From 4beab33e7183d46ea1456fdb7a8d6189b48f5cda Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 17 Jan 2024 19:51:24 -0800 Subject: [PATCH 001/150] attempted to solve toString() redundancy, unnecessary eslint-diable comment, changed a variable from x to gene to make it more clear what info the variable contains, reduced indentation by creating another method called expressionDataHandler, and created another function called expressionExportErrorHandler to reduce code repetition --- package-lock.json | 21613 ++------------------- server/dals/network-dal.js | 2 +- web-client/public/js/api/grnsight-api.js | 2 +- web-client/public/js/update-app.js | 2 +- web-client/public/js/upload.js | 126 +- 5 files changed, 1833 insertions(+), 19912 deletions(-) diff --git a/package-lock.json b/package-lock.json index bebb0710..b709fade 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,17794 +1,37 @@ { "name": "grnsight", - "version": "6.0.0", - "lockfileVersion": 2, + "version": "6.0.7", + "lockfileVersion": 1, "requires": true, - 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"integrity": "sha1-eNfL/B5tZjA/55g3NlmEUXsvbuE=", + "integrity": "sha512-jZ38TU/EBiGKrmyTNNZgnvCZHNowiRI4+w/I9noMlekHTZH3KyGgvJLmhSgykeAQ9j2SYPDosM0Bg3wHfzibAQ==", "dev": true, "requires": { "is-stream": "^1.0.1", "pinkie-promise": "^2.0.0" } }, + "hasown": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/hasown/-/hasown-2.0.0.tgz", + "integrity": "sha512-vUptKVTpIJhcczKBbgnS+RtcuYMB8+oNzPK2/Hp3hanz8JmpATdmmgLgSaadVREkDm+e2giHwY3ZRkyjSIDDFA==", + "requires": { + "function-bind": "^1.1.2" + } + }, "hawk": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/hawk/-/hawk-1.1.1.tgz", - "integrity": "sha1-h81JH5tG5OKurKM1QWdmiF0tHtk=", + "integrity": "sha512-am8sVA2bCJIw8fuuVcKvmmNnGFUGW8spTkVtj2fXTEZVkfN42bwFZFtDem57eFi+NSxurJB8EQ7Jd3uCHLn8Vw==", "requires": { "boom": "0.4.x", "cryptiles": "0.2.x", @@ -23381,7 +5383,7 @@ "hmac-drbg": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/hmac-drbg/-/hmac-drbg-1.0.1.tgz", - "integrity": "sha1-0nRXAQJabHdabFRXk+1QL8DGSaE=", + "integrity": "sha512-Tti3gMqLdZfhOQY1Mzf/AanLiqh1WTiJgEj26ZuYQ9fbkLomzGchCws4FyrSd4VkpBfiNhaE1On+lOz894jvXg==", "requires": { "hash.js": "^1.0.3", "minimalistic-assert": "^1.0.0", @@ -23391,12 +5393,12 @@ "hoek": { "version": "0.9.1", "resolved": "https://registry.npmjs.org/hoek/-/hoek-0.9.1.tgz", - 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"integrity": "sha1-euTsJXMC/XkNVXyxDJcQDYV7AFY=", + "integrity": "sha512-UwqFFU6yztduP6DXcjcIjrIyvWQMv/spvrK2vji37XiUykpCm1qTUUM3zO+ER7qjL3CtmbWKAoVC5+bO2HwiNA==", "dev": true }, "log-symbols": { @@ -25254,7 +7265,7 @@ "log-update": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/log-update/-/log-update-1.0.2.tgz", - "integrity": "sha1-GZKfZMQJPS0ucHWh2tivWcKWuNE=", + "integrity": "sha512-4vSow8gbiGnwdDNrpy1dyNaXWKSCIPop0EHdE8GrnngHoJujM3QhvHUN/igsYCgPoHo7pFOezlJ61Hlln0KHyA==", "dev": true, "requires": { "ansi-escapes": "^1.0.0", @@ -25310,17 +7321,17 @@ "map-cache": { "version": "0.2.2", "resolved": "https://registry.npmjs.org/map-cache/-/map-cache-0.2.2.tgz", - "integrity": "sha1-wyq9C9ZSXZsFFkW7TyasXcmKDb8=" + "integrity": "sha512-8y/eV9QQZCiyn1SprXSrCmqJN0yNRATe+PO8ztwqrvrbdRLA3eYJF0yaR0YayLWkMbsQSKWS9N2gPcGEc4UsZg==" }, "map-obj": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/map-obj/-/map-obj-1.0.1.tgz", - "integrity": "sha1-2TPOuSBdgr3PSIb2dCvcK03qFG0=" + "integrity": "sha512-7N/q3lyZ+LVCp7PzuxrJr4KMbBE2hW7BT7YNia330OFxIf4d3r5zVpicP2650l7CPN6RM9zOJRl3NGpqSiw3Eg==" }, "map-visit": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/map-visit/-/map-visit-1.0.0.tgz", - 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"integrity": "sha1-7/UuN1gknTO+QCuLuOVkuytdQDE=", + "integrity": "sha512-LeZY+DZDRnvP7eMuQ6LHfCzUGxAAIViUBliK24P3hWXL6y4SortgR6Nim6xrkfSLlmH0+k+9NYNwVC2s53ZrYQ==", "dev": true }, "async": { - "version": "2.6.3", - "resolved": "https://registry.npmjs.org/async/-/async-2.6.3.tgz", - "integrity": "sha512-zflvls11DCy+dQWzTW2dzuilv8Z5X/pjfmZOWba6TNIVDm+2UDaJmXSOXlasHKfNBs8oo3M0aT50fDEWfKZjXg==", + "version": "2.6.4", + "resolved": "https://registry.npmjs.org/async/-/async-2.6.4.tgz", + "integrity": "sha512-mzo5dfJYwAn29PeiJ0zvwTo04zj8HDJj0Mn8TD7sno7q12prdbnasKJHhkm2c1LgrhlJ0teaea8860oxi51mGA==", "dev": true, "requires": { "lodash": "^4.17.14" @@ -31929,7 +13825,7 @@ "dargs": { "version": "5.1.0", "resolved": "https://registry.npmjs.org/dargs/-/dargs-5.1.0.tgz", - "integrity": "sha1-7H6lDHhWTNNsnV7Bj2Yyn63ieCk=", + "integrity": "sha512-Mr5OxT76pdJv7BbLq3hF1gSP8zxlCyDA1afj2Iab2MPKmdAKV+aKGC8YJv6cT8ItdFXAf798JJQD7jmbWZcYTQ==", "dev": true }, "debug": { @@ -31954,7 +13850,7 @@ "github-username": { "version": "4.1.0", "resolved": "https://registry.npmjs.org/github-username/-/github-username-4.1.0.tgz", - "integrity": "sha1-y+KABBiDIG2kISrp5LXxacML9Bc=", + "integrity": "sha512-ABDfD5sjQOE8XDatHhN/WORUIAN1AGpgW4vegrKtby8x+jC/ALqCEuUDhCPlk9EXtjTHJWpuK25QdaehSUlCQg==", "dev": true, "requires": { "gh-got": "^6.0.0" @@ -31963,7 +13859,7 @@ "globby": { "version": "7.1.1", "resolved": "https://registry.npmjs.org/globby/-/globby-7.1.1.tgz", - "integrity": "sha1-+yzP+UAfhgCUXfral0QMypcrhoA=", + "integrity": "sha512-yANWAN2DUcBtuus5Cpd+SKROzXHs2iVXFZt/Ykrfz6SAXqacLX25NZpltE+39ceMexYF4TtEadjuSTw8+3wX4g==", "dev": true, "requires": { "array-union": "^1.0.1", @@ -31972,6 +13868,22 @@ "ignore": "^3.3.5", "pify": "^3.0.0", "slash": "^1.0.0" + }, + "dependencies": { + "glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "requires": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + } + } } }, "got": { @@ -32024,15 +13936,6 @@ "vinyl": "^2.0.1" } }, - "mkdirp": { - "version": "0.5.5", - "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-0.5.5.tgz", - "integrity": "sha512-NKmAlESf6jMGym1++R0Ra7wvhV+wFW63FaSOFPwRahvea0gMUcGUhVeAg/0BC0wiv9ih5NYPB1Wn1UEI1/L+xQ==", - "dev": true, - "requires": { - "minimist": "^1.2.5" - } - }, "ms": { "version": "2.1.3", "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz", @@ -32042,7 +13945,7 @@ "multimatch": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/multimatch/-/multimatch-2.1.0.tgz", - "integrity": "sha1-nHkGoi+0wCkZ4vX3UWG0zb1LKis=", + "integrity": "sha512-0mzK8ymiWdehTBiJh0vClAzGyQbdtyWqzSVx//EK4N/D+599RFlGfTAsKw2zMSABtDG9C6Ul2+t8f2Lbdjf5mA==", "dev": true, "requires": { "array-differ": "^1.0.0", @@ -32060,7 +13963,7 @@ "p-timeout": { "version": "1.2.1", "resolved": "https://registry.npmjs.org/p-timeout/-/p-timeout-1.2.1.tgz", - "integrity": "sha1-XrOzU7f86Z8QGhA4iAuwVOu+o4Y=", + "integrity": "sha512-gb0ryzr+K2qFqFv6qi3khoeqMZF/+ajxQipEF6NteZVnvz9tzdsfAVj3lYtn1gAXvH5lfLwfxEII799gt/mRIA==", "dev": true, "requires": { "p-finally": "^1.0.0" @@ -32069,13 +13972,13 @@ "pretty-bytes": { "version": "4.0.2", "resolved": "https://registry.npmjs.org/pretty-bytes/-/pretty-bytes-4.0.2.tgz", - "integrity": "sha1-sr+C5zUNZcbDOqlaqlpPYyf2HNk=", + "integrity": "sha512-yJAF+AjbHKlxQ8eezMd/34Mnj/YTQ3i6kLzvVsH4l/BfIFtp444n0wVbnsn66JimZ9uBofv815aRp1zCppxlWw==", "dev": true }, "read-chunk": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/read-chunk/-/read-chunk-2.1.0.tgz", - "integrity": "sha1-agTAkoAF7Z1C4aasVgDhnLx/9lU=", + "integrity": "sha512-QQqB2O9KX/BnztP1xkTRsBxABcWHCXTqQYmEm/DdNId1nw+leKkZvV/g5oCKUrXolGtU3zouoIxMLToAYyDgDw==", "dev": true, "requires": { "pify": "^3.0.0", @@ -32085,7 +13988,7 @@ "read-pkg": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/read-pkg/-/read-pkg-3.0.0.tgz", - "integrity": "sha1-nLxoaXj+5l0WwA4rGcI3/Pbjg4k=", + "integrity": "sha512-BLq/cCO9two+lBgiTYNqD6GdtK8s4NpaWrl6/rCO9w0TUS8oJl7cmToOZfRYllKTISY6nt1U7jQ53brmKqY6BA==", "dev": true, "requires": { "load-json-file": "^4.0.0", @@ -32096,7 +13999,7 @@ "read-pkg-up": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/read-pkg-up/-/read-pkg-up-3.0.0.tgz", - "integrity": "sha1-PtSWaF26D4/hGNBpHcUfSh/5bwc=", + "integrity": "sha512-YFzFrVvpC6frF1sz8psoHDBGF7fLPc+llq/8NB43oagqWkx8ar5zYtsTORtOjw9W2RHLpWP+zTWwBvf1bCmcSw==", "dev": true, "requires": { "find-up": "^2.0.0", diff --git a/server/dals/network-dal.js b/server/dals/network-dal.js index cd350f48..aeff6bf5 100644 --- a/server/dals/network-dal.js +++ b/server/dals/network-dal.js @@ -1,4 +1,3 @@ -/* eslint-disable max-len */ const Sequelize = require("sequelize"); require("dotenv").config(); var env = process.env.NODE_ENV || "development"; @@ -57,6 +56,7 @@ const buildQueryByType = function (queryType, query) { } }; +// const response = convertResponseToJSON(req.query.type, req.query, stdname); const convertResponseToJSON = function (queryType, query, totalOutput) { let JSONOutput = {}; switch (queryType) { diff --git a/web-client/public/js/api/grnsight-api.js b/web-client/public/js/api/grnsight-api.js index dea48043..884e4ddb 100644 --- a/web-client/public/js/api/grnsight-api.js +++ b/web-client/public/js/api/grnsight-api.js @@ -5,7 +5,7 @@ const buildQueryURL = function (path, parameters) { for (let p in parameters) { searchParams.append(p, parameters[p]); } - return `${path}?${searchParams.toString()}`; + return `${path}?${searchParams}`; }; const responseData = (database, formData, queryURL) => { diff --git a/web-client/public/js/update-app.js b/web-client/public/js/update-app.js index 559b6ca2..89566749 100644 --- a/web-client/public/js/update-app.js +++ b/web-client/public/js/update-app.js @@ -391,7 +391,7 @@ const loadExpressionDatabase = function (isTopDataset) { queryExpressionDatabase({ type:"ExpressionData", dataset, - genes : grnState.workbook.genes.map(x => {return x.name;}).join(","), + genes : grnState.workbook.genes.map(gene => {return gene.name;}).join(","), timepoints: timepointsResponse[dataset] }).then(function (response) { if (isTopDataset) { diff --git a/web-client/public/js/upload.js b/web-client/public/js/upload.js index 86cdf937..32987e8b 100644 --- a/web-client/public/js/upload.js +++ b/web-client/public/js/upload.js @@ -174,52 +174,55 @@ export const upload = function () { for (let sheet in finalExportSheets.expression) { startLoadingIcon(); const dataset = `${source}_${sheet.replace("_log2_expression", "")}`; + console.log('in handleExpressionDataAndExport') queryExpressionDatabase({ - type: "ExpressionTimePoints", - dataset - }).then(function (timepointsResponse) { + type: "ExpressionTimePoints", + dataset, + }) + .then(function(timepointsResponse) { queryExpressionDatabase({ - type: "ExpressionData", - dataset, - genes: grnState.workbook.genes.map(x => { - return x.name; - }).join(","), - timepoints: timepointsResponse[dataset] - }).then(function (response) { - finalExportSheets.expression[sheet] = response; - if (finalExportSheets.expression[sheet]) { - stopLoadingIcon(); - if (!Object.values(finalExportSheets.expression).includes(null)) { - // we have all of the expression sheets so lets initilize the export process - Object.keys(finalExportSheets.expression).forEach((sheet) => { - // make sure that the sheets we queried are populated with the correct data - if (!(finalExportSheets.expression[sheet].data && finalExportSheets.expression[sheet].timePoints)) { - // if the resulting query doesn't contains both the timePoint data and - // the gene data then don't export it. If not don't :) - finalExportSheets.expression[sheet] = null; - } - }); - if (finalExportSheets["optimization_parameters"] === null) { - finalExportSheets["optimization_parameters"] = updateOptimizationParameters(finalExportSheets); - } - grnState.workbook.exportSheets = finalExportSheets; - exportExcel(route, extension, sheetType); - } - } - }).catch(function (error) { - console.log(error.stack); - console.log(error.name); - console.log(error.message); - }); - }).catch(function (error) { - console.log(error.stack); - console.log(error.name); - console.log(error.message); - }); + type: "ExpressionData", + dataset, + genes: grnState.workbook.genes + .map((x) => { + return x.name; + }) + .join(","), + timepoints: timepointsResponse[dataset], + }) + .then((expressionData) => + expressionDataHandler(expressionData, sheet) + ) + .catch((error) => expressionExportErrorHandler(error)); + }) + .catch((error) => expressionExportErrorHandler(error)); } } }; + const expressionDataHandler = (expressionData, sheet) => { + console.log('in expression data handler') + finalExportSheets.expression[sheet] = expressionData; + if (finalExportSheets.expression[sheet]) { + stopLoadingIcon(); + if (!Object.values(finalExportSheets.expression).includes(null)) { + // we have all of the expression sheets so lets initilize the export process + Object.keys(finalExportSheets.expression).forEach((sheet) => { + // make sure that the sheets we queried are populated with the correct data + if (!(finalExportSheets.expression[sheet].data && finalExportSheets.expression[sheet].timePoints)) { + // if the resulting query doesn't contains both the timePoint data and + // the gene data then don't export it. If not don't :) + finalExportSheets.expression[sheet] = null; + } + }); + if (finalExportSheets["optimization_parameters"] === null) { + finalExportSheets["optimization_parameters"] = updateOptimizationParameters(finalExportSheets); + } + grnState.workbook.exportSheets = finalExportSheets; + exportExcel(route, extension, sheetType); + } + } + } const handleExportExcelButtonExport = (route, extension, sheetType, source) => { grnState.workbook.exportNetworkType = sheetType; @@ -302,23 +305,32 @@ export const upload = function () { } queryExpressionDatabase({ - type: twoColumnSheetType[sheet], - genes: grnState.workbook.genes.map(x => { - return x.name; - }).join(",") - }).then(function (response) { + type: twoColumnSheetType[sheet], + genes: grnState.workbook.genes + .map((x) => { + return x.name; + }) + .join(","), + }) + .then(function(response) { result.data = response; finalExportSheets.two_column_sheets[sheet] = result; - if (!Object.values(finalExportSheets.two_column_sheets).includes(null)) { - // if we got all of the two column sheets, then proceed with export - handleExpressionDataAndExport(route, extension, sheetType, source, finalExportSheets); + if ( + !Object.values( + finalExportSheets.two_column_sheets + ).includes(null) + ) { + // if we got all of the two column sheets, then proceed with export + handleExpressionDataAndExport( + route, + extension, + sheetType, + source, + finalExportSheets + ); } - - }).catch(function (error) { - console.log(error.stack); - console.log(error.name); - console.log(error.message); - }); + }) + .catch(error => expressionExportErrorHandler(error)); } } @@ -328,6 +340,12 @@ export const upload = function () { } }; + const expressionExportErrorHandler = (error) => { + console.log(error.stack); + console.log(error.name); + console.log(error.message); + }; + const determineWorkbookType = function () { const workbookSheets = $("input[name=workbookSheets]:checked"); for (const [key, value] of Object.entries(workbookSheets)) { From f19f1dc3e0b5e8868764698a56f01623e54789c9 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Sun, 21 Jan 2024 19:11:40 -0800 Subject: [PATCH 002/150] Fixed cell A1 of the spreadsheet. However, the test needs to change, will change in next commit --- server/controllers/exporters/xlsx.js | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/server/controllers/exporters/xlsx.js b/server/controllers/exporters/xlsx.js index 486abfd9..bba4b36d 100644 --- a/server/controllers/exporters/xlsx.js +++ b/server/controllers/exporters/xlsx.js @@ -10,7 +10,7 @@ const createArrayWithZeroes = function (length) { return Array.apply(null, Array(length)).map(() => 0); }; -const buildNetworkSheet = function (genes, links) { +const buildNetworkSheet = function (genes, links, workbookType) { const geneNameArray = buildGeneNameArray(genes); // The +1 to length is because we ALSO add the gene name to each of the network sheet arrays. const networkSheet = genes.map(() => createArrayWithZeroes(genes.length + 1)); @@ -18,7 +18,11 @@ const buildNetworkSheet = function (genes, links) { // Place the gene name in the beginning of the network sheet array. // EX: ["CIN5", 0, 0, 1] Object.keys(geneNameArray).forEach(index => networkSheet[index][0] = geneNameArray[index]); - geneNameArray.unshift("cols regulators/rows targets"); + if (workbookType === "grn") { + geneNameArray.unshift("cols regulators/rows targets"); + } else { + geneNameArray.unshift("protein 1/protein 2"); + } links.forEach((link) => { networkSheet[link.target][link.source + 1] = link.value; @@ -115,7 +119,7 @@ const buildXlsxSheet = function (workbook) { { "name": network, "data": buildNetworkSheet(workbook.exportSheets.networks[network].genes, - workbook.exportSheets.networks[network].links) + workbook.exportSheets.networks[network].links, workbook.meta.data.workbookType) } ); } From 0dab0ff172418bf7dd8ec0dcc1abb86f06541b6b Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sun, 21 Jan 2024 19:55:46 -0800 Subject: [PATCH 003/150] working on issue #1002. ran npm lint and revised method call for expressionDataHandler to be expressionDataHandler(expressionData, sheet, route, extension, sheetType, finalExportSheets) so that method gets all necessary info and fixed indentation in expressionExportErrorHandler. --- server/dals/network-dal.js | 9 +- web-client/public/js/upload.js | 150 ++++++++++++++++++--------------- 2 files changed, 87 insertions(+), 72 deletions(-) diff --git a/server/dals/network-dal.js b/server/dals/network-dal.js index aeff6bf5..2cad300a 100644 --- a/server/dals/network-dal.js +++ b/server/dals/network-dal.js @@ -22,10 +22,11 @@ const buildNetworkSourceQuery = function () { }; const buildNetworkGeneFromSourceQuery = function (gene, source, timestamp) { - return `SELECT DISTINCT gene_id, display_gene_id FROM gene_regulatory_network.network, gene_regulatory_network.gene WHERE - network.time_stamp='${timestamp}' AND network.source='${source}' AND - (gene.gene_id ='${gene}' OR gene.display_gene_id ='${gene}') AND - (gene.gene_id = network.regulator_gene_id OR gene.gene_id = network.target_gene_id);`; + return `SELECT DISTINCT gene_id, display_gene_id FROM + gene_regulatory_network.network, gene_regulatory_network.gene WHERE + network.time_stamp='${timestamp}' AND network.source='${source}' AND + (gene.gene_id ='${gene}' OR gene.display_gene_id ='${gene}') AND + (gene.gene_id = network.regulator_gene_id OR gene.gene_id = network.target_gene_id);`; }; const buildNetworkGenesQuery = function (geneString) { diff --git a/web-client/public/js/upload.js b/web-client/public/js/upload.js index 32987e8b..256ac672 100644 --- a/web-client/public/js/upload.js +++ b/web-client/public/js/upload.js @@ -161,6 +161,39 @@ export const upload = function () { return optimizationParameters; }; + // helper method for handleExpressionDataAndExport to reduce indentation + const expressionDataHandler = (expressionData, sheet, route, extension, sheetType, finalExportSheets) => { + finalExportSheets.expression[sheet] = expressionData; + if (finalExportSheets.expression[sheet]) { + stopLoadingIcon(); + if (!Object.values(finalExportSheets.expression).includes(null)) { + // we have all of the expression sheets so lets initilize the export process + Object.keys(finalExportSheets.expression).forEach((sheet) => { + // make sure that the sheets we queried are populated with the correct data + if (!(finalExportSheets.expression[sheet].data && finalExportSheets.expression[sheet].timePoints)) { + // if the resulting query doesn't contains both the timePoint data and + // the gene data then don't export it. If not don't :) + finalExportSheets.expression[sheet] = null; + } + }); + if (finalExportSheets["optimization_parameters"] === null) { + finalExportSheets[ + "optimization_parameters" + ] = updateOptimizationParameters(finalExportSheets); + } + grnState.workbook.exportSheets = finalExportSheets; + exportExcel(route, extension, sheetType); + } + } + }; + + // helper method for handleExpressionDataAndExport and handleExportExcelButtonExport to avoid redundant code + const expressionExportErrorHandler = (error) => { + console.log(error.stack); + console.log(error.name); + console.log(error.message); + }; + const handleExpressionDataAndExport = (route, extension, sheetType, source, finalExportSheets) => { if (source === "userInput" && grnState.workbook.expression) { // make sure that the optimization parameters sheet is actually properly formatted @@ -174,55 +207,47 @@ export const upload = function () { for (let sheet in finalExportSheets.expression) { startLoadingIcon(); const dataset = `${source}_${sheet.replace("_log2_expression", "")}`; - console.log('in handleExpressionDataAndExport') queryExpressionDatabase({ - type: "ExpressionTimePoints", - dataset, - }) - .then(function(timepointsResponse) { + type: "ExpressionTimePoints", + dataset + }).then(function (timepointsResponse) { queryExpressionDatabase({ - type: "ExpressionData", - dataset, - genes: grnState.workbook.genes - .map((x) => { - return x.name; - }) - .join(","), - timepoints: timepointsResponse[dataset], - }) - .then((expressionData) => - expressionDataHandler(expressionData, sheet) - ) - .catch((error) => expressionExportErrorHandler(error)); - }) - .catch((error) => expressionExportErrorHandler(error)); + type: "ExpressionData", + dataset, + genes: grnState.workbook.genes.map(x => { + return x.name; + }).join(","), + timepoints: timepointsResponse[dataset] + }).then((expressionData) => expressionDataHandler(expressionData, sheet, route, extension, sheetType, finalExportSheets)) + .catch((error) => expressionExportErrorHandler(error)); + }).catch((error) => expressionExportErrorHandler(error)); } } }; - const expressionDataHandler = (expressionData, sheet) => { - console.log('in expression data handler') - finalExportSheets.expression[sheet] = expressionData; - if (finalExportSheets.expression[sheet]) { - stopLoadingIcon(); - if (!Object.values(finalExportSheets.expression).includes(null)) { - // we have all of the expression sheets so lets initilize the export process - Object.keys(finalExportSheets.expression).forEach((sheet) => { - // make sure that the sheets we queried are populated with the correct data - if (!(finalExportSheets.expression[sheet].data && finalExportSheets.expression[sheet].timePoints)) { - // if the resulting query doesn't contains both the timePoint data and - // the gene data then don't export it. If not don't :) - finalExportSheets.expression[sheet] = null; - } - }); - if (finalExportSheets["optimization_parameters"] === null) { - finalExportSheets["optimization_parameters"] = updateOptimizationParameters(finalExportSheets); - } - grnState.workbook.exportSheets = finalExportSheets; - exportExcel(route, extension, sheetType); - } - } - } + + // .then(function (response) { + // finalExportSheets.expression[sheet] = response; + // if (finalExportSheets.expression[sheet]) { + // stopLoadingIcon(); + // if (!Object.values(finalExportSheets.expression).includes(null)) { + // // we have all of the expression sheets so lets initilize the export process + // Object.keys(finalExportSheets.expression).forEach((sheet) => { + // // make sure that the sheets we queried are populated with the correct data + // if (!(finalExportSheets.expression[sheet].data && finalExportSheets.expression[sheet].timePoints)) { + // // if the resulting query doesn't contains both the timePoint data and + // // the gene data then don't export it. If not don't :) + // finalExportSheets.expression[sheet] = null; + // } + // }); + // if (finalExportSheets["optimization_parameters"] === null) { + // finalExportSheets["optimization_parameters"] = updateOptimizationParameters(finalExportSheets); + // } + // grnState.workbook.exportSheets = finalExportSheets; + // exportExcel(route, extension, sheetType); + // } + // } + // } const handleExportExcelButtonExport = (route, extension, sheetType, source) => { grnState.workbook.exportNetworkType = sheetType; @@ -305,33 +330,28 @@ export const upload = function () { } queryExpressionDatabase({ - type: twoColumnSheetType[sheet], - genes: grnState.workbook.genes + type: twoColumnSheetType[sheet], + genes: grnState.workbook.genes .map((x) => { - return x.name; + return x.name; }) .join(","), }) - .then(function(response) { + .then(function (response) { result.data = response; finalExportSheets.two_column_sheets[sheet] = result; - if ( - !Object.values( - finalExportSheets.two_column_sheets - ).includes(null) - ) { - // if we got all of the two column sheets, then proceed with export - handleExpressionDataAndExport( - route, - extension, - sheetType, - source, - finalExportSheets - ); + if (!Object.values( finalExportSheets.two_column_sheets).includes(null)) { + // if we got all of the two column sheets, then proceed with export + handleExpressionDataAndExport( + route, + extension, + sheetType, + source, + finalExportSheets + ); } - }) + }) .catch(error => expressionExportErrorHandler(error)); - } } } else { @@ -340,12 +360,6 @@ export const upload = function () { } }; - const expressionExportErrorHandler = (error) => { - console.log(error.stack); - console.log(error.name); - console.log(error.message); - }; - const determineWorkbookType = function () { const workbookSheets = $("input[name=workbookSheets]:checked"); for (const [key, value] of Object.entries(workbookSheets)) { From 93d9033280876f050ac7917a90cfec7ecc010e23 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sun, 21 Jan 2024 21:36:38 -0800 Subject: [PATCH 004/150] Working on issue #1002. Fixed the verbose code with x !== false, fixed the inconsistent function style by making 2 functions next to each other both arrow functions, and changed the variable x to connection for clarity --- server/dals/network-dal.js | 8 ++++---- web-client/public/js/api/grnsight-api.js | 2 +- web-client/public/js/upload.js | 26 +----------------------- 3 files changed, 6 insertions(+), 30 deletions(-) diff --git a/server/dals/network-dal.js b/server/dals/network-dal.js index 2cad300a..0f53c713 100644 --- a/server/dals/network-dal.js +++ b/server/dals/network-dal.js @@ -63,10 +63,10 @@ const convertResponseToJSON = function (queryType, query, totalOutput) { switch (queryType) { case "NetworkSource": JSONOutput.sources = {}; - totalOutput.forEach(function (x) { - const timestamp = x.time_stamp; - const source = x.source; - const displayName = x.display_name; + totalOutput.forEach(function (connection) { + const timestamp = connection.time_stamp; + const source = connection.source; + const displayName = connection.display_name; JSONOutput.sources[`${displayName}: ${timestamp.toISOString().split("T")[0]}`] = {timestamp, source}; }); return JSONOutput; diff --git a/web-client/public/js/api/grnsight-api.js b/web-client/public/js/api/grnsight-api.js index 884e4ddb..402827b4 100644 --- a/web-client/public/js/api/grnsight-api.js +++ b/web-client/public/js/api/grnsight-api.js @@ -26,7 +26,7 @@ const responseData = (database, formData, queryURL) => { .done((data) => { resolve(data); }) - .error(function () { + .error(() => { console.log( `Error in accessing ${database} database. Result may just be loading.` ); diff --git a/web-client/public/js/upload.js b/web-client/public/js/upload.js index 256ac672..bfc29283 100644 --- a/web-client/public/js/upload.js +++ b/web-client/public/js/upload.js @@ -225,30 +225,6 @@ export const upload = function () { } }; - - // .then(function (response) { - // finalExportSheets.expression[sheet] = response; - // if (finalExportSheets.expression[sheet]) { - // stopLoadingIcon(); - // if (!Object.values(finalExportSheets.expression).includes(null)) { - // // we have all of the expression sheets so lets initilize the export process - // Object.keys(finalExportSheets.expression).forEach((sheet) => { - // // make sure that the sheets we queried are populated with the correct data - // if (!(finalExportSheets.expression[sheet].data && finalExportSheets.expression[sheet].timePoints)) { - // // if the resulting query doesn't contains both the timePoint data and - // // the gene data then don't export it. If not don't :) - // finalExportSheets.expression[sheet] = null; - // } - // }); - // if (finalExportSheets["optimization_parameters"] === null) { - // finalExportSheets["optimization_parameters"] = updateOptimizationParameters(finalExportSheets); - // } - // grnState.workbook.exportSheets = finalExportSheets; - // exportExcel(route, extension, sheetType); - // } - // } - // } - const handleExportExcelButtonExport = (route, extension, sheetType, source) => { grnState.workbook.exportNetworkType = sheetType; const workbookSheets = $("input[name=workbookSheets]:checked"); @@ -461,7 +437,7 @@ export const upload = function () { ] : [ (grnState.workbook.meta2 !== undefined && "optimization_diagnostics") ]; - additionalsheets = additionalsheets.filter(x => (x !== false && -1 !== optionalAdditionalSheets.indexOf(x))); + additionalsheets = additionalsheets.filter(sheet => (sheet && -1 !== optionalAdditionalSheets.indexOf(sheet))); additionalsheets = [...optionalAdditionalSheets, ...additionalsheets].sort(); additionalsheets = [...(new Set(additionalsheets))]; for (let n of networks) { From 895f8f629dfeeb4d0565e0aa912c38606ff27441 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sun, 21 Jan 2024 21:58:46 -0800 Subject: [PATCH 005/150] Issue #1002. Removed and fixed lingering /* eslint-disable max-len */ comment in server/dals/protein-dal.js --- server/dals/protein-dal.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/server/dals/protein-dal.js b/server/dals/protein-dal.js index bc039f19..bfd8dd3e 100644 --- a/server/dals/protein-dal.js +++ b/server/dals/protein-dal.js @@ -1,4 +1,3 @@ -/* eslint-disable max-len */ const Sequelize = require("sequelize"); require("dotenv").config(); var env = process.env.NODE_ENV || "development"; @@ -25,7 +24,8 @@ const buildNetworkSourceQuery = function () { const buildNetworkFromGeneProteinQuery = function (geneProtein) { return `SELECT DISTINCT gene_id, display_gene_id, standard_name, length, molecular_weight, PI FROM protein_protein_interactions.gene, protein_protein_interactions.protein WHERE - (LOWER(gene.gene_id)=LOWER('${geneProtein}') OR LOWER(gene.display_gene_id)=LOWER('${geneProtein}') OR LOWER(protein.standard_name) =LOWER('${geneProtein}')) AND + (LOWER(gene.gene_id)=LOWER('${geneProtein}') OR LOWER(gene.display_gene_id)=LOWER('${geneProtein}') + OR LOWER(protein.standard_name) =LOWER('${geneProtein}')) AND LOWER(gene.gene_id) = LOWER(protein.gene_systematic_name);`; }; From 360234290ed71bbe907f9ef3e5445442bf17e4b5 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 22 Jan 2024 19:58:40 -0800 Subject: [PATCH 006/150] Issue #1002. Worked on redundant code, made createMatrix method in generate_network.py --- .../scripts/generate_network.py | 38 ++++++++----------- 1 file changed, 15 insertions(+), 23 deletions(-) diff --git a/database/network-database/scripts/generate_network.py b/database/network-database/scripts/generate_network.py index 6627e7ea..8e3a2880 100644 --- a/database/network-database/scripts/generate_network.py +++ b/database/network-database/scripts/generate_network.py @@ -111,29 +111,21 @@ def create_regulator_to_target_row(target, all_regulators): if regulator != None: regulators_list.append(regulator) -print(f'Creating REGULATORS TO TARGETS MATRIX\n') -regulator_to_target_file = open(REGULATORS_TO_TARGETS_MATRIX, 'w') -headers = "cols regulators/rows targets" -headers += '\t'.join(regulators_list) -regulator_to_target_file.write(f'{headers}\n') -for target in targets: - result = create_regulator_to_target_row(target, regulators_to_targets) - if result != False: - regulator_to_target_file.write(f'{result}\n') -regulator_to_target_file.close() - -print(f'Creating REGULATORS TO TARGETS MATRIX\n') -regulator_to_regulator_file = open(REGULATORS_TO_REGULATORS_MATRIX, 'w') -headers = "cols regulators/rows targets" -headers += '\t'.join(regulators_list) -regulator_to_regulator_file.write(f'{headers}\n') -for target in targets: - result = create_regulator_to_target_row(target, regulators_to_targets) - if result != False: - regulator_to_regulator_file.write(f'{result}\n') -regulator_to_regulator_file.close() - - +def createMatrix(fileName: str): + statusMessage: str = 'Creating REGULATORS TO TARGETS MATRIX\n' if fileName == REGULATORS_TO_TARGETS_MATRIX else 'Creating REGULATORS TO REGULATORS MATRIX\n' + print(statusMessage) + regulator_to_target_file = open(fileName, 'w') + headers = "cols regulators/rows targets" + headers += '\t'.join(regulators_list) + regulator_to_target_file.write(f'{headers}\n') + for target in targets: + result = create_regulator_to_target_row(target, regulators_to_targets) + if result != False: + regulator_to_target_file.write(f'{result}\n') + regulator_to_target_file.close() + +createMatrix(REGULATORS_TO_TARGETS_MATRIX) +createMatrix(REGULATORS_TO_REGULATORS_MATRIX) # Create loader-files From 33eb3b65fb9403fc0048e1b8d2d5b8c803309ce8 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 22 Jan 2024 23:36:26 -0800 Subject: [PATCH 007/150] added createMatrix method to generate_new_network_version.py. adjusted createMatrix method in generate_network.py and generate_new_network.py to remove redundancy of if result != False --- .../scripts/generate_network.py | 2 +- .../scripts/generate_new_network_version.py | 39 ++++++++----------- 2 files changed, 17 insertions(+), 24 deletions(-) diff --git a/database/network-database/scripts/generate_network.py b/database/network-database/scripts/generate_network.py index 8e3a2880..fa0e1f94 100644 --- a/database/network-database/scripts/generate_network.py +++ b/database/network-database/scripts/generate_network.py @@ -120,7 +120,7 @@ def createMatrix(fileName: str): regulator_to_target_file.write(f'{headers}\n') for target in targets: result = create_regulator_to_target_row(target, regulators_to_targets) - if result != False: + if result: regulator_to_target_file.write(f'{result}\n') regulator_to_target_file.close() diff --git a/database/network-database/scripts/generate_new_network_version.py b/database/network-database/scripts/generate_new_network_version.py index 875aebde..fcd5487c 100644 --- a/database/network-database/scripts/generate_new_network_version.py +++ b/database/network-database/scripts/generate_new_network_version.py @@ -126,29 +126,22 @@ def create_regulator_to_target_row(target, all_regulators): if regulator != None: regulators_list.append(regulator) -print(f'Creating REGULATORS TO TARGETS MATRIX\n') -regulator_to_target_file = open(REGULATORS_TO_TARGETS_MATRIX, 'w') -headers = "cols regulators/rows targets" -headers += '\t'.join(regulators_list) -regulator_to_target_file.write(f'{headers}\n') -for target in targets: - result = create_regulator_to_target_row(target, regulators_to_targets) - if result != False: - regulator_to_target_file.write(f'{result}\n') -regulator_to_target_file.close() - -print(f'Creating REGULATORS TO TARGETS MATRIX\n') -regulator_to_regulator_file = open(REGULATORS_TO_REGULATORS_MATRIX, 'w') -headers = "cols regulators/rows targets" -headers += '\t'.join(regulators_list) -regulator_to_regulator_file.write(f'{headers}\n') -for target in targets: - result = create_regulator_to_target_row(target, regulators_to_targets) - if result != False: - regulator_to_regulator_file.write(f'{result}\n') -regulator_to_regulator_file.close() - - +# this is the same method used in generate_network.py to create Regulators to Targets Matrix and Regulators to Regulators Matrix +def createMatrix(fileName: str): + statusMessage: str = 'Creating REGULATORS TO TARGETS MATRIX\n' if fileName == REGULATORS_TO_TARGETS_MATRIX else 'Creating REGULATORS TO REGULATORS MATRIX\n' + print(statusMessage) + regulator_to_target_file = open(fileName, 'w') + headers = "cols regulators/rows targets" + headers += '\t'.join(regulators_list) + regulator_to_target_file.write(f'{headers}\n') + for target in targets: + result = create_regulator_to_target_row(target, regulators_to_targets) + if result: + regulator_to_target_file.write(f'{result}\n') + regulator_to_target_file.close() + +createMatrix(REGULATORS_TO_TARGETS_MATRIX) +createMatrix(REGULATORS_TO_REGULATORS_MATRIX) # Create loader-files From f93d15546e070d43dd89e8f03c19a565b320bbe7 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 23 Jan 2024 12:27:50 -0800 Subject: [PATCH 008/150] Fixing issue #1072. --- server/controllers/importers/sif.js | 12 ++++++++++++ test/import-sif-tests.js | 16 +++++++++++----- .../public/js/setup-load-and-import-handlers.js | 11 ++++++++--- 3 files changed, 31 insertions(+), 8 deletions(-) diff --git a/server/controllers/importers/sif.js b/server/controllers/importers/sif.js index 002046c9..5ef130b8 100644 --- a/server/controllers/importers/sif.js +++ b/server/controllers/importers/sif.js @@ -64,7 +64,18 @@ module.exports = function (sif) { var hasNumbers = relationships.some(isNumber); var allNumbers = relationships.every(isNumber); + + let networkMode = "grn"; + for (const relationship of relationships) { + if (relationship === "pp") { + networkMode = "protein-protein-physical-interaction"; + break; + } else if (relationship === "pd") { + break; + } + } return { + networkMode: networkMode, sheetType: allNumbers ? constants.WEIGHTED : constants.UNWEIGHTED, warnings: hasNumbers && !allNumbers ? constants.warnings.EDGES_WITHOUT_WEIGHTS : null, errors: errors @@ -134,6 +145,7 @@ module.exports = function (sif) { errors: errors, warnings: warnings, sheetType: workbookType.sheetType, + networkMode: workbookType.networkMode, positiveWeights: [], negativeWeights: [], meta: {}, diff --git a/test/import-sif-tests.js b/test/import-sif-tests.js index 2d1759db..cd5911e1 100644 --- a/test/import-sif-tests.js +++ b/test/import-sif-tests.js @@ -27,7 +27,8 @@ var expectedUnweightedWorkbook = initWorkbook({ negativeWeights: [], sheetType: "unweighted", meta: {}, - expression:{} + expression:{}, + networkMode: "grn" }); var expectedWeightedWorkbook = initWorkbook({ @@ -50,6 +51,7 @@ var expectedWeightedWorkbook = initWorkbook({ negativeWeights: [], sheetType: "weighted", meta: {}, + networkMode: "grn", expression:{} }); @@ -76,7 +78,8 @@ var expectedUnweightedWorkbookWithCycle = initWorkbook({ negativeWeights: [], sheetType: "unweighted", meta: {}, - expression:{} + expression:{}, + networkMode: "grn" }); var expectedWeightedWorkbookWithCycle = initWorkbook({ @@ -102,7 +105,8 @@ var expectedWeightedWorkbookWithCycle = initWorkbook({ negativeWeights: [], sheetType: "weighted", meta: {}, - expression:{} + expression:{}, + networkMode: "grn" }); // Unweighted SIF @@ -350,7 +354,8 @@ describe("Import from SIF", function () { negativeWeights: [], sheetType: "unweighted", meta: {}, - expression:{} + expression:{}, + networkMode: "grn" })); }); @@ -368,7 +373,8 @@ describe("Import from SIF", function () { negativeWeights: [], sheetType: "weighted", meta: {}, - expression:{} + expression:{}, + networkMode: "grn" })); }); diff --git a/web-client/public/js/setup-load-and-import-handlers.js b/web-client/public/js/setup-load-and-import-handlers.js index 7a7408c1..dfea2028 100644 --- a/web-client/public/js/setup-load-and-import-handlers.js +++ b/web-client/public/js/setup-load-and-import-handlers.js @@ -143,10 +143,15 @@ export const setupLoadAndImportHandlers = (grnState) => { break; } } - // TODO 👆🏼 The back end will add a `networkType` property to this object. - // The web app can then adjust various things based on that. grnState.workbook = workbook; - grnState.mode = workbook.meta.data.workbookType; + + if (grnState.name.includes(".sif")) { + grnState.mode = workbook.networkMode; + } else if (grnState.name.includes(".graphml")) { + grnState.mode = "grn"; + } else { + grnState.mode = workbook.meta.data.workbookType; + } grnState.workbook.expressionNames = Object.keys(workbook.expression); if (uploadRoute !== "upload") { grnState.annotateLinks(); From cb581d0a2b69f61c9eaf5bd4fe1c6d71a74c8de7 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Fri, 26 Jan 2024 14:34:26 -0800 Subject: [PATCH 009/150] Fixing and adding tests for cell A1 in issue #1054 --- server/controllers/network-sheet-parser.js | 43 ++++--- server/controllers/spreadsheet-controller.js | 5 +- test/export-tests.js | 128 ++++++++++++++++++- test/test.js | 2 +- 4 files changed, 156 insertions(+), 22 deletions(-) diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index 01024692..eb706b40 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -8,7 +8,6 @@ var semanticChecker = require(__dirname + "/semantic-checker"); var constants = require(__dirname + "/workbook-constants"); - // const NETWORK_SHEET_NAMES = ["network", "network_optimized_weights"]; // const isNetworkSheet = (sheetName) => { @@ -93,21 +92,6 @@ var parseNetworkSheet = function (sheet, network) { var columnChecker = []; var rowData = []; - // check for “cols regulators/rows targets” in cell A1 - const cellA1 = sheet.data[0][0]; - - // TODO There are now 2 valid values for cellA1. One indicates GRN, the other is PPI. - // If neither, then we continue with the warning. - - // Depending on the value of cellA1, we want to make a new property `networkType` which - // will indicate the network type. THe web app then reads this to decide what to do next. - if (cellA1 !== "cols regulators/rows targets") { - addWarning( - network, - constants.warnings.incorrectCellA1WorkbookWarning(sheet.name) - ); - } - // Get Source Genes for (let i = 1; i <= sheet.data[0].slice(1).length; i++) { currentGene = { name: sheet.data[0][i] }; @@ -284,8 +268,33 @@ var parseNetworkSheet = function (sheet, network) { return semanticChecker(network); }; +/* + * This method detect the network type of the workbook file either grn or protein-protein-physical-interactions + * If cellA1 = "cols regulators/ row targets" -> networkMode = grn + * If cellA1 = "protein 1/protein 2" -> networkMode = "protein-protein-physical-interaction" + * else undefined +*/ + +exports.networkMode = function (workbookFile) { + let networkMode = "grn"; + for (const sheet of workbookFile) { + if (sheet.name.toLowerCase() === "network") { + const cellA1 = sheet.data[0][0]; + + if (cellA1 === "cols regulators/rows targets") { + networkMode = "grn"; + } else if (cellA1 === "protein 1/protein 2") { + networkMode = "protein-protein-physical-interaction"; + } else { + networkMode = undefined; + } + break; + } + } + return networkMode; +}; -module.exports = function (workbookFile) { +exports.networks = function (workbookFile) { const networks = { network: {}, networkOptimizedWeights: {}, diff --git a/server/controllers/spreadsheet-controller.js b/server/controllers/spreadsheet-controller.js index 1e2f5532..515771ab 100644 --- a/server/controllers/spreadsheet-controller.js +++ b/server/controllers/spreadsheet-controller.js @@ -120,7 +120,9 @@ var crossSheetInteractions = function (workbookFile) { // Refactored the parseNetworkSheet function to preserve all network type sheets including "network", // "network_optimized_weights",and "network_weights" restructuring workbook object as a result - var networks = parseNetworkSheet(workbookFile); + + // var parseNetworkSheetData = parseNetworkSheet(workbookFile) + var networks = parseNetworkSheet.networks(workbookFile); // Parse expression and 2-column data, then add to workbook object // Eventually, will split this up into parsing for each type of sheet. @@ -194,6 +196,7 @@ var crossSheetInteractions = function (workbookFile) { } } + additionalData.meta.data.workbookType = parseNetworkSheet.networkMode(workbookFile); if (additionalData.meta.data.workbookType === undefined) { addWarning(workbook, constants.warnings.noWorkbookTypeDetected); additionalData.meta.data.workbookType = "grn"; diff --git a/test/export-tests.js b/test/export-tests.js index 9f8e65bb..efd56dab 100644 --- a/test/export-tests.js +++ b/test/export-tests.js @@ -407,6 +407,100 @@ describe("Export to GraphML", function () { }); }); +const inputPPIWorkbook = { + "genes": [ + { "name": "Aim32p" }, + { "name": "Ccr4p" }, + { "name": "Erv1p" } + ], + + "links": [ + { + "source": 0, + "target": 1, + "value": 1, + "type": "arrowhead", + "stroke": "black" + }, + { + "source": 1, + "target": 1, + "value": 1, + "type": "arrowhead", + "stroke": "black", + }, + { + "source": 0, + "target": 2, + "value": 1, + "type": "arrowhead", + "stroke": "black", + }, + { + "source": 2, + "target": 2, + "value": 1, + "type": "arrowhead", + "stroke": "black", + } + ], + + network: { + "genes": [ + { "name": "Aim32p" }, + { "name": "Ccr4p" }, + { "name": "Erv1p" } + ], + + "links": [ + { + "source": 0, + "target": 1, + "value": 1, + "type": "arrowhead", + "stroke": "black" + }, + { + "source": 1, + "target": 1, + "value": 1, + "type": "arrowhead", + "stroke": "black", + }, + { + "source": 0, + "target": 2, + "value": 1, + "type": "arrowhead", + "stroke": "black", + }, + { + "source": 2, + "target": 2, + "value": 1, + "type": "arrowhead", + "stroke": "black", + } + ], + }, + networkWeights: {}, + + "meta": { + data: { + "workbookType": "protein-protein-physical-interaction", + "species": "Saccharomyces cerevisiae", + "taxon_id": "559292", + } + }, +}; + +inputPPIWorkbook.exportSheets = { + networks: { + "network": inputPPIWorkbook.network + }, + "optimization_parameters": inputPPIWorkbook.meta +}; + const inputWorkbook = { "genes": [ { "name": "ACE2" }, @@ -550,7 +644,8 @@ const inputWorkbook = { "production_function": "testMM", "simulation_timepoints": [0, 0.1, 0.2], "species": "Saccharomyces cerevisiae", - "taxon_id": 559292 + "taxon_id": 559292, + "workbookType": "grn" } }, @@ -659,7 +754,7 @@ inputWorkbook.exportSheets = { }; describe("Export to spreadsheet", function () { - it("should export a workbook to a spreadsheet object properly", function () { + it("should export a workbook of gene regulatory network to a spreadsheet object properly", function () { const expectedSheet = [ { name: "network", @@ -701,7 +796,8 @@ describe("Export to spreadsheet", function () { ["production_function", "testMM"], ["simulation_timepoints", 0, 0.1, 0.2], ["species", "Saccharomyces cerevisiae"], - ["taxon_id", 559292] + ["taxon_id", 559292], + ["workbookType", "grn"] ] }, @@ -791,6 +887,32 @@ describe("Export to spreadsheet", function () { expect(actualSheet).to.deep.equal(xlsx.build(expectedSheet)); }); + it("should export a workbook of ppi to a spreadsheet object properly", function () { + const expectedSheet = [ + { + name: "network", + data: [ + ["protein 1/protein 2", "Aim32p", "Ccr4p", "Erv1p"], + ["Aim32p", 0, 0, 0], + ["Ccr4p", 1, 1, 0], + ["Erv1p", 1, 0, 1] + ] + }, + + { + name: "optimization_parameters", + data: [ + ["optimization_parameter", "value"], + ["workbookType", "protein-protein-physical-interaction"], + ["species", "Saccharomyces cerevisiae"], + ["taxon_id", "559292"] + ] + } + ]; + const actualSheet = exportController.grnsightToXlsx(inputPPIWorkbook); + expect(actualSheet).to.deep.equal(xlsx.build(expectedSheet)); + }); + it("should export a workbook exactly as the import", function () { // Commented out temporarily while reworking the export of the optimization diagnostics sheet diff --git a/test/test.js b/test/test.js index ee0bf508..28cf8f1c 100644 --- a/test/test.js +++ b/test/test.js @@ -14,7 +14,7 @@ var exportController = require(__dirname + "/../server/controllers/export-contro // changed network parser to preserve all network sheets instead of choosing the best and throwing awway rhe rest // this helper method chooses the best network sheet, so prior implemented test behaviour doesn't crash var parseNetworkSheet = (sheet) => { - var allNetworks = parseAllNetworkSheet(sheet); + var allNetworks = parseAllNetworkSheet.networks(sheet); if (typeof allNetworks.networkOptimizedWeights === "object" && Object.keys(allNetworks.networkOptimizedWeights).length !== 0) { return allNetworks.networkOptimizedWeights; From 9750efe6a6cb20e7f165b4a2fa87c7347b7e91c3 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Fri, 26 Jan 2024 14:40:28 -0800 Subject: [PATCH 010/150] Clean comment --- server/controllers/spreadsheet-controller.js | 1 - 1 file changed, 1 deletion(-) diff --git a/server/controllers/spreadsheet-controller.js b/server/controllers/spreadsheet-controller.js index 515771ab..67425827 100644 --- a/server/controllers/spreadsheet-controller.js +++ b/server/controllers/spreadsheet-controller.js @@ -121,7 +121,6 @@ var crossSheetInteractions = function (workbookFile) { // Refactored the parseNetworkSheet function to preserve all network type sheets including "network", // "network_optimized_weights",and "network_weights" restructuring workbook object as a result - // var parseNetworkSheetData = parseNetworkSheet(workbookFile) var networks = parseNetworkSheet.networks(workbookFile); // Parse expression and 2-column data, then add to workbook object From 3543466790c26ae689733bc3b6d694cadb7aa7c4 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Fri, 26 Jan 2024 20:10:21 -0800 Subject: [PATCH 011/150] Adding tests for PPI Unweighted Sif --- server/controllers/importers/sif.js | 34 +++++++++++-------- server/controllers/sif-constants.js | 2 +- test/import-sif-tests.js | 51 ++++++++++++++++++++++++----- 3 files changed, 64 insertions(+), 23 deletions(-) diff --git a/server/controllers/importers/sif.js b/server/controllers/importers/sif.js index 5ef130b8..0fda833a 100644 --- a/server/controllers/importers/sif.js +++ b/server/controllers/importers/sif.js @@ -44,7 +44,7 @@ module.exports = function (sif) { sifEntries.forEach(function (entry) { if (entry.length > TARGET) { if (!isNumber(entry[RELATIONSHIP])) { - if (entry[RELATIONSHIP] !== "pd") { + if (entry[RELATIONSHIP] !== "pd" && entry[RELATIONSHIP] !== 'pp') { unweightedRelationshipTypeErrorDetected = true; } } @@ -54,6 +54,24 @@ module.exports = function (sif) { } }); + let hasNumbers = relationships.some(isNumber); + let allNumbers = relationships.every(isNumber); + + let networkMode; + if (allNumbers) { + networkMode = "grn" + } else { + for (const relationship of relationships) { + if (relationship === "pp") { + networkMode = "protein-protein-physical-interaction"; + break; + } else if (relationship === "pd") { + networkMode = "grn" + break; + } + } + } + if (unweightedRelationshipTypeErrorDetected) { errors.push(sifConstants.errors.SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR); } @@ -61,19 +79,7 @@ module.exports = function (sif) { if (numRowsWithTwoColumns > 0) { errors.push(sifConstants.errors.SIF_MISSING_DATA_ERROR); } - - var hasNumbers = relationships.some(isNumber); - var allNumbers = relationships.every(isNumber); - - let networkMode = "grn"; - for (const relationship of relationships) { - if (relationship === "pp") { - networkMode = "protein-protein-physical-interaction"; - break; - } else if (relationship === "pd") { - break; - } - } + return { networkMode: networkMode, sheetType: allNumbers ? constants.WEIGHTED : constants.UNWEIGHTED, diff --git a/server/controllers/sif-constants.js b/server/controllers/sif-constants.js index e32445bb..eaf70107 100644 --- a/server/controllers/sif-constants.js +++ b/server/controllers/sif-constants.js @@ -13,7 +13,7 @@ module.exports = { SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR: { errorCode: "SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR", possibleCause: "The SIF importer detects an unweighted network with an unsupported relationship type.", - suggestedFix: "SIF files accepted by GRNsight must use 'pd' as the text string for the relationship" + + suggestedFix: "SIF files accepted by GRNsight must use 'pd' or 'pp' as the text string for the relationship" + " type in unweighted networks. Please review the SIF input documentation. Additionally, this" + " error may be have been caused by missing data in your file, which caused the importer to" + " incorrectly interpret a source or target as the relationship." diff --git a/test/import-sif-tests.js b/test/import-sif-tests.js index cd5911e1..0511c2fb 100644 --- a/test/import-sif-tests.js +++ b/test/import-sif-tests.js @@ -7,7 +7,7 @@ var importController = require(__dirname + "/../server/controllers" + "/import-c var constants = require(__dirname + "/../server/controllers" + "/constants"); var initWorkbook = require(__dirname + "/../server/controllers" + "/helpers.js").initWorkbook; -var expectedUnweightedWorkbook = initWorkbook({ +let expectedUnweightedGRNWorkbook = initWorkbook({ genes: [ { name: "A" }, { name: "B" }, @@ -31,6 +31,31 @@ var expectedUnweightedWorkbook = initWorkbook({ networkMode: "grn" }); +let expectedUnweightedPPIWorkbook = initWorkbook({ + genes: [ + { name: "A" }, + { name: "B" }, + { name: "C" }, + { name: "D" } + ], + + links: [ + { source: 1, target: 0 }, + { source: 1, target: 2 }, + { source: 2, target: 1 } + ], + + errors: [], + warnings: [], + positiveWeights: [], + negativeWeights: [], + sheetType: "unweighted", + meta: {}, + expression:{}, + networkMode: "protein-protein-physical-interaction" +}); + + var expectedWeightedWorkbook = initWorkbook({ genes: [ { name: "A" }, @@ -111,13 +136,20 @@ var expectedWeightedWorkbookWithCycle = initWorkbook({ // Unweighted SIF -var unweightedTestSif = [ +var unweightedGRNTestSif = [ "A", [ "B", "pd", "A", "C" ].join("\t"), [ "C", "pd", "B" ].join("\t"), "D" ].join("\r\n"); // Mix up linebreak types to test normalization. +var unweightedPPITestSif = [ + "A", + [ "B", "pp", "A", "C" ].join("\t"), + [ "C", "pp", "B" ].join("\t"), + "D" +].join("\r\n"); // Mix up linebreak types to test normalization. + var unweightedTestSifWithCycle = [ [ "A", "pd", "A" ].join("\t"), [ "B", "pd", "A", "C" ].join("\t"), @@ -287,8 +319,11 @@ var sifWithSemanticErrorOnly = [ describe("Import from SIF", function () { it("should import unweighted workbooks from SIF correctly", function () { expect( - importController.sifToGrnsight(unweightedTestSif) - ).to.deep.equal(expectedUnweightedWorkbook); + importController.sifToGrnsight(unweightedGRNTestSif) + ).to.deep.equal(expectedUnweightedGRNWorkbook); + expect( + importController.sifToGrnsight(unweightedPPITestSif) + ).to.deep.equal(expectedUnweightedPPIWorkbook); }); it("should import weighted workbooks from SIF correctly", function () { @@ -300,7 +335,7 @@ describe("Import from SIF", function () { it("should import inconsistently weighted workbooks from SIF as unweighted", function () { expect( importController.sifToGrnsight(inconsistentlyWeightedTestSif) - ).to.deep.equal(extend(true, {}, expectedUnweightedWorkbook, { + ).to.deep.equal(extend(true, {}, expectedUnweightedGRNWorkbook, { warnings: [ constants.warnings.EDGES_WITHOUT_WEIGHTS ] @@ -405,11 +440,11 @@ describe("Import from SIF syntactic checker", function () { it("should produce no warnings or errors for correct data", function () { expect( - importController.sifToGrnsight(unweightedTestSif).errors.length + importController.sifToGrnsight(unweightedGRNTestSif).errors.length ).to.equal(0); }); - it("should throw an error for unweighted graphs with relationship types other than 'pd'", function () { + it("should throw an error for unweighted graphs with relationship types other than 'pd' and 'pp", function () { expect( importController.sifToGrnsight(unweightedTestSifWithIncorrectRelationshipType).errors.length ).to.equal(1); @@ -476,7 +511,7 @@ describe("Import from SIF syntactic checker", function () { it("should accept trivially tabbed workbooks", function () { expect( importController.sifToGrnsight(triviallyTabbedUnweightedWorkbook) - ).to.deep.equal(expectedUnweightedWorkbook); + ).to.deep.equal(expectedUnweightedGRNWorkbook); }); }); From d9c56c2c8a3b01fb8c6e255cc9e1ba73268e2b49 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Fri, 26 Jan 2024 20:16:57 -0800 Subject: [PATCH 012/150] Clean lint errors --- server/controllers/importers/sif.js | 8 ++++---- server/controllers/sif-constants.js | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/server/controllers/importers/sif.js b/server/controllers/importers/sif.js index 0fda833a..c9f5e363 100644 --- a/server/controllers/importers/sif.js +++ b/server/controllers/importers/sif.js @@ -44,7 +44,7 @@ module.exports = function (sif) { sifEntries.forEach(function (entry) { if (entry.length > TARGET) { if (!isNumber(entry[RELATIONSHIP])) { - if (entry[RELATIONSHIP] !== "pd" && entry[RELATIONSHIP] !== 'pp') { + if (entry[RELATIONSHIP] !== "pd" && entry[RELATIONSHIP] !== "pp") { unweightedRelationshipTypeErrorDetected = true; } } @@ -59,14 +59,14 @@ module.exports = function (sif) { let networkMode; if (allNumbers) { - networkMode = "grn" + networkMode = "grn"; } else { for (const relationship of relationships) { if (relationship === "pp") { networkMode = "protein-protein-physical-interaction"; break; } else if (relationship === "pd") { - networkMode = "grn" + networkMode = "grn"; break; } } @@ -79,7 +79,7 @@ module.exports = function (sif) { if (numRowsWithTwoColumns > 0) { errors.push(sifConstants.errors.SIF_MISSING_DATA_ERROR); } - + return { networkMode: networkMode, sheetType: allNumbers ? constants.WEIGHTED : constants.UNWEIGHTED, diff --git a/server/controllers/sif-constants.js b/server/controllers/sif-constants.js index eaf70107..eedf9e87 100644 --- a/server/controllers/sif-constants.js +++ b/server/controllers/sif-constants.js @@ -13,10 +13,10 @@ module.exports = { SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR: { errorCode: "SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR", possibleCause: "The SIF importer detects an unweighted network with an unsupported relationship type.", - suggestedFix: "SIF files accepted by GRNsight must use 'pd' or 'pp' as the text string for the relationship" + - " type in unweighted networks. Please review the SIF input documentation. Additionally, this" + - " error may be have been caused by missing data in your file, which caused the importer to" + - " incorrectly interpret a source or target as the relationship." + suggestedFix: "SIF files accepted by GRNsight must use 'pd' or 'pp' as the text string for the" + + " relationship type in unweighted networks. Please review the SIF input documentation." + + " Additionally, this error may be have been caused by missing data in your file, which caused " + + "the importer to incorrectly interpret a source or target as the relationship." }, SIF_MISSING_DATA_ERROR: { From e9c3755e26d3cd5a092580ac9e311f63fcbfc328 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 29 Jan 2024 20:14:12 -0800 Subject: [PATCH 013/150] On Issue #1002, removing my package-lock.json from pull request since does not need to be pushed --- package-lock.json | 21619 ++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 19858 insertions(+), 1761 deletions(-) diff --git a/package-lock.json b/package-lock.json index b709fade..bebb0710 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,37 +1,17794 @@ { "name": "grnsight", - "version": "6.0.7", - "lockfileVersion": 1, + "version": "6.0.0", + "lockfileVersion": 2, "requires": true, + "packages": { + "": { + "name": "grnsight", + "version": "6.0.0", + 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@@ -1570,7 +19514,7 @@ "boom": { "version": "0.4.2", "resolved": "https://registry.npmjs.org/boom/-/boom-0.4.2.tgz", - "integrity": "sha512-OvfN8y1oAxxphzkl2SnCS+ztV/uVKTATtgLjWYg/7KwcNyf3rzpHxNQJZCKtsZd4+MteKczhWbSjtEX4bGgU9g==", + "integrity": "sha1-emNune1O/O+xnO9JR6PGffrukRs=", "requires": { "hoek": "0.9.x" } @@ -1592,7 +19536,7 @@ "camelcase": { "version": "4.1.0", "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-4.1.0.tgz", - "integrity": "sha512-FxAv7HpHrXbh3aPo4o2qxHay2lkLY3x5Mw3KeE4KQE8ysVfziWeRZDwcjauvwBSGEC/nXUPzZy8zeh4HokqOnw==" + "integrity": "sha1-1UVjW+HjPFQmScaRc+Xeas+uNN0=" } } }, @@ -1625,7 +19569,7 @@ "extend-shallow": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/extend-shallow/-/extend-shallow-2.0.1.tgz", - "integrity": "sha512-zCnTtlxNoAiDc3gqY2aYAWFx7XWWiasuF2K8Me5WbN8otHKTUKBwjPtNpRs/rbUZm7KxWAaNj7P1a/p52GbVug==", + "integrity": "sha1-Ua99YUrZqfYQ6huvu5idaxxWiQ8=", "requires": { "is-extendable": "^0.1.0" } @@ -1635,7 +19579,7 @@ 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"sha1-MeohpzS6ubuw8yRm2JOupR5KPGQ=", "dev": true, "requires": { "is-buffer": "^1.1.5" @@ -4006,7 +22003,7 @@ "expand-tilde": { "version": "2.0.2", "resolved": "https://registry.npmjs.org/expand-tilde/-/expand-tilde-2.0.2.tgz", - "integrity": "sha512-A5EmesHW6rfnZ9ysHQjPdJRni0SRar0tjtG5MNtm9n5TUvsYU8oozprtRD4AqHxcZWWlVuAmQo2nWKfN9oyjTw==", + "integrity": "sha1-l+gBqgUt8CRU3kawK/YhZCzchQI=", "dev": true, "requires": { "homedir-polyfill": "^1.0.1" @@ -4015,7 +22012,7 @@ "express": { "version": "4.16.0", "resolved": "https://registry.npmjs.org/express/-/express-4.16.0.tgz", - "integrity": "sha512-mBhv3wUcA4u0UyVlxjwJYmvdrDu1eBj9w9/8go1WCRqMDH2Rs0i+GFoWutMHtYlEkfjz9C4aQeEleWxT//ZYKg==", + "integrity": "sha1-tRljjk61jnF4yBtJjvIveYyy4lU=", "requires": { "accepts": "~1.3.4", "array-flatten": "1.1.1", @@ -4052,7 +22049,7 @@ "serve-static": { "version": "1.13.0", "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.13.0.tgz", - "integrity": 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"path-dirname": "^1.0.0" @@ -5012,7 +23041,7 @@ "is-glob": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/is-glob/-/is-glob-3.1.0.tgz", - "integrity": "sha512-UFpDDrPgM6qpnFNI+rh/p3bUaq9hKLZN8bMUWzxmcnZVS3omf4IPK+BrewlnWjO1WmUsMYuSjKh4UJuV4+Lqmw==", + "integrity": "sha1-e6WuJCF4BKxwcHuWkiVnSGzD6Eo=", "requires": { "is-extglob": "^2.1.0" } @@ -5022,13 +23051,13 @@ "glob-to-regexp": { "version": "0.3.0", "resolved": "https://registry.npmjs.org/glob-to-regexp/-/glob-to-regexp-0.3.0.tgz", - "integrity": "sha512-Iozmtbqv0noj0uDDqoL0zNq0VBEfK2YFoMAZoxJe4cwphvLR+JskfF30QhXHOR4m3KrE6NLRYw+U9MRXvifyig==", + "integrity": "sha1-jFoUlNIGbFcMw7/kSWF1rMTVAqs=", "dev": true }, "global-dirs": { "version": "0.1.1", "resolved": "https://registry.npmjs.org/global-dirs/-/global-dirs-0.1.1.tgz", - "integrity": "sha512-NknMLn7F2J7aflwFOlGdNIuCDpN3VGoSoB+aap3KABFWbHVn1TCgFC+np23J8W2BiZbjfEw3BFBycSMv1AFblg==", + "integrity": "sha1-sxnA3UYH81PzvpzKTHL8FIxJ9EU=", "requires": { "ini": "^1.3.4" } @@ -5047,7 +23076,7 @@ "global-prefix": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/global-prefix/-/global-prefix-1.0.2.tgz", - "integrity": "sha512-5lsx1NUDHtSjfg0eHlmYvZKv8/nVqX4ckFbM+FrGcQ+04KWcWFo9P5MxPZYSzUvyzmdTbI7Eix8Q4IbELDqzKg==", + "integrity": "sha1-2/dDxsFJklk8ZVVoy2btMsASLr4=", "dev": true, "requires": { "expand-tilde": "^2.0.2", @@ -5076,28 +23105,12 @@ "ignore": "^3.3.5", "pify": "^3.0.0", "slash": "^1.0.0" - }, - "dependencies": { - "glob": { - "version": "7.2.3", - "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", - "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", - "dev": true, - "requires": { - "fs.realpath": "^1.0.0", - "inflight": "^1.0.4", - "inherits": "2", - "minimatch": "^3.1.1", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" - } - } } }, "googleapis": { "version": "1.1.5", "resolved": "https://registry.npmjs.org/googleapis/-/googleapis-1.1.5.tgz", - "integrity": 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"version": "1.4.1", @@ -5267,10 +23267,16 @@ "has-symbols": "^1.0.2" } }, + "has-unicode": { + "version": "2.0.1", + "resolved": "https://registry.npmjs.org/has-unicode/-/has-unicode-2.0.1.tgz", + "integrity": "sha1-4Ob+aijPUROIVeCG0Wkedx3iqLk=", + "peer": true + }, "has-value": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/has-value/-/has-value-1.0.0.tgz", - "integrity": "sha512-IBXk4GTsLYdQ7Rvt+GRBrFSVEkmuOUy4re0Xjd9kJSUQpnTrWR4/y9RpfexN9vkAPMFuQoeWKwqzPozRTlasGw==", + "integrity": "sha1-GLKB2lhbHFxR3vJMkw7SmgvmsXc=", "requires": { "get-value": "^2.0.6", "has-values": "^1.0.0", @@ -5280,7 +23286,7 @@ "has-values": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/has-values/-/has-values-1.0.0.tgz", - "integrity": "sha512-ODYZC64uqzmtfGMEAX/FvZiRyWLpAC3vYnNunURUnkGVTS+mI0smVsWaPydRBsE3g+ok7h960jChO8mFcWlHaQ==", + "integrity": "sha1-lbC2P+whRmGab+V/51Yo1aOe/k8=", "requires": { "is-number": "^3.0.0", "kind-of": "^4.0.0" @@ -5289,7 +23295,7 @@ "kind-of": { 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"jwa": "~1.0.0" @@ -6858,7 +24848,7 @@ "kew": { "version": "0.7.0", "resolved": "https://registry.npmjs.org/kew/-/kew-0.7.0.tgz", - "integrity": "sha512-IG6nm0+QtAMdXt9KvbgbGdvY50RSrw+U4sGZg+KlrSKPJEwVE5JVoI3d7RWfSMdBQneRheeAOj3lIjX5VL/9RQ==", + "integrity": "sha1-edk9LTM2PW/dKXCzNdkUGtWR15s=", "dev": true }, "keyv": { @@ -6878,7 +24868,7 @@ "klaw": { "version": "1.3.1", "resolved": "https://registry.npmjs.org/klaw/-/klaw-1.3.1.tgz", - "integrity": "sha512-TED5xi9gGQjGpNnvRWknrwAB1eL5GciPfVFOt3Vk1OJCVDQbzuSfrF3hkUQKlsgKrG1F+0t5W0m+Fje1jIt8rw==", + "integrity": "sha1-QIhDO0azsbolnXh4XY6W9zugJDk=", "dev": true, "requires": { "graceful-fs": "^4.1.9" @@ -6887,7 +24877,7 @@ "latest-version": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/latest-version/-/latest-version-3.1.0.tgz", - "integrity": "sha512-Be1YRHWWlZaSsrz2U+VInk+tO0EwLIyV+23RhWLINJYwg/UIikxjlj3MhH37/6/EDCAusjajvMkMMUXRaMWl/w==", + "integrity": "sha1-ogU4P+oyKzO1rjsYq+4NwvNW7hU=", "requires": { "package-json": 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} @@ -7161,7 +25151,7 @@ "load-json-file": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/load-json-file/-/load-json-file-4.0.0.tgz", - "integrity": "sha512-Kx8hMakjX03tiGTLAIdJ+lL0htKnXjEZN6hk/tozf/WOuYGdZBJrZ+rCJRbVCugsjB3jMLn9746NsQIf5VjBMw==", + "integrity": "sha1-L19Fq5HjMhYjT9U62rZo607AmTs=", "dev": true, "requires": { "graceful-fs": "^4.1.2", @@ -7173,7 +25163,7 @@ "parse-json": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/parse-json/-/parse-json-4.0.0.tgz", - "integrity": "sha512-aOIos8bujGN93/8Ox/jPLh7RwVnPEysynVFE+fQZyg6jKELEHwzgKdLRFHUgXJL6kylijVSBC4BvN9OmsB48Rw==", + "integrity": "sha1-vjX1Qlvh9/bHRxhPmKeIy5lHfuA=", "dev": true, "requires": { "error-ex": "^1.3.1", @@ -7188,9 +25178,9 @@ "integrity": "sha512-Jsmr89RcXGIwivFY21FcRrisYZfvLMTWx5kOLc+JTxtpBOG6xML0vzbc6SEQG2FO9/4Fc3wW4LVcB5DmGflaRw==" }, "loader-utils": { - "version": "1.4.2", - "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-1.4.2.tgz", - "integrity": 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@@ -12951,13 +31077,13 @@ "require-main-filename": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/require-main-filename/-/require-main-filename-1.0.1.tgz", - "integrity": "sha512-IqSUtOVP4ksd1C/ej5zeEh/BIP2ajqpn8c5x+q99gvcIG/Qf0cud5raVnE/Dwd0ua9TXYDoDc0RE5hBSdz22Ug==", + "integrity": "sha1-l/cXtp1IeE9fUmpsWqj/3aBVpNE=", "dev": true }, "wrap-ansi": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-2.1.0.tgz", - "integrity": "sha512-vAaEaDM946gbNpH5pLVNR+vX2ht6n0Bt3GXwVB1AuAqZosOvHNF3P7wDnh8KLkSqgUh0uh77le7Owgoz+Z9XBw==", + "integrity": "sha1-2Pw9KE3QV5T+hJc8rs3Rz4JP3YU=", "dev": true, "requires": { "string-width": "^1.0.1", @@ -12967,7 +31093,7 @@ "string-width": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/string-width/-/string-width-1.0.2.tgz", - "integrity": "sha512-0XsVpQLnVCXHJfyEs8tC0zpTVIr5PKKsQtkT29IwupnPTjtPmQ3xT/4yCREF9hYkV/3M3kzcUTSAZT6a6h81tw==", + "integrity": "sha1-EYvfW4zcUaKn5w0hHgfisLmxB9M=", "dev": true, 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"integrity": "sha512-LeZY+DZDRnvP7eMuQ6LHfCzUGxAAIViUBliK24P3hWXL6y4SortgR6Nim6xrkfSLlmH0+k+9NYNwVC2s53ZrYQ==", + "integrity": "sha1-7/UuN1gknTO+QCuLuOVkuytdQDE=", "dev": true }, "async": { - "version": "2.6.4", - "resolved": "https://registry.npmjs.org/async/-/async-2.6.4.tgz", - "integrity": "sha512-mzo5dfJYwAn29PeiJ0zvwTo04zj8HDJj0Mn8TD7sno7q12prdbnasKJHhkm2c1LgrhlJ0teaea8860oxi51mGA==", + "version": "2.6.3", + "resolved": "https://registry.npmjs.org/async/-/async-2.6.3.tgz", + "integrity": "sha512-zflvls11DCy+dQWzTW2dzuilv8Z5X/pjfmZOWba6TNIVDm+2UDaJmXSOXlasHKfNBs8oo3M0aT50fDEWfKZjXg==", "dev": true, "requires": { "lodash": "^4.17.14" @@ -13825,7 +31929,7 @@ "dargs": { "version": "5.1.0", "resolved": "https://registry.npmjs.org/dargs/-/dargs-5.1.0.tgz", - "integrity": "sha512-Mr5OxT76pdJv7BbLq3hF1gSP8zxlCyDA1afj2Iab2MPKmdAKV+aKGC8YJv6cT8ItdFXAf798JJQD7jmbWZcYTQ==", + "integrity": "sha1-7H6lDHhWTNNsnV7Bj2Yyn63ieCk=", "dev": true }, "debug": { @@ -13850,7 +31954,7 @@ "github-username": { "version": "4.1.0", "resolved": "https://registry.npmjs.org/github-username/-/github-username-4.1.0.tgz", - "integrity": "sha512-ABDfD5sjQOE8XDatHhN/WORUIAN1AGpgW4vegrKtby8x+jC/ALqCEuUDhCPlk9EXtjTHJWpuK25QdaehSUlCQg==", + "integrity": "sha1-y+KABBiDIG2kISrp5LXxacML9Bc=", "dev": true, "requires": { "gh-got": "^6.0.0" @@ -13859,7 +31963,7 @@ "globby": { "version": "7.1.1", "resolved": "https://registry.npmjs.org/globby/-/globby-7.1.1.tgz", - "integrity": "sha512-yANWAN2DUcBtuus5Cpd+SKROzXHs2iVXFZt/Ykrfz6SAXqacLX25NZpltE+39ceMexYF4TtEadjuSTw8+3wX4g==", + "integrity": "sha1-+yzP+UAfhgCUXfral0QMypcrhoA=", "dev": true, "requires": { "array-union": "^1.0.1", @@ -13868,22 +31972,6 @@ "ignore": "^3.3.5", "pify": "^3.0.0", "slash": "^1.0.0" - }, - "dependencies": { - "glob": { - "version": "7.2.3", - "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", - "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", - "dev": true, - "requires": { - "fs.realpath": "^1.0.0", - "inflight": "^1.0.4", - "inherits": "2", - "minimatch": "^3.1.1", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" - } - } } }, "got": { @@ -13936,6 +32024,15 @@ "vinyl": "^2.0.1" } }, + "mkdirp": { + "version": "0.5.5", + "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-0.5.5.tgz", + "integrity": "sha512-NKmAlESf6jMGym1++R0Ra7wvhV+wFW63FaSOFPwRahvea0gMUcGUhVeAg/0BC0wiv9ih5NYPB1Wn1UEI1/L+xQ==", + "dev": true, + "requires": { + "minimist": "^1.2.5" + } + }, "ms": { "version": "2.1.3", "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz", @@ -13945,7 +32042,7 @@ "multimatch": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/multimatch/-/multimatch-2.1.0.tgz", - "integrity": "sha512-0mzK8ymiWdehTBiJh0vClAzGyQbdtyWqzSVx//EK4N/D+599RFlGfTAsKw2zMSABtDG9C6Ul2+t8f2Lbdjf5mA==", + "integrity": "sha1-nHkGoi+0wCkZ4vX3UWG0zb1LKis=", "dev": true, "requires": { "array-differ": "^1.0.0", @@ -13963,7 +32060,7 @@ "p-timeout": { "version": "1.2.1", "resolved": "https://registry.npmjs.org/p-timeout/-/p-timeout-1.2.1.tgz", - "integrity": "sha512-gb0ryzr+K2qFqFv6qi3khoeqMZF/+ajxQipEF6NteZVnvz9tzdsfAVj3lYtn1gAXvH5lfLwfxEII799gt/mRIA==", + "integrity": "sha1-XrOzU7f86Z8QGhA4iAuwVOu+o4Y=", "dev": true, "requires": { "p-finally": "^1.0.0" @@ -13972,13 +32069,13 @@ "pretty-bytes": { "version": "4.0.2", "resolved": "https://registry.npmjs.org/pretty-bytes/-/pretty-bytes-4.0.2.tgz", - "integrity": "sha512-yJAF+AjbHKlxQ8eezMd/34Mnj/YTQ3i6kLzvVsH4l/BfIFtp444n0wVbnsn66JimZ9uBofv815aRp1zCppxlWw==", + "integrity": "sha1-sr+C5zUNZcbDOqlaqlpPYyf2HNk=", "dev": true }, "read-chunk": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/read-chunk/-/read-chunk-2.1.0.tgz", - "integrity": "sha512-QQqB2O9KX/BnztP1xkTRsBxABcWHCXTqQYmEm/DdNId1nw+leKkZvV/g5oCKUrXolGtU3zouoIxMLToAYyDgDw==", + "integrity": "sha1-agTAkoAF7Z1C4aasVgDhnLx/9lU=", "dev": true, "requires": { "pify": "^3.0.0", @@ -13988,7 +32085,7 @@ "read-pkg": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/read-pkg/-/read-pkg-3.0.0.tgz", - "integrity": "sha512-BLq/cCO9two+lBgiTYNqD6GdtK8s4NpaWrl6/rCO9w0TUS8oJl7cmToOZfRYllKTISY6nt1U7jQ53brmKqY6BA==", + "integrity": "sha1-nLxoaXj+5l0WwA4rGcI3/Pbjg4k=", "dev": true, "requires": { "load-json-file": "^4.0.0", @@ -13999,7 +32096,7 @@ "read-pkg-up": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/read-pkg-up/-/read-pkg-up-3.0.0.tgz", - "integrity": "sha512-YFzFrVvpC6frF1sz8psoHDBGF7fLPc+llq/8NB43oagqWkx8ar5zYtsTORtOjw9W2RHLpWP+zTWwBvf1bCmcSw==", + "integrity": "sha1-PtSWaF26D4/hGNBpHcUfSh/5bwc=", "dev": true, "requires": { "find-up": "^2.0.0", From f2570bdc4c8403f241869a22d13381a3ecb1a6a3 Mon Sep 17 00:00:00 2001 From: dondi Date: Tue, 30 Jan 2024 10:22:55 -0800 Subject: [PATCH 014/150] Version bump. --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 3e03a883..9ec726c3 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "grnsight", - "version": "7.0.8", + "version": "7.0.9", "description": "Web app and service for visualizing models of gene regulatory networks", "directories": { "test": "test" From 5903498bb5d64623bd5774e8ab2e74963745b07a Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 2 Feb 2024 18:47:26 -0800 Subject: [PATCH 015/150] Working on issue #1091. Fixed issue caught in PR #1085 with file test-files/semantic-error-test-files/empty-network-xlsx-with-network-tab.xlsx. Added a try-catch that makes error modal pop up --- server/controllers/network-sheet-parser.js | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index 01024692..8f231f3b 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -94,7 +94,13 @@ var parseNetworkSheet = function (sheet, network) { var rowData = []; // check for “cols regulators/rows targets” in cell A1 - const cellA1 = sheet.data[0][0]; + let cellA1 = ""; + try { + cellA1 = sheet.data[0][0]; + } catch (err) { + addError(network, constants.errors.missingValueError(row, column)); + return network; + } // TODO There are now 2 valid values for cellA1. One indicates GRN, the other is PPI. // If neither, then we continue with the warning. From 5db14720237adb237aadb16efe34a92be9ec783c Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 2 Feb 2024 19:05:12 -0800 Subject: [PATCH 016/150] Working on issue #1091 that found issue in PR #1085. Adjusted code for lint errors --- server/controllers/network-sheet-parser.js | 2 ++ 1 file changed, 2 insertions(+) diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index 8f231f3b..6f714ea9 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -98,6 +98,8 @@ var parseNetworkSheet = function (sheet, network) { try { cellA1 = sheet.data[0][0]; } catch (err) { + const row = 0; + const column = 0; addError(network, constants.errors.missingValueError(row, column)); return network; } From ff0d8e44ba75cb74d921c1f5e1f8ebe4f5063b30 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 2 Feb 2024 20:15:29 -0800 Subject: [PATCH 017/150] Issue #1083. D-pad and slider can show again. Need to decide whether want the user to be able to use the D-pad and zoom slider or disable them --- web-client/public/js/graph.js | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index ef69b6c3..76746589 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -163,12 +163,14 @@ export var drawGraph = function (workbook) { zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; $container.removeClass(CURSOR_CLASSES).addClass("cursorGrabbing"); + // this prevents the zoom from zooming in and out if (!adaptive) { $container.removeClass(CURSOR_CLASSES); } }; var zoomDragged = function () { + // this only allows the zoom slider to be dragged if adaptive if (adaptive) { var scale = 1; if (zoomContainer.attr("transform")) { @@ -182,6 +184,7 @@ export var drawGraph = function (workbook) { }; var zoomDragEnded = function () { + // this only allows the zoom slider to be dragged if adaptive $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); if (!adaptive) { $container.removeClass(CURSOR_CLASSES); @@ -243,7 +246,12 @@ export var drawGraph = function (workbook) { const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); - } else if (!adaptive && zoomScale >= MIDDLE_SCALE) { + } // this only allows the zoom slider to be dragged if adaptive -> new code + // else if (zoomScale >= MIDDLE_SCALE) { + // $container.removeClass(CURSOR_CLASSES); + // } + // this prevents the zoom slider to be dragged if not adaptive -> old code + else if (!adaptive && zoomScale >= MIDDLE_SCALE) { $container.removeClass(CURSOR_CLASSES); } var container = zoomContainer; @@ -257,7 +265,7 @@ export var drawGraph = function (workbook) { let zoomScaleSliderRight; const updateAppBasedOnZoomValue = () => { - + // sets constant zoomvalue if not adaptive if (!adaptive) { grnState.zoomValue = 100.0; } @@ -369,10 +377,12 @@ export var drawGraph = function (workbook) { center(); } else if (fixed) { $("#restrict-graph-to-viewport span").addClass("glyphicon-ok"); + // this checks the box that restricts viewport $("input[name=viewport]").prop("checked", "checked"); - $(document).ready(function () { - $(".scale-and-scroll").hide(); - }); + // this hides the dpad and the scroll + // $(document).ready(function () { + // $(".scale-and-scroll").hide(); + // }); adaptive = false; $container.removeClass(CURSOR_CLASSES); if (grnState.zoomValue > ZOOM_DISPLAY_MIDDLE) { From 00f490ce5dfedc46d1852a7503d1082946b831bb Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 5 Feb 2024 13:04:55 -0800 Subject: [PATCH 018/150] can scroll the zoom slider less than 100, but the zoom does not go below 100. need to figure out how to stop the slider from moving --- web-client/public/js/graph.js | 53 +++++++++++++++++++++++++++-------- 1 file changed, 42 insertions(+), 11 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 76746589..d8521f49 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -164,9 +164,9 @@ export var drawGraph = function (workbook) { zoomDragPrevY = d3.event.y; $container.removeClass(CURSOR_CLASSES).addClass("cursorGrabbing"); // this prevents the zoom from zooming in and out - if (!adaptive) { - $container.removeClass(CURSOR_CLASSES); - } + // if (!adaptive) { + // $container.removeClass(CURSOR_CLASSES); + // } }; var zoomDragged = function () { @@ -180,15 +180,32 @@ export var drawGraph = function (workbook) { zoom.translateBy(zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY)); zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; + } else { + var scale = 1; + if (zoomContainer.attr("transform")) { + var string = zoomContainer.attr("transform"); + scale = 1 / +string.match(/scale\(([^\)]+)\)/)[1]; + } + if (d3.event.x >= ZOOM_DISPLAY_MIDDLE) { + zoom.translateBy( + zoomContainer, + scale * (d3.event.x - zoomDragPrevX), + scale * (d3.event.y - zoomDragPrevY) + ); + zoomDragPrevX = d3.event.x; + zoomDragPrevY = d3.event.y; + } + + } }; var zoomDragEnded = function () { // this only allows the zoom slider to be dragged if adaptive $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); - if (!adaptive) { - $container.removeClass(CURSOR_CLASSES); - } + // if (!adaptive) { + // $container.removeClass(CURSOR_CLASSES); + // } }; var zoomDrag = d3.drag() @@ -265,13 +282,27 @@ export var drawGraph = function (workbook) { let zoomScaleSliderRight; const updateAppBasedOnZoomValue = () => { - // sets constant zoomvalue if not adaptive - if (!adaptive) { - grnState.zoomValue = 100.0; - } + // TODO: sets constant zoomvalue if not adaptive. This is the line that keeps it constant + // if (!adaptive) { + // grnState.zoomValue = 100.0; + // } const zoomDisplay = grnState.zoomValue; - setGraphZoom((zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)(zoomDisplay)); + if (adaptive) { + setGraphZoom( + (zoomDisplay <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleLeft + : zoomScaleRight)(zoomDisplay) + ); + } else { + if (grnState.zoomValue >= ZOOM_DISPLAY_MIDDLE) { + setGraphZoom( + (zoomDisplay <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleLeft + : zoomScaleRight)(zoomDisplay) + ); + } + } const finalDisplay = grnState.zoomValue; $(ZOOM_PERCENT).text(`${finalDisplay}%`); From c5c9c46917b80c55f16e511187b6343a45be41b2 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 5 Feb 2024 13:24:18 -0800 Subject: [PATCH 019/150] Issue #1083. Zoom slider minimum value is 100%, or ZOOM_DISPLAY_MIDDLE, and the zoom slider can only be moved to 100% as well --- web-client/public/js/graph.js | 49 +++++++++++++++++++---------------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index d8521f49..e14c4ae1 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -195,8 +195,6 @@ export var drawGraph = function (workbook) { zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; } - - } }; @@ -263,13 +261,6 @@ export var drawGraph = function (workbook) { const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); - } // this only allows the zoom slider to be dragged if adaptive -> new code - // else if (zoomScale >= MIDDLE_SCALE) { - // $container.removeClass(CURSOR_CLASSES); - // } - // this prevents the zoom slider to be dragged if not adaptive -> old code - else if (!adaptive && zoomScale >= MIDDLE_SCALE) { - $container.removeClass(CURSOR_CLASSES); } var container = zoomContainer; zoom.scaleTo(container, zoomScale); @@ -282,10 +273,10 @@ export var drawGraph = function (workbook) { let zoomScaleSliderRight; const updateAppBasedOnZoomValue = () => { - // TODO: sets constant zoomvalue if not adaptive. This is the line that keeps it constant - // if (!adaptive) { - // grnState.zoomValue = 100.0; - // } + // If !adaptive, set Zoomvalue to ZOOM_DISPLAY_MIDDLE, 100, so do not zoom outside Ggr + if (!adaptive && grnState.zoomValue < ZOOM_DISPLAY_MIDDLE) { + grnState.zoomValue = ZOOM_DISPLAY_MIDDLE; + } const zoomDisplay = grnState.zoomValue; if (adaptive) { @@ -294,14 +285,12 @@ export var drawGraph = function (workbook) { ? zoomScaleLeft : zoomScaleRight)(zoomDisplay) ); - } else { - if (grnState.zoomValue >= ZOOM_DISPLAY_MIDDLE) { - setGraphZoom( - (zoomDisplay <= ZOOM_DISPLAY_MIDDLE - ? zoomScaleLeft - : zoomScaleRight)(zoomDisplay) - ); - } + } else if (!adaptive && grnState.zoomValue >= ZOOM_DISPLAY_MIDDLE){ + setGraphZoom( + (zoomDisplay <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleLeft + : zoomScaleRight)(zoomDisplay) + ); } const finalDisplay = grnState.zoomValue; @@ -314,8 +303,22 @@ export var drawGraph = function (workbook) { $(ZOOM_INPUT).val(finalDisplay); } - $(ZOOM_SLIDER).val((finalDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleSliderLeft : zoomScaleSliderRight) - .invert(finalDisplay)); + if (adaptive) { + $(ZOOM_SLIDER).val( + (finalDisplay <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleSliderLeft + : zoomScaleSliderRight + ).invert(finalDisplay) + ); + } else if (!adaptive && grnState.zoomValue >= ZOOM_DISPLAY_MIDDLE) { + // only allow minimum zoom value to be 100% so that do not go outside of viewport + $(ZOOM_SLIDER).val( + (finalDisplay <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleSliderLeft + : zoomScaleSliderRight + ).invert(finalDisplay) + ); + } }; /** From a08395fc177df5509bf41291243008ba1667f66f Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 5 Feb 2024 13:25:54 -0800 Subject: [PATCH 020/150] Issue #1083. Deleted unnecessary comment --- web-client/public/js/graph.js | 5 ----- 1 file changed, 5 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index e14c4ae1..db5ccd89 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -411,12 +411,7 @@ export var drawGraph = function (workbook) { center(); } else if (fixed) { $("#restrict-graph-to-viewport span").addClass("glyphicon-ok"); - // this checks the box that restricts viewport $("input[name=viewport]").prop("checked", "checked"); - // this hides the dpad and the scroll - // $(document).ready(function () { - // $(".scale-and-scroll").hide(); - // }); adaptive = false; $container.removeClass(CURSOR_CLASSES); if (grnState.zoomValue > ZOOM_DISPLAY_MIDDLE) { From 073cd6783a421e4ca1a0c654e5704a1969cb723b Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 5 Feb 2024 22:30:21 -0800 Subject: [PATCH 021/150] Issue #1083. Can use arrows on D-pad to move graph, sometimes can see border of graph though. Need to make sure that can only move cursor to area in graph as well --- web-client/public/js/graph.js | 76 +++++++++++++++++++++++++---------- 1 file changed, 54 insertions(+), 22 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index db5ccd89..6da9682d 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -163,10 +163,6 @@ export var drawGraph = function (workbook) { zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; $container.removeClass(CURSOR_CLASSES).addClass("cursorGrabbing"); - // this prevents the zoom from zooming in and out - // if (!adaptive) { - // $container.removeClass(CURSOR_CLASSES); - // } }; var zoomDragged = function () { @@ -199,11 +195,7 @@ export var drawGraph = function (workbook) { }; var zoomDragEnded = function () { - // this only allows the zoom slider to be dragged if adaptive $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); - // if (!adaptive) { - // $container.removeClass(CURSOR_CLASSES); - // } }; var zoomDrag = d3.drag() @@ -249,10 +241,11 @@ export var drawGraph = function (workbook) { .attr("stroke", "none" ) .append("g"); + // this controls the D-pad d3.selectAll(".scrollBtn").on("click", null); // Remove event handlers, if there were any. var arrowMovement = [ "Up", "Left", "Right", "Down" ]; arrowMovement.forEach(function (direction) { - d3.select(".scroll" + direction).on("click", function () { + d3.select(".scroll" + direction).on("click", function() { move(direction.toLowerCase()); }); }); @@ -447,9 +440,48 @@ export var drawGraph = function (workbook) { } function move (direction) { - var width = direction === "left" ? -50 : (direction === "right" ? 50 : 0); - var height = direction === "up" ? -50 : (direction === "down" ? 50 : 0); - zoom.translateBy(zoomContainer, width, height); + // TODO: move is what moves the graph!!! + var width = + direction === "left" ? -50 : direction === "right" ? 50 : 0; + var height = + direction === "up" ? -50 : direction === "down" ? 50 : 0; + + if (adaptive) { + zoom.translateBy(zoomContainer, width, height); + } else if (!adaptive && grnState.zoomValue != ZOOM_DISPLAY_MIDDLE) { + // we parse through transform attribute of zoomContainer which contains information about the scale of the graph + const graphScale = parseFloat( + zoomContainer + .attr("transform") + .split("(")[2].split(")")[0] + ); + + const xTranslation = parseFloat(zoomContainer + .attr("transform") + .split("(")[1].split(",")[0]) + + const yTranslation = parseFloat(zoomContainer + .attr("transform") + .split("(")[1].split(",")[1].split(")")[0]) + + const zoomContainerWidth = parseInt(zoomContainer.attr("width")); + const zoomContainerHeight = parseInt(zoomContainer.attr("height")); + + // right: abs(new x coordinate) / zoomContainerWidth - 1.0 == all digits after decimal point if graphscale > 1 and < 2 or graphScale - 1 if graphScale >= 2 + // bottom: abs(new y coordinate) / zoomContainerHeight - 1.0 == all digits after decimal point if graphscale > 1 and < 2 or graphScale - 1 if graphScale >= 2 + // top: y coordinate rounded == -0 + // left: y coordinate rounded == -0 + if ( + Math.abs(xTranslation + width) / zoomContainerWidth <= + graphScale - 1.0 && + Math.abs(yTranslation + height) / zoomContainerHeight <= + graphScale - 1.0 && + xTranslation + width <= 0 && + yTranslation + height <= 0 + ) { + zoom.translateBy(zoomContainer, width, height); + } + } } var defs = boundingBoxContainer.append("defs"); @@ -1365,6 +1397,7 @@ export var drawGraph = function (workbook) { var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; + // this controls movement and position of nodes try { node.attr("x", function (d) { var selfReferringEdge = getSelfReferringEdge(d); @@ -1406,17 +1439,16 @@ export var drawGraph = function (workbook) { height += OFFSET_VALUE; boundingBoxContainer.attr("height", height); link - .attr("y1", function (d) { - return d.source.y; - }) - .attr("y2", function (d) { - return d.target.y; - }); + .attr("y1", function(d) { + return d.source.y; + }) + .attr("y2", function(d) { + return d.target.y; + }); - node - .attr("y", function (d) { - return d.y; - }); + node.attr("y", function(d) { + return d.y; + }); } } return d.y = currentYPos; From 69165d67e7ce7a1dcdd26c9eb46bbfb0335e08c1 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 5 Feb 2024 22:54:20 -0800 Subject: [PATCH 022/150] Issue #1083. In updateAppBasedOnZoomValue, center() graph whenever zoom value changed and in restrict graph to viewpoint so that do not exceed viewport borders. Also cleaned up code in zoomDragged to be cleaner --- web-client/public/js/graph.js | 32 +++++++++++++------------------- 1 file changed, 13 insertions(+), 19 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 6da9682d..d380c4e0 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -165,33 +165,24 @@ export var drawGraph = function (workbook) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrabbing"); }; + // allows zoom slider to be moved and limits movement when !adaptive var zoomDragged = function () { - // this only allows the zoom slider to be dragged if adaptive - if (adaptive) { var scale = 1; if (zoomContainer.attr("transform")) { var string = zoomContainer.attr("transform"); scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } - zoom.translateBy(zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY)); - zoomDragPrevX = d3.event.x; - zoomDragPrevY = d3.event.y; - } else { - var scale = 1; - if (zoomContainer.attr("transform")) { - var string = zoomContainer.attr("transform"); - scale = 1 / +string.match(/scale\(([^\)]+)\)/)[1]; + if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE) { + zoom.translateBy( + zoomContainer, + scale * (d3.event.x - zoomDragPrevX), + scale * (d3.event.y - zoomDragPrevY) + ); + } else if (adaptive) { + zoom.translateBy(zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY)); } - if (d3.event.x >= ZOOM_DISPLAY_MIDDLE) { - zoom.translateBy( - zoomContainer, - scale * (d3.event.x - zoomDragPrevX), - scale * (d3.event.y - zoomDragPrevY) - ); zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; - } - } }; var zoomDragEnded = function () { @@ -284,6 +275,7 @@ export var drawGraph = function (workbook) { ? zoomScaleLeft : zoomScaleRight)(zoomDisplay) ); + center(); } const finalDisplay = grnState.zoomValue; @@ -407,10 +399,12 @@ export var drawGraph = function (workbook) { $("input[name=viewport]").prop("checked", "checked"); adaptive = false; $container.removeClass(CURSOR_CLASSES); + $container.removeClass("cursorGrab"); if (grnState.zoomValue > ZOOM_DISPLAY_MIDDLE) { grnState.zoomValue = ZOOM_DISPLAY_MIDDLE; updateAppBasedOnZoomValue(); $container.removeClass(CURSOR_CLASSES); + $container.removeClass("cursorGrabbing"); } width = $container.width(); height = $container.height(); @@ -439,8 +433,8 @@ export var drawGraph = function (workbook) { zoom.translateTo(zoomContainer, viewportWidth / 2, viewportHeight / 2); } + // move: moves graph with D-pad function move (direction) { - // TODO: move is what moves the graph!!! var width = direction === "left" ? -50 : direction === "right" ? 50 : 0; var height = From 03aff586676e41c8af2badec834135db074fc85b Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 6 Feb 2024 10:33:42 -0800 Subject: [PATCH 023/150] Version bump --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 9ec726c3..bda06576 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "grnsight", - "version": "7.0.9", + "version": "7.0.10", "description": "Web app and service for visualizing models of gene regulatory networks", "directories": { "test": "test" From c4e70f59e22c2a3a82bd3c0dc41227b7b75d9e17 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Thu, 8 Feb 2024 14:34:54 -0800 Subject: [PATCH 024/150] now stay in bounds with D-pad. had to make calculation of new movement to include graphScale and needed to add a Math.floor calculation because noticed pattern that results of the calculation Math.abs(xTranslation + width * graphScale) / zoomContainerWidth in the decimal tenths place like 0.5 were in bounds but ratios like 0.05 in the hundreths place were out of bounds --- web-client/public/js/graph.js | 129 +++++++++++++++++++++++----------- 1 file changed, 89 insertions(+), 40 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index d380c4e0..70c3ac4c 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -159,6 +159,7 @@ export var drawGraph = function (workbook) { var zoomDragPrevX = 0; var zoomDragPrevY = 0; + var zoomDragStarted = function () { zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; @@ -167,22 +168,22 @@ export var drawGraph = function (workbook) { // allows zoom slider to be moved and limits movement when !adaptive var zoomDragged = function () { - var scale = 1; - if (zoomContainer.attr("transform")) { - var string = zoomContainer.attr("transform"); - scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); - } - if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE) { - zoom.translateBy( - zoomContainer, - scale * (d3.event.x - zoomDragPrevX), - scale * (d3.event.y - zoomDragPrevY) - ); - } else if (adaptive) { - zoom.translateBy(zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY)); - } - zoomDragPrevX = d3.event.x; - zoomDragPrevY = d3.event.y; + var scale = 1; + if (zoomContainer.attr("transform")) { + var string = zoomContainer.attr("transform"); + scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); + } + if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE) { + zoom.translateBy( + zoomContainer, + scale * (d3.event.x - zoomDragPrevX), + scale * (d3.event.y - zoomDragPrevY) + ); + } else if (adaptive) { + zoom.translateBy(zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY)); + } + zoomDragPrevX = d3.event.x; + zoomDragPrevY = d3.event.y; }; var zoomDragEnded = function () { @@ -236,7 +237,7 @@ export var drawGraph = function (workbook) { d3.selectAll(".scrollBtn").on("click", null); // Remove event handlers, if there were any. var arrowMovement = [ "Up", "Left", "Right", "Down" ]; arrowMovement.forEach(function (direction) { - d3.select(".scroll" + direction).on("click", function() { + d3.select(".scroll" + direction).on("click", function () { move(direction.toLowerCase()); }); }); @@ -259,7 +260,7 @@ export var drawGraph = function (workbook) { const updateAppBasedOnZoomValue = () => { // If !adaptive, set Zoomvalue to ZOOM_DISPLAY_MIDDLE, 100, so do not zoom outside Ggr if (!adaptive && grnState.zoomValue < ZOOM_DISPLAY_MIDDLE) { - grnState.zoomValue = ZOOM_DISPLAY_MIDDLE; + grnState.zoomValue = ZOOM_DISPLAY_MIDDLE; } const zoomDisplay = grnState.zoomValue; @@ -269,7 +270,7 @@ export var drawGraph = function (workbook) { ? zoomScaleLeft : zoomScaleRight)(zoomDisplay) ); - } else if (!adaptive && grnState.zoomValue >= ZOOM_DISPLAY_MIDDLE){ + } else if (!adaptive && grnState.zoomValue >= ZOOM_DISPLAY_MIDDLE) { setGraphZoom( (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft @@ -386,9 +387,6 @@ export var drawGraph = function (workbook) { var restrictGraphToViewport = function (fixed) { if (!fixed) { $("#restrict-graph-to-viewport span").removeClass("glyphicon-ok"); - $(document).ready(function () { - $(".scale-and-scroll").show(); - }); $("input[name=viewport]").removeProp("checked"); $container.addClass("cursorGrabbing"); adaptive = true; @@ -397,14 +395,15 @@ export var drawGraph = function (workbook) { } else if (fixed) { $("#restrict-graph-to-viewport span").addClass("glyphicon-ok"); $("input[name=viewport]").prop("checked", "checked"); + // $(document).ready(function() { + // $(".scale-and-scroll").hide(); + // }); adaptive = false; $container.removeClass(CURSOR_CLASSES); - $container.removeClass("cursorGrab"); if (grnState.zoomValue > ZOOM_DISPLAY_MIDDLE) { grnState.zoomValue = ZOOM_DISPLAY_MIDDLE; updateAppBasedOnZoomValue(); $container.removeClass(CURSOR_CLASSES); - $container.removeClass("cursorGrabbing"); } width = $container.width(); height = $container.height(); @@ -441,9 +440,11 @@ export var drawGraph = function (workbook) { direction === "up" ? -50 : direction === "down" ? 50 : 0; if (adaptive) { - zoom.translateBy(zoomContainer, width, height); - } else if (!adaptive && grnState.zoomValue != ZOOM_DISPLAY_MIDDLE) { - // we parse through transform attribute of zoomContainer which contains information about the scale of the graph + zoom.translateBy(zoomContainer, width, height); + } else if (!adaptive && grnState.zoomValue !== ZOOM_DISPLAY_MIDDLE) { + /* transform attribute of zoomContainer contains translation info about graph */ + /* we parse through transform attribute of zoomContainer which + contains information about the scale of the graph */ const graphScale = parseFloat( zoomContainer .attr("transform") @@ -452,30 +453,78 @@ export var drawGraph = function (workbook) { const xTranslation = parseFloat(zoomContainer .attr("transform") - .split("(")[1].split(",")[0]) + .split("(")[1].split(",")[0]); const yTranslation = parseFloat(zoomContainer .attr("transform") - .split("(")[1].split(",")[1].split(")")[0]) + .split("(")[1].split(",")[1].split(")")[0]); const zoomContainerWidth = parseInt(zoomContainer.attr("width")); const zoomContainerHeight = parseInt(zoomContainer.attr("height")); + console.log(" ") + console.log("graphScale", graphScale) + /* + "new translation", + width + xTranslation + zoomContainerWidth, - // right: abs(new x coordinate) / zoomContainerWidth - 1.0 == all digits after decimal point if graphscale > 1 and < 2 or graphScale - 1 if graphScale >= 2 - // bottom: abs(new y coordinate) / zoomContainerHeight - 1.0 == all digits after decimal point if graphscale > 1 and < 2 or graphScale - 1 if graphScale >= 2 - // top: y coordinate rounded == -0 - // left: y coordinate rounded == -0 + "height + yTranslation", + height + yTranslation + zoomContainerHidth, + */ + console.log( + "width", + zoomContainerWidth, + "xTranslation", + xTranslation, + "movement width", + width * graphScale, + "test for new width move", + Math.abs(xTranslation + width * graphScale) / zoomContainerWidth + ); + console.log("height", + zoomContainerHeight, + "yTranslation", + yTranslation, + "movement height", + height * graphScale, + "total new height translation", + height + yTranslation + zoomContainerHeight, + "test for new y move", + Math.abs(yTranslation + height * graphScale) / zoomContainerHeight + ); + // make sure new position within bounds of graph + //TODO: tried multiplying width by graphScale? + // const newWidth = width * graphScale + xTranslation + zoomContainerWidth <= zoomContainerWidth; + // const newHeight = height * graphScale + yTranslation + zoomContainerHeight <= zoomContainerHeight + + // if (0 <= newWidth && zoomContainerWidth >= newWidth && 0 <= newHeight && zoomContainerHeight >= newHeight) { + // zoom.translateBy(zoomContainer, width, height); + // } + + /* + * right: abs(new x coordinate) / zoomContainerWidth - 1.0 == all digits after decimal point if + graphscale > 1 and < 2 or graphScale - 1 if graphScale >= 2 + * bottom: abs(new y coordinate) / zoomContainerHeight - 1.0 == all digits after decimal point if + graphscale > 1 and < 2 or graphScale - 1 if graphScale >= 2 + * top: y coordinate rounded == -0 + * left: y coordinate rounded == -0 + * Amount of movement is dependent on graphScale, so actual movement is not just the width or height + but width or height multiplied by graphScale + * multiply Math.abs(yTranslation + height * graphScale) / zoomContainerHeight by 10 because + decimals like 0.5 are in bounds but decimals like 0.05 are out of bounds + */ if ( - Math.abs(xTranslation + width) / zoomContainerWidth <= + Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 && - Math.abs(yTranslation + height) / zoomContainerHeight <= + Math.floor(Math.abs(xTranslation + width * graphScale) / zoomContainerWidth * 10 ) !== 0 && + Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= graphScale - 1.0 && + Math.floor(Math.abs(yTranslation + height * graphScale) / zoomContainerHeight * 10) != 0 && xTranslation + width <= 0 && yTranslation + height <= 0 ) { zoom.translateBy(zoomContainer, width, height); } - } + } } var defs = boundingBoxContainer.append("defs"); @@ -1433,15 +1482,15 @@ export var drawGraph = function (workbook) { height += OFFSET_VALUE; boundingBoxContainer.attr("height", height); link - .attr("y1", function(d) { + .attr("y1", function (d) { return d.source.y; }) - .attr("y2", function(d) { + .attr("y2", function (d) { return d.target.y; }); - node.attr("y", function(d) { - return d.y; + node.attr("y", function (d) { + return d.y; }); } } From cbea2b1262c797cf58f6c22e36cf9ca0ef5f1de1 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Thu, 8 Feb 2024 14:36:12 -0800 Subject: [PATCH 025/150] deleted some unecessary comments --- web-client/public/js/graph.js | 45 ++++------------------------------- 1 file changed, 4 insertions(+), 41 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 70c3ac4c..f950b9f3 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -442,9 +442,10 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, width, height); } else if (!adaptive && grnState.zoomValue !== ZOOM_DISPLAY_MIDDLE) { - /* transform attribute of zoomContainer contains translation info about graph */ - /* we parse through transform attribute of zoomContainer which - contains information about the scale of the graph */ + /* + * transform attribute of zoomContainer contains translation info about graph + * we parse through transform attribute of zoomContainer which + contains information about the scale of the graph */ const graphScale = parseFloat( zoomContainer .attr("transform") @@ -461,44 +462,6 @@ export var drawGraph = function (workbook) { const zoomContainerWidth = parseInt(zoomContainer.attr("width")); const zoomContainerHeight = parseInt(zoomContainer.attr("height")); - console.log(" ") - console.log("graphScale", graphScale) - /* - "new translation", - width + xTranslation + zoomContainerWidth, - - "height + yTranslation", - height + yTranslation + zoomContainerHidth, - */ - console.log( - "width", - zoomContainerWidth, - "xTranslation", - xTranslation, - "movement width", - width * graphScale, - "test for new width move", - Math.abs(xTranslation + width * graphScale) / zoomContainerWidth - ); - console.log("height", - zoomContainerHeight, - "yTranslation", - yTranslation, - "movement height", - height * graphScale, - "total new height translation", - height + yTranslation + zoomContainerHeight, - "test for new y move", - Math.abs(yTranslation + height * graphScale) / zoomContainerHeight - ); - // make sure new position within bounds of graph - //TODO: tried multiplying width by graphScale? - // const newWidth = width * graphScale + xTranslation + zoomContainerWidth <= zoomContainerWidth; - // const newHeight = height * graphScale + yTranslation + zoomContainerHeight <= zoomContainerHeight - - // if (0 <= newWidth && zoomContainerWidth >= newWidth && 0 <= newHeight && zoomContainerHeight >= newHeight) { - // zoom.translateBy(zoomContainer, width, height); - // } /* * right: abs(new x coordinate) / zoomContainerWidth - 1.0 == all digits after decimal point if From 890a6e8d232abf3dd6c516a62848f2b50b8c5ee9 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Thu, 8 Feb 2024 18:41:29 -0800 Subject: [PATCH 026/150] Issue #1083. Can now register click event on the graph, changed up some comments and moved the instantiation of CURSOR_CLASSES to an earlier line --- web-client/public/js/graph.js | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index f950b9f3..6750b52a 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -50,6 +50,7 @@ export var updaters = { export var drawGraph = function (workbook) { /* eslint-enable no-unused-vars */ var $container = $(".grnsight-container"); + var CURSOR_CLASSES = "cursorGrab cursorGrabbing"; d3.selectAll("svg").remove(); $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); // allow graph dragging right away @@ -61,8 +62,6 @@ export var drawGraph = function (workbook) { var dashedLine = $("#dashedGrayLineButton").prop("checked"); - var CURSOR_CLASSES = "cursorGrab cursorGrabbing"; - $("#warningMessage").html(workbook.warnings.length !== 0 ? "Click here in order to view warnings." : ""); var getNodeWidth = function (node) { @@ -243,6 +242,12 @@ export var drawGraph = function (workbook) { }); d3.select(".center").on("click", center); + const boundingBoxListener = () => { + console.log("boundingBox clicked") + } + + zoomContainer.on("click", boundingBoxListener) + const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); @@ -395,9 +400,6 @@ export var drawGraph = function (workbook) { } else if (fixed) { $("#restrict-graph-to-viewport span").addClass("glyphicon-ok"); $("input[name=viewport]").prop("checked", "checked"); - // $(document).ready(function() { - // $(".scale-and-scroll").hide(); - // }); adaptive = false; $container.removeClass(CURSOR_CLASSES); if (grnState.zoomValue > ZOOM_DISPLAY_MIDDLE) { @@ -464,16 +466,16 @@ export var drawGraph = function (workbook) { const zoomContainerHeight = parseInt(zoomContainer.attr("height")); /* - * right: abs(new x coordinate) / zoomContainerWidth - 1.0 == all digits after decimal point if - graphscale > 1 and < 2 or graphScale - 1 if graphScale >= 2 - * bottom: abs(new y coordinate) / zoomContainerHeight - 1.0 == all digits after decimal point if - graphscale > 1 and < 2 or graphScale - 1 if graphScale >= 2 + * right: Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 + * bottom: Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= + graphScale - 1.0 && * top: y coordinate rounded == -0 * left: y coordinate rounded == -0 * Amount of movement is dependent on graphScale, so actual movement is not just the width or height but width or height multiplied by graphScale * multiply Math.abs(yTranslation + height * graphScale) / zoomContainerHeight by 10 because - decimals like 0.5 are in bounds but decimals like 0.05 are out of bounds + decimals like 0.5 are in bounds but decimals like 0.05 or less are out of bounds, then + get floor to ensure that decimal does not have 0 in tenths place */ if ( Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= @@ -1581,11 +1583,13 @@ export var drawGraph = function (workbook) { if (!d3.event.active) { simulation.alphaTarget(0.3).restart(); } + d.fx = d.x; d.fy = d.y; } function dragged (d) { + console.log("dragged"); d.fx = d3.event.x; d.fy = d3.event.y; } From 95a9b3e49d9782fd0ee73c32277510f1676947f9 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 9 Feb 2024 00:24:37 -0800 Subject: [PATCH 027/150] cursor still goes out of bounds, but restructured code so that inBounds(width, height) tracks if the graph is in bounds, and updateZoomContainerInfo is called from inside that function that updates variables that store zoomContainerInfo so that code easier to read. Issue #1083. --- web-client/public/js/graph.js | 144 +++++++++++++++++++++++----------- 1 file changed, 99 insertions(+), 45 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 6750b52a..94294fd1 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -242,11 +242,107 @@ export var drawGraph = function (workbook) { }); d3.select(".center").on("click", center); + let graphScale = 0; + let xTranslation = 0; + let yTranslation = 0; + let zoomContainerWidth = 0; + let zoomContainerHeight = 0; + + const updateZoomContainerInfo = () => { + /* + * transform attribute of zoomContainer contains translation info about graph + * we parse through transform attribute of zoomContainer which + contains information about the scale of the graph */ + graphScale = parseFloat( + zoomContainer + .attr("transform") + .split("(")[2].split(")")[0] + ); + + xTranslation = parseFloat(zoomContainer + .attr("transform") + .split("(")[1].split(",")[0]); + + yTranslation = parseFloat(zoomContainer + .attr("transform") + .split("(")[1].split(",")[1].split(")")[0]); + + zoomContainerWidth = parseInt(zoomContainer.attr("width")); + zoomContainerHeight = parseInt(zoomContainer.attr("height")); + } + + const inBounds = (width, height) => { + /* + * right: Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 + * bottom: Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= graphScale - 1.0 + * top: y coordinate == -0, left: x coordinate == -0 + * Amount of movement is dependent on graphScale, so actual movement is not just the width or height + but width or height multiplied by graphScale + * multiply Math.abs(yTranslation + height * graphScale) / zoomContainerHeight by 10 because + decimals like 0.5 are in bounds but decimals like 0.05 or less are out of bounds, then + get floor to ensure that decimal does not have 0 in tenths place + */ + updateZoomContainerInfo() + + return ( + Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 && + Math.floor((Math.abs(xTranslation + width * graphScale) / zoomContainerWidth) * 10) !== 0 && + Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= + graphScale - 1.0 && + Math.floor((Math.abs(yTranslation + height * graphScale) / zoomContainerHeight) * 10) != 0 && + xTranslation + width <= 0 && + yTranslation + height <= 0 + ); + } + const boundingBoxListener = () => { - console.log("boundingBox clicked") + console.log("boundingBox mousedown"); + // TODO: change to !adaptive only, || adaptive for testing + if (!adaptive || adaptive && !inBounds(width=0, height=0)) { + /* + * stack overflow combine mouseover and mousemove: + https://stackoverflow.com/questions/55987499/prevent-panning-outside-of-map-bounds-in-d3v5 + */ + var e = d3.event; + console.log(e) + + var scale = 1; + if (zoomContainer.attr("transform")) { + var string = zoomContainer.attr("transform"); + scale = 1 / +string.match(/scale\(([^\)]+)\)/)[1]; + } + var tx = Math.min(0, Math.max(e.x, width - width * scale)); + var ty = Math.min(0, Math.max(e.y, height - height * scale)); + zoom.translateBy(zoomContainer, tx, ty); + // zoomContainer.attr( + // "transform", + // [ + // "translate(" + [tx, ty] + ")", + // "scale(" + scale + ")", + // ].join(" ") + // ); + console.log("not in bounds") + } + // console.log(tx, ty) + // console.log("e event info", e.x, e.y, e.scale, e.k) } - zoomContainer.on("click", boundingBoxListener) + zoomContainer.on("mouseover", boundingBoxListener) + + // let isMouseDown = false; + // zoomContainer.on("mousedown", () => { + // isMouseDown = true; + // }) + + // zoomContainer.on("mousemove", () => { + // if (isMouseDown) { + // boundingBoxListener(); + // } + // }); + + // zoomContainer.on("mouseup", () => { + // isMouseDown = false; + // }) const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { @@ -444,49 +540,7 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, width, height); } else if (!adaptive && grnState.zoomValue !== ZOOM_DISPLAY_MIDDLE) { - /* - * transform attribute of zoomContainer contains translation info about graph - * we parse through transform attribute of zoomContainer which - contains information about the scale of the graph */ - const graphScale = parseFloat( - zoomContainer - .attr("transform") - .split("(")[2].split(")")[0] - ); - - const xTranslation = parseFloat(zoomContainer - .attr("transform") - .split("(")[1].split(",")[0]); - - const yTranslation = parseFloat(zoomContainer - .attr("transform") - .split("(")[1].split(",")[1].split(")")[0]); - - const zoomContainerWidth = parseInt(zoomContainer.attr("width")); - const zoomContainerHeight = parseInt(zoomContainer.attr("height")); - - /* - * right: Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 - * bottom: Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= - graphScale - 1.0 && - * top: y coordinate rounded == -0 - * left: y coordinate rounded == -0 - * Amount of movement is dependent on graphScale, so actual movement is not just the width or height - but width or height multiplied by graphScale - * multiply Math.abs(yTranslation + height * graphScale) / zoomContainerHeight by 10 because - decimals like 0.5 are in bounds but decimals like 0.05 or less are out of bounds, then - get floor to ensure that decimal does not have 0 in tenths place - */ - if ( - Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= - graphScale - 1.0 && - Math.floor(Math.abs(xTranslation + width * graphScale) / zoomContainerWidth * 10 ) !== 0 && - Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= - graphScale - 1.0 && - Math.floor(Math.abs(yTranslation + height * graphScale) / zoomContainerHeight * 10) != 0 && - xTranslation + width <= 0 && - yTranslation + height <= 0 - ) { + if (inBounds(width, height)) { zoom.translateBy(zoomContainer, width, height); } } From 66dac3ad447916e87323c37cdc604a1789bb0c38 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 9 Feb 2024 00:34:11 -0800 Subject: [PATCH 028/150] Although graph does not stop at border, can now register that graph is in or out of bounds with mouseover, need to change so that only tracks mouse movement when cursorGrabbing --- web-client/public/js/graph.js | 45 +++++++++++++++++++++++++++-------- 1 file changed, 35 insertions(+), 10 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 94294fd1..8b4e524a 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -283,22 +283,48 @@ export var drawGraph = function (workbook) { get floor to ensure that decimal does not have 0 in tenths place */ updateZoomContainerInfo() + console.log("inBounds function ran") + if (width == 0 && height == 0) { + console.log("width and height change = 0") + + // console.log("in bounds?", + // Math.abs(xTranslation) / zoomContainerWidth <= graphScale - 1.0 && + // Math.floor( + // (Math.abs(xTranslation) / zoomContainerWidth) * 10 + // ) !== 0 && + // Math.abs(yTranslation) / zoomContainerHeight <= + // graphScale - 1.0 && + // Math.floor( + // (Math.abs(yTranslation) / zoomContainerHeight) * 10 + // ) != 0 && + // xTranslation + width <= 0 && + // yTranslation + height <= 0 + // ); + return ( + Math.abs(xTranslation) / zoomContainerWidth <= graphScale - 1.0 && + Math.floor((Math.abs(xTranslation) / zoomContainerWidth) * 10) !== 0 && + Math.abs(yTranslation) / zoomContainerHeight <= graphScale - 1.0 && + Math.floor((Math.abs(yTranslation) / zoomContainerHeight) * 10) != 0 && + xTranslation + width <= 0 && + yTranslation + height <= 0) + + } return ( - Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 && - Math.floor((Math.abs(xTranslation + width * graphScale) / zoomContainerWidth) * 10) !== 0 && - Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= - graphScale - 1.0 && - Math.floor((Math.abs(yTranslation + height * graphScale) / zoomContainerHeight) * 10) != 0 && - xTranslation + width <= 0 && - yTranslation + height <= 0 + Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 && + Math.floor((Math.abs(xTranslation + width * graphScale) / zoomContainerWidth) * 10) !== 0 && + Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= + graphScale - 1.0 && + Math.floor((Math.abs(yTranslation + height * graphScale) / zoomContainerHeight) * 10) != 0 && + xTranslation + width <= 0 && + yTranslation + height <= 0 ); } const boundingBoxListener = () => { console.log("boundingBox mousedown"); // TODO: change to !adaptive only, || adaptive for testing - if (!adaptive || adaptive && !inBounds(width=0, height=0)) { + if (!adaptive && !inBounds(width=0, height=0)) { /* * stack overflow combine mouseover and mousemove: https://stackoverflow.com/questions/55987499/prevent-panning-outside-of-map-bounds-in-d3v5 @@ -320,8 +346,7 @@ export var drawGraph = function (workbook) { // "translate(" + [tx, ty] + ")", // "scale(" + scale + ")", // ].join(" ") - // ); - console.log("not in bounds") + // ) } // console.log(tx, ty) // console.log("e event info", e.x, e.y, e.scale, e.k) From bf2dfb1a4c328edf6bece59aa766ecbb2c6860f8 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 9 Feb 2024 02:13:04 -0800 Subject: [PATCH 029/150] can now observe if in bounds with mutationObserver, and hope to use this to see if cursorGrab is on or not, but for some reason mutation observer fires 4 times when click. Issue #1083 --- web-client/public/js/graph.js | 136 +++++++++++++++++----------------- 1 file changed, 68 insertions(+), 68 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 8b4e524a..c74cbdde 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -215,7 +215,6 @@ export var drawGraph = function (workbook) { svg.style("pointer-events", "all").call(zoomDrag) .style("font-family", "sans-serif"); - function zoomed () { zoomContainer.attr("transform", d3.event.transform); } @@ -284,31 +283,27 @@ export var drawGraph = function (workbook) { */ updateZoomContainerInfo() console.log("inBounds function ran") - if (width == 0 && height == 0) { - console.log("width and height change = 0") - - // console.log("in bounds?", - // Math.abs(xTranslation) / zoomContainerWidth <= graphScale - 1.0 && - // Math.floor( - // (Math.abs(xTranslation) / zoomContainerWidth) * 10 - // ) !== 0 && - // Math.abs(yTranslation) / zoomContainerHeight <= - // graphScale - 1.0 && - // Math.floor( - // (Math.abs(yTranslation) / zoomContainerHeight) * 10 - // ) != 0 && - // xTranslation + width <= 0 && - // yTranslation + height <= 0 - // ); - return ( - Math.abs(xTranslation) / zoomContainerWidth <= graphScale - 1.0 && - Math.floor((Math.abs(xTranslation) / zoomContainerWidth) * 10) !== 0 && - Math.abs(yTranslation) / zoomContainerHeight <= graphScale - 1.0 && - Math.floor((Math.abs(yTranslation) / zoomContainerHeight) * 10) != 0 && - xTranslation + width <= 0 && - yTranslation + height <= 0) - - } + + console.log( + "in bounds?", + Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= + graphScale - 1.0 && + Math.floor( + (Math.abs(xTranslation + width * graphScale) / + zoomContainerWidth) * + 10 + ) !== 0 && + Math.abs(yTranslation + height * graphScale) / + zoomContainerHeight <= + graphScale - 1.0 && + Math.floor( + (Math.abs(yTranslation + height * graphScale) / + zoomContainerHeight) * + 10 + ) != 0 && + xTranslation + width <= 0 && + yTranslation + height <= 0 + ); return ( Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 && @@ -323,51 +318,56 @@ export var drawGraph = function (workbook) { const boundingBoxListener = () => { console.log("boundingBox mousedown"); - // TODO: change to !adaptive only, || adaptive for testing - if (!adaptive && !inBounds(width=0, height=0)) { - /* - * stack overflow combine mouseover and mousemove: - https://stackoverflow.com/questions/55987499/prevent-panning-outside-of-map-bounds-in-d3v5 - */ + /* hardcode width and height as 0 since this is special case where we just want to check + if the current xTranslation and yTranslation are inBounds + */ + if (!adaptive && !inBounds((width = 0), (height = 0))) { + /* + * stack overflow combine mouseover and mousemove: + https://stackoverflow.com/questions/55987499/prevent-panning-outside-of-map-bounds-in-d3v5 + */ var e = d3.event; - console.log(e) - - var scale = 1; - if (zoomContainer.attr("transform")) { - var string = zoomContainer.attr("transform"); - scale = 1 / +string.match(/scale\(([^\)]+)\)/)[1]; + if (e) { + var scale = 1; + if (zoomContainer.attr("transform")) { + var string = zoomContainer.attr("transform"); + scale = 1 / +string.match(/scale\(([^\)]+)\)/)[1]; + } + var tx = Math.min(0, Math.max(e.x, width - width * scale)); + var ty = Math.min(0, Math.max(e.y, height - height * scale)); + zoom.translateBy(zoomContainer, tx, ty); + // zoomContainer.attr( + // "transform", + // [ + // "translate(" + [tx, ty] + ")", + // "scale(" + scale + ")", + // ].join(" ") + // ) } - var tx = Math.min(0, Math.max(e.x, width - width * scale)); - var ty = Math.min(0, Math.max(e.y, height - height * scale)); - zoom.translateBy(zoomContainer, tx, ty); - // zoomContainer.attr( - // "transform", - // [ - // "translate(" + [tx, ty] + ")", - // "scale(" + scale + ")", - // ].join(" ") - // ) - } - // console.log(tx, ty) - // console.log("e event info", e.x, e.y, e.scale, e.k) + } } + + // Thanks for MutationObserver help from: https://www.seanmcp.com/articles/listen-for-class-change-in-javascript/ + let lastContainerClassList = $container.attr("class"); + let mutationCallback2 = null; + const cursorDownObserver = new MutationObserver((mutationsList, observer) => { + let classList = $container.attr("class") + console.log(mutationsList) + if (typeof mutationCallback2 === "function") { + for (const item of mutationsList) { + if (item.attributeName === "class" && classList !== lastContainerClassList) { + // console.log("current list", classList); + // console.log("lastclasslist", lastContainerClassList); + lastContainerClassList = classList; + mutationCallback2(); + } + } + } + }); - zoomContainer.on("mouseover", boundingBoxListener) - - // let isMouseDown = false; - // zoomContainer.on("mousedown", () => { - // isMouseDown = true; - // }) - - // zoomContainer.on("mousemove", () => { - // if (isMouseDown) { - // boundingBoxListener(); - // } - // }); - - // zoomContainer.on("mouseup", () => { - // isMouseDown = false; - // }) + mutationCallback2 = boundingBoxListener; + cursorDownObserver.disconnect(); + cursorDownObserver.observe($container.get(0), { attributeFilter: ["class"] }); const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { @@ -514,7 +514,7 @@ export var drawGraph = function (workbook) { if (!fixed) { $("#restrict-graph-to-viewport span").removeClass("glyphicon-ok"); $("input[name=viewport]").removeProp("checked"); - $container.addClass("cursorGrabbing"); + // $container.addClass("cursorGrabbing"); adaptive = true; d3.select("rect").attr("stroke", "none"); center(); From dad3673cd021607b0f2c080c6f12262edd56bfd4 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 9 Feb 2024 02:22:34 -0800 Subject: [PATCH 030/150] Issue #1083. Now the graph stop s in the boundaries but gets stuck at the edges --- web-client/public/js/graph.js | 45 +++++++++++++++++++---------------- 1 file changed, 24 insertions(+), 21 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index c74cbdde..7926c76f 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -163,6 +163,7 @@ export var drawGraph = function (workbook) { zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; $container.removeClass(CURSOR_CLASSES).addClass("cursorGrabbing"); + console.log("zoomDragStarted", $container.attr("class")) }; // allows zoom slider to be moved and limits movement when !adaptive @@ -172,7 +173,7 @@ export var drawGraph = function (workbook) { var string = zoomContainer.attr("transform"); scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } - if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE) { + if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE && inBounds(width=5, height=5)) { zoom.translateBy( zoomContainer, scale * (d3.event.x - zoomDragPrevX), @@ -189,6 +190,7 @@ export var drawGraph = function (workbook) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); }; + // TODO: this is what keeps track of cursorGrabbing! var zoomDrag = d3.drag() .on("start", zoomDragStarted) .on("drag", zoomDragged) @@ -212,6 +214,7 @@ export var drawGraph = function (workbook) { .scaleExtent([MIN_SCALE, ZOOM_ADAPTIVE_MAX_SCALE]) .on("zoom", zoomed); + // this is how we keep track of mousedrags svg.style("pointer-events", "all").call(zoomDrag) .style("font-family", "sans-serif"); @@ -348,26 +351,26 @@ export var drawGraph = function (workbook) { } // Thanks for MutationObserver help from: https://www.seanmcp.com/articles/listen-for-class-change-in-javascript/ - let lastContainerClassList = $container.attr("class"); - let mutationCallback2 = null; - const cursorDownObserver = new MutationObserver((mutationsList, observer) => { - let classList = $container.attr("class") - console.log(mutationsList) - if (typeof mutationCallback2 === "function") { - for (const item of mutationsList) { - if (item.attributeName === "class" && classList !== lastContainerClassList) { - // console.log("current list", classList); - // console.log("lastclasslist", lastContainerClassList); - lastContainerClassList = classList; - mutationCallback2(); - } - } - } - }); - - mutationCallback2 = boundingBoxListener; - cursorDownObserver.disconnect(); - cursorDownObserver.observe($container.get(0), { attributeFilter: ["class"] }); + // let lastContainerClassList = $container.attr("class"); + // let mutationCallback2 = null; + // const cursorDownObserver = new MutationObserver((mutationsList, observer) => { + // let classList = $container.attr("class") + // // console.log(mutationsList) + // if (typeof mutationCallback2 === "function") { + // for (const item of mutationsList) { + // if (item.attributeName === "class" && classList !== lastContainerClassList) { + // // console.log("current list", classList); + // // console.log("lastclasslist", lastContainerClassList); + // lastContainerClassList = classList; + // mutationCallback2(); + // } + // } + // } + // }); + + // mutationCallback2 = boundingBoxListener; + // cursorDownObserver.disconnect(); + // cursorDownObserver.observe($container.get(0), { attributeFilter: ["class"] }); const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { From b20171f6ba9cc414b0c873b1733c017b542fc2c0 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 9 Feb 2024 02:35:19 -0800 Subject: [PATCH 031/150] Cursor successfully not allowed to move graph outside of viewport now. Still need to run lint and test to ensure that everything working. Issue #1083 --- web-client/public/js/graph.js | 88 +++-------------------------------- 1 file changed, 6 insertions(+), 82 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 7926c76f..380f3b96 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -173,11 +173,11 @@ export var drawGraph = function (workbook) { var string = zoomContainer.attr("transform"); scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } - if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE && inBounds(width=5, height=5)) { + if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE && inBounds(d3.event.dx, d3.event.dy)) { zoom.translateBy( - zoomContainer, - scale * (d3.event.x - zoomDragPrevX), - scale * (d3.event.y - zoomDragPrevY) + zoomContainer, + scale * (d3.event.x - zoomDragPrevX), + scale * (d3.event.y - zoomDragPrevY) ); } else if (adaptive) { zoom.translateBy(zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY)); @@ -190,7 +190,7 @@ export var drawGraph = function (workbook) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); }; - // TODO: this is what keeps track of cursorGrabbing! + // zoomDrag keeps track of cursor position var zoomDrag = d3.drag() .on("start", zoomDragStarted) .on("drag", zoomDragged) @@ -214,7 +214,6 @@ export var drawGraph = function (workbook) { .scaleExtent([MIN_SCALE, ZOOM_ADAPTIVE_MAX_SCALE]) .on("zoom", zoomed); - // this is how we keep track of mousedrags svg.style("pointer-events", "all").call(zoomDrag) .style("font-family", "sans-serif"); @@ -285,29 +284,7 @@ export var drawGraph = function (workbook) { get floor to ensure that decimal does not have 0 in tenths place */ updateZoomContainerInfo() - console.log("inBounds function ran") - - console.log( - "in bounds?", - Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= - graphScale - 1.0 && - Math.floor( - (Math.abs(xTranslation + width * graphScale) / - zoomContainerWidth) * - 10 - ) !== 0 && - Math.abs(yTranslation + height * graphScale) / - zoomContainerHeight <= - graphScale - 1.0 && - Math.floor( - (Math.abs(yTranslation + height * graphScale) / - zoomContainerHeight) * - 10 - ) != 0 && - xTranslation + width <= 0 && - yTranslation + height <= 0 - ); - + return ( Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 && Math.floor((Math.abs(xTranslation + width * graphScale) / zoomContainerWidth) * 10) !== 0 && @@ -319,59 +296,6 @@ export var drawGraph = function (workbook) { ); } - const boundingBoxListener = () => { - console.log("boundingBox mousedown"); - /* hardcode width and height as 0 since this is special case where we just want to check - if the current xTranslation and yTranslation are inBounds - */ - if (!adaptive && !inBounds((width = 0), (height = 0))) { - /* - * stack overflow combine mouseover and mousemove: - https://stackoverflow.com/questions/55987499/prevent-panning-outside-of-map-bounds-in-d3v5 - */ - var e = d3.event; - if (e) { - var scale = 1; - if (zoomContainer.attr("transform")) { - var string = zoomContainer.attr("transform"); - scale = 1 / +string.match(/scale\(([^\)]+)\)/)[1]; - } - var tx = Math.min(0, Math.max(e.x, width - width * scale)); - var ty = Math.min(0, Math.max(e.y, height - height * scale)); - zoom.translateBy(zoomContainer, tx, ty); - // zoomContainer.attr( - // "transform", - // [ - // "translate(" + [tx, ty] + ")", - // "scale(" + scale + ")", - // ].join(" ") - // ) - } - } - } - - // Thanks for MutationObserver help from: https://www.seanmcp.com/articles/listen-for-class-change-in-javascript/ - // let lastContainerClassList = $container.attr("class"); - // let mutationCallback2 = null; - // const cursorDownObserver = new MutationObserver((mutationsList, observer) => { - // let classList = $container.attr("class") - // // console.log(mutationsList) - // if (typeof mutationCallback2 === "function") { - // for (const item of mutationsList) { - // if (item.attributeName === "class" && classList !== lastContainerClassList) { - // // console.log("current list", classList); - // // console.log("lastclasslist", lastContainerClassList); - // lastContainerClassList = classList; - // mutationCallback2(); - // } - // } - // } - // }); - - // mutationCallback2 = boundingBoxListener; - // cursorDownObserver.disconnect(); - // cursorDownObserver.observe($container.get(0), { attributeFilter: ["class"] }); - const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); From 9ab6c075e77bc7835f91c61df8f801c441c436a3 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 9 Feb 2024 02:40:04 -0800 Subject: [PATCH 032/150] Issue #1083 lint and test all passing --- web-client/public/js/graph.js | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 380f3b96..51ca1a1c 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -163,7 +163,6 @@ export var drawGraph = function (workbook) { zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; $container.removeClass(CURSOR_CLASSES).addClass("cursorGrabbing"); - console.log("zoomDragStarted", $container.attr("class")) }; // allows zoom slider to be moved and limits movement when !adaptive @@ -250,7 +249,7 @@ export var drawGraph = function (workbook) { let zoomContainerHeight = 0; const updateZoomContainerInfo = () => { - /* + /* * transform attribute of zoomContainer contains translation info about graph * we parse through transform attribute of zoomContainer which contains information about the scale of the graph */ @@ -270,31 +269,31 @@ export var drawGraph = function (workbook) { zoomContainerWidth = parseInt(zoomContainer.attr("width")); zoomContainerHeight = parseInt(zoomContainer.attr("height")); - } + }; const inBounds = (width, height) => { /* * right: Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 * bottom: Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= graphScale - 1.0 * top: y coordinate == -0, left: x coordinate == -0 - * Amount of movement is dependent on graphScale, so actual movement is not just the width or height + * Amount of movement is dependent on graphScale, so actual movement is not just the width or height but width or height multiplied by graphScale - * multiply Math.abs(yTranslation + height * graphScale) / zoomContainerHeight by 10 because - decimals like 0.5 are in bounds but decimals like 0.05 or less are out of bounds, then + * multiply Math.abs(yTranslation + height * graphScale) / zoomContainerHeight by 10 because + decimals like 0.5 are in bounds but decimals like 0.05 or less are out of bounds, then get floor to ensure that decimal does not have 0 in tenths place */ - updateZoomContainerInfo() + updateZoomContainerInfo(); return ( Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 && Math.floor((Math.abs(xTranslation + width * graphScale) / zoomContainerWidth) * 10) !== 0 && Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= graphScale - 1.0 && - Math.floor((Math.abs(yTranslation + height * graphScale) / zoomContainerHeight) * 10) != 0 && + Math.floor((Math.abs(yTranslation + height * graphScale) / zoomContainerHeight) * 10) !== 0 && xTranslation + width <= 0 && yTranslation + height <= 0 ); - } + }; const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { @@ -1589,13 +1588,11 @@ export var drawGraph = function (workbook) { if (!d3.event.active) { simulation.alphaTarget(0.3).restart(); } - d.fx = d.x; d.fy = d.y; } function dragged (d) { - console.log("dragged"); d.fx = d3.event.x; d.fy = d3.event.y; } From ea4e33e59d25faebe5dbccf451e661e48b413805 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 9 Feb 2024 13:32:35 -0800 Subject: [PATCH 033/150] changed zoomContainerWidth and zoomContainerHeight to .width() and .height(). experiencing issue where cannot move graph all the way to top nor all the way to left so nodes hidden at top and to the left, which must be something to do with xTranslation + width * graphScale and yTranslation + height * graphScale since that is what controls the top and left borders. Issue #1083 --- web-client/public/js/graph.js | 76 ++++++++++++++++++++++++++--------- 1 file changed, 58 insertions(+), 18 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 51ca1a1c..9556deed 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -172,12 +172,26 @@ export var drawGraph = function (workbook) { var string = zoomContainer.attr("transform"); scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } - if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE && inBounds(d3.event.dx, d3.event.dy)) { - zoom.translateBy( - zoomContainer, - scale * (d3.event.x - zoomDragPrevX), - scale * (d3.event.y - zoomDragPrevY) - ); + if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE ) { + if ( + inBounds(d3.event.dx, d3.event.dy) || + inBounds(d3.event.x * graphScale, d3.event.x * graphScale) + ) { + // zoom.translateExtent([0,0], [zoomContainerWidth, zoomContainerHeight]) + zoom.translateBy( + zoomContainer, + scale * (d3.event.x - zoomDragPrevX), + scale * (d3.event.y - zoomDragPrevY) + ); + } + // } else if (!inBounds(d3.event.x * graphScale, d3.event.x * graphScale)) { + // console.log(d3.event) + // zoom.translateBy( + // zoomContainer, + // scale * (d3.event.x - zoomDragPrevX), + // scale * (d3.event.y - zoomDragPrevY) + // ); + // } } else if (adaptive) { zoom.translateBy(zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY)); } @@ -267,8 +281,6 @@ export var drawGraph = function (workbook) { .attr("transform") .split("(")[1].split(",")[1].split(")")[0]); - zoomContainerWidth = parseInt(zoomContainer.attr("width")); - zoomContainerHeight = parseInt(zoomContainer.attr("height")); }; const inBounds = (width, height) => { @@ -284,15 +296,45 @@ export var drawGraph = function (workbook) { */ updateZoomContainerInfo(); - return ( - Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 && - Math.floor((Math.abs(xTranslation + width * graphScale) / zoomContainerWidth) * 10) !== 0 && - Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= - graphScale - 1.0 && - Math.floor((Math.abs(yTranslation + height * graphScale) / zoomContainerHeight) * 10) !== 0 && + console.log( + Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= + graphScale - 1.0 && + Math.floor( + (Math.abs(xTranslation + width * graphScale) / + zoomContainerWidth) * + 10 + ) !== 0 && + Math.abs(yTranslation + height * graphScale) / + zoomContainerHeight <= + graphScale - 1.0 && + Math.floor( + (Math.abs(yTranslation + height * graphScale) / + zoomContainerHeight) * + 10 + ) !== 0 && xTranslation + width <= 0 && yTranslation + height <= 0 ); + + // console.log($container.width(), $container.height(), zoomContainerWidth, zoomContainerHeight) + + return ( + Math.abs(xTranslation + width * graphScale) / $container.width() <= + graphScale - 1.0 && + Math.floor( + (Math.abs(xTranslation + width * graphScale) / $container.width()) * + 10 + ) !== 0 && + Math.abs(yTranslation + height * graphScale) / $container.height() <= + graphScale - 1.0 && + Math.floor( + (Math.abs(yTranslation + height * graphScale) / + $container.height()) * + 10 + ) !== 0 && + xTranslation + width * graphScale <= 0 && + yTranslation + height * graphScale <= 0 + ); }; const setGraphZoom = zoomScale => { @@ -490,10 +532,8 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, width, height); - } else if (!adaptive && grnState.zoomValue !== ZOOM_DISPLAY_MIDDLE) { - if (inBounds(width, height)) { - zoom.translateBy(zoomContainer, width, height); - } + } else if (!adaptive && grnState.zoomValue !== ZOOM_DISPLAY_MIDDLE && inBounds(width, height)) { + zoom.translateBy(zoomContainer, width, height); } } From 819da1030fe70bb89c5138fd2326a2de1d2f3dda Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 9 Feb 2024 14:25:12 -0800 Subject: [PATCH 034/150] Now can correctly see nodes in all 4 corners and on all edges in graph when restrict to viewport. Changed graphZoom so that assigned in setGraphZoom. In the equation: Math.floor((Math.abs(xTranslation + width * graphZoom) / .width()) * 1000) !== 0, had to multiply by 1000 instead of 10 which I did before because the ratio of the scale is not inBounds only when that ratio has a significant digit in the thousandths place or less. all lint and test passing. Issue #1083 --- web-client/public/js/graph.js | 90 +++++++++-------------------------- 1 file changed, 23 insertions(+), 67 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 9556deed..3d370d1e 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -173,25 +173,13 @@ export var drawGraph = function (workbook) { scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE ) { - if ( - inBounds(d3.event.dx, d3.event.dy) || - inBounds(d3.event.x * graphScale, d3.event.x * graphScale) - ) { - // zoom.translateExtent([0,0], [zoomContainerWidth, zoomContainerHeight]) + if (inBounds(d3.event.dx, d3.event.dy)) { zoom.translateBy( zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY) ); } - // } else if (!inBounds(d3.event.x * graphScale, d3.event.x * graphScale)) { - // console.log(d3.event) - // zoom.translateBy( - // zoomContainer, - // scale * (d3.event.x - zoomDragPrevX), - // scale * (d3.event.y - zoomDragPrevY) - // ); - // } } else if (adaptive) { zoom.translateBy(zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY)); } @@ -256,23 +244,12 @@ export var drawGraph = function (workbook) { }); d3.select(".center").on("click", center); - let graphScale = 0; + let graphZoom = 0; let xTranslation = 0; let yTranslation = 0; - let zoomContainerWidth = 0; - let zoomContainerHeight = 0; const updateZoomContainerInfo = () => { - /* - * transform attribute of zoomContainer contains translation info about graph - * we parse through transform attribute of zoomContainer which - contains information about the scale of the graph */ - graphScale = parseFloat( - zoomContainer - .attr("transform") - .split("(")[2].split(")")[0] - ); - + // transform attribute of zoomContainer contains translation info about graph xTranslation = parseFloat(zoomContainer .attr("transform") .split("(")[1].split(",")[0]); @@ -280,60 +257,37 @@ export var drawGraph = function (workbook) { yTranslation = parseFloat(zoomContainer .attr("transform") .split("(")[1].split(",")[1].split(")")[0]); - }; const inBounds = (width, height) => { /* - * right: Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= graphScale - 1.0 - * bottom: Math.abs(yTranslation + height * graphScale) / zoomContainerHeight <= graphScale - 1.0 + * right: Math.abs(xTranslation + width * graphZoom) / zoomContainerWidth <= graphZoom - 1.0 + * bottom: Math.abs(yTranslation + height * graphZoom) / zoomContainerHeight <= graphZoom - 1.0 * top: y coordinate == -0, left: x coordinate == -0 - * Amount of movement is dependent on graphScale, so actual movement is not just the width or height - but width or height multiplied by graphScale - * multiply Math.abs(yTranslation + height * graphScale) / zoomContainerHeight by 10 because - decimals like 0.5 are in bounds but decimals like 0.05 or less are out of bounds, then - get floor to ensure that decimal does not have 0 in tenths place + * Amount of movement is dependent on graphZoom, so actual movement is not just the width or height + but width or height multiplied by graphZoom + * multiply Math.abs(yTranslation + height * graphZoom) / zoomContainerHeight by 1000 because + decimals like 0.005 (in the thousandths place) or less are out of bounds, + then get floor of that to ensure that decimal does not have 0 in hundredths place */ updateZoomContainerInfo(); - console.log( - Math.abs(xTranslation + width * graphScale) / zoomContainerWidth <= - graphScale - 1.0 && - Math.floor( - (Math.abs(xTranslation + width * graphScale) / - zoomContainerWidth) * - 10 - ) !== 0 && - Math.abs(yTranslation + height * graphScale) / - zoomContainerHeight <= - graphScale - 1.0 && - Math.floor( - (Math.abs(yTranslation + height * graphScale) / - zoomContainerHeight) * - 10 - ) !== 0 && - xTranslation + width <= 0 && - yTranslation + height <= 0 - ); - - // console.log($container.width(), $container.height(), zoomContainerWidth, zoomContainerHeight) - return ( - Math.abs(xTranslation + width * graphScale) / $container.width() <= - graphScale - 1.0 && + Math.abs(xTranslation + width * graphZoom) / $container.width() <= + graphZoom - 1.0 && Math.floor( - (Math.abs(xTranslation + width * graphScale) / $container.width()) * - 10 + (Math.abs(xTranslation + width * graphZoom) / $container.width()) * + 1000 ) !== 0 && - Math.abs(yTranslation + height * graphScale) / $container.height() <= - graphScale - 1.0 && + Math.abs(yTranslation + height * graphZoom) / $container.height() <= + graphZoom - 1.0 && Math.floor( - (Math.abs(yTranslation + height * graphScale) / + (Math.abs(yTranslation + height * graphZoom) / $container.height()) * - 10 + 1000 ) !== 0 && - xTranslation + width * graphScale <= 0 && - yTranslation + height * graphScale <= 0 + xTranslation + width * graphZoom <= 0 && + yTranslation + height * graphZoom <= 0 ); }; @@ -343,6 +297,8 @@ export var drawGraph = function (workbook) { } var container = zoomContainer; zoom.scaleTo(container, zoomScale); + // graphZoom is used in inBounds(width, height) to check if graph in zoomContainer when restricted to viewport + graphZoom = zoomScale; }; // See setupZoomElements below to see how these are initialized. They are declared here because @@ -352,7 +308,7 @@ export var drawGraph = function (workbook) { let zoomScaleSliderRight; const updateAppBasedOnZoomValue = () => { - // If !adaptive, set Zoomvalue to ZOOM_DISPLAY_MIDDLE, 100, so do not zoom outside Ggr + // If !adaptive, set Zoomvalue to ZOOM_DISPLAY_MIDDLE, 100, so do not zoom outside graph if (!adaptive && grnState.zoomValue < ZOOM_DISPLAY_MIDDLE) { grnState.zoomValue = ZOOM_DISPLAY_MIDDLE; } From 110af2a78d95f7602e5ae10d7a0b0dcdbad471d3 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Mon, 12 Feb 2024 23:02:12 -0800 Subject: [PATCH 035/150] Fixing the export sif file, and changing networkMode variable to workbookType to match with other custom workbook, easier for exporting --- .../controllers/custom-workbook-controller.js | 2 +- server/controllers/exporters/sif.js | 4 ++- server/controllers/importers/sif.js | 28 +++++++++---------- server/controllers/network-sheet-parser.js | 16 +++++------ server/controllers/spreadsheet-controller.js | 2 +- test/export-tests.js | 12 +++++--- test/import-sif-tests.js | 14 +++++----- .../js/setup-load-and-import-handlers.js | 2 +- 8 files changed, 43 insertions(+), 37 deletions(-) diff --git a/server/controllers/custom-workbook-controller.js b/server/controllers/custom-workbook-controller.js index b0cbe0be..73791f59 100644 --- a/server/controllers/custom-workbook-controller.js +++ b/server/controllers/custom-workbook-controller.js @@ -46,7 +46,7 @@ const createCustomWorkbook = (genesString, linksString, networkType) => { data: { species: "Saccharomyces cerevisiae", taxon_id: 559292, - workbookType: networkType, + workbookType: networkType } }, meta2: {}, diff --git a/server/controllers/exporters/sif.js b/server/controllers/exporters/sif.js index 915cd172..89366d3b 100644 --- a/server/controllers/exporters/sif.js +++ b/server/controllers/exporters/sif.js @@ -7,7 +7,9 @@ var exportEdges = function (workbook, gene, geneIndex) { if (link.source === geneIndex) { result += [ gene.name, - workbook.sheetType === constants.UNWEIGHTED ? "pd" : link.value, + workbook.sheetType === constants.WEIGHTED ? + link.value : workbook.workbookType === "protein-protein-physical-interactions" ? + "pp" : "pd", workbook.genes[link.target].name ].join("\t") + "\n"; } diff --git a/server/controllers/importers/sif.js b/server/controllers/importers/sif.js index c9f5e363..b7804b3c 100644 --- a/server/controllers/importers/sif.js +++ b/server/controllers/importers/sif.js @@ -57,16 +57,16 @@ module.exports = function (sif) { let hasNumbers = relationships.some(isNumber); let allNumbers = relationships.every(isNumber); - let networkMode; + let workbookType; if (allNumbers) { - networkMode = "grn"; + workbookType = "grn"; } else { for (const relationship of relationships) { if (relationship === "pp") { - networkMode = "protein-protein-physical-interaction"; + workbookType = "protein-protein-physical-interaction"; break; } else if (relationship === "pd") { - networkMode = "grn"; + workbookType = "grn"; break; } } @@ -81,7 +81,7 @@ module.exports = function (sif) { } return { - networkMode: networkMode, + workbookType: workbookType, sheetType: allNumbers ? constants.WEIGHTED : constants.UNWEIGHTED, warnings: hasNumbers && !allNumbers ? constants.warnings.EDGES_WITHOUT_WEIGHTS : null, errors: errors @@ -94,7 +94,7 @@ module.exports = function (sif) { var genes = []; var links = []; - var workbookType = "unweighted"; + var workbookMeta = "unweighted"; var nullEntries = entries.filter(function (entry) { return entry === null; @@ -109,13 +109,13 @@ module.exports = function (sif) { } }); - workbookType = sifWorkbookType(entries); - if (workbookType.warnings) { - warnings.push(workbookType.warnings); + workbookMeta = sifWorkbookType(entries); + if (workbookMeta.warnings) { + warnings.push(workbookMeta.warnings); } - if (workbookType.errors) { - workbookType.errors.forEach(function (error) { + if (workbookMeta.errors) { + workbookMeta.errors.forEach(function (error) { errors.push(error); }); } @@ -134,7 +134,7 @@ module.exports = function (sif) { source: sourceIndex, target: targetIndex }; - if (workbookType.sheetType === constants.WEIGHTED) { + if (workbookMeta.sheetType === constants.WEIGHTED) { link.value = +entry[RELATIONSHIP]; } links.push(link); @@ -150,8 +150,8 @@ module.exports = function (sif) { links: links, errors: errors, warnings: warnings, - sheetType: workbookType.sheetType, - networkMode: workbookType.networkMode, + sheetType: workbookMeta.sheetType, + workbookType: workbookMeta.workbookType, positiveWeights: [], negativeWeights: [], meta: {}, diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index 5d0d83e9..203e7e6e 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -293,28 +293,28 @@ var parseNetworkSheet = function (sheet, network) { /* * This method detect the network type of the workbook file either grn or protein-protein-physical-interactions - * If cellA1 = "cols regulators/ row targets" -> networkMode = grn - * If cellA1 = "protein 1/protein 2" -> networkMode = "protein-protein-physical-interaction" + * If cellA1 = "cols regulators/ row targets" -> workbookType = grn + * If cellA1 = "protein 1/protein 2" -> workbookType = "protein-protein-physical-interaction" * else undefined */ -exports.networkMode = function (workbookFile) { - let networkMode = "grn"; +exports.workbookType = function (workbookFile) { + let workbookType = "grn"; for (const sheet of workbookFile) { if (sheet.name.toLowerCase() === "network") { const cellA1 = sheet.data[0][0]; if (cellA1 === "cols regulators/rows targets") { - networkMode = "grn"; + workbookType = "grn"; } else if (cellA1 === "protein 1/protein 2") { - networkMode = "protein-protein-physical-interaction"; + workbookType = "protein-protein-physical-interaction"; } else { - networkMode = undefined; + workbookType = undefined; } break; } } - return networkMode; + return workbookType; }; exports.networks = function (workbookFile) { diff --git a/server/controllers/spreadsheet-controller.js b/server/controllers/spreadsheet-controller.js index 67425827..2c68fc3e 100644 --- a/server/controllers/spreadsheet-controller.js +++ b/server/controllers/spreadsheet-controller.js @@ -195,7 +195,7 @@ var crossSheetInteractions = function (workbookFile) { } } - additionalData.meta.data.workbookType = parseNetworkSheet.networkMode(workbookFile); + additionalData.meta.data.workbookType = parseNetworkSheet.workbookType(workbookFile); if (additionalData.meta.data.workbookType === undefined) { addWarning(workbook, constants.warnings.noWorkbookTypeDetected); additionalData.meta.data.workbookType = "grn"; diff --git a/test/export-tests.js b/test/export-tests.js index efd56dab..45c4cd0a 100644 --- a/test/export-tests.js +++ b/test/export-tests.js @@ -20,7 +20,8 @@ var unweightedTestWorkbook = { ], errors: [], warnings: [], - sheetType: "unweighted" + sheetType: "unweighted", + workbookType: "grn" }; var weightedTestWorkbook = { @@ -37,7 +38,8 @@ var weightedTestWorkbook = { ], errors: [], warnings: [], - sheetType: "weighted" + sheetType: "weighted", + workbookType: "grn" }; var unweightedTestWorkbookWithCycle = { @@ -57,7 +59,8 @@ var unweightedTestWorkbookWithCycle = { ], errors: [], warnings: [], - sheetType: "unweighted" + sheetType: "unweighted", + workbookType: "grn" }; var weightedTestWorkbookWithCycle = { @@ -77,7 +80,8 @@ var weightedTestWorkbookWithCycle = { ], errors: [], warnings: [], - sheetType: "weighted" + sheetType: "weighted", + workbookType: "grn" }; describe("Export to SIF", function () { diff --git a/test/import-sif-tests.js b/test/import-sif-tests.js index 0511c2fb..d0a35ec8 100644 --- a/test/import-sif-tests.js +++ b/test/import-sif-tests.js @@ -28,7 +28,7 @@ let expectedUnweightedGRNWorkbook = initWorkbook({ sheetType: "unweighted", meta: {}, expression:{}, - networkMode: "grn" + workbookType: "grn" }); let expectedUnweightedPPIWorkbook = initWorkbook({ @@ -52,7 +52,7 @@ let expectedUnweightedPPIWorkbook = initWorkbook({ sheetType: "unweighted", meta: {}, expression:{}, - networkMode: "protein-protein-physical-interaction" + workbookType: "protein-protein-physical-interaction" }); @@ -76,7 +76,7 @@ var expectedWeightedWorkbook = initWorkbook({ negativeWeights: [], sheetType: "weighted", meta: {}, - networkMode: "grn", + workbookType: "grn", expression:{} }); @@ -104,7 +104,7 @@ var expectedUnweightedWorkbookWithCycle = initWorkbook({ sheetType: "unweighted", meta: {}, expression:{}, - networkMode: "grn" + workbookType: "grn" }); var expectedWeightedWorkbookWithCycle = initWorkbook({ @@ -131,7 +131,7 @@ var expectedWeightedWorkbookWithCycle = initWorkbook({ sheetType: "weighted", meta: {}, expression:{}, - networkMode: "grn" + workbookType: "grn" }); // Unweighted SIF @@ -390,7 +390,7 @@ describe("Import from SIF", function () { sheetType: "unweighted", meta: {}, expression:{}, - networkMode: "grn" + workbookType: "grn" })); }); @@ -409,7 +409,7 @@ describe("Import from SIF", function () { sheetType: "weighted", meta: {}, expression:{}, - networkMode: "grn" + workbookType: "grn" })); }); diff --git a/web-client/public/js/setup-load-and-import-handlers.js b/web-client/public/js/setup-load-and-import-handlers.js index dfea2028..d3e12ce8 100644 --- a/web-client/public/js/setup-load-and-import-handlers.js +++ b/web-client/public/js/setup-load-and-import-handlers.js @@ -146,7 +146,7 @@ export const setupLoadAndImportHandlers = (grnState) => { grnState.workbook = workbook; if (grnState.name.includes(".sif")) { - grnState.mode = workbook.networkMode; + grnState.mode = workbook.workbookType; } else if (grnState.name.includes(".graphml")) { grnState.mode = "grn"; } else { From fcb706bdc959ab669d6511ef0ef1b54520c35a01 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 13 Feb 2024 01:51:32 -0800 Subject: [PATCH 036/150] fixed D-pad controls so can go to edge of graph with D-pad. Had to change move function. Issue #1083 --- web-client/public/js/graph.js | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 3d370d1e..bb10387d 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -481,15 +481,22 @@ export var drawGraph = function (workbook) { // move: moves graph with D-pad function move (direction) { - var width = - direction === "left" ? -50 : direction === "right" ? 50 : 0; - var height = - direction === "up" ? -50 : direction === "down" ? 50 : 0; - + var width = direction === "left" ? -50 : direction === "right" ? 50 : 0; + var height = direction === "up" ? -50 : direction === "down" ? 50 : 0; if (adaptive) { zoom.translateBy(zoomContainer, width, height); - } else if (!adaptive && grnState.zoomValue !== ZOOM_DISPLAY_MIDDLE && inBounds(width, height)) { - zoom.translateBy(zoomContainer, width, height); + } else if (!adaptive && grnState.zoomValue !== ZOOM_DISPLAY_MIDDLE) { + if (inBounds(width, height)) { + zoom.translateBy(zoomContainer, width, height); + } else if (inBounds(0, 0)) { + // ^check if current position in bounds but still not at border, + // then move remaining amount left in graph + if (width !== 0 && inBounds(width / graphZoom / 3, height)) { + zoom.translateBy(zoomContainer, width / graphZoom / 3, height); + } else if (height !== 0 && inBounds(width, height / graphZoom / 3)) { + zoom.translateBy(zoomContainer, width, height / graphZoom / 3); + } + } } } From 5216dad93eb9e1622ba7d448c780b996bf3aaf08 Mon Sep 17 00:00:00 2001 From: Cecilia Zaragoza <105010308+ceciliazaragoza@users.noreply.github.com> Date: Tue, 13 Feb 2024 10:49:11 -0800 Subject: [PATCH 037/150] Update package.json --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index bda06576..33183392 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "grnsight", - "version": "7.0.10", + "version": "7.0.11", "description": "Web app and service for visualizing models of gene regulatory networks", "directories": { "test": "test" From f26e8e22bc1f9f71cd4bd0bbd624b4f26e79e790 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 19 Feb 2024 21:21:16 -0800 Subject: [PATCH 038/150] a box with a black outline contains most of the nodes, but nodes inside the box cannot be dragged and some nodes are outside the border. when zoomed, the container size does not stay constant and stays the same size as the borderBox --- web-client/public/js/graph.js | 37 +++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index bb10387d..817302e9 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -33,6 +33,9 @@ import { * Resize detection logic: to avoid "listener leaks," this is set up a single time here, with an assignable * updateFunction being set when needed. */ + +// Stack overflow link for trying to create a box containing the graph: +// https://stackoverflow.com/questions/47544041/how-to-visualize-groups-of-nodes-in-a-d3-force-directed-graph-layout let mutationCallback = null; const resizeObserver = new MutationObserver((mutationsList, observer) => { if (typeof(mutationCallback) === "function") { @@ -211,6 +214,13 @@ export var drawGraph = function (workbook) { var boundingBoxContainer = zoomContainer.append("g"); // appended another g here... + var flexibleContainerRect = svg + .append("rect") + .attr("class", "boundingBox") + .attr("stroke", "black") + .attr("stroke-width", 1) + .attr("fill", "none") + var zoom = d3.zoom() .scaleExtent([MIN_SCALE, ZOOM_ADAPTIVE_MAX_SCALE]) .on("zoom", zoomed); @@ -1394,6 +1404,25 @@ export var drawGraph = function (workbook) { } }; + + //need to manipulate tick so that box changes whenever the nodes move + + //node has all the nodes + var nodes = simulation.nodes() + + const calculateFlexibleBox = (nodes) => { + const xValues = nodes.map(node => node.x) + const yValues = nodes.map(node => node.y) + const minX = Math.min(...xValues) + const minY = Math.min(...yValues) + const maxX = Math.max(...xValues) + const maxY = Math.max(...yValues) + + return {x: minX, y: minY, width: maxX - minX, height: maxY - minY} + } + + let flexibleContainer = calculateFlexibleBox(nodes) + // Tick only runs while the graph physics are still running. // (I.e. when the graph is completely relaxed, tick stops running.) function tick () { @@ -1413,6 +1442,14 @@ export var drawGraph = function (workbook) { var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; + flexibleContainer = calculateFlexibleBox(nodes) + + flexibleContainerRect + .attr("x", flexibleContainer.x) + .attr("y", flexibleContainer.y) + .attr("width", flexibleContainer.width) + .attr("height", flexibleContainer.height) + // this controls movement and position of nodes try { node.attr("x", function (d) { From da713b76b89f29f0c9dbe94478a67250a2146cab Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 19 Feb 2024 22:09:05 -0800 Subject: [PATCH 039/150] Issue #1083. FlexibleContainerRect contains most of the nodes, and the rect changes size if zoom in or out. need to see how can include node edges in box as well --- web-client/public/js/graph.js | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 817302e9..3a968400 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -214,12 +214,12 @@ export var drawGraph = function (workbook) { var boundingBoxContainer = zoomContainer.append("g"); // appended another g here... - var flexibleContainerRect = svg - .append("rect") + var flexibleContainerRect = boundingBoxContainer.append("rect") .attr("class", "boundingBox") .attr("stroke", "black") .attr("stroke-width", 1) .attr("fill", "none") + // .append("g") var zoom = d3.zoom() .scaleExtent([MIN_SCALE, ZOOM_ADAPTIVE_MAX_SCALE]) @@ -228,6 +228,7 @@ export var drawGraph = function (workbook) { svg.style("pointer-events", "all").call(zoomDrag) .style("font-family", "sans-serif"); + // this is why drag happens inside the flexibleContainerRect function zoomed () { zoomContainer.attr("transform", d3.event.transform); } @@ -1404,13 +1405,10 @@ export var drawGraph = function (workbook) { } }; - - //need to manipulate tick so that box changes whenever the nodes move - //node has all the nodes var nodes = simulation.nodes() - const calculateFlexibleBox = (nodes) => { + function calcFlexiBox (nodes) { const xValues = nodes.map(node => node.x) const yValues = nodes.map(node => node.y) const minX = Math.min(...xValues) @@ -1421,7 +1419,7 @@ export var drawGraph = function (workbook) { return {x: minX, y: minY, width: maxX - minX, height: maxY - minY} } - let flexibleContainer = calculateFlexibleBox(nodes) + let flexibleContainer = calcFlexiBox(nodes) // Tick only runs while the graph physics are still running. // (I.e. when the graph is completely relaxed, tick stops running.) @@ -1442,7 +1440,7 @@ export var drawGraph = function (workbook) { var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; - flexibleContainer = calculateFlexibleBox(nodes) + flexibleContainer = calcFlexiBox(nodes); flexibleContainerRect .attr("x", flexibleContainer.x) From a7c0e73ba431f1e7c583ca071dc653b48146828f Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 19 Feb 2024 22:24:16 -0800 Subject: [PATCH 040/150] Issue #1083. FlexiBox now contains total height of node. had to make sure to account for height of node when calculating max x position of node since seems like x position calculated at top left of node --- web-client/public/js/graph.js | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 3a968400..9773b1a8 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1409,17 +1409,24 @@ export var drawGraph = function (workbook) { var nodes = simulation.nodes() function calcFlexiBox (nodes) { + // let nodeHeight = 0 + // let height = 0 + // if (nodes.length > 0) { + // width = nodes[0].width + // height = nodes[0].height + // } const xValues = nodes.map(node => node.x) const yValues = nodes.map(node => node.y) const minX = Math.min(...xValues) const minY = Math.min(...yValues) const maxX = Math.max(...xValues) - const maxY = Math.max(...yValues) + const maxY = Math.max(...yValues) + nodeHeight return {x: minX, y: minY, width: maxX - minX, height: maxY - minY} } - let flexibleContainer = calcFlexiBox(nodes) + // don't set flexibleContainer = calcFlexiBox or else the function does not stop running, only want to run on tick + let flexibleContainer = null // Tick only runs while the graph physics are still running. // (I.e. when the graph is completely relaxed, tick stops running.) From 281435ad3358a1e47a12c033c83036135a59989b Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 19 Feb 2024 22:47:10 -0800 Subject: [PATCH 041/150] Issue #1083. now all nodes contained in flexibox, had to account for width of node. --- web-client/public/js/graph.js | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 9773b1a8..66f88952 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1409,19 +1409,17 @@ export var drawGraph = function (workbook) { var nodes = simulation.nodes() function calcFlexiBox (nodes) { - // let nodeHeight = 0 - // let height = 0 - // if (nodes.length > 0) { - // width = nodes[0].width - // height = nodes[0].height - // } + let nodeWidth = 0 + if (nodes.length > 0) { + nodeWidth = nodes[0].textWidth + 8 + } const xValues = nodes.map(node => node.x) const yValues = nodes.map(node => node.y) const minX = Math.min(...xValues) const minY = Math.min(...yValues) - const maxX = Math.max(...xValues) + + const maxX = Math.max(...xValues) + nodeWidth const maxY = Math.max(...yValues) + nodeHeight - return {x: minX, y: minY, width: maxX - minX, height: maxY - minY} } @@ -1447,13 +1445,15 @@ export var drawGraph = function (workbook) { var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; - flexibleContainer = calcFlexiBox(nodes); + if (!adaptive) { + flexibleContainer = calcFlexiBox(nodes); - flexibleContainerRect - .attr("x", flexibleContainer.x) - .attr("y", flexibleContainer.y) - .attr("width", flexibleContainer.width) - .attr("height", flexibleContainer.height) + flexibleContainerRect + .attr("x", flexibleContainer.x) + .attr("y", flexibleContainer.y) + .attr("width", flexibleContainer.width) + .attr("height", flexibleContainer.height) + } // this controls movement and position of nodes try { From 7d6c173ef1d19fc3cfa31c984813f4882c7e3eb4 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 19 Feb 2024 22:57:45 -0800 Subject: [PATCH 042/150] Issue #1083, can move zoom to any number now, but now the boundingBox container isn't showing up anymore --- web-client/public/js/graph.js | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 66f88952..5e9aa456 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -175,6 +175,7 @@ export var drawGraph = function (workbook) { var string = zoomContainer.attr("transform"); scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } + // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE ) { if (inBounds(d3.event.dx, d3.event.dy)) { zoom.translateBy( @@ -212,14 +213,15 @@ export var drawGraph = function (workbook) { .attr("width", width) .attr("height", height); - var boundingBoxContainer = zoomContainer.append("g"); // appended another g here... + var boundingBoxContainer = zoomContainer.append("g") + .attr("stroke", "black") + .attr("stroke-width", 1); // appended another g here... var flexibleContainerRect = boundingBoxContainer.append("rect") .attr("class", "boundingBox") .attr("stroke", "black") .attr("stroke-width", 1) .attr("fill", "none") - // .append("g") var zoom = d3.zoom() .scaleExtent([MIN_SCALE, ZOOM_ADAPTIVE_MAX_SCALE]) @@ -320,9 +322,7 @@ export var drawGraph = function (workbook) { const updateAppBasedOnZoomValue = () => { // If !adaptive, set Zoomvalue to ZOOM_DISPLAY_MIDDLE, 100, so do not zoom outside graph - if (!adaptive && grnState.zoomValue < ZOOM_DISPLAY_MIDDLE) { - grnState.zoomValue = ZOOM_DISPLAY_MIDDLE; - } + // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds const zoomDisplay = grnState.zoomValue; if (adaptive) { @@ -331,7 +331,9 @@ export var drawGraph = function (workbook) { ? zoomScaleLeft : zoomScaleRight)(zoomDisplay) ); - } else if (!adaptive && grnState.zoomValue >= ZOOM_DISPLAY_MIDDLE) { + } + // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds + else if (!adaptive) { setGraphZoom( (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft @@ -357,7 +359,9 @@ export var drawGraph = function (workbook) { : zoomScaleSliderRight ).invert(finalDisplay) ); - } else if (!adaptive && grnState.zoomValue >= ZOOM_DISPLAY_MIDDLE) { + } + // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds + else if (!adaptive) { // only allow minimum zoom value to be 100% so that do not go outside of viewport $(ZOOM_SLIDER).val( (finalDisplay <= ZOOM_DISPLAY_MIDDLE From d2105330f417d7d093db29a9be071aba660919ee Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 19 Feb 2024 23:32:39 -0800 Subject: [PATCH 043/150] Issue #1083, had to change order that boundingBoxContainer.append(rect) comes first to ensure that boundingBoxContainer border rectangle created before flexibleContainerRect. now can see both rectangles --- web-client/public/js/graph.js | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 5e9aa456..852ad4ef 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -213,9 +213,17 @@ export var drawGraph = function (workbook) { .attr("width", width) .attr("height", height); - var boundingBoxContainer = zoomContainer.append("g") - .attr("stroke", "black") - .attr("stroke-width", 1); // appended another g here... + var boundingBoxContainer = zoomContainer.append("g"); // appended another g here... + + // This rectangle catches all of the mousewheel and pan events, without letting + // them bubble up to the body. + boundingBoxContainer.append("rect") + .attr("width", width) + .attr("height", height) + .style("fill", "none") + .style("pointer-events", "all") + .attr("stroke", "none" ) + .append("g"); var flexibleContainerRect = boundingBoxContainer.append("rect") .attr("class", "boundingBox") @@ -237,16 +245,6 @@ export var drawGraph = function (workbook) { d3.select("svg").on("dblclick.zoom", null); // disables double click zooming - // This rectangle catches all of the mousewheel and pan events, without letting - // them bubble up to the body. - boundingBoxContainer.append("rect") - .attr("width", width) - .attr("height", height) - .style("fill", "none") - .style("pointer-events", "all") - .attr("stroke", "none" ) - .append("g"); - // this controls the D-pad d3.selectAll(".scrollBtn").on("click", null); // Remove event handlers, if there were any. var arrowMovement = [ "Up", "Left", "Right", "Down" ]; From d7d5dcd52a50bf5d24e082bf719ee17ebf24ea9f Mon Sep 17 00:00:00 2001 From: akaiap <109131321+akaiap@users.noreply.github.com> Date: Tue, 20 Feb 2024 10:52:06 -0800 Subject: [PATCH 044/150] Update Beta Version 7.0.12 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 33183392..8d7e2ceb 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "grnsight", - "version": "7.0.11", + "version": "7.0.12", "description": "Web app and service for visualizing models of gene regulatory networks", "directories": { "test": "test" From bb127c115b3d9452194df4c9ea09cb705a90a207 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Sun, 25 Feb 2024 17:35:13 -0800 Subject: [PATCH 045/150] Fixing the network mode for export function. Originall the network mode for ppi was mistyped. --- server/controllers/exporters/sif.js | 2 +- server/controllers/network-sheet-parser.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/server/controllers/exporters/sif.js b/server/controllers/exporters/sif.js index 89366d3b..0ef4df88 100644 --- a/server/controllers/exporters/sif.js +++ b/server/controllers/exporters/sif.js @@ -8,7 +8,7 @@ var exportEdges = function (workbook, gene, geneIndex) { result += [ gene.name, workbook.sheetType === constants.WEIGHTED ? - link.value : workbook.workbookType === "protein-protein-physical-interactions" ? + link.value : workbook.workbookType === "protein-protein-physical-interaction" ? "pp" : "pd", workbook.genes[link.target].name ].join("\t") + "\n"; diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index 203e7e6e..95faf45a 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -299,7 +299,7 @@ var parseNetworkSheet = function (sheet, network) { */ exports.workbookType = function (workbookFile) { - let workbookType = "grn"; + let workbookType; for (const sheet of workbookFile) { if (sheet.name.toLowerCase() === "network") { const cellA1 = sheet.data[0][0]; From 05597825c79a35b8844bb3fa77ff5202a2c402b9 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Sun, 25 Feb 2024 17:44:52 -0800 Subject: [PATCH 046/150] Renamed protein 1/protein 2 to cols protein1/ rows protein2 --- server/controllers/exporters/xlsx.js | 2 +- server/controllers/network-sheet-parser.js | 4 ++-- test/export-tests.js | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/server/controllers/exporters/xlsx.js b/server/controllers/exporters/xlsx.js index bba4b36d..c93bb4bb 100644 --- a/server/controllers/exporters/xlsx.js +++ b/server/controllers/exporters/xlsx.js @@ -21,7 +21,7 @@ const buildNetworkSheet = function (genes, links, workbookType) { if (workbookType === "grn") { geneNameArray.unshift("cols regulators/rows targets"); } else { - geneNameArray.unshift("protein 1/protein 2"); + geneNameArray.unshift("cols protein1/ rows protein2"); } links.forEach((link) => { diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index 203e7e6e..d131056c 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -294,7 +294,7 @@ var parseNetworkSheet = function (sheet, network) { /* * This method detect the network type of the workbook file either grn or protein-protein-physical-interactions * If cellA1 = "cols regulators/ row targets" -> workbookType = grn - * If cellA1 = "protein 1/protein 2" -> workbookType = "protein-protein-physical-interaction" + * If cellA1 = "cols protein1/ rows protein2" -> workbookType = "protein-protein-physical-interaction" * else undefined */ @@ -306,7 +306,7 @@ exports.workbookType = function (workbookFile) { if (cellA1 === "cols regulators/rows targets") { workbookType = "grn"; - } else if (cellA1 === "protein 1/protein 2") { + } else if (cellA1 === "cols protein1/ rows protein2") { workbookType = "protein-protein-physical-interaction"; } else { workbookType = undefined; diff --git a/test/export-tests.js b/test/export-tests.js index 45c4cd0a..2678e490 100644 --- a/test/export-tests.js +++ b/test/export-tests.js @@ -896,7 +896,7 @@ describe("Export to spreadsheet", function () { { name: "network", data: [ - ["protein 1/protein 2", "Aim32p", "Ccr4p", "Erv1p"], + ["cols protein1/ rows protein2", "Aim32p", "Ccr4p", "Erv1p"], ["Aim32p", 0, 0, 0], ["Ccr4p", 1, 1, 0], ["Erv1p", 1, 0, 1] From 052a634f74d9030733b2a5bff8fa1a064c82ac52 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Sun, 25 Feb 2024 20:13:28 -0800 Subject: [PATCH 047/150] Adding data-expression for each menu demo selection and only load demo if selected --- .../public/js/setup-load-and-import-handlers.js | 10 ++++++---- web-client/views/components/demo.pug | 12 ++++++------ 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/web-client/public/js/setup-load-and-import-handlers.js b/web-client/public/js/setup-load-and-import-handlers.js index d3e12ce8..6362273e 100644 --- a/web-client/public/js/setup-load-and-import-handlers.js +++ b/web-client/public/js/setup-load-and-import-handlers.js @@ -183,10 +183,12 @@ export const setupLoadAndImportHandlers = (grnState) => { }; const initializeDemoFile = (demoClass, demoPath, demoName) => { - // Deleted parameter `event` - $(demoClass).on("click", () => { - loadDemo(demoPath, demoClass, demoName); - }); + $(".dropdown-menu li a").on("click", (event) => { + const selected = event.target.dataset.expression; + if (`.${selected}` === demoClass) { + loadDemo(demoPath, demoClass, demoName); + } + }) $("#demoSourceDropdown").on("change", () => { const selected = `.${$("#demoSourceDropdown").val()}`; if (selected === demoClass) { diff --git a/web-client/views/components/demo.pug b/web-client/views/components/demo.pug index db2003ea..c29f8734 100644 --- a/web-client/views/components/demo.pug +++ b/web-client/views/components/demo.pug @@ -1,12 +1,12 @@ -ul(class='dropdown-menu' role='menu') +ul(class='dropdown-menu' role='menu' id="demo-dropdown") li - a(href='#' class='unweighted') Demo #1: Unweighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data) + a(href='#' class='unweighted' data-expression="unweighted") Demo #1: Unweighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data) li - a(href='#' class='weighted') Demo #2: Weighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data) + a(href='#' class='weighted' data-expression="weighted") Demo #2: Weighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data) li - a(href='#' class='schadeInput') Demo #3: Unweighted GRN (21 genes, 31 edges) + a(href='#' class='schadeInput' data-expression="schadeInput") Demo #3: Unweighted GRN (21 genes, 31 edges) li - a(href='#' class='schadeOutput') Demo #4: Weighted GRN (21 genes, 31 edges, Schade et al. 2004 data) + a(href='#' class='schadeOutput' data-expression="schadeOutput") Demo #4: Weighted GRN (21 genes, 31 edges, Schade et al. 2004 data) li - a(href='#' class='ppi') Demo #5: PPI (18 proteins, 81 edges) + a(href='#' class='ppi' data-expression="ppi") Demo #5: PPI (18 proteins, 81 edges) \ No newline at end of file From 9c5a39aebe63687364686ef855ed73943bff45ac Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Sun, 25 Feb 2024 20:15:20 -0800 Subject: [PATCH 048/150] Fix lint error, forgot ; at the end of line --- web-client/public/js/setup-load-and-import-handlers.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web-client/public/js/setup-load-and-import-handlers.js b/web-client/public/js/setup-load-and-import-handlers.js index 6362273e..b2d45fb0 100644 --- a/web-client/public/js/setup-load-and-import-handlers.js +++ b/web-client/public/js/setup-load-and-import-handlers.js @@ -188,7 +188,7 @@ export const setupLoadAndImportHandlers = (grnState) => { if (`.${selected}` === demoClass) { loadDemo(demoPath, demoClass, demoName); } - }) + }); $("#demoSourceDropdown").on("change", () => { const selected = `.${$("#demoSourceDropdown").val()}`; if (selected === demoClass) { From 63ca684687289e86b45229eabde2ee9f17f4fc2b Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 27 Feb 2024 11:36:49 -0800 Subject: [PATCH 049/150] Issue #1083. when restrict to graph viewport clicked, graph now refreshes without graph having to be clicked by user because call tick() function once restricted to viewport. trying to add paths in calculation for flexiBox, but when switch to different graphs, all nodes in one corner. Commented out that code for now, so this version works without any errors --- web-client/public/js/graph.js | 65 +++++++++++++++++++++++------------ 1 file changed, 43 insertions(+), 22 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 852ad4ef..91f61445 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -484,6 +484,8 @@ export var drawGraph = function (workbook) { d3.selectAll("input[name=viewport]").on("change", function () { var fixed = $(this).prop("checked"); restrictGraphToViewport(fixed); + // refresh the graph so that nodes and paths are restricted + tick() }); function center () { @@ -1408,21 +1410,41 @@ export var drawGraph = function (workbook) { }; //node has all the nodes - var nodes = simulation.nodes() + let nodes = simulation.nodes() + // let paths = link.selectAll("path").data() function calcFlexiBox (nodes) { - let nodeWidth = 0 - if (nodes.length > 0) { - nodeWidth = nodes[0].textWidth + 8 + // paths = link.selectAll("path").data(); + // if (nodes && paths) { + if (nodes) { + let nodeWidth = 0; + if (nodes.length > 0) { + nodeWidth = nodes[0].textWidth + 8; + } + + // const xValuesPaths = paths.map((path) => path.label.x); + // const yValuesPaths = paths.map((path) => path.label.y); + + const xValuesNodes = nodes.map((node) => node.x); + const yValuesNodes = nodes.map((node) => node.y); + + // const xValues = xValuesPaths.concat(xValuesNodes); + // const yValues = yValuesPaths.concat(yValuesNodes); + const xValues = xValuesNodes + const yValues = yValuesNodes + + const minX = Math.min(...xValues); + const minY = Math.min(...yValues); + + const maxX = Math.max(...xValues) + nodeWidth; + const maxY = Math.max(...yValues) + nodeHeight; + return { + x: minX, + y: minY, + width: maxX - minX, + height: maxY - minY, + }; } - const xValues = nodes.map(node => node.x) - const yValues = nodes.map(node => node.y) - const minX = Math.min(...xValues) - const minY = Math.min(...yValues) - - const maxX = Math.max(...xValues) + nodeWidth - const maxY = Math.max(...yValues) + nodeHeight - return {x: minX, y: minY, width: maxX - minX, height: maxY - minY} } // don't set flexibleContainer = calcFlexiBox or else the function does not stop running, only want to run on tick @@ -1447,18 +1469,17 @@ export var drawGraph = function (workbook) { var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; - if (!adaptive) { - flexibleContainer = calcFlexiBox(nodes); - - flexibleContainerRect - .attr("x", flexibleContainer.x) - .attr("y", flexibleContainer.y) - .attr("width", flexibleContainer.width) - .attr("height", flexibleContainer.height) - } - // this controls movement and position of nodes try { + if (!adaptive) { + flexibleContainer = calcFlexiBox(nodes); + + flexibleContainerRect + .attr("x", flexibleContainer.x) + .attr("y", flexibleContainer.y) + .attr("width", flexibleContainer.width) + .attr("height", flexibleContainer.height); + } node.attr("x", function (d) { var selfReferringEdge = getSelfReferringEdge(d); From b7e9370bc147b71965893ae72c9812873fbd24b3 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 27 Feb 2024 12:10:41 -0800 Subject: [PATCH 050/150] Issue #1083. Tried adding the x and y of the node path, but paths still not contained in box. will find other way to take control points into account. can switch between demos withought any errors though --- web-client/public/js/graph.js | 41 ++++++++++++++++++++++++----------- 1 file changed, 28 insertions(+), 13 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 91f61445..51346cac 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1424,14 +1424,28 @@ export var drawGraph = function (workbook) { // const xValuesPaths = paths.map((path) => path.label.x); // const yValuesPaths = paths.map((path) => path.label.y); + let xValuesPaths = [] + let yValuesPaths = [] + link.selectAll("path").attr("d", (pathData) => { + if (pathData.label) { + // have to make sure paths are rendered before reading label + // console.log(pathData.label.x) + xValuesPaths.push(pathData.label.x) + yValuesPaths.push(pathData.label.y) + // console.log(pathData.label.y) + } + }) + // let xValuesPaths = paths.map(path => console.log(path)) + + // console.log(xValuesPaths, yValuesPaths) const xValuesNodes = nodes.map((node) => node.x); const yValuesNodes = nodes.map((node) => node.y); - // const xValues = xValuesPaths.concat(xValuesNodes); - // const yValues = yValuesPaths.concat(yValuesNodes); - const xValues = xValuesNodes - const yValues = yValuesNodes + const xValues = xValuesPaths.concat(xValuesNodes); + const yValues = yValuesPaths.concat(yValuesNodes); + // const xValues = xValuesNodes + // const yValues = yValuesNodes const minX = Math.min(...xValues); const minY = Math.min(...yValues); @@ -1469,17 +1483,18 @@ export var drawGraph = function (workbook) { var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; + if (!adaptive) { + flexibleContainer = calcFlexiBox(nodes); + + flexibleContainerRect + .attr("x", flexibleContainer.x) + .attr("y", flexibleContainer.y) + .attr("width", flexibleContainer.width) + .attr("height", flexibleContainer.height); + } + // this controls movement and position of nodes try { - if (!adaptive) { - flexibleContainer = calcFlexiBox(nodes); - - flexibleContainerRect - .attr("x", flexibleContainer.x) - .attr("y", flexibleContainer.y) - .attr("width", flexibleContainer.width) - .attr("height", flexibleContainer.height); - } node.attr("x", function (d) { var selfReferringEdge = getSelfReferringEdge(d); From e3bc4e670254fb5ded7e46ce2483cfebebf12ad0 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 27 Feb 2024 21:08:11 -0800 Subject: [PATCH 051/150] Issue #1083. all nodes and edges contained in flexiContainer, but there is extra space in the box. now will work on collision with edge of box --- web-client/public/js/graph.js | 54 +++++++++++++++++++---------------- 1 file changed, 30 insertions(+), 24 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 51346cac..a182681b 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -270,7 +270,7 @@ export var drawGraph = function (workbook) { .split("(")[1].split(",")[1].split(")")[0]); }; - const inBounds = (width, height) => { + function inBounds(width, height) { /* * right: Math.abs(xTranslation + width * graphZoom) / zoomContainerWidth <= graphZoom - 1.0 * bottom: Math.abs(yTranslation + height * graphZoom) / zoomContainerHeight <= graphZoom - 1.0 @@ -1414,50 +1414,56 @@ export var drawGraph = function (workbook) { // let paths = link.selectAll("path").data() function calcFlexiBox (nodes) { - // paths = link.selectAll("path").data(); - // if (nodes && paths) { if (nodes) { let nodeWidth = 0; if (nodes.length > 0) { nodeWidth = nodes[0].textWidth + 8; } - // const xValuesPaths = paths.map((path) => path.label.x); - // const yValuesPaths = paths.map((path) => path.label.y); let xValuesPaths = [] let yValuesPaths = [] - link.selectAll("path").attr("d", (pathData) => { - if (pathData.label) { - // have to make sure paths are rendered before reading label - // console.log(pathData.label.x) - xValuesPaths.push(pathData.label.x) - yValuesPaths.push(pathData.label.y) - // console.log(pathData.label.y) - } - }) - // let xValuesPaths = paths.map(path => console.log(path)) - // console.log(xValuesPaths, yValuesPaths) + // this would reassign the values of pathData, since no value being assigned, then the value would be null + link.selectAll("path").each( function(pathData) { + if (pathData.source) { + // Log the "d" attribute for each path + const controlPoints = d3.select(this).attr("d"); + if (controlPoints.includes("A")) { + const splitSpaces = controlPoints.split(" "); + const controlPoint1 = splitSpaces[0].split("M")[1].split(","); + const controlPoint1X = controlPoint1[0]; + const controlPoint1Y = controlPoint1[1]; + console.log("A contains", controlPoint1X, controlPoint1Y); + } + else { + const splitC = controlPoints.split("C"); + const splitM = splitC[0].split("M")[1].split(","); + xValuesPaths.push(splitM[0]); + yValuesPaths.push(splitM[1]); + + splitC[1].split(",").forEach((coordinates) => { + const splitSpaces = coordinates.split(" "); + const xValue = splitSpaces[splitSpaces.length - 2] + const yValue = splitSpaces[splitSpaces.length - 1]; + xValuesPaths.push(xValue) + yValuesPaths.push(yValue) + }) + } + } + }); const xValuesNodes = nodes.map((node) => node.x); const yValuesNodes = nodes.map((node) => node.y); const xValues = xValuesPaths.concat(xValuesNodes); const yValues = yValuesPaths.concat(yValuesNodes); - // const xValues = xValuesNodes - // const yValues = yValuesNodes const minX = Math.min(...xValues); const minY = Math.min(...yValues); const maxX = Math.max(...xValues) + nodeWidth; const maxY = Math.max(...yValues) + nodeHeight; - return { - x: minX, - y: minY, - width: maxX - minX, - height: maxY - minY, - }; + return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } } From a0bb2ed83fe991757853d95d81a326c8fc9f5c54 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 27 Feb 2024 21:33:14 -0800 Subject: [PATCH 052/150] Issue #1083. added calculation so that self-regulating gene positions are taken into account --- web-client/public/js/graph.js | 69 +++++++++++++++++------------------ 1 file changed, 34 insertions(+), 35 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index a182681b..1a91fa3a 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1414,57 +1414,56 @@ export var drawGraph = function (workbook) { // let paths = link.selectAll("path").data() function calcFlexiBox (nodes) { - if (nodes) { - let nodeWidth = 0; - if (nodes.length > 0) { - nodeWidth = nodes[0].textWidth + 8; - } + let nodeWidth = 0; + if (nodes.length > 0) { + nodeWidth = nodes[0].textWidth + 8; + } - let xValuesPaths = [] - let yValuesPaths = [] + let xValuesPaths = [] + let yValuesPaths = [] - // this would reassign the values of pathData, since no value being assigned, then the value would be null - link.selectAll("path").each( function(pathData) { - if (pathData.source) { - // Log the "d" attribute for each path - const controlPoints = d3.select(this).attr("d"); + // this would reassign the values of pathData, since no value being assigned, then the value would be null + link.selectAll("path").each( function(pathData) { + if (pathData.source) { + // Log the "d" attribute for each path + const controlPoints = d3.select(this).attr("d"); + if (controlPoints) { if (controlPoints.includes("A")) { const splitSpaces = controlPoints.split(" "); - const controlPoint1 = splitSpaces[0].split("M")[1].split(","); - const controlPoint1X = controlPoint1[0]; - const controlPoint1Y = controlPoint1[1]; - console.log("A contains", controlPoint1X, controlPoint1Y); + const controlPoint = splitSpaces[0].split("M")[1].split(","); + const controlPointX = controlPoint[0]; + const controlPointY = controlPoint[1]; + // console.log(typeof(controlPointX), typeof(controlPointY)) + xValuesPaths.push(parseFloat(controlPointX)) + yValuesPaths.push(parseFloat(controlPointY)) } - else { + else if (controlPoints.includes("C")) { const splitC = controlPoints.split("C"); - const splitM = splitC[0].split("M")[1].split(","); - xValuesPaths.push(splitM[0]); - yValuesPaths.push(splitM[1]); splitC[1].split(",").forEach((coordinates) => { const splitSpaces = coordinates.split(" "); - const xValue = splitSpaces[splitSpaces.length - 2] + const xValue = splitSpaces[splitSpaces.length - 2]; const yValue = splitSpaces[splitSpaces.length - 1]; - xValuesPaths.push(xValue) - yValuesPaths.push(yValue) - }) + xValuesPaths.push(parseFloat(xValue)); + yValuesPaths.push(parseFloat(yValue)); + }); } } - }); + } + }); - const xValuesNodes = nodes.map((node) => node.x); - const yValuesNodes = nodes.map((node) => node.y); + const xValuesNodes = nodes.map((node) => node.x); + const yValuesNodes = nodes.map((node) => node.y); - const xValues = xValuesPaths.concat(xValuesNodes); - const yValues = yValuesPaths.concat(yValuesNodes); + const xValues = xValuesPaths.concat(xValuesNodes); + const yValues = yValuesPaths.concat(yValuesNodes); - const minX = Math.min(...xValues); - const minY = Math.min(...yValues); + const minX = Math.min(...xValues); + const minY = Math.min(...yValues); - const maxX = Math.max(...xValues) + nodeWidth; - const maxY = Math.max(...yValues) + nodeHeight; - return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; - } + const maxX = Math.max(...xValues) + nodeWidth; + const maxY = Math.max(...yValues) + nodeHeight; + return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } // don't set flexibleContainer = calcFlexiBox or else the function does not stop running, only want to run on tick From e88caec68ceb64ec222551ae52db742343f104c9 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 1 Mar 2024 22:18:52 -0800 Subject: [PATCH 053/150] Issue #1083. cleaned up updateAppBasedOnZoomValue and zoomDragged --- web-client/public/js/graph.js | 68 ++++++++++++++--------------------- 1 file changed, 27 insertions(+), 41 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 1a91fa3a..9b8a57ff 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -176,16 +176,12 @@ export var drawGraph = function (workbook) { scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (!adaptive && d3.event.x >= ZOOM_DISPLAY_MIDDLE ) { - if (inBounds(d3.event.dx, d3.event.dy)) { - zoom.translateBy( - zoomContainer, - scale * (d3.event.x - zoomDragPrevX), - scale * (d3.event.y - zoomDragPrevY) - ); - } - } else if (adaptive) { - zoom.translateBy(zoomContainer, scale * (d3.event.x - zoomDragPrevX), scale * (d3.event.y - zoomDragPrevY)); + if (adaptive && (!adaptive && inBounds(d3.event.dx, d3.event.dy))) { + zoom.translateBy( + zoomContainer, + scale * (d3.event.x - zoomDragPrevX), + scale * (d3.event.y - zoomDragPrevY) + ); } zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; @@ -323,20 +319,14 @@ export var drawGraph = function (workbook) { // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds const zoomDisplay = grnState.zoomValue; - if (adaptive) { - setGraphZoom( - (zoomDisplay <= ZOOM_DISPLAY_MIDDLE - ? zoomScaleLeft - : zoomScaleRight)(zoomDisplay) - ); - } + setGraphZoom( + (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)( + zoomDisplay + ) + ); + // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - else if (!adaptive) { - setGraphZoom( - (zoomDisplay <= ZOOM_DISPLAY_MIDDLE - ? zoomScaleLeft - : zoomScaleRight)(zoomDisplay) - ); + if (!adaptive) { center(); } @@ -350,7 +340,8 @@ export var drawGraph = function (workbook) { $(ZOOM_INPUT).val(finalDisplay); } - if (adaptive) { + // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds + if (adaptive || !adaptive) { $(ZOOM_SLIDER).val( (finalDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleSliderLeft @@ -358,16 +349,6 @@ export var drawGraph = function (workbook) { ).invert(finalDisplay) ); } - // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - else if (!adaptive) { - // only allow minimum zoom value to be 100% so that do not go outside of viewport - $(ZOOM_SLIDER).val( - (finalDisplay <= ZOOM_DISPLAY_MIDDLE - ? zoomScaleSliderLeft - : zoomScaleSliderRight - ).invert(finalDisplay) - ); - } }; /** @@ -1409,11 +1390,8 @@ export var drawGraph = function (workbook) { } }; - //node has all the nodes - let nodes = simulation.nodes() - // let paths = link.selectAll("path").data() - - function calcFlexiBox (nodes) { + function calcFlexiBox () { + const nodes = simulation.nodes() let nodeWidth = 0; if (nodes.length > 0) { nodeWidth = nodes[0].textWidth + 8; @@ -1433,7 +1411,6 @@ export var drawGraph = function (workbook) { const controlPoint = splitSpaces[0].split("M")[1].split(","); const controlPointX = controlPoint[0]; const controlPointY = controlPoint[1]; - // console.log(typeof(controlPointX), typeof(controlPointY)) xValuesPaths.push(parseFloat(controlPointX)) yValuesPaths.push(parseFloat(controlPointY)) } @@ -1466,6 +1443,14 @@ export var drawGraph = function (workbook) { return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } + function flexiCollision(flexibleContainer) { + if (flexibleContainer) { + console.log("flexiCollision"); + console.log(flexibleContainer.x, flexibleContainer.y, zoomContainer.attr("transform")) + console.log(svg.attr("width"), svg.attr("height")) + } + } + // don't set flexibleContainer = calcFlexiBox or else the function does not stop running, only want to run on tick let flexibleContainer = null @@ -1489,7 +1474,8 @@ export var drawGraph = function (workbook) { var OFFSET_VALUE = 5; if (!adaptive) { - flexibleContainer = calcFlexiBox(nodes); + flexibleContainer = calcFlexiBox(); + flexiCollision(flexibleContainer) flexibleContainerRect .attr("x", flexibleContainer.x) From 29bd515dff19f48fa9551395f8c30536d50768f4 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 4 Mar 2024 22:56:29 -0800 Subject: [PATCH 054/150] Issue #1083. Now the flexibleContainerRect appears when restricted to viewport and goes away when not restricted to viewport --- web-client/public/js/graph.js | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 9b8a57ff..006aca9c 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -226,6 +226,7 @@ export var drawGraph = function (workbook) { .attr("stroke", "black") .attr("stroke-width", 1) .attr("fill", "none") + .attr("id", "flexibleContainerRect"); var zoom = d3.zoom() .scaleExtent([MIN_SCALE, ZOOM_ADAPTIVE_MAX_SCALE]) @@ -234,7 +235,6 @@ export var drawGraph = function (workbook) { svg.style("pointer-events", "all").call(zoomDrag) .style("font-family", "sans-serif"); - // this is why drag happens inside the flexibleContainerRect function zoomed () { zoomContainer.attr("transform", d3.event.transform); } @@ -432,9 +432,9 @@ export var drawGraph = function (workbook) { if (!fixed) { $("#restrict-graph-to-viewport span").removeClass("glyphicon-ok"); $("input[name=viewport]").removeProp("checked"); - // $container.addClass("cursorGrabbing"); adaptive = true; d3.select("rect").attr("stroke", "none"); + d3.select("#flexibleContainerRect").attr("stroke", "none") center(); } else if (fixed) { $("#restrict-graph-to-viewport span").addClass("glyphicon-ok"); @@ -448,10 +448,12 @@ export var drawGraph = function (workbook) { } width = $container.width(); height = $container.height(); + // put a border with a gray stroke around the original container size d3.select("rect").attr("stroke", "#9A9A9A") .attr("width", width) .attr("height", height); $(".boundingBox").attr("width", width).attr("height", height); + d3.select("#flexibleContainerRect").attr("stroke", "black"); center(); } updateAppBasedOnZoomValue(); // Update zoom value within bounds @@ -1477,6 +1479,7 @@ export var drawGraph = function (workbook) { flexibleContainer = calcFlexiBox(); flexiCollision(flexibleContainer) + // TODO: do I need to make this transform and translate? This is firing too much flexibleContainerRect .attr("x", flexibleContainer.x) .attr("y", flexibleContainer.y) @@ -1538,6 +1541,8 @@ export var drawGraph = function (workbook) { }); } } + // height += OFFSET_VALUE; + // boundingBoxContainer.attr("height", height); return d.y = currentYPos; }).attr("transform", function (d) { return "translate(" + d.x + "," + d.y + ")"; From 238f8a12d9be6b60a762cf18e7b5908db933ffe2 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 5 Mar 2024 11:44:04 -0800 Subject: [PATCH 055/150] Issue #1081. Can get the node tab to hide, but still want the option to enable Enable Node Coloring and do not like the look of the empty list elements --- web-client/public/js/update-app.js | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/web-client/public/js/update-app.js b/web-client/public/js/update-app.js index 89566749..2399051b 100644 --- a/web-client/public/js/update-app.js +++ b/web-client/public/js/update-app.js @@ -515,8 +515,8 @@ const showNodeColoringMenus = () => { const disableNodeColoringMenus = () => { $(NODE_COLORING_SIDEBAR_PANEL).addClass("disabled"); $(NODE_COLORING_SIDEBAR_PANEL).removeClass("in"); - $(NODE_COLORING_MENU).addClass("disabled"); $(NODE_COLORING_MENU_CLASS).addClass("disabled"); + $(NODE_COLORING_MENU).addClass("disabled"); $(NODE_COLORING_SIDEBAR_HEADER_LINK).attr("data-toggle", ""); }; @@ -873,6 +873,7 @@ export const updateApp = grnState => { $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", true); $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).val(DEFAULT_MAX_LOG_FOLD_CHANGE); $(NODE_COLORING_SIDEBAR_BODY).removeClass("hidden"); + $(NODE_COLORING_MENU_CLASS).removeClass("hidden") if (grnState.database.expressionDatasets.includes(grnState.nodeColoring.topDataset) && grnState.workbook.expression[grnState.nodeColoring.topDataset] === undefined) { if ($(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked")) { @@ -931,6 +932,7 @@ export const updateApp = grnState => { } } else if (grnState.workbook !== null && !grnState.nodeColoring.nodeColoringEnabled) { $(NODE_COLORING_SIDEBAR_BODY).addClass("hidden"); + $(NODE_COLORING_MENU_CLASS).addClass("hidden") $(`${NODE_COLORING_TOGGLE_MENU} span`).removeClass("glyphicon-ok"); $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", false); } From 223ed527d1182b544b61434bf7894577b452217b Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 5 Mar 2024 18:43:25 -0800 Subject: [PATCH 056/150] Issue #1081. Can now enable and disable node tab list elements in navbar, but the css in the list elements in the node tab are a little off (not centered, the text is blue) --- web-client/public/js/update-app.js | 9 +++-- web-client/views/upload.pug | 53 +++++++++++++++--------------- 2 files changed, 34 insertions(+), 28 deletions(-) diff --git a/web-client/public/js/update-app.js b/web-client/public/js/update-app.js index 2399051b..5f66c7ae 100644 --- a/web-client/public/js/update-app.js +++ b/web-client/public/js/update-app.js @@ -873,7 +873,9 @@ export const updateApp = grnState => { $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", true); $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).val(DEFAULT_MAX_LOG_FOLD_CHANGE); $(NODE_COLORING_SIDEBAR_BODY).removeClass("hidden"); - $(NODE_COLORING_MENU_CLASS).removeClass("hidden") + $(NODE_COLORING_MENU).removeClass("hidden"); + $("#node-coloring-options").removeClass("hidden"); + console.log("node coloring menus shown") if (grnState.database.expressionDatasets.includes(grnState.nodeColoring.topDataset) && grnState.workbook.expression[grnState.nodeColoring.topDataset] === undefined) { if ($(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked")) { @@ -932,8 +934,11 @@ export const updateApp = grnState => { } } else if (grnState.workbook !== null && !grnState.nodeColoring.nodeColoringEnabled) { $(NODE_COLORING_SIDEBAR_BODY).addClass("hidden"); - $(NODE_COLORING_MENU_CLASS).addClass("hidden") + $(NODE_COLORING_MENU).addClass("disabled"); + $("#node-coloring-options").addClass("hidden"); $(`${NODE_COLORING_TOGGLE_MENU} span`).removeClass("glyphicon-ok"); + + console.log("node coloring hidden") $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", false); } diff --git a/web-client/views/upload.pug b/web-client/views/upload.pug index 40f431ee..70bca72c 100644 --- a/web-client/views/upload.pug +++ b/web-client/views/upload.pug @@ -118,32 +118,33 @@ html a(href='#' id='node-coloring-toggle-menu' class='nodeColoringToggle') span(class='glyphicon') |   Enable Node Coloring - li(class='divider') - li(class='node-coloring-menu dropdown-submenu disabled') - a(href='#') - span(class='glyphicon invisible') - |   Select Top Dataset - ul(class='dropdown-menu' id='topDatasetDropdownMenu') - li(class='node-coloring-menu disabled') - a(href='#' id='averageDataTopMenu' class='nodeColoring') - span(class='glyphicon') - |   Average Replicate Values for Top Dataset - li(class='divider') - li(class='node-coloring-menu dropdown-submenu disabled') - a(href='#') - span(class='glyphicon invisible') - |   Select Bottom Dataset - ul(class='dropdown-menu' id='bottomDatasetDropdownMenu') - li(class='node-coloring-menu disabled') - a(href='#' id='averageDataBottomMenu' class='viewportOption') - span(class='glyphicon') - |   Average Replicate Values for Bottom Dataset - li(class='divider') - li(class='node-coloring-menu disabled') - a(href='#' class='nodeOptions with-input') - span(class='glyphicon invisible') - |   Log Fold Change Max Value (0.01 - 100):   - input(type='number' min="0.01" max="100" id='log-fold-change-max-value-menu' class='logFoldChangeMaxValue keepopen' aria-describedby='basic-addon1') + div(id='node-coloring-options') + li(class='divider') + li(class='node-coloring-menu dropdown-submenu disabled') + a(href='#') + span(class='glyphicon invisible') + |   Select Top Dataset + ul(class='dropdown-menu' id='topDatasetDropdownMenu') + li(class='node-coloring-menu disabled') + a(href='#' id='averageDataTopMenu' class='nodeColoring') + span(class='glyphicon') + |   Average Replicate Values for Top Dataset + li(class='divider') + li(class='node-coloring-menu dropdown-submenu disabled') + a(href='#') + span(class='glyphicon invisible') + |   Select Bottom Dataset + ul(class='dropdown-menu' id='bottomDatasetDropdownMenu') + li(class='node-coloring-menu disabled') + a(href='#' id='averageDataBottomMenu' class='viewportOption') + span(class='glyphicon') + |   Average Replicate Values for Bottom Dataset + li(class='divider') + li(class='node-coloring-menu disabled') + a(href='#' class='nodeOptions with-input') + span(class='glyphicon invisible') + |   Log Fold Change Max Value (0.01 - 100):   + input(type='number' min="0.01" max="100" id='log-fold-change-max-value-menu' class='logFoldChangeMaxValue keepopen' aria-describedby='basic-addon1') li(class='dropdown') a(href='#' class='dropdown-toggle' data-toggle='dropdown') Edge From 34fb304e6a20bb9aeb09bebb1abf1b0357b7387e Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 5 Mar 2024 18:49:48 -0800 Subject: [PATCH 057/150] Issue #1081. added node coloring constant to constants.js --- web-client/public/js/constants.js | 1 + web-client/public/js/update-app.js | 5 +++-- web-client/views/upload.pug | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/web-client/public/js/constants.js b/web-client/public/js/constants.js index 3da3b8ab..1e412565 100644 --- a/web-client/public/js/constants.js +++ b/web-client/public/js/constants.js @@ -131,6 +131,7 @@ export const EXPRESSION_DB_LOADER_TEXT = ".expression-db-loader export const DATA_SET_SELECT = "#data-set-select"; export const NODE_COLORING_MENU = ".node-coloring"; export const NODE_COLORING_MENU_CLASS = ".node-coloring-menu"; +export const NODE_COLORING_NAVBAR_OPTIONS = "#node-coloring-navbar-options"; export const NODE_COLORING_SIDEBAR_PANEL = "#nodeColoringSidebarPanel"; export const NODE_COLORING_SIDEBAR_HEADER_LINK = "#nodeColoringHeaderLink"; export const NODE_COLORING_SIDEBAR_BODY = ".nodeColoringSidebarBody"; diff --git a/web-client/public/js/update-app.js b/web-client/public/js/update-app.js index 5f66c7ae..7101b01a 100644 --- a/web-client/public/js/update-app.js +++ b/web-client/public/js/update-app.js @@ -49,6 +49,7 @@ import { NODE_COLORING_MENU, NODE_COLORING_TOGGLE_MENU, NODE_COLORING_MENU_CLASS, + NODE_COLORING_NAVBAR_OPTIONS, NODE_COLORING_SIDEBAR_BODY, NODE_COLORING_SIDEBAR_PANEL, NODE_COLORING_SIDEBAR_HEADER_LINK, @@ -874,7 +875,7 @@ export const updateApp = grnState => { $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).val(DEFAULT_MAX_LOG_FOLD_CHANGE); $(NODE_COLORING_SIDEBAR_BODY).removeClass("hidden"); $(NODE_COLORING_MENU).removeClass("hidden"); - $("#node-coloring-options").removeClass("hidden"); + $(NODE_COLORING_NAVBAR_OPTIONS).removeClass("hidden"); console.log("node coloring menus shown") if (grnState.database.expressionDatasets.includes(grnState.nodeColoring.topDataset) && grnState.workbook.expression[grnState.nodeColoring.topDataset] === undefined) { @@ -935,7 +936,7 @@ export const updateApp = grnState => { } else if (grnState.workbook !== null && !grnState.nodeColoring.nodeColoringEnabled) { $(NODE_COLORING_SIDEBAR_BODY).addClass("hidden"); $(NODE_COLORING_MENU).addClass("disabled"); - $("#node-coloring-options").addClass("hidden"); + $(NODE_COLORING_NAVBAR_OPTIONS).addClass("hidden"); $(`${NODE_COLORING_TOGGLE_MENU} span`).removeClass("glyphicon-ok"); console.log("node coloring hidden") diff --git a/web-client/views/upload.pug b/web-client/views/upload.pug index 70bca72c..f3230144 100644 --- a/web-client/views/upload.pug +++ b/web-client/views/upload.pug @@ -118,7 +118,7 @@ html a(href='#' id='node-coloring-toggle-menu' class='nodeColoringToggle') span(class='glyphicon') |   Enable Node Coloring - div(id='node-coloring-options') + div(id='node-coloring-navbar-options') li(class='divider') li(class='node-coloring-menu dropdown-submenu disabled') a(href='#') From 2f89ff1fd34402c1f9ba5203e308b446def6f85b Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 5 Mar 2024 19:39:39 -0800 Subject: [PATCH 058/150] Issue #1081, trying to change CSS styling in grnsight.styl with .dropdown-submenu, but still not working --- web-client/public/stylesheets/grnsight.styl | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/web-client/public/stylesheets/grnsight.styl b/web-client/public/stylesheets/grnsight.styl index 35196707..94f51503 100644 --- a/web-client/public/stylesheets/grnsight.styl +++ b/web-client/public/stylesheets/grnsight.styl @@ -255,10 +255,10 @@ nav.navbar.navbar-default -moz-border-radius:0 6px 6px 6px border-radius:0 6px 6px 6px -.dropdown-submenu:hover>.dropdown-menu +.dropdown-submenu:hover>.dropdown-menu, #node-coloring-navbar-options>.dropdown-submenu:hover>.dropdown-menu display:block -.dropdown-submenu>a:after +.dropdown-submenu>a:after, #node-coloring-navbar-options>.dropdown-submenu:hover>a:after display:block content:" " float:right @@ -271,13 +271,13 @@ nav.navbar.navbar-default margin-top:5px margin-right:-10px -.dropdown-submenu:hover>a:after +.dropdown-submenu:hover>a:after, #node-coloring-navbar-options>.dropdown-submenu:hover>a:after border-left-color:#ffffff -.dropdown-submenu.pull-left +.dropdown-submenu.pull-left, #node-coloring-navbar-options>.dropdown-submenu.pull-left float:none -.dropdown-submenu.pull-left>.dropdown-menu +.dropdown-submenu.pull-left>.dropdown-menu, #node-coloring-navbar-options>.dropdown-submenu.pull-left>.dropdown-menu left:-100% margin-left:10px -webkit-border-radius:6px 0 6px 6px From 59cb9897420408352b859a6d1b573bb682d33b81 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 5 Mar 2024 22:28:40 -0800 Subject: [PATCH 059/150] Issue #1083. Cursorgrab wasn't working, so fixed that can cursorgrab within bounding box --- web-client/public/js/graph.js | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 006aca9c..59281fd7 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -176,7 +176,7 @@ export var drawGraph = function (workbook) { scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (adaptive && (!adaptive && inBounds(d3.event.dx, d3.event.dy))) { + if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy))) { zoom.translateBy( zoomContainer, scale * (d3.event.x - zoomDragPrevX), @@ -1541,8 +1541,6 @@ export var drawGraph = function (workbook) { }); } } - // height += OFFSET_VALUE; - // boundingBoxContainer.attr("height", height); return d.y = currentYPos; }).attr("transform", function (d) { return "translate(" + d.x + "," + d.y + ")"; From f6bb7d8a2bed07724d1d38ad21f0269c5b985d2a Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 5 Mar 2024 22:45:21 -0800 Subject: [PATCH 060/150] Issue #1083. Now there is a bounding box, called viewportBoundingBox, that is consisntently the size of the exportContainer. Although the border for the boundingBoxContainer no longer shows since its border properties (width and color) now belong to the viewportBoundingBox, the boundingBoxContainer still works the same as before --- web-client/public/js/graph.js | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 59281fd7..c1c5d165 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -204,6 +204,17 @@ export var drawGraph = function (workbook) { .attr("height", height) .attr("id", "exportContainer"); + var viewportBoundingBox = svg + .append("g") + .append("rect") + .attr("class", "boundingBox") + .attr("width", width) + .attr("height", height) + .style("fill", "none") + // .attr("stroke", "black") + // .attr("stroke-width", 2) + .attr("id", "viewportBoundingBox"); + var zoomContainer = svg.append("g") // required for zoom to work .attr("class", "boundingBox") .attr("width", width) From ad4ef0f0542e6d724cad30d0eedfa657f93db440 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 5 Mar 2024 23:39:16 -0800 Subject: [PATCH 061/150] Issue #1083. Temporarily commented out viewportBoundingBox so that can see BoundingBox again. now the flexibleRect does not exceed the bottom or right boundaries of the boundingBox, but still exceeds right and top boundaries. probably has something to do with x == 0 or y == 0 for boundaries --- web-client/public/js/graph.js | 59 ++++++++++++++++++++++++++--------- 1 file changed, 44 insertions(+), 15 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index c1c5d165..cb0ff524 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -204,16 +204,14 @@ export var drawGraph = function (workbook) { .attr("height", height) .attr("id", "exportContainer"); - var viewportBoundingBox = svg - .append("g") - .append("rect") - .attr("class", "boundingBox") - .attr("width", width) - .attr("height", height) - .style("fill", "none") - // .attr("stroke", "black") - // .attr("stroke-width", 2) - .attr("id", "viewportBoundingBox"); + // var viewportBoundingBox = svg + // .append("g") + // .append("rect") + // .attr("class", "boundingBox") + // .attr("width", width) + // .attr("height", height) + // .style("fill", "none") + // .attr("id", "viewportBoundingBox"); var zoomContainer = svg.append("g") // required for zoom to work .attr("class", "boundingBox") @@ -1458,15 +1456,22 @@ export var drawGraph = function (workbook) { function flexiCollision(flexibleContainer) { if (flexibleContainer) { - console.log("flexiCollision"); - console.log(flexibleContainer.x, flexibleContainer.y, zoomContainer.attr("transform")) - console.log(svg.attr("width"), svg.attr("height")) + // console.log("flexiCollision"); + // console.log(flexibleContainer.x, flexibleContainer.y, zoomContainer.attr("transform")) + // console.log(svg.attr("width"), svg.attr("height")) } } + function flexiRectInBounds() { + const xInBounds = flexibleContainer.width - flexibleContainer.x <= width * graphZoom; + const yInBounds = flexibleContainer.height - flexibleContainer.y <= height * graphZoom; + + return {x: xInBounds, y: yInBounds}; + } + // don't set flexibleContainer = calcFlexiBox or else the function does not stop running, only want to run on tick let flexibleContainer = null - + // Tick only runs while the graph physics are still running. // (I.e. when the graph is completely relaxed, tick stops running.) function tick () { @@ -1490,12 +1495,36 @@ export var drawGraph = function (workbook) { flexibleContainer = calcFlexiBox(); flexiCollision(flexibleContainer) - // TODO: do I need to make this transform and translate? This is firing too much + console.log(flexiRectInBounds()) + const flexiRectValidation = flexiRectInBounds() + + // if outside x or y bounds, set flexiRect width or height to max size of bounding box + if (!flexiRectValidation.x) { + flexibleContainer.width = width - flexibleContainer.x; + } + + if (!flexiRectValidation.y) { + flexibleContainer.height = height - flexibleContainer.y; + } + + // console.log("d3 events", d3.event) + // const flexiRectValidation = flexiRectInBounds(d3.event.dx, d3.event.dy) + // if ( + // d3.event.x &&d3.event.dy && flexiRectValidation[0] &&flexiRectValidation[1] + // ) + // { flexibleContainerRect .attr("x", flexibleContainer.x) .attr("y", flexibleContainer.y) .attr("width", flexibleContainer.width) .attr("height", flexibleContainer.height); + // } else { + // flexibleContainerRect + // .attr("x", flexibleContainer.x) + // .attr("y", flexibleContainer.y) + // .attr("width", flexibleContainer.width) + // .attr("height", flexibleContainer.height); + // } } // this controls movement and position of nodes From 0fc0a99bae89a9192ee51016316017d18e9675ee Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 5 Mar 2024 23:51:21 -0800 Subject: [PATCH 062/150] Issue #1083. Now flexibleContainerRect is limited to the size of the bounding box and cannot exceed iteven if the user drags their mouse outside of the box --- web-client/public/js/graph.js | 56 +++++++++++++++-------------------- 1 file changed, 24 insertions(+), 32 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index cb0ff524..609eb287 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1462,16 +1462,32 @@ export var drawGraph = function (workbook) { } } - function flexiRectInBounds() { - const xInBounds = flexibleContainer.width - flexibleContainer.x <= width * graphZoom; - const yInBounds = flexibleContainer.height - flexibleContainer.y <= height * graphZoom; - - return {x: xInBounds, y: yInBounds}; - } // don't set flexibleContainer = calcFlexiBox or else the function does not stop running, only want to run on tick let flexibleContainer = null + function flexiRectInBounds() { + // x left bound + if (flexibleContainer.x < 0) { + flexibleContainer.x = 0 + } + + // x right bound + if (!(flexibleContainer.width - flexibleContainer.x <= width * graphZoom)) { + flexibleContainer.width = width - flexibleContainer.x; + } + + // y top bound + if (flexibleContainer.y < 0) { + flexibleContainer.y = 0; + } + + // y bottom bound + if (!(flexibleContainer.height - flexibleContainer.y <= height * graphZoom)) { + flexibleContainer.height = height - flexibleContainer.y; + } + } + // Tick only runs while the graph physics are still running. // (I.e. when the graph is completely relaxed, tick stops running.) function tick () { @@ -1493,38 +1509,14 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(); - flexiCollision(flexibleContainer) + flexiRectInBounds(); + // flexiCollision(flexibleContainer) - console.log(flexiRectInBounds()) - const flexiRectValidation = flexiRectInBounds() - - // if outside x or y bounds, set flexiRect width or height to max size of bounding box - if (!flexiRectValidation.x) { - flexibleContainer.width = width - flexibleContainer.x; - } - - if (!flexiRectValidation.y) { - flexibleContainer.height = height - flexibleContainer.y; - } - - // console.log("d3 events", d3.event) - // const flexiRectValidation = flexiRectInBounds(d3.event.dx, d3.event.dy) - // if ( - // d3.event.x &&d3.event.dy && flexiRectValidation[0] &&flexiRectValidation[1] - // ) - // { flexibleContainerRect .attr("x", flexibleContainer.x) .attr("y", flexibleContainer.y) .attr("width", flexibleContainer.width) .attr("height", flexibleContainer.height); - // } else { - // flexibleContainerRect - // .attr("x", flexibleContainer.x) - // .attr("y", flexibleContainer.y) - // .attr("width", flexibleContainer.width) - // .attr("height", flexibleContainer.height); - // } } // this controls movement and position of nodes From 968f3778982626bca8404393a8991c3357e0d164 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 6 Mar 2024 01:14:12 -0800 Subject: [PATCH 063/150] Issue #1083, for some reason the flexiRectInBounds won't run after flexiContainerRect exceeds the export box. added flexiRectInBounds throughout code, must be something to do with flexiContainerRect being underneath the zoom bar when dragging, but the graph still zooms in --- web-client/public/js/graph.js | 97 ++++++++++++++++++++--------------- 1 file changed, 57 insertions(+), 40 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 609eb287..72164eaf 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -170,13 +170,14 @@ export var drawGraph = function (workbook) { // allows zoom slider to be moved and limits movement when !adaptive var zoomDragged = function () { + console.log("zoom dragged ran") var scale = 1; if (zoomContainer.attr("transform")) { var string = zoomContainer.attr("transform"); scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy))) { + if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy) && flexiRectInBounds())) { zoom.translateBy( zoomContainer, scale * (d3.event.x - zoomDragPrevX), @@ -204,15 +205,6 @@ export var drawGraph = function (workbook) { .attr("height", height) .attr("id", "exportContainer"); - // var viewportBoundingBox = svg - // .append("g") - // .append("rect") - // .attr("class", "boundingBox") - // .attr("width", width) - // .attr("height", height) - // .style("fill", "none") - // .attr("id", "viewportBoundingBox"); - var zoomContainer = svg.append("g") // required for zoom to work .attr("class", "boundingBox") .attr("width", width) @@ -236,6 +228,15 @@ export var drawGraph = function (workbook) { .attr("stroke-width", 1) .attr("fill", "none") .attr("id", "flexibleContainerRect"); + + // var viewportBoundingBox = svg + // .append("g") + // .append("rect") + // .attr("class", "boundingBox") + // .attr("width", width) + // .attr("height", height) + // .style("fill", "none") + // .attr("id", "viewportBoundingBox"); var zoom = d3.zoom() .scaleExtent([MIN_SCALE, ZOOM_ADAPTIVE_MAX_SCALE]) @@ -335,7 +336,7 @@ export var drawGraph = function (workbook) { ); // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (!adaptive) { + if (!adaptive && flexiRectInBounds()) { center(); } @@ -349,13 +350,13 @@ export var drawGraph = function (workbook) { $(ZOOM_INPUT).val(finalDisplay); } - // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (adaptive || !adaptive) { + // TODO:instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds + if (adaptive || (!adaptive && flexiRectInBounds())) { $(ZOOM_SLIDER).val( - (finalDisplay <= ZOOM_DISPLAY_MIDDLE + (finalDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleSliderLeft : zoomScaleSliderRight - ).invert(finalDisplay) + ).invert(finalDisplay) ); } }; @@ -1454,38 +1455,54 @@ export var drawGraph = function (workbook) { return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } - function flexiCollision(flexibleContainer) { - if (flexibleContainer) { - // console.log("flexiCollision"); - // console.log(flexibleContainer.x, flexibleContainer.y, zoomContainer.attr("transform")) - // console.log(svg.attr("width"), svg.attr("height")) - } - } - - // don't set flexibleContainer = calcFlexiBox or else the function does not stop running, only want to run on tick let flexibleContainer = null function flexiRectInBounds() { - // x left bound - if (flexibleContainer.x < 0) { - flexibleContainer.x = 0 + if (flexibleContainer) { + if (flexibleContainer.width * graphZoom > width) { + return false; + } else if (flexibleContainer.height * graphZoom > height) { + return false; + } + console.log("widths of flexible and viewport", flexibleContainer.width * graphZoom, width) + console.log("heights of flexible and viewport", flexibleContainer.height * graphZoom, height) } + return true + } - // x right bound - if (!(flexibleContainer.width - flexibleContainer.x <= width * graphZoom)) { - flexibleContainer.width = width - flexibleContainer.x; - } + function flexiRectLimitBounds() { + // TODO: with collision, if any of these are true then that means that graph is colliding with boundingBox + // can also determine if collide with edge of graph here to see if can zoom in or not + let flexiBoxInBounds = true; + if (flexibleContainer != null) { + // x left bound + // TODO: if graphZoom < 1, then do borders based on viewport? + if (flexibleContainer.x < 0) { + flexibleContainer.x = 0; + flexiBoxInBounds = false; + } - // y top bound - if (flexibleContainer.y < 0) { - flexibleContainer.y = 0; - } - - // y bottom bound - if (!(flexibleContainer.height - flexibleContainer.y <= height * graphZoom)) { - flexibleContainer.height = height - flexibleContainer.y; + // x right bound + if (!(flexibleContainer.width - flexibleContainer.x <= width * graphZoom)) { + flexibleContainer.width = width - flexibleContainer.x; + flexiBoxInBounds = false; + } + + // y top bound + if (flexibleContainer.y < 0) { + flexibleContainer.y = 0; + flexiBoxInBounds = false; + } + + // y bottom bound + if (!(flexibleContainer.height - flexibleContainer.y <= height * graphZoom)) { + flexibleContainer.height = height - flexibleContainer.y; + flexiBoxInBounds = false; + } } + + return flexiBoxInBounds; } // Tick only runs while the graph physics are still running. @@ -1509,8 +1526,8 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(); + flexiRectLimitBounds(); flexiRectInBounds(); - // flexiCollision(flexibleContainer) flexibleContainerRect .attr("x", flexibleContainer.x) From 5172c8e11db36cee4b0b95b43ae09dfa23c5c4c3 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 6 Mar 2024 18:15:01 -0800 Subject: [PATCH 064/150] Issue #1083. flexiContainerRect does not zoom in any further when next zoomScale will exceed viewport bounds, but cannot zoom back out --- web-client/public/js/graph.js | 77 +++++++++++++++++++---------------- 1 file changed, 41 insertions(+), 36 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 72164eaf..e345272a 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -168,16 +168,14 @@ export var drawGraph = function (workbook) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrabbing"); }; - // allows zoom slider to be moved and limits movement when !adaptive var zoomDragged = function () { - console.log("zoom dragged ran") var scale = 1; if (zoomContainer.attr("transform")) { var string = zoomContainer.attr("transform"); scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy) && flexiRectInBounds())) { + if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy) && flexRectInBounds())) { zoom.translateBy( zoomContainer, scale * (d3.event.x - zoomDragPrevX), @@ -192,7 +190,7 @@ export var drawGraph = function (workbook) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); }; - // zoomDrag keeps track of cursor position + // zoomDrag and all functions that it calls handles cursor dragging var zoomDrag = d3.drag() .on("start", zoomDragStarted) .on("drag", zoomDragged) @@ -228,15 +226,6 @@ export var drawGraph = function (workbook) { .attr("stroke-width", 1) .attr("fill", "none") .attr("id", "flexibleContainerRect"); - - // var viewportBoundingBox = svg - // .append("g") - // .append("rect") - // .attr("class", "boundingBox") - // .attr("width", width) - // .attr("height", height) - // .style("fill", "none") - // .attr("id", "viewportBoundingBox"); var zoom = d3.zoom() .scaleExtent([MIN_SCALE, ZOOM_ADAPTIVE_MAX_SCALE]) @@ -264,6 +253,7 @@ export var drawGraph = function (workbook) { let graphZoom = 0; let xTranslation = 0; let yTranslation = 0; + let flexibleContainer = null; const updateZoomContainerInfo = () => { // transform attribute of zoomContainer contains translation info about graph @@ -313,7 +303,9 @@ export var drawGraph = function (workbook) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); } var container = zoomContainer; - zoom.scaleTo(container, zoomScale); + if (adaptive || (!adaptive && flexRectInBounds())) { + zoom.scaleTo(container, zoomScale); + } // graphZoom is used in inBounds(width, height) to check if graph in zoomContainer when restricted to viewport graphZoom = zoomScale; }; @@ -329,17 +321,13 @@ export var drawGraph = function (workbook) { // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds const zoomDisplay = grnState.zoomValue; + console.log("zoomDisplay", zoomDisplay) setGraphZoom( (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)( zoomDisplay ) ); - // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (!adaptive && flexiRectInBounds()) { - center(); - } - const finalDisplay = grnState.zoomValue; $(ZOOM_PERCENT).text(`${finalDisplay}%`); @@ -351,7 +339,12 @@ export var drawGraph = function (workbook) { } // TODO:instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (adaptive || (!adaptive && flexiRectInBounds())) { + if (adaptive || (!adaptive && flexRectInBounds())) { + + if (!adaptive) { + center(); + } + $(ZOOM_SLIDER).val( (finalDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleSliderLeft @@ -399,10 +392,22 @@ export var drawGraph = function (workbook) { }).blur(() => $(ZOOM_INPUT).val(grnState.zoomValue)); d3.select(ZOOM_SLIDER).on("input", function () { - const sliderValue = +$(this).val(); - grnState.zoomValue = Math.floor( - (sliderValue <= sliderMidpoint ? zoomScaleSliderLeft : zoomScaleSliderRight)(sliderValue) - ); + const sliderValue = $(this).val(); + let maxZoomValue = 2; + if (flexibleContainerRect) { + maxZoomValue = width / flexibleContainerRect.attr("width"); + } + + console.log(maxZoomValue, graphZoom) + + if (adaptive || (!adaptive && (graphZoom + 0.5 < maxZoomValue))) { + console.log("zoom slider value changed") + grnState.zoomValue = Math.floor( + (sliderValue <= sliderMidpoint + ? zoomScaleSliderLeft + : zoomScaleSliderRight)(sliderValue) + ); + } updateAppBasedOnZoomValue(); }).on("mousedown", function () { manualZoom = true; @@ -446,7 +451,7 @@ export var drawGraph = function (workbook) { d3.select("rect").attr("stroke", "none"); d3.select("#flexibleContainerRect").attr("stroke", "none") center(); - } else if (fixed) { + } else { $("#restrict-graph-to-viewport span").addClass("glyphicon-ok"); $("input[name=viewport]").prop("checked", "checked"); adaptive = false; @@ -1455,27 +1460,26 @@ export var drawGraph = function (workbook) { return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } - // don't set flexibleContainer = calcFlexiBox or else the function does not stop running, only want to run on tick - let flexibleContainer = null - - function flexiRectInBounds() { + function flexRectInBounds() { if (flexibleContainer) { if (flexibleContainer.width * graphZoom > width) { + // console.log("width check", flexibleContainer.width * graphZoom > width); return false; } else if (flexibleContainer.height * graphZoom > height) { + // console.log("height check", flexibleContainer.height * graphZoom > height); return false; } - console.log("widths of flexible and viewport", flexibleContainer.width * graphZoom, width) - console.log("heights of flexible and viewport", flexibleContainer.height * graphZoom, height) + // console.log("widths of flexible and viewport", flexibleContainer.width * graphZoom, width) + // console.log("heights of flexible and viewport", flexibleContainer.height * graphZoom, height) } return true } - function flexiRectLimitBounds() { + function flexRectLimitBounds() { // TODO: with collision, if any of these are true then that means that graph is colliding with boundingBox // can also determine if collide with edge of graph here to see if can zoom in or not let flexiBoxInBounds = true; - if (flexibleContainer != null) { + if (flexibleContainer) { // x left bound // TODO: if graphZoom < 1, then do borders based on viewport? if (flexibleContainer.x < 0) { @@ -1526,8 +1530,7 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(); - flexiRectLimitBounds(); - flexiRectInBounds(); + flexRectLimitBounds(); flexibleContainerRect .attr("x", flexibleContainer.x) @@ -1536,7 +1539,7 @@ export var drawGraph = function (workbook) { .attr("height", flexibleContainer.height); } - // this controls movement and position of nodes + // this controls movement and position of nodes, clamps the nodes to boundary try { node.attr("x", function (d) { var selfReferringEdge = getSelfReferringEdge(d); @@ -1544,6 +1547,7 @@ export var drawGraph = function (workbook) { var selfReferringEdgeWidth = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + 2 : 0); var rightBoundary = width - (d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN - selfReferringEdgeWidth; + // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentXPos = Math.max(BOUNDARY_MARGIN, Math.min(rightBoundary, d.x)); if (adaptive && width < MAX_WIDTH && (currentXPos === BOUNDARY_MARGIN || currentXPos === rightBoundary)) { @@ -1571,6 +1575,7 @@ export var drawGraph = function (workbook) { var selfReferringEdgeHeight = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + SELF_REFERRING_Y_OFFSET + 0.5 : 0); var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN - selfReferringEdgeHeight; + // currentYPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentYPos = Math.max(BOUNDARY_MARGIN, Math.min(bottomBoundary, d.y)); if (adaptive && height < MAX_HEIGHT && (currentYPos === BOUNDARY_MARGIN || currentYPos === bottomBoundary)) { From 5cfbdd5dfcfb186ecd7d1e468144206bfb205f4f Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 6 Mar 2024 19:33:59 -0800 Subject: [PATCH 065/150] Issue #1083. Can now zoom in and zoom back out from flexContainer. have to change how determine the next zoom level though, because still slightly zoom in a little too far in some cases --- web-client/public/js/graph.js | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index e345272a..297fa0a0 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -315,13 +315,13 @@ export var drawGraph = function (workbook) { let sliderMidpoint; let zoomScaleSliderLeft; let zoomScaleSliderRight; + let prevGrnstateZoomVal; const updateAppBasedOnZoomValue = () => { // If !adaptive, set Zoomvalue to ZOOM_DISPLAY_MIDDLE, 100, so do not zoom outside graph // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds const zoomDisplay = grnState.zoomValue; - console.log("zoomDisplay", zoomDisplay) setGraphZoom( (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)( zoomDisplay @@ -387,6 +387,7 @@ export var drawGraph = function (workbook) { }; $(ZOOM_INPUT).on("input", () => { + prevGrnstateZoomVal = grnState.zoomValue grnState.zoomValue = zoomInputValidator(+$(ZOOM_INPUT).val()); updateAppBasedOnZoomValue(); }).blur(() => $(ZOOM_INPUT).val(grnState.zoomValue)); @@ -397,10 +398,18 @@ export var drawGraph = function (workbook) { if (flexibleContainerRect) { maxZoomValue = width / flexibleContainerRect.attr("width"); } - - console.log(maxZoomValue, graphZoom) - if (adaptive || (!adaptive && (graphZoom + 0.5 < maxZoomValue))) { + console.log(maxZoomValue, graphZoom, graphZoom + 0.5 < maxZoomValue); + + let validZoom = false + // cannot zoom in any farther if exceed maxZoomValue, but can zoom back out to smaller value + if (graphZoom + 0.5 > maxZoomValue && sliderValue < prevGrnstateZoomVal) { + validZoom = true + } else if (!prevGrnstateZoomVal) { + validZoom = true + } + + if (adaptive || (!adaptive && validZoom)) { console.log("zoom slider value changed") grnState.zoomValue = Math.floor( (sliderValue <= sliderMidpoint @@ -408,6 +417,7 @@ export var drawGraph = function (workbook) { : zoomScaleSliderRight)(sliderValue) ); } + updateAppBasedOnZoomValue(); }).on("mousedown", function () { manualZoom = true; From da2513ecf7d66bab5c0aee5cbba840d67c42c9c4 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Thu, 7 Mar 2024 11:16:34 -0800 Subject: [PATCH 066/150] Adding constant for 'cols regulatory/ rows target' and 'cols protein1/ rows protein2' in the server side --- server/controllers/constants.js | 2 ++ server/controllers/export-constants.js | 5 +++-- server/controllers/exporters/xlsx.js | 5 +++-- server/controllers/network-sheet-parser.js | 7 ++++--- server/controllers/workbook-constants.js | 3 ++- test/export-tests.js | 7 ++++--- 6 files changed, 18 insertions(+), 11 deletions(-) diff --git a/server/controllers/constants.js b/server/controllers/constants.js index 30588cb2..1be24dd3 100644 --- a/server/controllers/constants.js +++ b/server/controllers/constants.js @@ -4,6 +4,8 @@ module.exports = { NOT_FOUND: -1, WEIGHTED: "weighted", UNWEIGHTED: "unweighted", + CELL_A1_PPI: "cols protein1/ rows protein2", + CELL_A1_GRN: "cols regulators/rows targets", GRNSIGHT_FILENAME_HEADER: "X-GRNsight-Filename", diff --git a/server/controllers/export-constants.js b/server/controllers/export-constants.js index 3b2eeb5d..2c96f515 100644 --- a/server/controllers/export-constants.js +++ b/server/controllers/export-constants.js @@ -37,8 +37,9 @@ module.exports = { warningCode: "INCORRECT_NETWORK_SHEET_EXPORT_WARNING", errorDescription: "GRNsight has detected that the 'network' sheet or the 'network_optimized_weights'" + " sheet is improperly formattedPlease look over your exported workbook and ensure that network" + - " sheets have cell A1 as 'cols regulators/rows targets' exactly, and all gene are using the naming" + - " conventions listed at: \nhttps://dondi.github.io/GRNsight/documentation.html." + " sheets have cell A1 as 'cols regulators/rows targets' or 'cols protein1/ rows protein2' exactly" + + " and all gene are using the naming conventions listed at:" + + " \nhttps://dondi.github.io/GRNsight/documentation.html." }, // Missing Source Genes MISSING_SOURCE_GENES_EXPORT_WARNING: { diff --git a/server/controllers/exporters/xlsx.js b/server/controllers/exporters/xlsx.js index c93bb4bb..148fa881 100644 --- a/server/controllers/exporters/xlsx.js +++ b/server/controllers/exporters/xlsx.js @@ -1,5 +1,6 @@ // const { meta } = require("eslint/lib/rules/*"); const xlsx = require("node-xlsx"); +const { CELL_A1_GRN, CELL_A1_PPI } = require("../constants"); const buildGeneNameArray = function (genes) { const geneNameArray = genes.map(gene => gene["name"]); @@ -19,9 +20,9 @@ const buildNetworkSheet = function (genes, links, workbookType) { // EX: ["CIN5", 0, 0, 1] Object.keys(geneNameArray).forEach(index => networkSheet[index][0] = geneNameArray[index]); if (workbookType === "grn") { - geneNameArray.unshift("cols regulators/rows targets"); + geneNameArray.unshift(CELL_A1_GRN); } else { - geneNameArray.unshift("cols protein1/ rows protein2"); + geneNameArray.unshift(CELL_A1_PPI); } links.forEach((link) => { diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index d131056c..898b82b3 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -2,6 +2,7 @@ // var path = require("path"); // var demoWorkbooks = require(__dirname + "/demo-workbooks"); +const { CELL_A1_GRN, CELL_A1_PPI } = require("./constants"); const { initWorkbook } = require("./helpers"); var semanticChecker = require(__dirname + "/semantic-checker"); @@ -108,7 +109,7 @@ var parseNetworkSheet = function (sheet, network) { // Depending on the value of cellA1, we want to make a new property `networkType` which // will indicate the network type. THe web app then reads this to decide what to do next. - if (cellA1 !== "cols regulators/rows targets") { + if (cellA1 !== CELL_A1_GRN || cellA1 !== CELL_A1_PPI) { addWarning( network, constants.warnings.incorrectCellA1WorkbookWarning(sheet.name) @@ -304,9 +305,9 @@ exports.workbookType = function (workbookFile) { if (sheet.name.toLowerCase() === "network") { const cellA1 = sheet.data[0][0]; - if (cellA1 === "cols regulators/rows targets") { + if (cellA1 === CELL_A1_GRN) { workbookType = "grn"; - } else if (cellA1 === "cols protein1/ rows protein2") { + } else if (cellA1 === CELL_A1_PPI) { workbookType = "protein-protein-physical-interaction"; } else { workbookType = undefined; diff --git a/server/controllers/workbook-constants.js b/server/controllers/workbook-constants.js index 2571c5b7..a44af985 100644 --- a/server/controllers/workbook-constants.js +++ b/server/controllers/workbook-constants.js @@ -102,7 +102,8 @@ module.exports = { return { warningCode: "MISLABELED_NETWORK_CELL_A1", errorDescription: `The top left cell of the ${sheetName} sheet is mislabeled. - Replace the incorrect label with \'cols regulators/rows targets\' exactly.` + Replace the incorrect label with \'cols regulators/ rows targets\' or \'cols + protein1/ rows protein2'\ exactly.` }; }, diff --git a/test/export-tests.js b/test/export-tests.js index 2678e490..965c968b 100644 --- a/test/export-tests.js +++ b/test/export-tests.js @@ -2,6 +2,7 @@ var expect = require("chai").expect; var extend = require("jquery-extend"); var xlsx = require("node-xlsx"); var test = require("./test"); +const { CELL_A1_PPI, CELL_A1_GRN } = require("../server/controllers/constants"); var exportController = require(__dirname + "/../server/controllers/export-controller")(); var constants = require(__dirname + "/../server/controllers/constants"); @@ -763,7 +764,7 @@ describe("Export to spreadsheet", function () { { name: "network", data: [ - ["cols regulators/rows targets", "ACE2", "AFT2", "CIN5"], + [CELL_A1_GRN, "ACE2", "AFT2", "CIN5"], ["ACE2", 1, 0, 0], ["AFT2", 0, 1, 1], ["CIN5", 0, 0, 1] @@ -773,7 +774,7 @@ describe("Export to spreadsheet", function () { { name: "network_weights", data: [ - ["cols regulators/rows targets", "ACE2", "AFT2", "CIN5"], + [CELL_A1_GRN, "ACE2", "AFT2", "CIN5"], ["ACE2", 1, 0, 0], ["AFT2", 0, 1, 1], ["CIN5", 0, 0, 1] @@ -896,7 +897,7 @@ describe("Export to spreadsheet", function () { { name: "network", data: [ - ["cols protein1/ rows protein2", "Aim32p", "Ccr4p", "Erv1p"], + [CELL_A1_PPI, "Aim32p", "Ccr4p", "Erv1p"], ["Aim32p", 0, 0, 0], ["Ccr4p", 1, 1, 0], ["Erv1p", 1, 0, 1] From e7e771977f5b747625fdc876918edbc90e72075f Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Thu, 7 Mar 2024 16:46:14 -0800 Subject: [PATCH 067/150] #1079 Previous merge only correct if importing a sif file then export it, but this new commit fixed the export when exporting SIF to SIF or Excel workbook to SIF and this commit create constant variables for grn and protein-protein-physical-interaction --- server/controllers/constants.js | 3 +++ server/controllers/demo-workbooks.js | 12 ++++++---- server/controllers/exporters/sif.js | 5 +++- server/controllers/exporters/xlsx.js | 3 ++- server/controllers/importers/sif.js | 6 ++--- server/controllers/network-sheet-parser.js | 5 ++-- server/controllers/spreadsheet-controller.js | 11 +++++---- test/export-tests.js | 14 +++++------ test/import-sif-tests.js | 14 +++++------ web-client/public/js/constants.js | 3 ++- web-client/public/js/generateNetwork.js | 24 +++++++++---------- web-client/public/js/graph.js | 3 ++- web-client/public/js/grnstate.js | 5 ++-- .../js/setup-load-and-import-handlers.js | 10 ++++---- web-client/public/js/update-app.js | 18 +++++++------- web-client/public/js/upload.js | 13 +++++----- 16 files changed, 84 insertions(+), 65 deletions(-) diff --git a/server/controllers/constants.js b/server/controllers/constants.js index 30588cb2..14ee5bda 100644 --- a/server/controllers/constants.js +++ b/server/controllers/constants.js @@ -5,6 +5,9 @@ module.exports = { WEIGHTED: "weighted", UNWEIGHTED: "unweighted", + NETWORK_PPI_MODE: "protein-protein-physical-interaction", + NETWORK_GRN_MODE: "grn", + GRNSIGHT_FILENAME_HEADER: "X-GRNsight-Filename", warnings: { diff --git a/server/controllers/demo-workbooks.js b/server/controllers/demo-workbooks.js index fecef526..3bdc0536 100644 --- a/server/controllers/demo-workbooks.js +++ b/server/controllers/demo-workbooks.js @@ -1,3 +1,5 @@ +const constants = require("./constants"); + /* eslint-disable camelcase */ var helpers = require(__dirname + "/helpers"); @@ -530,7 +532,7 @@ var demoWorkbook1 = function (path, res, app) { simulation_timepoints: [0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60], species: "Saccharomyces cerevisiae", taxon_id: 559292, - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE } }, twoColumnSheets: { @@ -2694,7 +2696,7 @@ var demoWorkbook2 = function (path, res, app) { simulation_timepoints: [0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60], species: "Saccharomyces cerevisiae", taxon_id: 559292, - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE } }, twoColumnSheets: { @@ -4622,7 +4624,7 @@ var demoWorkbook3 = function (path, res, app) { TolX: 0.00001, species: "Saccharomyces cerevisiae", taxon_id: 559292, - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE } }, twoColumnSheets: {}, @@ -5684,7 +5686,7 @@ var demoWorkbook4 = function (path, res, app) { TolX: 0.00001, species: "Saccharomyces cerevisiae", taxon_id: 559292, - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE } }, twoColumnSheets: {}, @@ -6680,7 +6682,7 @@ var demoWorkbook5 = function (path, res, app) { sheetType: "unweighted", meta: { data: { - workbookType: "protein-protein-physical-interaction", + workbookType: constants.NETWORK_PPI_MODE, species: "Saccharomyces cerevisiae", taxon_id: "559292", }, diff --git a/server/controllers/exporters/sif.js b/server/controllers/exporters/sif.js index 0ef4df88..ddbbec96 100644 --- a/server/controllers/exporters/sif.js +++ b/server/controllers/exporters/sif.js @@ -8,7 +8,10 @@ var exportEdges = function (workbook, gene, geneIndex) { result += [ gene.name, workbook.sheetType === constants.WEIGHTED ? - link.value : workbook.workbookType === "protein-protein-physical-interaction" ? + link.value : (workbook.meta) ? + (workbook.meta.data.workbookType === constants.NETWORK_PPI_MODE ? + "pp" : "pd") : + workbook.workbookType === constants.NETWORK_PPI_MODE ? "pp" : "pd", workbook.genes[link.target].name ].join("\t") + "\n"; diff --git a/server/controllers/exporters/xlsx.js b/server/controllers/exporters/xlsx.js index bba4b36d..1702ca28 100644 --- a/server/controllers/exporters/xlsx.js +++ b/server/controllers/exporters/xlsx.js @@ -1,5 +1,6 @@ // const { meta } = require("eslint/lib/rules/*"); const xlsx = require("node-xlsx"); +const { NETWORK_GRN_MODE } = require("../constants"); const buildGeneNameArray = function (genes) { const geneNameArray = genes.map(gene => gene["name"]); @@ -18,7 +19,7 @@ const buildNetworkSheet = function (genes, links, workbookType) { // Place the gene name in the beginning of the network sheet array. // EX: ["CIN5", 0, 0, 1] Object.keys(geneNameArray).forEach(index => networkSheet[index][0] = geneNameArray[index]); - if (workbookType === "grn") { + if (workbookType === NETWORK_GRN_MODE) { geneNameArray.unshift("cols regulators/rows targets"); } else { geneNameArray.unshift("protein 1/protein 2"); diff --git a/server/controllers/importers/sif.js b/server/controllers/importers/sif.js index b7804b3c..34acbfad 100644 --- a/server/controllers/importers/sif.js +++ b/server/controllers/importers/sif.js @@ -59,14 +59,14 @@ module.exports = function (sif) { let workbookType; if (allNumbers) { - workbookType = "grn"; + workbookType = constants.NETWORK_GRN_MODE; } else { for (const relationship of relationships) { if (relationship === "pp") { - workbookType = "protein-protein-physical-interaction"; + workbookType = constants.NETWORK_PPI_MODE; break; } else if (relationship === "pd") { - workbookType = "grn"; + workbookType = constants.NETWORK_GRN_MODE; break; } } diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index 95faf45a..9480e0f3 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -2,6 +2,7 @@ // var path = require("path"); // var demoWorkbooks = require(__dirname + "/demo-workbooks"); +const { NETWORK_PPI_MODE, NETWORK_GRN_MODE } = require("./constants"); const { initWorkbook } = require("./helpers"); var semanticChecker = require(__dirname + "/semantic-checker"); @@ -305,9 +306,9 @@ exports.workbookType = function (workbookFile) { const cellA1 = sheet.data[0][0]; if (cellA1 === "cols regulators/rows targets") { - workbookType = "grn"; + workbookType = NETWORK_GRN_MODE; } else if (cellA1 === "protein 1/protein 2") { - workbookType = "protein-protein-physical-interaction"; + workbookType = NETWORK_PPI_MODE; } else { workbookType = undefined; } diff --git a/server/controllers/spreadsheet-controller.js b/server/controllers/spreadsheet-controller.js index 2c68fc3e..2b8a1fff 100644 --- a/server/controllers/spreadsheet-controller.js +++ b/server/controllers/spreadsheet-controller.js @@ -1,6 +1,7 @@ var multiparty = require("multiparty"); var xlsx = require("node-xlsx"); var path = require("path"); +const { NETWORK_GRN_MODE, NETWORK_PPI_MODE } = require("./constants"); var parseAdditionalSheets = require(__dirname + "/additional-sheet-parser"); var parseExpressionSheets = require(__dirname + "/expression-sheet-parser"); var parseNetworkSheet = require(__dirname + "/network-sheet-parser"); @@ -22,8 +23,8 @@ var SPECIES = [ ]; const WORKBOOK_TYPES = [ - "grn", - "protein-protein-physical-interaction" + NETWORK_GRN_MODE, + NETWORK_PPI_MODE ]; var TAXON_ID = ["3702", "6293", "7227", "9606", "10090", "4932", "559292"]; @@ -198,7 +199,7 @@ var crossSheetInteractions = function (workbookFile) { additionalData.meta.data.workbookType = parseNetworkSheet.workbookType(workbookFile); if (additionalData.meta.data.workbookType === undefined) { addWarning(workbook, constants.warnings.noWorkbookTypeDetected); - additionalData.meta.data.workbookType = "grn"; + additionalData.meta.data.workbookType = NETWORK_GRN_MODE; } else if (!supportWorkbookType(additionalData.meta.data.workbookType)) { addWarning( workbook, @@ -206,7 +207,7 @@ var crossSheetInteractions = function (workbookFile) { additionalData.meta.data.workbookType ) ); - additionalData.meta.data.workbookType = "grn"; + additionalData.meta.data.workbookType = NETWORK_GRN_MODE; } if (additionalData.meta.data.species === undefined && additionalData.meta.data.taxon_id === undefined) { @@ -232,7 +233,7 @@ var crossSheetInteractions = function (workbookFile) { // FUTURE IMPROVEMENT: not all expression sheets are specifically named 'wt_log2_expression.' // We need to account for all the different possible expression sheet names. if (expressionData) { - if (additionalData.meta.data.workbookType === "grn") { + if (additionalData.meta.data.workbookType === constants.NETWORK_GRN_MODE) { if (expressionData["expression"] && Object.keys(expressionData["expression"]).length === 0) { addWarning(expressionData, constants.warnings.missingExpressionWarning()); } diff --git a/test/export-tests.js b/test/export-tests.js index 45c4cd0a..059818d9 100644 --- a/test/export-tests.js +++ b/test/export-tests.js @@ -21,7 +21,7 @@ var unweightedTestWorkbook = { errors: [], warnings: [], sheetType: "unweighted", - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE }; var weightedTestWorkbook = { @@ -39,7 +39,7 @@ var weightedTestWorkbook = { errors: [], warnings: [], sheetType: "weighted", - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE }; var unweightedTestWorkbookWithCycle = { @@ -60,7 +60,7 @@ var unweightedTestWorkbookWithCycle = { errors: [], warnings: [], sheetType: "unweighted", - workbookType: "grn" + workbookType: "constants.NETWORK_GRN_MODE" }; var weightedTestWorkbookWithCycle = { @@ -81,7 +81,7 @@ var weightedTestWorkbookWithCycle = { errors: [], warnings: [], sheetType: "weighted", - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE }; describe("Export to SIF", function () { @@ -649,7 +649,7 @@ const inputWorkbook = { "simulation_timepoints": [0, 0.1, 0.2], "species": "Saccharomyces cerevisiae", "taxon_id": 559292, - "workbookType": "grn" + "workbookType": constants.NETWORK_GRN_MODE } }, @@ -801,7 +801,7 @@ describe("Export to spreadsheet", function () { ["simulation_timepoints", 0, 0.1, 0.2], ["species", "Saccharomyces cerevisiae"], ["taxon_id", 559292], - ["workbookType", "grn"] + ["workbookType", constants.NETWORK_GRN_MODE] ] }, @@ -907,7 +907,7 @@ describe("Export to spreadsheet", function () { name: "optimization_parameters", data: [ ["optimization_parameter", "value"], - ["workbookType", "protein-protein-physical-interaction"], + ["workbookType", constants.NETWORK_PPI_MODE], ["species", "Saccharomyces cerevisiae"], ["taxon_id", "559292"] ] diff --git a/test/import-sif-tests.js b/test/import-sif-tests.js index d0a35ec8..c0aea2e9 100644 --- a/test/import-sif-tests.js +++ b/test/import-sif-tests.js @@ -28,7 +28,7 @@ let expectedUnweightedGRNWorkbook = initWorkbook({ sheetType: "unweighted", meta: {}, expression:{}, - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE }); let expectedUnweightedPPIWorkbook = initWorkbook({ @@ -52,7 +52,7 @@ let expectedUnweightedPPIWorkbook = initWorkbook({ sheetType: "unweighted", meta: {}, expression:{}, - workbookType: "protein-protein-physical-interaction" + workbookType: constants.NETWORK_PPI_MODE }); @@ -76,7 +76,7 @@ var expectedWeightedWorkbook = initWorkbook({ negativeWeights: [], sheetType: "weighted", meta: {}, - workbookType: "grn", + workbookType: constants.NETWORK_GRN_MODE, expression:{} }); @@ -104,7 +104,7 @@ var expectedUnweightedWorkbookWithCycle = initWorkbook({ sheetType: "unweighted", meta: {}, expression:{}, - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE }); var expectedWeightedWorkbookWithCycle = initWorkbook({ @@ -131,7 +131,7 @@ var expectedWeightedWorkbookWithCycle = initWorkbook({ sheetType: "weighted", meta: {}, expression:{}, - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE }); // Unweighted SIF @@ -390,7 +390,7 @@ describe("Import from SIF", function () { sheetType: "unweighted", meta: {}, expression:{}, - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE })); }); @@ -409,7 +409,7 @@ describe("Import from SIF", function () { sheetType: "weighted", meta: {}, expression:{}, - workbookType: "grn" + workbookType: constants.NETWORK_GRN_MODE })); }); diff --git a/web-client/public/js/constants.js b/web-client/public/js/constants.js index 3da3b8ab..4611f2c7 100644 --- a/web-client/public/js/constants.js +++ b/web-client/public/js/constants.js @@ -193,5 +193,6 @@ export const VIEWPORT_SIZE_FIT_SIDEBAR = "#boundBoxFit"; export const VIEWPORT_OPTION_CLASS = ".viewportOption"; export const VIEWPORT_OPTION_CLASS_SIDEBAR = ".boundBoxSize"; - +export const NETWORK_PPI_MODE = "protein-protein-physical-interaction"; +export const NETWORK_GRN_MODE = "grn"; diff --git a/web-client/public/js/generateNetwork.js b/web-client/public/js/generateNetwork.js index 8557686b..b475958f 100644 --- a/web-client/public/js/generateNetwork.js +++ b/web-client/public/js/generateNetwork.js @@ -1,5 +1,5 @@ /* eslint-disable max-len */ -import {CREATE_NETWORK_CLASS, CREATE_NETWORK_MODAL} from "./constants"; +import { CREATE_NETWORK_CLASS, CREATE_NETWORK_MODAL, NETWORK_PPI_MODE, NETWORK_GRN_MODE} from "./constants"; import { queryNetworkDatabase, queryProteinProteinDatabase, uploadCustomWorkbook } from "./api/grnsight-api"; import { grnState } from "./grnstate"; @@ -13,7 +13,7 @@ export const generateNetwork = function () { "MF(ALPHA)2" : "YGL089C" }; const createHTMLforForm = (sources, source, networkType) => { - const geneProtein = networkType === "protein-protein-physical-interaction" ? "protein" : "gene"; + const geneProtein = networkType === NETWORK_PPI_MODE ? "protein" : "gene"; let result = `

Generate Network

@@ -64,8 +64,8 @@ export const generateNetwork = function () {
`; for (let gene in grnState.customWorkbook.genes) { - const primaryName = grnState.customWorkbook.type === "grn" ? grnState.customWorkbook.genes[gene] : gene; - const secondaryName = grnState.customWorkbook.type === "grn" ? gene : + const primaryName = grnState.customWorkbook.type === NETWORK_GRN_MODE ? grnState.customWorkbook.genes[gene] : gene; + const secondaryName = grnState.customWorkbook.type === NETWORK_GRN_MODE ? gene : `${grnState.customWorkbook.genes[gene].displayGeneID} | ${grnState.customWorkbook.genes[gene].geneID}`; result += `
@@ -104,7 +104,7 @@ export const generateNetwork = function () { return ""; }; const addGene = function () { - const userGeneProtein = grnState.customWorkbook.type === "grn" ? "Gene" : "Protein"; + const userGeneProtein = grnState.customWorkbook.type === NETWORK_GRN_MODE ? "Gene" : "Protein"; const searchGeneProtein = `${$("#network-search-bar").val()}`; $("#network-search-bar").val(""); const geneProtein = validGene(searchGeneProtein.toUpperCase()); @@ -113,7 +113,7 @@ export const generateNetwork = function () { containing "-", "_", and alpha-numeric characters only`); } else { let source = grnState.customWorkbook.source; - if (grnState.customWorkbook.type === "grn") { + if (grnState.customWorkbook.type === NETWORK_GRN_MODE) { let headers = { type:"NetworkGeneFromSource", gene: geneProtein, @@ -134,7 +134,7 @@ containing "-", "_", and alpha-numeric characters only`); console.log(error.name); console.log(error.message); }); - } else if (grnState.customWorkbook.type === "protein-protein-physical-interaction") { + } else if (grnState.customWorkbook.type === NETWORK_PPI_MODE) { let headers = { type:"NetworkFromGeneProtein", geneProtein: geneProtein, @@ -177,7 +177,7 @@ containing "-", "_", and alpha-numeric characters only`); $("#generateNetworkFooter-container").append(createHTMLforModalButtons()); grnState.customWorkbook = { genes : {}, - type: "grn", + type: NETWORK_GRN_MODE, source : null, sources : { proteinProteinInteractions : null, @@ -213,12 +213,12 @@ containing "-", "_", and alpha-numeric characters only`); $("body").on("change", "#network-type", function (event) { grnState.customWorkbook.type = $("#network-type").val(); grnState.customWorkbook.genes = {}; - if (grnState.customWorkbook.type === "protein-protein-physical-interaction") { + if (grnState.customWorkbook.type === NETWORK_PPI_MODE) { grnState.customWorkbook.source = Object.keys(grnState.customWorkbook.sources.proteinProteinInteractions).length >= 1 ? Object.keys(grnState.customWorkbook.sources.proteinProteinInteractions)[0] : null; $("#generateNetworkFormContainer").remove(); $("#generateNetworkQuestions-container").append(createHTMLforForm(Object.keys(grnState.customWorkbook.sources.proteinProteinInteractions), grnState.customWorkbook.source, grnState.customWorkbook.type)); - } else if (grnState.customWorkbook.type === "grn") { + } else if (grnState.customWorkbook.type === NETWORK_GRN_MODE) { grnState.customWorkbook.source = Object.keys(grnState.customWorkbook.sources.proteinProteinInteractions).length >= 1 ? Object.keys(grnState.customWorkbook.sources.geneRegulation)[0] : null; $("#generateNetworkFormContainer").remove(); @@ -241,7 +241,7 @@ containing "-", "_", and alpha-numeric characters only`); alert(`GRNsight is only capable of handling 75 genes at most. Your proposed network contains ${genesAmount} genes. Please remove some genes from your proposed network.`); } else { - if (grnState.customWorkbook.type === "grn") { + if (grnState.customWorkbook.type === NETWORK_GRN_MODE) { const genes = Object.keys(grnState.customWorkbook.genes); const displayGenes = Object.keys(grnState.customWorkbook.genes).map(g => grnState.customWorkbook.genes[g]); const source = grnState.customWorkbook.source; @@ -277,7 +277,7 @@ containing "-", "_", and alpha-numeric characters only`); console.log(error.name); console.log(error.message); }); - } else if (grnState.customWorkbook.type === "protein-protein-physical-interaction") { + } else if (grnState.customWorkbook.type === NETWORK_PPI_MODE) { const proteins = Object.keys(grnState.customWorkbook.genes); const source = grnState.customWorkbook.source; const headers = { diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index bb10387d..868f8730 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -11,6 +11,7 @@ import { ZOOM_DISPLAY_MAXIMUM_VALUE, ZOOM_DISPLAY_MIDDLE, ZOOM_ADAPTIVE_MAX_SCALE, + NETWORK_GRN_MODE } from "./constants"; /* globals d3 */ @@ -682,7 +683,7 @@ export var drawGraph = function (workbook) { }); } else { // Arrowheads - if (grnState.mode === "grn") { + if (grnState.mode === NETWORK_GRN_MODE) { if (d.strokeWidth === 2) { d.strokeWidth = 4; } diff --git a/web-client/public/js/grnstate.js b/web-client/public/js/grnstate.js index 5dde708a..67b0d011 100644 --- a/web-client/public/js/grnstate.js +++ b/web-client/public/js/grnstate.js @@ -10,7 +10,8 @@ import { DEFAULT_MAX_LOG_FOLD_CHANGE, DEFAULT_ZOOM_VALUE, FORCE_GRAPH, - VIEWPORT_INIT + VIEWPORT_INIT, + NETWORK_GRN_MODE } from "./constants"; let currentWorkbook = null; @@ -41,7 +42,7 @@ const annotateLinks = workbook => { }; export const grnState = { - mode: "grn", // GRNsight will display GRN view unless specified + mode: NETWORK_GRN_MODE, // GRNsight will display GRN view unless specified name: null, simulation: undefined, newWorkbook: false, diff --git a/web-client/public/js/setup-load-and-import-handlers.js b/web-client/public/js/setup-load-and-import-handlers.js index b2d45fb0..1e52fd5e 100644 --- a/web-client/public/js/setup-load-and-import-handlers.js +++ b/web-client/public/js/setup-load-and-import-handlers.js @@ -12,7 +12,9 @@ import { SCHADE_OUTPUT_NAME, PPI_DEMO_PATH, PPI_DEMO_NAME, - FORCE_GRAPH + FORCE_GRAPH, + NETWORK_PPI_MODE, + NETWORK_GRN_MODE } from "./constants"; import { getWorkbookFromForm, getWorkbookFromUrl } from "./api/grnsight-api"; @@ -148,7 +150,7 @@ export const setupLoadAndImportHandlers = (grnState) => { if (grnState.name.includes(".sif")) { grnState.mode = workbook.workbookType; } else if (grnState.name.includes(".graphml")) { - grnState.mode = "grn"; + grnState.mode = NETWORK_GRN_MODE; } else { grnState.mode = workbook.meta.data.workbookType; } @@ -218,10 +220,10 @@ export const setupLoadAndImportHandlers = (grnState) => { export const responseCustomWorkbookData = (grnState, queryURL, name) => { const uploadRoute = queryURL; getWorkbookFromUrl(uploadRoute).done((workbook) => { - if (workbook.meta.data.workbookType === "protein-protein-physical-interaction") { + if (workbook.meta.data.workbookType === NETWORK_PPI_MODE) { grnState.mode = workbook.meta.data.workbookType; } else { - grnState.mode = "grn"; + grnState.mode = NETWORK_GRN_MODE; } grnState.name = name; grnState.workbook = workbook; diff --git a/web-client/public/js/update-app.js b/web-client/public/js/update-app.js index 89566749..c6c7c06b 100644 --- a/web-client/public/js/update-app.js +++ b/web-client/public/js/update-app.js @@ -107,6 +107,8 @@ import { NETWORK_MODE_PROTEIN_PHYS, NETWORK_MODE_GRN, EXPORT_TO_UNWEIGHTED_GML_MENU, + NETWORK_GRN_MODE, + NETWORK_PPI_MODE // EXPRESSION_SOURCE, } from "./constants"; @@ -532,21 +534,21 @@ const updateModeViews = () =>{ $(`${NETWORK_MODE_DROPDOWN} option[value="${grnState.mode}"]`).prop("selected", true); // Select the correct menu items $(`${NETWORK_MODE_CLASS} option`).removeAttr("checked"); - if (grnState.mode === "grn") { + if (grnState.mode === NETWORK_GRN_MODE) { toggleLayout(NETWORK_MODE_GRN, NETWORK_MODE_PROTEIN_PHYS); - } else if (grnState.mode === "protein-protein-physical-interaction") { + } else if (grnState.mode === NETWORK_PPI_MODE) { toggleLayout(NETWORK_MODE_PROTEIN_PHYS, NETWORK_MODE_GRN); } }; const checkWorkbookModeSettings = () => { - if (grnState.mode === "protein-protein-physical-interaction") { + if (grnState.mode === NETWORK_PPI_MODE) { grnState.nodeColoring.nodeColoringEnabled = false; grnState.colorOptimal = false; disableNodeColoringMenus(); hideEdgeWeightOptions(); updateModeViews(); - } else if (grnState.mode === "grn") { + } else if (grnState.mode === NETWORK_GRN_MODE) { grnState.nodeColoring.nodeColoringEnabled = true; grnState.colorOptimal = true; showNodeColoringMenus(); @@ -556,9 +558,9 @@ const checkWorkbookModeSettings = () => { }; $("body").on("click", () => { - if (grnState.mode === "protein-protein-physical-interaction") { + if (grnState.mode === NETWORK_PPI_MODE) { $(EXPORT_TO_UNWEIGHTED_GML_MENU).addClass("disabled"); - } else if (grnState.mode === "grn") { + } else if (grnState.mode === NETWORK_GRN_MODE) { $(EXPORT_TO_UNWEIGHTED_GML_MENU).removeClass("disabled"); } }); @@ -569,12 +571,12 @@ $(NETWORK_MODE_DROPDOWN).on("change", () => { refreshApp(); }); $(NETWORK_MODE_PROTEIN_PHYS).on("click", () => { - grnState.mode = "protein-protein-physical-interaction"; + grnState.mode = NETWORK_PPI_MODE; checkWorkbookModeSettings(); refreshApp(); }); $(NETWORK_MODE_GRN).on("click", () => { - grnState.mode = "grn"; + grnState.mode = NETWORK_GRN_MODE; checkWorkbookModeSettings(); refreshApp(); }); diff --git a/web-client/public/js/upload.js b/web-client/public/js/upload.js index bfc29283..50ac8d39 100644 --- a/web-client/public/js/upload.js +++ b/web-client/public/js/upload.js @@ -12,6 +12,7 @@ import { } from "./update-app"; import { queryExpressionDatabase } from "./api/grnsight-api.js"; +import { NETWORK_PPI_MODE, NETWORK_GRN_MODE } from "./constants.js"; const EXPRESSION_SHEET_SUFFIXES = ["_expression", "_optimized_expression", "_sigmas"]; @@ -118,7 +119,7 @@ export const upload = function () { const updateOptimizationParameters = (finalExportSheets) => { let optimizationParameters = { - data: grnState.mode === "grn" ? { + data: grnState.mode === NETWORK_GRN_MODE ? { alpha: 0.002, "kk_max": 1, MaxIter: 100000000, @@ -133,14 +134,14 @@ export const upload = function () { "fix_b": 0, species: "Saccharomyces cerevisiae", "taxon_id":559292, - workbookType: "grn" + workbookType: NETWORK_GRN_MODE } : { species: "Saccharomyces cerevisiae", "taxon_id":559292, - workbookType: "protein-protein-physical-interaction" + workbookType: NETWORK_PPI_MODE } }; - if (grnState.mode === "grn") { + if (grnState.mode === NETWORK_GRN_MODE) { const expression = Object.keys(finalExportSheets.expression); let expTimepoints = expression.length > 0 ? finalExportSheets.expression[expression[0]].timePoints : null; expTimepoints = expTimepoints ? [...(new Set(expTimepoints))].sort(function (a, b) { @@ -581,7 +582,7 @@ export const upload = function () { $("#Export-Excel-Button").on("click", performExport("export-to-excel", "xlsx", null, source)); }; const handleExportExcelModal = function () { - if (grnState.mode === "grn") { + if (grnState.mode === NETWORK_GRN_MODE) { $("#exportExcelForm").remove(); $("#exportExcelFooter").remove(); $("#exportExcelQuestions-containter").append(createHTMLforGRNForm); @@ -600,7 +601,7 @@ export const upload = function () { } }); handleExpressionSheetsFromSource(source); - } else if (grnState.mode === "protein-protein-physical-interaction") { + } else if (grnState.mode === NETWORK_PPI_MODE) { const source = "userInput"; $("#exportExcelForm").remove(); $("#exportExcelFooter").remove(); From c0e07de003c881d92fc93c03e3c99891d577916a Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 8 Mar 2024 20:58:45 -0800 Subject: [PATCH 068/150] Issue #1083. Tried predicting nextZoomValue, but will try to ignore nextZoomValue for now and focus on slider movement stopping and resuming --- web-client/public/js/graph.js | 115 ++++++++++++++++++++-------------- 1 file changed, 69 insertions(+), 46 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 297fa0a0..d1a69edd 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -174,8 +174,10 @@ export var drawGraph = function (workbook) { var string = zoomContainer.attr("transform"); scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } + + // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy) && flexRectInBounds())) { + if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy) && flexRectInBounds(scale, 2))) { zoom.translateBy( zoomContainer, scale * (d3.event.x - zoomDragPrevX), @@ -298,16 +300,21 @@ export var drawGraph = function (workbook) { ); }; + // controls reading movement of zoomSlider and scaling graph to that zoomScale const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); } var container = zoomContainer; - if (adaptive || (!adaptive && flexRectInBounds())) { - zoom.scaleTo(container, zoomScale); - } // graphZoom is used in inBounds(width, height) to check if graph in zoomContainer when restricted to viewport graphZoom = zoomScale; + var nextZoomValue = graphZoom + 0.25; + console.log("graphZoom", graphZoom, "nextZoomValue", nextZoomValue) + if (adaptive || (!adaptive && flexRectInBounds(nextZoomValue, width / flexibleContainerRect.attr("width")))) { + zoom.scaleTo(container, zoomScale); + } + + }; // See setupZoomElements below to see how these are initialized. They are declared here because @@ -320,8 +327,36 @@ export var drawGraph = function (workbook) { const updateAppBasedOnZoomValue = () => { // If !adaptive, set Zoomvalue to ZOOM_DISPLAY_MIDDLE, 100, so do not zoom outside graph // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds + let nextZoomValue = (grnState.zoomValue + 6 <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)(grnState.zoomValue + 6); + let maxZoomValue = 2; + console.log(width, flexibleContainerRect.attr("width")); + if (!adaptive && flexibleContainer) { + flexibleContainer = calcFlexiBox() + maxZoomValue = width / flexibleContainerRect.attr("width"); + } const zoomDisplay = grnState.zoomValue; + + // if (!adaptive && !flexRectInBounds(nextZoomValue, maxZoomValue) && prevGrnstateZoomVal) { + // grnState.zoomValue = prevGrnstateZoomVal + // } + + + + console.log( + "zoomDisplay", + zoomDisplay, + "set graphzoom value", + (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)( + zoomDisplay + ), + "nextZoomValue", + nextZoomValue, + flexRectInBounds(nextZoomValue, maxZoomValue), + "maxZoomValue", + maxZoomValue + ); + setGraphZoom( (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)( zoomDisplay @@ -339,18 +374,25 @@ export var drawGraph = function (workbook) { } // TODO:instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (adaptive || (!adaptive && flexRectInBounds())) { - - if (!adaptive) { - center(); - } - - $(ZOOM_SLIDER).val( - (finalDisplay <= ZOOM_DISPLAY_MIDDLE - ? zoomScaleSliderLeft - : zoomScaleSliderRight - ).invert(finalDisplay) - ); + if ( + adaptive || + (!adaptive && + flexRectInBounds( + (zoomDisplay <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleLeft + : zoomScaleRight)(zoomDisplay) + )) + ) { + if (!adaptive) { + center(); + } + + $(ZOOM_SLIDER).val( + (finalDisplay <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleSliderLeft + : zoomScaleSliderRight + ).invert(finalDisplay) + ); } }; @@ -387,36 +429,19 @@ export var drawGraph = function (workbook) { }; $(ZOOM_INPUT).on("input", () => { - prevGrnstateZoomVal = grnState.zoomValue grnState.zoomValue = zoomInputValidator(+$(ZOOM_INPUT).val()); updateAppBasedOnZoomValue(); }).blur(() => $(ZOOM_INPUT).val(grnState.zoomValue)); d3.select(ZOOM_SLIDER).on("input", function () { const sliderValue = $(this).val(); - let maxZoomValue = 2; - if (flexibleContainerRect) { - maxZoomValue = width / flexibleContainerRect.attr("width"); - } - - console.log(maxZoomValue, graphZoom, graphZoom + 0.5 < maxZoomValue); - - let validZoom = false - // cannot zoom in any farther if exceed maxZoomValue, but can zoom back out to smaller value - if (graphZoom + 0.5 > maxZoomValue && sliderValue < prevGrnstateZoomVal) { - validZoom = true - } else if (!prevGrnstateZoomVal) { - validZoom = true - } + prevGrnstateZoomVal = grnState.zoomValue; - if (adaptive || (!adaptive && validZoom)) { - console.log("zoom slider value changed") - grnState.zoomValue = Math.floor( - (sliderValue <= sliderMidpoint - ? zoomScaleSliderLeft - : zoomScaleSliderRight)(sliderValue) - ); - } + grnState.zoomValue = Math.floor( + (sliderValue <= sliderMidpoint + ? zoomScaleSliderLeft + : zoomScaleSliderRight)(sliderValue) + ); updateAppBasedOnZoomValue(); }).on("mousedown", function () { @@ -1470,17 +1495,15 @@ export var drawGraph = function (workbook) { return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } - function flexRectInBounds() { + function flexRectInBounds(nextZoom, maxZoomValue) { if (flexibleContainer) { - if (flexibleContainer.width * graphZoom > width) { - // console.log("width check", flexibleContainer.width * graphZoom > width); + if (nextZoom > maxZoomValue) { + return false + } else if (flexibleContainer.width * nextZoom > width) { return false; - } else if (flexibleContainer.height * graphZoom > height) { - // console.log("height check", flexibleContainer.height * graphZoom > height); + } else if (flexibleContainer.height * nextZoom > height) { return false; } - // console.log("widths of flexible and viewport", flexibleContainer.width * graphZoom, width) - // console.log("heights of flexible and viewport", flexibleContainer.height * graphZoom, height) } return true } From 8c58fea80eb6232940799d17617d2e35f6e12f18 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Fri, 8 Mar 2024 22:07:59 -0800 Subject: [PATCH 069/150] Issue #1083. Now the flexRect stays in bounds and the slider stops moving right before the flex rect is out of bounds! Had to manage when zoomDisplay = grnState.zoomValue in updateAppBasedOnZoomValue and do not need to calculate the next value, so had to change flexRectInBounds as well --- web-client/public/js/graph.js | 47 +++++++++++++++-------------------- 1 file changed, 20 insertions(+), 27 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index d1a69edd..d2d2dc62 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -308,9 +308,9 @@ export var drawGraph = function (workbook) { var container = zoomContainer; // graphZoom is used in inBounds(width, height) to check if graph in zoomContainer when restricted to viewport graphZoom = zoomScale; - var nextZoomValue = graphZoom + 0.25; - console.log("graphZoom", graphZoom, "nextZoomValue", nextZoomValue) - if (adaptive || (!adaptive && flexRectInBounds(nextZoomValue, width / flexibleContainerRect.attr("width")))) { + // var nextZoomValue = graphZoom + 0.25; + // console.log("graphZoom", graphZoom, "nextZoomValue", nextZoomValue) + if (adaptive || (!adaptive && flexRectInBounds(graphZoom))) { zoom.scaleTo(container, zoomScale); } @@ -327,21 +327,18 @@ export var drawGraph = function (workbook) { const updateAppBasedOnZoomValue = () => { // If !adaptive, set Zoomvalue to ZOOM_DISPLAY_MIDDLE, 100, so do not zoom outside graph // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - let nextZoomValue = (grnState.zoomValue + 6 <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)(grnState.zoomValue + 6); - let maxZoomValue = 2; - console.log(width, flexibleContainerRect.attr("width")); - if (!adaptive && flexibleContainer) { - flexibleContainer = calcFlexiBox() - maxZoomValue = width / flexibleContainerRect.attr("width"); - } - - const zoomDisplay = grnState.zoomValue; - // if (!adaptive && !flexRectInBounds(nextZoomValue, maxZoomValue) && prevGrnstateZoomVal) { - // grnState.zoomValue = prevGrnstateZoomVal - // } + let zoomDisplay; - + if (adaptive) { + zoomDisplay = grnState.zoomValue + } else if (!adaptive && flexRectInBounds((grnState.zoomValue <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)(grnState.zoomValue)) ) { + zoomDisplay = grnState.zoomValue; + } else { + console.log("statement false") + grnState.zoomValue = prevGrnstateZoomVal; + zoomDisplay = grnState.zoomValue; + } console.log( "zoomDisplay", @@ -349,12 +346,7 @@ export var drawGraph = function (workbook) { "set graphzoom value", (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)( zoomDisplay - ), - "nextZoomValue", - nextZoomValue, - flexRectInBounds(nextZoomValue, maxZoomValue), - "maxZoomValue", - maxZoomValue + ) ); setGraphZoom( @@ -1495,13 +1487,14 @@ export var drawGraph = function (workbook) { return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } - function flexRectInBounds(nextZoom, maxZoomValue) { + function flexRectInBounds(zoomValue) { if (flexibleContainer) { - if (nextZoom > maxZoomValue) { - return false - } else if (flexibleContainer.width * nextZoom > width) { + if (flexibleContainer.width * zoomValue > width) { + console.log(flexibleContainer.width, zoomValue, width, flexibleContainer.width * zoomValue > width); + console.log("width exceeds") return false; - } else if (flexibleContainer.height * nextZoom > height) { + } else if (flexibleContainer.height * zoomValue > height) { + console.log("height exceeds") return false; } } From 1df0122e2f5820a0a961adde85d87253dc782d32 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 9 Mar 2024 00:50:22 -0800 Subject: [PATCH 070/150] Issue #1083. Can now drag graph to always be in bounds at 100%, need to refine calculation for when graph is greater than 100% --- web-client/public/js/graph.js | 198 ++++++++++++++++++---------------- 1 file changed, 108 insertions(+), 90 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index d2d2dc62..a1f2a361 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -161,6 +161,7 @@ export var drawGraph = function (workbook) { var zoomDragPrevX = 0; var zoomDragPrevY = 0; + let graphZoom = 0; var zoomDragStarted = function () { zoomDragPrevX = d3.event.x; @@ -175,9 +176,11 @@ export var drawGraph = function (workbook) { scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } + // console.log("scale", scale, "graphZoom", graphZoom) + // inBounds(d3.event.dx, d3.event.dy) && flexRectInBounds(graphZoom) - // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy) && flexRectInBounds(scale, 2))) { + if (adaptive || (!adaptive && flexRectInBounds(graphZoom) && inBounds(graphZoom, d3.event.dx, d3.event.dy))) { + // if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy) && flexRectInBounds(graphZoom))) { zoom.translateBy( zoomContainer, scale * (d3.event.x - zoomDragPrevX), @@ -252,12 +255,11 @@ export var drawGraph = function (workbook) { }); d3.select(".center").on("click", center); - let graphZoom = 0; let xTranslation = 0; let yTranslation = 0; let flexibleContainer = null; - const updateZoomContainerInfo = () => { + function updateZoomContainerInfo() { // transform attribute of zoomContainer contains translation info about graph xTranslation = parseFloat(zoomContainer .attr("transform") @@ -268,36 +270,60 @@ export var drawGraph = function (workbook) { .split("(")[1].split(",")[1].split(")")[0]); }; - function inBounds(width, height) { - /* - * right: Math.abs(xTranslation + width * graphZoom) / zoomContainerWidth <= graphZoom - 1.0 - * bottom: Math.abs(yTranslation + height * graphZoom) / zoomContainerHeight <= graphZoom - 1.0 - * top: y coordinate == -0, left: x coordinate == -0 - * Amount of movement is dependent on graphZoom, so actual movement is not just the width or height - but width or height multiplied by graphZoom - * multiply Math.abs(yTranslation + height * graphZoom) / zoomContainerHeight by 1000 because - decimals like 0.005 (in the thousandths place) or less are out of bounds, - then get floor of that to ensure that decimal does not have 0 in hundredths place - */ + function inBounds(graphZoom, dx, dy) { updateZoomContainerInfo(); + // if ((xTranslation < 0 && Math.abs(xTranslation) * graphZoom >= Math.floor(flexibleContainer.x + dx)) || + // (xTranslation > 0 && (flexibleContainer.width + flexibleContainer.x + xTranslation) + dx >= width / graphZoom)) { + /*(xTranslation < 0 && + ((graphZoom <= 1 && + Math.abs(xTranslation) * graphZoom >= + Math.floor(flexibleContainer.x + dx)) || + flexibleContainer.width + flexibleContainer.x + Math.abs(xTranslation) >= width * graphZoom)) ||*/ + if ( + (xTranslation < 0 && + Math.abs(xTranslation) * graphZoom >= + Math.floor(flexibleContainer.x + dx)) || + (xTranslation > 0 && + flexibleContainer.width + flexibleContainer.x + xTranslation + dx >= + width / graphZoom) + ) { + console.log( + Math.abs(xTranslation) * graphZoom >= + Math.floor(flexibleContainer.x + dx), + xTranslation, + xTranslation * graphZoom, + flexibleContainer.x + ); + return false; + } else if ( + (yTranslation < 0 && + Math.abs(yTranslation) * graphZoom >= + Math.floor(flexibleContainer.y + dy)) || + (yTranslation > 0 && + flexibleContainer.height + + flexibleContainer.y + + yTranslation + + dy >= + height / graphZoom) + ) { + // validations for up/down cursor drag and movement + console.log( + "flexContainer.y", + flexibleContainer.y, + "flexibleContainer.height", + flexibleContainer.height, + "yTranslation", + yTranslation, + "total height", + height + ); + console.log(" "); + return false + } + console.log("flexContainer.x",flexibleContainer.x,"flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "total width", width); + console.log("flexContainer height and width in bounds"); - return ( - Math.abs(xTranslation + width * graphZoom) / $container.width() <= - graphZoom - 1.0 && - Math.floor( - (Math.abs(xTranslation + width * graphZoom) / $container.width()) * - 1000 - ) !== 0 && - Math.abs(yTranslation + height * graphZoom) / $container.height() <= - graphZoom - 1.0 && - Math.floor( - (Math.abs(yTranslation + height * graphZoom) / - $container.height()) * - 1000 - ) !== 0 && - xTranslation + width * graphZoom <= 0 && - yTranslation + height * graphZoom <= 0 - ); + return true }; // controls reading movement of zoomSlider and scaling graph to that zoomScale @@ -308,8 +334,6 @@ export var drawGraph = function (workbook) { var container = zoomContainer; // graphZoom is used in inBounds(width, height) to check if graph in zoomContainer when restricted to viewport graphZoom = zoomScale; - // var nextZoomValue = graphZoom + 0.25; - // console.log("graphZoom", graphZoom, "nextZoomValue", nextZoomValue) if (adaptive || (!adaptive && flexRectInBounds(graphZoom))) { zoom.scaleTo(container, zoomScale); } @@ -325,9 +349,6 @@ export var drawGraph = function (workbook) { let prevGrnstateZoomVal; const updateAppBasedOnZoomValue = () => { - // If !adaptive, set Zoomvalue to ZOOM_DISPLAY_MIDDLE, 100, so do not zoom outside graph - // TODO: instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - let zoomDisplay; if (adaptive) { @@ -335,25 +356,15 @@ export var drawGraph = function (workbook) { } else if (!adaptive && flexRectInBounds((grnState.zoomValue <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)(grnState.zoomValue)) ) { zoomDisplay = grnState.zoomValue; } else { - console.log("statement false") grnState.zoomValue = prevGrnstateZoomVal; zoomDisplay = grnState.zoomValue; } - console.log( - "zoomDisplay", - zoomDisplay, - "set graphzoom value", - (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)( - zoomDisplay - ) - ); + const calcGraphZoom = (zoomDisplay <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleLeft + : zoomScaleRight)(zoomDisplay); - setGraphZoom( - (zoomDisplay <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)( - zoomDisplay - ) - ); + setGraphZoom(calcGraphZoom); const finalDisplay = grnState.zoomValue; $(ZOOM_PERCENT).text(`${finalDisplay}%`); @@ -365,26 +376,20 @@ export var drawGraph = function (workbook) { $(ZOOM_INPUT).val(finalDisplay); } - // TODO:instead of d3.event.x >= ZOOM_DISPLAY_MIDDLE, need to make sure that box in bounds - if ( - adaptive || - (!adaptive && - flexRectInBounds( - (zoomDisplay <= ZOOM_DISPLAY_MIDDLE - ? zoomScaleLeft - : zoomScaleRight)(zoomDisplay) - )) - ) { - if (!adaptive) { - center(); - } + // This controls actual movement of slider + if (adaptive || (!adaptive && flexRectInBounds(calcGraphZoom))) { + // don't really want to center anymore for zooming since don't care if see bounding box anymore + // if don't center, then get issue of zooming into the box since not inside the width of the viewport + if (!adaptive) { + center(); + } - $(ZOOM_SLIDER).val( - (finalDisplay <= ZOOM_DISPLAY_MIDDLE - ? zoomScaleSliderLeft - : zoomScaleSliderRight - ).invert(finalDisplay) - ); + $(ZOOM_SLIDER).val( + (finalDisplay <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleSliderLeft + : zoomScaleSliderRight + ).invert(finalDisplay) + ); } }; @@ -525,18 +530,20 @@ export var drawGraph = function (workbook) { var height = direction === "up" ? -50 : direction === "down" ? 50 : 0; if (adaptive) { zoom.translateBy(zoomContainer, width, height); - } else if (!adaptive && grnState.zoomValue !== ZOOM_DISPLAY_MIDDLE) { - if (inBounds(width, height)) { + } else if (!adaptive) { + // if (inBounds(width, height) && flexRectInBounds(graphZoom)) { + if (flexRectInBounds(graphZoom)) { zoom.translateBy(zoomContainer, width, height); - } else if (inBounds(0, 0)) { - // ^check if current position in bounds but still not at border, - // then move remaining amount left in graph - if (width !== 0 && inBounds(width / graphZoom / 3, height)) { - zoom.translateBy(zoomContainer, width / graphZoom / 3, height); - } else if (height !== 0 && inBounds(width, height / graphZoom / 3)) { - zoom.translateBy(zoomContainer, width, height / graphZoom / 3); - } - } + } + // else if (inBounds(0, 0)) { + // // ^check if current position in bounds but still not at border, + // // then move remaining amount left in graph + // if (width !== 0 && inBounds(width / graphZoom / 3, height)) { + // zoom.translateBy(zoomContainer, width / graphZoom / 3, height); + // } else if (height !== 0 && inBounds(width, height / graphZoom / 3)) { + // zoom.translateBy(zoomContainer, width, height / graphZoom / 3); + // } + // } } } @@ -1444,7 +1451,6 @@ export var drawGraph = function (workbook) { let xValuesPaths = [] let yValuesPaths = [] - // this would reassign the values of pathData, since no value being assigned, then the value would be null link.selectAll("path").each( function(pathData) { if (pathData.source) { // Log the "d" attribute for each path @@ -1489,25 +1495,37 @@ export var drawGraph = function (workbook) { function flexRectInBounds(zoomValue) { if (flexibleContainer) { - if (flexibleContainer.width * zoomValue > width) { - console.log(flexibleContainer.width, zoomValue, width, flexibleContainer.width * zoomValue > width); - console.log("width exceeds") + updateZoomContainerInfo(); + // validations for zoom and left/right cursor drag and D-pad movement + if (flexibleContainer.width * zoomValue > width ) { + console.log( + "width exceeds", + flexibleContainer.width * zoomValue, + "total width", + width, + "graphZoom", + graphZoom, + "zoomValue", + zoomValue + ); return false; } else if (flexibleContainer.height * zoomValue > height) { - console.log("height exceeds") + console.log( + "height exceeds", + flexibleContainer.height * zoomValue, + "total height", + height + ); return false; - } + } } return true } function flexRectLimitBounds() { - // TODO: with collision, if any of these are true then that means that graph is colliding with boundingBox - // can also determine if collide with edge of graph here to see if can zoom in or not let flexiBoxInBounds = true; if (flexibleContainer) { // x left bound - // TODO: if graphZoom < 1, then do borders based on viewport? if (flexibleContainer.x < 0) { flexibleContainer.x = 0; flexiBoxInBounds = false; From 49568d25d6daf796eb1e0507a4732381c654a114 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 9 Mar 2024 01:44:24 -0800 Subject: [PATCH 071/150] Issue #1083. Can move the graph with d-pad, but there is an edge case I am experiencing where when the graph starts out almost the height of the container, the graph exceeds the bounds --- web-client/public/js/graph.js | 81 ++++++++++++++++++----------------- 1 file changed, 41 insertions(+), 40 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index a1f2a361..8cd2db72 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -176,11 +176,7 @@ export var drawGraph = function (workbook) { scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } - // console.log("scale", scale, "graphZoom", graphZoom) - // inBounds(d3.event.dx, d3.event.dy) && flexRectInBounds(graphZoom) - - if (adaptive || (!adaptive && flexRectInBounds(graphZoom) && inBounds(graphZoom, d3.event.dx, d3.event.dy))) { - // if (adaptive || (!adaptive && inBounds(d3.event.dx, d3.event.dy) && flexRectInBounds(graphZoom))) { + if (adaptive || (!adaptive && flexRectInBounds(graphZoom) && inBounds(graphZoom, d3.event.dx, d3.event.dy, false))) { zoom.translateBy( zoomContainer, scale * (d3.event.x - zoomDragPrevX), @@ -270,8 +266,9 @@ export var drawGraph = function (workbook) { .split("(")[1].split(",")[1].split(")")[0]); }; - function inBounds(graphZoom, dx, dy) { + function inBounds(graphZoom, dx, dy, dPad) { updateZoomContainerInfo(); + console.log("dx", dx, "dy", dy, "yTranslation", yTranslation) // if ((xTranslation < 0 && Math.abs(xTranslation) * graphZoom >= Math.floor(flexibleContainer.x + dx)) || // (xTranslation > 0 && (flexibleContainer.width + flexibleContainer.x + xTranslation) + dx >= width / graphZoom)) { /*(xTranslation < 0 && @@ -279,26 +276,42 @@ export var drawGraph = function (workbook) { Math.abs(xTranslation) * graphZoom >= Math.floor(flexibleContainer.x + dx)) || flexibleContainer.width + flexibleContainer.x + Math.abs(xTranslation) >= width * graphZoom)) ||*/ + + if (dPad) { + // if () { + console.log("flexContainer.y", flexibleContainer.y, "flexibleContainer.height", + flexibleContainer.height,"yTranslation",yTranslation, "dy", dy, "total height",height); + // } else { + console.log((yTranslation < 0 && + Math.abs(yTranslation) * graphZoom >= + Math.floor(flexibleContainer.y + dy)) || + (yTranslation > 0 && + flexibleContainer.height + + flexibleContainer.y + + yTranslation + + dy >= + height / graphZoom)) + console.log("dPad violated") + // } + + } + if ( (xTranslation < 0 && Math.abs(xTranslation) * graphZoom >= Math.floor(flexibleContainer.x + dx)) || (xTranslation > 0 && - flexibleContainer.width + flexibleContainer.x + xTranslation + dx >= - width / graphZoom) + flexibleContainer.width + + flexibleContainer.x + + xTranslation + + dx >= + width / graphZoom) ) { - console.log( - Math.abs(xTranslation) * graphZoom >= - Math.floor(flexibleContainer.x + dx), - xTranslation, - xTranslation * graphZoom, - flexibleContainer.x - ); return false; } else if ( (yTranslation < 0 && - Math.abs(yTranslation) * graphZoom >= - Math.floor(flexibleContainer.y + dy)) || + Math.abs(yTranslation) * graphZoom >= + Math.floor(flexibleContainer.y + dy)) || (yTranslation > 0 && flexibleContainer.height + flexibleContainer.y + @@ -306,21 +319,9 @@ export var drawGraph = function (workbook) { dy >= height / graphZoom) ) { - // validations for up/down cursor drag and movement - console.log( - "flexContainer.y", - flexibleContainer.y, - "flexibleContainer.height", - flexibleContainer.height, - "yTranslation", - yTranslation, - "total height", - height - ); - console.log(" "); return false } - console.log("flexContainer.x",flexibleContainer.x,"flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "total width", width); + // console.log("flexContainer.x",flexibleContainer.x,"flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "total width", width); console.log("flexContainer height and width in bounds"); return true @@ -526,22 +527,22 @@ export var drawGraph = function (workbook) { // move: moves graph with D-pad function move (direction) { - var width = direction === "left" ? -50 : direction === "right" ? 50 : 0; - var height = direction === "up" ? -50 : direction === "down" ? 50 : 0; + var moveWidth = direction === "left" ? -50 : direction === "right" ? 50 : 0; + var moveHeight = direction === "up" ? -50 : direction === "down" ? 50 : 0; if (adaptive) { - zoom.translateBy(zoomContainer, width, height); + zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { // if (inBounds(width, height) && flexRectInBounds(graphZoom)) { - if (flexRectInBounds(graphZoom)) { - zoom.translateBy(zoomContainer, width, height); + if (flexRectInBounds(graphZoom) && inBounds(graphZoom, moveWidth, moveHeight, true)) { + zoom.translateBy(zoomContainer, moveWidth, moveHeight); } - // else if (inBounds(0, 0)) { + // else if (inBounds(graphZoom, 0, 0)) { // // ^check if current position in bounds but still not at border, // // then move remaining amount left in graph - // if (width !== 0 && inBounds(width / graphZoom / 3, height)) { - // zoom.translateBy(zoomContainer, width / graphZoom / 3, height); - // } else if (height !== 0 && inBounds(width, height / graphZoom / 3)) { - // zoom.translateBy(zoomContainer, width, height / graphZoom / 3); + // if (moveWidth !== 0 && inBounds(graphZoom, moveWidth / 3, moveHeight)) { + // zoom.translateBy(zoomContainer, moveWidth / 3, moveHeight); + // } else if (moveHeight !== 0 && inBounds(graphZoom, moveWidth, moveHeight / 3)) { + // zoom.translateBy(zoomContainer, moveWidth, moveHeight / 3); // } // } } From 3ed3e1c6761dc6f5332bd97e07679ed465128a5a Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Sun, 10 Mar 2024 19:23:27 -0700 Subject: [PATCH 072/150] Fix merge --- server/controllers/constants.js | 2 ++ server/controllers/export-constants.js | 5 +++-- server/controllers/exporters/xlsx.js | 6 +++--- server/controllers/network-sheet-parser.js | 10 +++++----- server/controllers/workbook-constants.js | 3 ++- test/export-tests.js | 7 ++++--- 6 files changed, 19 insertions(+), 14 deletions(-) diff --git a/server/controllers/constants.js b/server/controllers/constants.js index 14ee5bda..7b147c64 100644 --- a/server/controllers/constants.js +++ b/server/controllers/constants.js @@ -4,6 +4,8 @@ module.exports = { NOT_FOUND: -1, WEIGHTED: "weighted", UNWEIGHTED: "unweighted", + CELL_A1_PPI: "cols protein1/ rows protein2", + CELL_A1_GRN: "cols regulators/rows targets", NETWORK_PPI_MODE: "protein-protein-physical-interaction", NETWORK_GRN_MODE: "grn", diff --git a/server/controllers/export-constants.js b/server/controllers/export-constants.js index 3b2eeb5d..2c96f515 100644 --- a/server/controllers/export-constants.js +++ b/server/controllers/export-constants.js @@ -37,8 +37,9 @@ module.exports = { warningCode: "INCORRECT_NETWORK_SHEET_EXPORT_WARNING", errorDescription: "GRNsight has detected that the 'network' sheet or the 'network_optimized_weights'" + " sheet is improperly formattedPlease look over your exported workbook and ensure that network" + - " sheets have cell A1 as 'cols regulators/rows targets' exactly, and all gene are using the naming" + - " conventions listed at: \nhttps://dondi.github.io/GRNsight/documentation.html." + " sheets have cell A1 as 'cols regulators/rows targets' or 'cols protein1/ rows protein2' exactly" + + " and all gene are using the naming conventions listed at:" + + " \nhttps://dondi.github.io/GRNsight/documentation.html." }, // Missing Source Genes MISSING_SOURCE_GENES_EXPORT_WARNING: { diff --git a/server/controllers/exporters/xlsx.js b/server/controllers/exporters/xlsx.js index 1702ca28..f36bcb4c 100644 --- a/server/controllers/exporters/xlsx.js +++ b/server/controllers/exporters/xlsx.js @@ -1,6 +1,6 @@ // const { meta } = require("eslint/lib/rules/*"); const xlsx = require("node-xlsx"); -const { NETWORK_GRN_MODE } = require("../constants"); +const { CELL_A1_GRN, CELL_A1_PPI, NETWORK_GRN_MODE } = require("../constants"); const buildGeneNameArray = function (genes) { const geneNameArray = genes.map(gene => gene["name"]); @@ -20,9 +20,9 @@ const buildNetworkSheet = function (genes, links, workbookType) { // EX: ["CIN5", 0, 0, 1] Object.keys(geneNameArray).forEach(index => networkSheet[index][0] = geneNameArray[index]); if (workbookType === NETWORK_GRN_MODE) { - geneNameArray.unshift("cols regulators/rows targets"); + geneNameArray.unshift(CELL_A1_GRN); } else { - geneNameArray.unshift("protein 1/protein 2"); + geneNameArray.unshift(CELL_A1_PPI); } links.forEach((link) => { diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index 9480e0f3..a8bc58f2 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -2,7 +2,7 @@ // var path = require("path"); // var demoWorkbooks = require(__dirname + "/demo-workbooks"); -const { NETWORK_PPI_MODE, NETWORK_GRN_MODE } = require("./constants"); +const { NETWORK_PPI_MODE, NETWORK_GRN_MODE, CELL_A1_GRN, CELL_A1_PPI } = require("./constants"); const { initWorkbook } = require("./helpers"); var semanticChecker = require(__dirname + "/semantic-checker"); @@ -109,7 +109,7 @@ var parseNetworkSheet = function (sheet, network) { // Depending on the value of cellA1, we want to make a new property `networkType` which // will indicate the network type. THe web app then reads this to decide what to do next. - if (cellA1 !== "cols regulators/rows targets") { + if (cellA1 !== CELL_A1_GRN && cellA1 !== CELL_A1_PPI) { addWarning( network, constants.warnings.incorrectCellA1WorkbookWarning(sheet.name) @@ -295,7 +295,7 @@ var parseNetworkSheet = function (sheet, network) { /* * This method detect the network type of the workbook file either grn or protein-protein-physical-interactions * If cellA1 = "cols regulators/ row targets" -> workbookType = grn - * If cellA1 = "protein 1/protein 2" -> workbookType = "protein-protein-physical-interaction" + * If cellA1 = "cols protein1/ rows protein2" -> workbookType = "protein-protein-physical-interaction" * else undefined */ @@ -305,9 +305,9 @@ exports.workbookType = function (workbookFile) { if (sheet.name.toLowerCase() === "network") { const cellA1 = sheet.data[0][0]; - if (cellA1 === "cols regulators/rows targets") { + if (cellA1 === CELL_A1_GRN) { workbookType = NETWORK_GRN_MODE; - } else if (cellA1 === "protein 1/protein 2") { + } else if (cellA1 === CELL_A1_PPI) { workbookType = NETWORK_PPI_MODE; } else { workbookType = undefined; diff --git a/server/controllers/workbook-constants.js b/server/controllers/workbook-constants.js index 2571c5b7..a44af985 100644 --- a/server/controllers/workbook-constants.js +++ b/server/controllers/workbook-constants.js @@ -102,7 +102,8 @@ module.exports = { return { warningCode: "MISLABELED_NETWORK_CELL_A1", errorDescription: `The top left cell of the ${sheetName} sheet is mislabeled. - Replace the incorrect label with \'cols regulators/rows targets\' exactly.` + Replace the incorrect label with \'cols regulators/ rows targets\' or \'cols + protein1/ rows protein2'\ exactly.` }; }, diff --git a/test/export-tests.js b/test/export-tests.js index 059818d9..bd8a0f75 100644 --- a/test/export-tests.js +++ b/test/export-tests.js @@ -2,6 +2,7 @@ var expect = require("chai").expect; var extend = require("jquery-extend"); var xlsx = require("node-xlsx"); var test = require("./test"); +const { CELL_A1_PPI, CELL_A1_GRN } = require("../server/controllers/constants"); var exportController = require(__dirname + "/../server/controllers/export-controller")(); var constants = require(__dirname + "/../server/controllers/constants"); @@ -763,7 +764,7 @@ describe("Export to spreadsheet", function () { { name: "network", data: [ - ["cols regulators/rows targets", "ACE2", "AFT2", "CIN5"], + [CELL_A1_GRN, "ACE2", "AFT2", "CIN5"], ["ACE2", 1, 0, 0], ["AFT2", 0, 1, 1], ["CIN5", 0, 0, 1] @@ -773,7 +774,7 @@ describe("Export to spreadsheet", function () { { name: "network_weights", data: [ - ["cols regulators/rows targets", "ACE2", "AFT2", "CIN5"], + [CELL_A1_GRN, "ACE2", "AFT2", "CIN5"], ["ACE2", 1, 0, 0], ["AFT2", 0, 1, 1], ["CIN5", 0, 0, 1] @@ -896,7 +897,7 @@ describe("Export to spreadsheet", function () { { name: "network", data: [ - ["protein 1/protein 2", "Aim32p", "Ccr4p", "Erv1p"], + [CELL_A1_PPI, "Aim32p", "Ccr4p", "Erv1p"], ["Aim32p", 0, 0, 0], ["Ccr4p", 1, 1, 0], ["Erv1p", 1, 0, 1] From 930bc422828f20d6d78caadb7b0703f5bb7960f3 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sun, 10 Mar 2024 23:26:15 -0700 Subject: [PATCH 073/150] Issue #1083, can now use D-pad, zoom slider, and cursor drag on graph, but experiencing issue where graph gets stuch at bottom of viewport sometimes --- web-client/public/js/graph.js | 53 ++++------------------------------- 1 file changed, 5 insertions(+), 48 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 8cd2db72..732034ef 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -269,39 +269,12 @@ export var drawGraph = function (workbook) { function inBounds(graphZoom, dx, dy, dPad) { updateZoomContainerInfo(); console.log("dx", dx, "dy", dy, "yTranslation", yTranslation) - // if ((xTranslation < 0 && Math.abs(xTranslation) * graphZoom >= Math.floor(flexibleContainer.x + dx)) || - // (xTranslation > 0 && (flexibleContainer.width + flexibleContainer.x + xTranslation) + dx >= width / graphZoom)) { - /*(xTranslation < 0 && - ((graphZoom <= 1 && - Math.abs(xTranslation) * graphZoom >= - Math.floor(flexibleContainer.x + dx)) || - flexibleContainer.width + flexibleContainer.x + Math.abs(xTranslation) >= width * graphZoom)) ||*/ - - if (dPad) { - // if () { - console.log("flexContainer.y", flexibleContainer.y, "flexibleContainer.height", - flexibleContainer.height,"yTranslation",yTranslation, "dy", dy, "total height",height); - // } else { - console.log((yTranslation < 0 && - Math.abs(yTranslation) * graphZoom >= - Math.floor(flexibleContainer.y + dy)) || - (yTranslation > 0 && - flexibleContainer.height + - flexibleContainer.y + - yTranslation + - dy >= - height / graphZoom)) - console.log("dPad violated") - // } - - } if ( - (xTranslation < 0 && + ((dx < 0 || xTranslation < 0) && Math.abs(xTranslation) * graphZoom >= Math.floor(flexibleContainer.x + dx)) || - (xTranslation > 0 && - flexibleContainer.width + + (flexibleContainer.width + flexibleContainer.x + xTranslation + dx >= @@ -309,16 +282,16 @@ export var drawGraph = function (workbook) { ) { return false; } else if ( - (yTranslation < 0 && + ((dy < 0 || yTranslation < 0) && Math.abs(yTranslation) * graphZoom >= Math.floor(flexibleContainer.y + dy)) || - (yTranslation > 0 && - flexibleContainer.height + + (flexibleContainer.height + flexibleContainer.y + yTranslation + dy >= height / graphZoom) ) { + console.log("yTranslation returned FALSE") return false } // console.log("flexContainer.x",flexibleContainer.x,"flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "total width", width); @@ -1499,24 +1472,8 @@ export var drawGraph = function (workbook) { updateZoomContainerInfo(); // validations for zoom and left/right cursor drag and D-pad movement if (flexibleContainer.width * zoomValue > width ) { - console.log( - "width exceeds", - flexibleContainer.width * zoomValue, - "total width", - width, - "graphZoom", - graphZoom, - "zoomValue", - zoomValue - ); return false; } else if (flexibleContainer.height * zoomValue > height) { - console.log( - "height exceeds", - flexibleContainer.height * zoomValue, - "total height", - height - ); return false; } } From 602badd9651dac65e3a03cdf1afff74844a45fd8 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sun, 10 Mar 2024 23:59:40 -0700 Subject: [PATCH 074/150] Issue #1083. Adjusted calcFlexiBox to more accurately calculate the flexibox for self-referring nodes. Still experiencing Issue with PPI demo graph where get stuck at bottom of viewport --- web-client/public/js/graph.js | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 732034ef..49b6a3fc 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -268,7 +268,9 @@ export var drawGraph = function (workbook) { function inBounds(graphZoom, dx, dy, dPad) { updateZoomContainerInfo(); - console.log("dx", dx, "dy", dy, "yTranslation", yTranslation) + console.log("dx", dx, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport height", height) + console.log("dy", dy, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport width", width) + console.log(" ") if ( ((dx < 0 || xTranslation < 0) && @@ -1432,9 +1434,9 @@ export var drawGraph = function (workbook) { if (controlPoints) { if (controlPoints.includes("A")) { const splitSpaces = controlPoints.split(" "); - const controlPoint = splitSpaces[0].split("M")[1].split(","); - const controlPointX = controlPoint[0]; - const controlPointY = controlPoint[1]; + const controlPointXY = splitSpaces[2].split(",") + const controlPointX = controlPointXY[0]; + const controlPointY = controlPointXY[1]; xValuesPaths.push(parseFloat(controlPointX)) yValuesPaths.push(parseFloat(controlPointY)) } From 20b6c965ff84feeaf83290cf71664a2f96398158 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 11 Mar 2024 00:59:50 -0700 Subject: [PATCH 075/150] Issue #1083. Fixed issue with the graph sticking to the edge of the viewport, it was when a self-referring edge was right next to one of the graph edges. Now experiencing another issue where the graph exceeds the left and top of the graph --- web-client/public/js/graph.js | 61 +++++++++++++++++------------------ 1 file changed, 30 insertions(+), 31 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 49b6a3fc..165f3e97 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -176,7 +176,7 @@ export var drawGraph = function (workbook) { scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } - if (adaptive || (!adaptive && flexRectInBounds(graphZoom) && inBounds(graphZoom, d3.event.dx, d3.event.dy, false))) { + if (adaptive || (!adaptive && flexRectInBounds(graphZoom) && inBounds(graphZoom, d3.event.dx, d3.event.dy))) { zoom.translateBy( zoomContainer, scale * (d3.event.x - zoomDragPrevX), @@ -266,40 +266,51 @@ export var drawGraph = function (workbook) { .split("(")[1].split(",")[1].split(")")[0]); }; - function inBounds(graphZoom, dx, dy, dPad) { + function inBounds(graphZoom, dx, dy) { updateZoomContainerInfo(); - console.log("dx", dx, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport height", height) - console.log("dy", dy, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport width", width) - console.log(" ") if ( ((dx < 0 || xTranslation < 0) && Math.abs(xTranslation) * graphZoom >= - Math.floor(flexibleContainer.x + dx)) || + Math.floor(flexibleContainer.x) + dx) && + !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx) || (dx > 0 && (flexibleContainer.width + flexibleContainer.x + xTranslation + dx >= - width / graphZoom) + width / graphZoom)) ) { - return false; + console.log("dx", dx, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) + return false; } else if ( ((dy < 0 || yTranslation < 0) && Math.abs(yTranslation) * graphZoom >= - Math.floor(flexibleContainer.y + dy)) || + Math.floor(flexibleContainer.y) + dy) && + !(Math.abs(yTranslation) * graphZoom - flexibleContainer.y > dy) || (dy > 0 && (flexibleContainer.height + flexibleContainer.y + yTranslation + dy >= - height / graphZoom) + height / graphZoom)) ) { console.log("yTranslation returned FALSE") + console.log("dy", dy, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) + console.log("first statement dy or y Translation", (dy < 0 || yTranslation < 0)) + console.log("first truth move up", Math.abs(yTranslation) * graphZoom >= + Math.floor(flexibleContainer.y + dy), Math.abs(yTranslation) * graphZoom, ">=", Math.floor(flexibleContainer.y + dy)) + console.log("first statement move down", (flexibleContainer.height + + flexibleContainer.y + + yTranslation + + dy >= + height / graphZoom)) + return false + } else { + // console.log("flexContainer.x",flexibleContainer.x,"flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "total width", width); + console.log("flexContainer height and width in bounds"); + return true } - // console.log("flexContainer.x",flexibleContainer.x,"flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "total width", width); - console.log("flexContainer height and width in bounds"); - - return true + }; // controls reading movement of zoomSlider and scaling graph to that zoomScale @@ -313,8 +324,6 @@ export var drawGraph = function (workbook) { if (adaptive || (!adaptive && flexRectInBounds(graphZoom))) { zoom.scaleTo(container, zoomScale); } - - }; // See setupZoomElements below to see how these are initialized. They are declared here because @@ -507,19 +516,9 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { - // if (inBounds(width, height) && flexRectInBounds(graphZoom)) { - if (flexRectInBounds(graphZoom) && inBounds(graphZoom, moveWidth, moveHeight, true)) { + if (flexRectInBounds(graphZoom) && inBounds(graphZoom, moveWidth, moveHeight)) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); - } - // else if (inBounds(graphZoom, 0, 0)) { - // // ^check if current position in bounds but still not at border, - // // then move remaining amount left in graph - // if (moveWidth !== 0 && inBounds(graphZoom, moveWidth / 3, moveHeight)) { - // zoom.translateBy(zoomContainer, moveWidth / 3, moveHeight); - // } else if (moveHeight !== 0 && inBounds(graphZoom, moveWidth, moveHeight / 3)) { - // zoom.translateBy(zoomContainer, moveWidth, moveHeight / 3); - // } - // } + } } } @@ -1477,7 +1476,7 @@ export var drawGraph = function (workbook) { return false; } else if (flexibleContainer.height * zoomValue > height) { return false; - } + } } return true } @@ -1493,7 +1492,7 @@ export var drawGraph = function (workbook) { // x right bound if (!(flexibleContainer.width - flexibleContainer.x <= width * graphZoom)) { - flexibleContainer.width = width - flexibleContainer.x; + flexibleContainer.width = (width - flexibleContainer.x) * graphZoom; flexiBoxInBounds = false; } @@ -1505,7 +1504,7 @@ export var drawGraph = function (workbook) { // y bottom bound if (!(flexibleContainer.height - flexibleContainer.y <= height * graphZoom)) { - flexibleContainer.height = height - flexibleContainer.y; + flexibleContainer.height = (height - flexibleContainer.y) * graphZoom; flexiBoxInBounds = false; } } From 13769b0d69b5a649ae812d6f4b25e3907b600516 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 11 Mar 2024 01:57:30 -0700 Subject: [PATCH 076/150] Issue #1083, graph still getting stuck at borders of viewport --- web-client/public/js/graph.js | 63 ++++++++++++++++++----------------- 1 file changed, 32 insertions(+), 31 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 165f3e97..efa86f66 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -268,49 +268,51 @@ export var drawGraph = function (workbook) { function inBounds(graphZoom, dx, dy) { updateZoomContainerInfo(); + // console.log("dy", dy, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) + // console.log("dx", dx, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) + // console.log(Math.abs(xTranslation) < flexibleContainer.x, !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx)) + // handle left border of viewport + if ((Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx)) { + return false + } + if (Math.abs(yTranslation) * graphZoom - flexibleContainer.y > dy) { + return false; + } + + // handle right border if ( - ((dx < 0 || xTranslation < 0) && + ((dx < 0 || (xTranslation < 0 && Math.abs(xTranslation) > flexibleContainer.x)) && Math.abs(xTranslation) * graphZoom >= - Math.floor(flexibleContainer.x) + dx) && - !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx) || (dx > 0 && + Math.floor(flexibleContainer.x) + dx) + || (dx > 0 && (flexibleContainer.width + flexibleContainer.x + xTranslation + dx >= width / graphZoom)) ) { - console.log("dx", dx, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) - return false; - } else if ( - ((dy < 0 || yTranslation < 0) && + return false + } + + // handle bottom border + if ( + ((dy < 0 || (yTranslation < 0 && Math.abs(yTranslation) > flexibleContainer.y)) && Math.abs(yTranslation) * graphZoom >= - Math.floor(flexibleContainer.y) + dy) && - !(Math.abs(yTranslation) * graphZoom - flexibleContainer.y > dy) || (dy > 0 && - (flexibleContainer.height + + Math.floor(flexibleContainer.y) + dy) + || (dy > 0 && + (flexibleContainer.height + flexibleContainer.y + yTranslation + dy >= height / graphZoom)) ) { console.log("yTranslation returned FALSE") - console.log("dy", dy, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) - console.log("first statement dy or y Translation", (dy < 0 || yTranslation < 0)) - console.log("first truth move up", Math.abs(yTranslation) * graphZoom >= - Math.floor(flexibleContainer.y + dy), Math.abs(yTranslation) * graphZoom, ">=", Math.floor(flexibleContainer.y + dy)) - console.log("first statement move down", (flexibleContainer.height + - flexibleContainer.y + - yTranslation + - dy >= - height / graphZoom)) - return false - } else { - // console.log("flexContainer.x",flexibleContainer.x,"flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "total width", width); - console.log("flexContainer height and width in bounds"); - return true } - + // console.log("flexContainer.x",flexibleContainer.x,"flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "total width", width); + console.log("flexContainer height and width in bounds"); + return true }; // controls reading movement of zoomSlider and scaling graph to that zoomScale @@ -1482,34 +1484,33 @@ export var drawGraph = function (workbook) { } function flexRectLimitBounds() { - let flexiBoxInBounds = true; if (flexibleContainer) { // x left bound if (flexibleContainer.x < 0) { flexibleContainer.x = 0; - flexiBoxInBounds = false; + return false } // x right bound if (!(flexibleContainer.width - flexibleContainer.x <= width * graphZoom)) { flexibleContainer.width = (width - flexibleContainer.x) * graphZoom; - flexiBoxInBounds = false; + return false } // y top bound if (flexibleContainer.y < 0) { flexibleContainer.y = 0; - flexiBoxInBounds = false; + return false } // y bottom bound if (!(flexibleContainer.height - flexibleContainer.y <= height * graphZoom)) { flexibleContainer.height = (height - flexibleContainer.y) * graphZoom; - flexiBoxInBounds = false; + return false } } - return flexiBoxInBounds; + // return flexiBoxInBounds; } // Tick only runs while the graph physics are still running. From 20ca39552bab99eeb7bd47fc5b091ce0362ecddc Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Mon, 11 Mar 2024 21:56:09 -0700 Subject: [PATCH 077/150] Fix merge, hopefully this one works --- server/controllers/exporters/xlsx.js | 4 ---- server/controllers/network-sheet-parser.js | 10 ---------- 2 files changed, 14 deletions(-) diff --git a/server/controllers/exporters/xlsx.js b/server/controllers/exporters/xlsx.js index c294a642..f36bcb4c 100644 --- a/server/controllers/exporters/xlsx.js +++ b/server/controllers/exporters/xlsx.js @@ -1,10 +1,6 @@ // const { meta } = require("eslint/lib/rules/*"); const xlsx = require("node-xlsx"); -<<<<<<< HEAD const { CELL_A1_GRN, CELL_A1_PPI, NETWORK_GRN_MODE } = require("../constants"); -======= -const { CELL_A1_GRN, CELL_A1_PPI } = require("../constants"); ->>>>>>> beta const buildGeneNameArray = function (genes) { const geneNameArray = genes.map(gene => gene["name"]); diff --git a/server/controllers/network-sheet-parser.js b/server/controllers/network-sheet-parser.js index 2a8fe28c..a8bc58f2 100644 --- a/server/controllers/network-sheet-parser.js +++ b/server/controllers/network-sheet-parser.js @@ -2,11 +2,7 @@ // var path = require("path"); // var demoWorkbooks = require(__dirname + "/demo-workbooks"); -<<<<<<< HEAD const { NETWORK_PPI_MODE, NETWORK_GRN_MODE, CELL_A1_GRN, CELL_A1_PPI } = require("./constants"); -======= -const { CELL_A1_GRN, CELL_A1_PPI } = require("./constants"); ->>>>>>> beta const { initWorkbook } = require("./helpers"); var semanticChecker = require(__dirname + "/semantic-checker"); @@ -310,15 +306,9 @@ exports.workbookType = function (workbookFile) { const cellA1 = sheet.data[0][0]; if (cellA1 === CELL_A1_GRN) { -<<<<<<< HEAD workbookType = NETWORK_GRN_MODE; } else if (cellA1 === CELL_A1_PPI) { workbookType = NETWORK_PPI_MODE; -======= - workbookType = "grn"; - } else if (cellA1 === CELL_A1_PPI) { - workbookType = "protein-protein-physical-interaction"; ->>>>>>> beta } else { workbookType = undefined; } From 05401da5bb3f40277122e186cde1bd3bad37d8cb Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Mon, 11 Mar 2024 23:58:57 -0700 Subject: [PATCH 078/150] Update version to 7.0.13 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 8d7e2ceb..93012c73 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "grnsight", - "version": "7.0.12", + "version": "7.0.13", "description": "Web app and service for visualizing models of gene regulatory networks", "directories": { "test": "test" From 8f9d553d9bb3afef9662e4fc9a768e9159125575 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 12 Mar 2024 01:50:08 -0700 Subject: [PATCH 079/150] Issue #1083. Can now clamp the graph when zoom in to ensure the graph does not exceed viewport --- web-client/public/js/graph.js | 79 +++++++++++++++++++++-------------- 1 file changed, 48 insertions(+), 31 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index efa86f66..5928baa4 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -271,47 +271,50 @@ export var drawGraph = function (workbook) { // console.log("dy", dy, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) // console.log("dx", dx, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) // console.log(Math.abs(xTranslation) < flexibleContainer.x, !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx)) - // handle left border of viewport - if ((Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx)) { + // TODO: this handles left border, but the graph still goes through the left edge + // console.log(!(Math.abs(xTranslation) < flexibleContainer.x), !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx)); + if (!(Math.abs(yTranslation) < flexibleContainer.y) && (Math.abs(yTranslation) * graphZoom - flexibleContainer.y > dy)) { return false } - if (Math.abs(yTranslation) * graphZoom - flexibleContainer.y > dy) { - return false; - } - // handle right border if ( ((dx < 0 || (xTranslation < 0 && Math.abs(xTranslation) > flexibleContainer.x)) && Math.abs(xTranslation) * graphZoom >= - Math.floor(flexibleContainer.x) + dx) - || (dx > 0 && + Math.floor(flexibleContainer.x) + dx)) { + // BOUNDARY_MARGIN_X = graphZoom > 1 ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + return false + } + + if (dx > 0 && (flexibleContainer.width + flexibleContainer.x + xTranslation + dx >= - width / graphZoom)) - ) { + width / graphZoom)) { + // BOUNDARY_MARGIN_X = width / graphZoom; return false } - // handle bottom border if ( - ((dy < 0 || (yTranslation < 0 && Math.abs(yTranslation) > flexibleContainer.y)) && + ((dy < 0 || yTranslation < 0) && (Math.abs(yTranslation) > flexibleContainer.y) && Math.abs(yTranslation) * graphZoom >= - Math.floor(flexibleContainer.y) + dy) - || (dy > 0 && - (flexibleContainer.height + - flexibleContainer.y + - yTranslation + - dy >= - height / graphZoom)) + Math.floor(flexibleContainer.y) + dy)) + { + // console.log("yTranslation returned FALSE") + // BOUNDARY_MARGIN_Y = graphZoom > 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; + return false + } + + if ( + dy > 0 && + flexibleContainer.height + flexibleContainer.y + yTranslation + dy >= + height / graphZoom ) { - console.log("yTranslation returned FALSE") + // BOUNDARY_MARGIN_Y = height / graphZoom; return false } - // console.log("flexContainer.x",flexibleContainer.x,"flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "total width", width); - console.log("flexContainer height and width in bounds"); + // console.log("flexContainer height and width in bounds"); return true }; @@ -1467,6 +1470,7 @@ export var drawGraph = function (workbook) { const maxX = Math.max(...xValues) + nodeWidth; const maxY = Math.max(...yValues) + nodeHeight; + return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } @@ -1509,8 +1513,6 @@ export var drawGraph = function (workbook) { return false } } - - // return flexiBoxInBounds; } // Tick only runs while the graph physics are still running. @@ -1526,11 +1528,21 @@ export var drawGraph = function (workbook) { var getSelfReferringRadius = function (edge) { return edge ? 17 + (getEdgeThickness(edge) / 2) : 0; }; - var BOUNDARY_MARGIN = 5; + + + + let BOUNDARY_MARGIN = 5; + + let BOUNDARY_MARGIN_X = adaptive? BOUNDARY_MARGIN : graphZoom > 1 ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + let BOUNDARY_MARGIN_Y = adaptive? BOUNDARY_MARGIN: graphZoom > 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; + // let BOUNDARY_MARGIN_X = BOUNDARY_MARGIN + // let BOUNDARY_MARGIN_Y = BOUNDARY_MARGIN var SELF_REFERRING_Y_OFFSET = 6; var MAX_WIDTH = 5000; var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; + console.log("xboundary margin", BOUNDARY_MARGIN_X); + console.log("yboundary margin", BOUNDARY_MARGIN_Y); if (!adaptive) { flexibleContainer = calcFlexiBox(); @@ -1550,11 +1562,16 @@ export var drawGraph = function (workbook) { var selfReferringEdgeWidth = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + 2 : 0); - var rightBoundary = width - (d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN - selfReferringEdgeWidth; + // var rightBoundary = width - + // (d.textWidth + OFFSET_VALUE) - + // BOUNDARY_MARGIN_X - + // selfReferringEdgeWidth + // ; + var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X - selfReferringEdgeWidth; // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentXPos = Math.max(BOUNDARY_MARGIN, Math.min(rightBoundary, d.x)); + var currentXPos = Math.max(BOUNDARY_MARGIN_X, Math.min(rightBoundary, d.x)); if (adaptive && width < MAX_WIDTH && - (currentXPos === BOUNDARY_MARGIN || currentXPos === rightBoundary)) { + (currentXPos === BOUNDARY_MARGIN_X || currentXPos === rightBoundary)) { if (!d3.select(this).classed("fixed")) { width += OFFSET_VALUE; boundingBoxContainer.attr("width", width); @@ -1578,11 +1595,11 @@ export var drawGraph = function (workbook) { var selfReferringEdge = getSelfReferringEdge(d); var selfReferringEdgeHeight = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + SELF_REFERRING_Y_OFFSET + 0.5 : 0); - var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN - selfReferringEdgeHeight; + var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN_Y - selfReferringEdgeHeight; // currentYPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentYPos = Math.max(BOUNDARY_MARGIN, Math.min(bottomBoundary, d.y)); + var currentYPos = Math.max(BOUNDARY_MARGIN_Y, Math.min(bottomBoundary, d.y)); if (adaptive && height < MAX_HEIGHT && - (currentYPos === BOUNDARY_MARGIN || currentYPos === bottomBoundary)) { + (currentYPos === BOUNDARY_MARGIN_Y || currentYPos === bottomBoundary)) { if (!d3.select(this).classed("fixed")) { height += OFFSET_VALUE; boundingBoxContainer.attr("height", height); From dfa366bb06024cdbc167048d42d1bbd8027b04d0 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 12 Mar 2024 09:10:33 -0700 Subject: [PATCH 080/150] Issue #1083, this works for dragging left and right but borders smaller than should be whenfirst zoom in on graph --- web-client/public/js/graph.js | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 5928baa4..222193e8 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -337,6 +337,7 @@ export var drawGraph = function (workbook) { let zoomScaleSliderLeft; let zoomScaleSliderRight; let prevGrnstateZoomVal; + let centerXCoord; const updateAppBasedOnZoomValue = () => { let zoomDisplay; @@ -372,6 +373,7 @@ export var drawGraph = function (workbook) { // if don't center, then get issue of zooming into the box since not inside the width of the viewport if (!adaptive) { center(); + centerXCoord = xTranslation } $(ZOOM_SLIDER).val( @@ -1488,6 +1490,7 @@ export var drawGraph = function (workbook) { } function flexRectLimitBounds() { + //prevent flexContainer from having bounds outside of bounding box if (flexibleContainer) { // x left bound if (flexibleContainer.x < 0) { @@ -1532,17 +1535,19 @@ export var drawGraph = function (workbook) { let BOUNDARY_MARGIN = 5; - - let BOUNDARY_MARGIN_X = adaptive? BOUNDARY_MARGIN : graphZoom > 1 ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; - let BOUNDARY_MARGIN_Y = adaptive? BOUNDARY_MARGIN: graphZoom > 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; + // xTranslation > 0 -> moved to the left? wo right boundary hidden, left is too short + let BOUNDARY_MARGIN_X_LEFT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation <= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + let BOUNDARY_MARGIN_X_RIGHT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation >= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + let BOUNDARY_MARGIN_Y = adaptive? BOUNDARY_MARGIN: graphZoom >= 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; // let BOUNDARY_MARGIN_X = BOUNDARY_MARGIN // let BOUNDARY_MARGIN_Y = BOUNDARY_MARGIN var SELF_REFERRING_Y_OFFSET = 6; var MAX_WIDTH = 5000; var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; - console.log("xboundary margin", BOUNDARY_MARGIN_X); + console.log("xboundary margin", BOUNDARY_MARGIN_X_LEFT, BOUNDARY_MARGIN_X_RIGHT); console.log("yboundary margin", BOUNDARY_MARGIN_Y); + console.log("xTranslation", xTranslation) if (!adaptive) { flexibleContainer = calcFlexiBox(); @@ -1562,16 +1567,13 @@ export var drawGraph = function (workbook) { var selfReferringEdgeWidth = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + 2 : 0); - // var rightBoundary = width - - // (d.textWidth + OFFSET_VALUE) - - // BOUNDARY_MARGIN_X - - // selfReferringEdgeWidth - // ; - var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X - selfReferringEdgeWidth; + // this creates too much whitespace, want it to be the BOUNDARY_MARGIN_X when can see right side of borerbox + + var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X_RIGHT - selfReferringEdgeWidth; // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentXPos = Math.max(BOUNDARY_MARGIN_X, Math.min(rightBoundary, d.x)); + var currentXPos = Math.max(BOUNDARY_MARGIN_X_LEFT, Math.min(rightBoundary, d.x)); if (adaptive && width < MAX_WIDTH && - (currentXPos === BOUNDARY_MARGIN_X || currentXPos === rightBoundary)) { + (currentXPos === BOUNDARY_MARGIN_X_LEFT || currentXPos === rightBoundary)) { if (!d3.select(this).classed("fixed")) { width += OFFSET_VALUE; boundingBoxContainer.attr("width", width); From 805fb8973257a2b3e116db812e4f97b65a123cd1 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 18 Mar 2024 01:04:47 -0700 Subject: [PATCH 081/150] Issue #1083. There was an issue where the box would exceed the bounding box, this was because returning a value and therefore exiting the function before validating entire perimeter of flexContainer. also did not need to take graphZoom into account for the function like I was doing before. I commented out clamping code for now --- web-client/public/js/graph.js | 32 +++++++++++++++----------------- 1 file changed, 15 insertions(+), 17 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 222193e8..c8f08928 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -369,10 +369,11 @@ export var drawGraph = function (workbook) { // This controls actual movement of slider if (adaptive || (!adaptive && flexRectInBounds(calcGraphZoom))) { - // don't really want to center anymore for zooming since don't care if see bounding box anymore + // TODO: don't really want to center anymore for zooming since don't care if see bounding box anymore // if don't center, then get issue of zooming into the box since not inside the width of the viewport if (!adaptive) { center(); + updateZoomContainerInfo(); centerXCoord = xTranslation } @@ -1495,25 +1496,21 @@ export var drawGraph = function (workbook) { // x left bound if (flexibleContainer.x < 0) { flexibleContainer.x = 0; - return false } // x right bound - if (!(flexibleContainer.width - flexibleContainer.x <= width * graphZoom)) { - flexibleContainer.width = (width - flexibleContainer.x) * graphZoom; - return false + if (flexibleContainer.width > width - flexibleContainer.x) { + flexibleContainer.width = width - flexibleContainer.x; } // y top bound if (flexibleContainer.y < 0) { flexibleContainer.y = 0; - return false } // y bottom bound - if (!(flexibleContainer.height - flexibleContainer.y <= height * graphZoom)) { - flexibleContainer.height = (height - flexibleContainer.y) * graphZoom; - return false + if (flexibleContainer.height > height - flexibleContainer.y) { + flexibleContainer.height = height - flexibleContainer.y; } } } @@ -1532,15 +1529,14 @@ export var drawGraph = function (workbook) { return edge ? 17 + (getEdgeThickness(edge) / 2) : 0; }; - - let BOUNDARY_MARGIN = 5; // xTranslation > 0 -> moved to the left? wo right boundary hidden, left is too short - let BOUNDARY_MARGIN_X_LEFT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation <= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; - let BOUNDARY_MARGIN_X_RIGHT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation >= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; - let BOUNDARY_MARGIN_Y = adaptive? BOUNDARY_MARGIN: graphZoom >= 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; - // let BOUNDARY_MARGIN_X = BOUNDARY_MARGIN - // let BOUNDARY_MARGIN_Y = BOUNDARY_MARGIN + // let BOUNDARY_MARGIN_X_LEFT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation <= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + // let BOUNDARY_MARGIN_X_RIGHT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation >= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + // let BOUNDARY_MARGIN_Y = adaptive? BOUNDARY_MARGIN: graphZoom >= 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; + let BOUNDARY_MARGIN_X_LEFT = BOUNDARY_MARGIN + let BOUNDARY_MARGIN_X_RIGHT = BOUNDARY_MARGIN + let BOUNDARY_MARGIN_Y = BOUNDARY_MARGIN var SELF_REFERRING_Y_OFFSET = 6; var MAX_WIDTH = 5000; var MAX_HEIGHT = 5000; @@ -1568,7 +1564,9 @@ export var drawGraph = function (workbook) { var selfReferringEdgeWidth = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + 2 : 0); // this creates too much whitespace, want it to be the BOUNDARY_MARGIN_X when can see right side of borerbox - + // a stack overflow link to look at: https://stackoverflow.com/questions/26781129/d3-v2-prevent-zooming-and-panning-chart-outside-viewport + // could also look at this: https://observablehq.com/@john-guerra/force-directed-adjusted + // and look at this too: https://www.w3.org/TR/SVG/coords.html var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X_RIGHT - selfReferringEdgeWidth; // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentXPos = Math.max(BOUNDARY_MARGIN_X_LEFT, Math.min(rightBoundary, d.x)); From 7c1ff3d3c1a0d85bdf8529b6db9641bc56b8fb66 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 18 Mar 2024 02:52:33 -0700 Subject: [PATCH 082/150] experiencing issue with exportBoundsMoveDrag, cannot correctly detect edges of graph anymore, move through edges of graph --- web-client/public/js/graph.js | 89 ++++++++++++++++++++--------------- 1 file changed, 52 insertions(+), 37 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index c8f08928..6afb09a6 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -176,12 +176,18 @@ export var drawGraph = function (workbook) { scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } - if (adaptive || (!adaptive && flexRectInBounds(graphZoom) && inBounds(graphZoom, d3.event.dx, d3.event.dy))) { - zoom.translateBy( - zoomContainer, - scale * (d3.event.x - zoomDragPrevX), - scale * (d3.event.y - zoomDragPrevY) - ); + // if (adaptive || (!adaptive && flexRectInBounds(graphZoom) && exportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy))) { + if ( + adaptive || + (!adaptive && + flexRectInBounds(graphZoom) && + exportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy)) + ) { + zoom.translateBy( + zoomContainer, + scale * (d3.event.x - zoomDragPrevX), + scale * (d3.event.y - zoomDragPrevY) + ); } zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; @@ -266,55 +272,63 @@ export var drawGraph = function (workbook) { .split("(")[1].split(",")[1].split(")")[0]); }; - function inBounds(graphZoom, dx, dy) { + // TODO: issue with this, might also have to do with boundaries of graph and clamping + // does not allow flexbox to go outside of container when move or drag, have to incorporate into tick somehow? + function exportBoundsMoveDrag(graphZoom, dx, dy) { updateZoomContainerInfo(); - // console.log("dy", dy, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) - // console.log("dx", dx, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) - // console.log(Math.abs(xTranslation) < flexibleContainer.x, !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx)) + console.log("dx", dx, dx * graphZoom, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) + console.log("dy", dy, dy * graphZoom, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) // TODO: this handles left border, but the graph still goes through the left edge // console.log(!(Math.abs(xTranslation) < flexibleContainer.x), !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx)); - if (!(Math.abs(yTranslation) < flexibleContainer.y) && (Math.abs(yTranslation) * graphZoom - flexibleContainer.y > dy)) { - return false - } + + // if (!(Math.abs(yTranslation) < flexibleContainer.y) && (Math.abs(yTranslation) * graphZoom - flexibleContainer.y > dy * graphZoom)) { + // console.log("first statement false") + // return false + // } + if ( - ((dx < 0 || (xTranslation < 0 && Math.abs(xTranslation) > flexibleContainer.x)) && + ((dx * graphZoom < 0 || (xTranslation < 0 && Math.abs(xTranslation) > flexibleContainer.x)) && Math.abs(xTranslation) * graphZoom >= - Math.floor(flexibleContainer.x) + dx)) { + Math.floor(flexibleContainer.x) + dx * graphZoom)) { // BOUNDARY_MARGIN_X = graphZoom > 1 ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + console.log("second statement false") return false } - if (dx > 0 && + if (dx * graphZoom > 0 && (flexibleContainer.width + flexibleContainer.x + xTranslation + - dx >= + dx * graphZoom >= width / graphZoom)) { + console.log("third statement false") // BOUNDARY_MARGIN_X = width / graphZoom; return false } if ( - ((dy < 0 || yTranslation < 0) && (Math.abs(yTranslation) > flexibleContainer.y) && + ((dy * graphZoom < 0 || yTranslation < 0) && (Math.abs(yTranslation) > flexibleContainer.y) && Math.abs(yTranslation) * graphZoom >= - Math.floor(flexibleContainer.y) + dy)) + Math.floor(flexibleContainer.y) + dy * graphZoom)) { // console.log("yTranslation returned FALSE") // BOUNDARY_MARGIN_Y = graphZoom > 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; + console.log("fourth statement false") return false } if ( - dy > 0 && - flexibleContainer.height + flexibleContainer.y + yTranslation + dy >= + dy * graphZoom > 0 && + flexibleContainer.height + flexibleContainer.y + yTranslation + dy * graphZoom >= height / graphZoom ) { // BOUNDARY_MARGIN_Y = height / graphZoom; + console.log("fifth statement false") return false } - // console.log("flexContainer height and width in bounds"); + console.log("flexContainer height and width in bounds"); return true }; @@ -324,7 +338,7 @@ export var drawGraph = function (workbook) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); } var container = zoomContainer; - // graphZoom is used in inBounds(width, height) to check if graph in zoomContainer when restricted to viewport + // graphZoom is current zoom of graphZoom = zoomScale; if (adaptive || (!adaptive && flexRectInBounds(graphZoom))) { zoom.scaleTo(container, zoomScale); @@ -524,7 +538,7 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { - if (flexRectInBounds(graphZoom) && inBounds(graphZoom, moveWidth, moveHeight)) { + if (exportBoundsMoveDrag(graphZoom, moveWidth, moveHeight)) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } } @@ -1424,6 +1438,7 @@ export var drawGraph = function (workbook) { } }; + // there is too much whitespace in flexiContainer function calcFlexiBox () { const nodes = simulation.nodes() let nodeWidth = 0; @@ -1474,16 +1489,19 @@ export var drawGraph = function (workbook) { const maxX = Math.max(...xValues) + nodeWidth; const maxY = Math.max(...yValues) + nodeHeight; + // console.log("minX", minX, "minY", minY, "width", maxX - minX, "height", maxY - minY); return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } + // this checks if zoomInValue is in bounds when zoom in and out function flexRectInBounds(zoomValue) { if (flexibleContainer) { updateZoomContainerInfo(); - // validations for zoom and left/right cursor drag and D-pad movement if (flexibleContainer.width * zoomValue > width ) { + console.log("width out of bounds") return false; } else if (flexibleContainer.height * zoomValue > height) { + console.log("height out of bounds") return false; } } @@ -1491,26 +1509,24 @@ export var drawGraph = function (workbook) { } function flexRectLimitBounds() { - //prevent flexContainer from having bounds outside of bounding box + // limit flexContainer from exceeding bounding box + // TODO: add 5 so never hit edges exactly if (flexibleContainer) { // x left bound if (flexibleContainer.x < 0) { - flexibleContainer.x = 0; + flexibleContainer.x = 0 + 5; } - // x right bound if (flexibleContainer.width > width - flexibleContainer.x) { - flexibleContainer.width = width - flexibleContainer.x; + flexibleContainer.width = width - flexibleContainer.x - 5; } - // y top bound if (flexibleContainer.y < 0) { - flexibleContainer.y = 0; + flexibleContainer.y = 0 + 5; } - // y bottom bound if (flexibleContainer.height > height - flexibleContainer.y) { - flexibleContainer.height = height - flexibleContainer.y; + flexibleContainer.height = height - flexibleContainer.y - 5; } } } @@ -1532,7 +1548,9 @@ export var drawGraph = function (workbook) { let BOUNDARY_MARGIN = 5; // xTranslation > 0 -> moved to the left? wo right boundary hidden, left is too short // let BOUNDARY_MARGIN_X_LEFT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation <= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; - // let BOUNDARY_MARGIN_X_RIGHT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation >= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + // let BOUNDARY_MARGIN_X_LEFT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation <= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + + // let BOUNDARY_MARGIN_X_RIGHT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation >= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; // let BOUNDARY_MARGIN_Y = adaptive? BOUNDARY_MARGIN: graphZoom >= 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; let BOUNDARY_MARGIN_X_LEFT = BOUNDARY_MARGIN let BOUNDARY_MARGIN_X_RIGHT = BOUNDARY_MARGIN @@ -1541,9 +1559,6 @@ export var drawGraph = function (workbook) { var MAX_WIDTH = 5000; var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; - console.log("xboundary margin", BOUNDARY_MARGIN_X_LEFT, BOUNDARY_MARGIN_X_RIGHT); - console.log("yboundary margin", BOUNDARY_MARGIN_Y); - console.log("xTranslation", xTranslation) if (!adaptive) { flexibleContainer = calcFlexiBox(); From cfc3b4640e44811465ed22d5ff0594c9c9d33cba Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 18 Mar 2024 21:41:23 -0700 Subject: [PATCH 083/150] Now stay within top and bottom border when dragging in 100% view, but top and bottom border shifted up when move with d-pad --- web-client/public/js/graph.js | 98 ++++++++++++++++++----------------- 1 file changed, 51 insertions(+), 47 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 6afb09a6..72115860 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -181,7 +181,7 @@ export var drawGraph = function (workbook) { adaptive || (!adaptive && flexRectInBounds(graphZoom) && - exportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy)) + exportBoundsMoveDragY(graphZoom, d3.event.dx, d3.event.dy)) ) { zoom.translateBy( zoomContainer, @@ -274,61 +274,63 @@ export var drawGraph = function (workbook) { // TODO: issue with this, might also have to do with boundaries of graph and clamping // does not allow flexbox to go outside of container when move or drag, have to incorporate into tick somehow? - function exportBoundsMoveDrag(graphZoom, dx, dy) { + // NEED TO USE PREVIOUS POSITION + // let prevUpwardMoveViolated = false + // issue where if drag graph and then move with arrows, exceed bounds, has something to do with yTranslation since for some reason the old value is kept + // when use cursor, top and bottom bound are shifted up by same amount + function exportBoundsMoveDragY(graphZoom, dx, dy) { updateZoomContainerInfo(); - console.log("dx", dx, dx * graphZoom, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) + // console.log("dx", dx, dx * graphZoom, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) console.log("dy", dy, dy * graphZoom, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) + // if ( + // ((dx < 0 || xTranslation < 0) && + // Math.abs(xTranslation) * graphZoom >= + // Math.floor(flexibleContainer.x) + dx * graphZoom && + // !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx * graphZoom)) || + // (dx > 0 && + // flexibleContainer.width + flexibleContainer.x + xTranslation + dx * graphZoom >= + // width / graphZoom) + // ) { + // return false; + // } + // TODO: this handles left border, but the graph still goes through the left edge // console.log(!(Math.abs(xTranslation) < flexibleContainer.x), !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx)); - - // if (!(Math.abs(yTranslation) < flexibleContainer.y) && (Math.abs(yTranslation) * graphZoom - flexibleContainer.y > dy * graphZoom)) { - // console.log("first statement false") - // return false - // } - + // this allows to move up and down from bottom border, but goes through top border if ( - ((dx * graphZoom < 0 || (xTranslation < 0 && Math.abs(xTranslation) > flexibleContainer.x)) && - Math.abs(xTranslation) * graphZoom >= - Math.floor(flexibleContainer.x) + dx * graphZoom)) { - // BOUNDARY_MARGIN_X = graphZoom > 1 ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; - console.log("second statement false") - return false + dy < 0 && Math.abs(yTranslation) * graphZoom > + Math.floor(flexibleContainer.y) + dy * graphZoom + && + !( + Math.abs(yTranslation) * graphZoom - flexibleContainer.y > + dy * graphZoom + ) + ) { + return false; } - if (dx * graphZoom > 0 && - (flexibleContainer.width + - flexibleContainer.x + - xTranslation + - dx * graphZoom >= - width / graphZoom)) { - console.log("third statement false") - // BOUNDARY_MARGIN_X = width / graphZoom; - return false + if ((flexibleContainer.y <= 5 || + yTranslation < 0) && + Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) && + (dy < 0 || + (dy > 0 && + Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) + dy )) + ) { + return false; } - - if ( - ((dy * graphZoom < 0 || yTranslation < 0) && (Math.abs(yTranslation) > flexibleContainer.y) && - Math.abs(yTranslation) * graphZoom >= - Math.floor(flexibleContainer.y) + dy * graphZoom)) - { - // console.log("yTranslation returned FALSE") - // BOUNDARY_MARGIN_Y = graphZoom > 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; - console.log("fourth statement false") + + if (dy > 0 && + flexibleContainer.height + + flexibleContainer.y + + yTranslation + + dy * graphZoom >= + height / graphZoom) { + console.log("downward movement returning false") return false } - if ( - dy * graphZoom > 0 && - flexibleContainer.height + flexibleContainer.y + yTranslation + dy * graphZoom >= - height / graphZoom - ) { - // BOUNDARY_MARGIN_Y = height / graphZoom; - console.log("fifth statement false") - return false - } - console.log("flexContainer height and width in bounds"); return true }; @@ -538,8 +540,10 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { - if (exportBoundsMoveDrag(graphZoom, moveWidth, moveHeight)) { + if (exportBoundsMoveDragY(graphZoom, moveWidth, moveHeight)) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); + updateZoomContainerInfo(); + console.log("new yTranslation value", yTranslation) } } } @@ -1517,15 +1521,15 @@ export var drawGraph = function (workbook) { flexibleContainer.x = 0 + 5; } // x right bound - if (flexibleContainer.width > width - flexibleContainer.x) { - flexibleContainer.width = width - flexibleContainer.x - 5; + if (flexibleContainer.width > width - flexibleContainer.x - 5) { + flexibleContainer.width = width - flexibleContainer.x - 5; } // y top bound if (flexibleContainer.y < 0) { flexibleContainer.y = 0 + 5; } // y bottom bound - if (flexibleContainer.height > height - flexibleContainer.y) { + if (flexibleContainer.height > height - flexibleContainer.y - 5) { flexibleContainer.height = height - flexibleContainer.y - 5; } } From f958c6e5849073df1836ff0b94e71b575b6ec4f1 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 18 Mar 2024 21:51:22 -0700 Subject: [PATCH 084/150] handle d-pad movement on y-axis at 100% now --- web-client/public/js/graph.js | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 72115860..a7ecbb53 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -181,7 +181,7 @@ export var drawGraph = function (workbook) { adaptive || (!adaptive && flexRectInBounds(graphZoom) && - exportBoundsMoveDragY(graphZoom, d3.event.dx, d3.event.dy)) + exportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy, false)) ) { zoom.translateBy( zoomContainer, @@ -278,11 +278,10 @@ export var drawGraph = function (workbook) { // let prevUpwardMoveViolated = false // issue where if drag graph and then move with arrows, exceed bounds, has something to do with yTranslation since for some reason the old value is kept // when use cursor, top and bottom bound are shifted up by same amount - function exportBoundsMoveDragY(graphZoom, dx, dy) { + function exportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { updateZoomContainerInfo(); // console.log("dx", dx, dx * graphZoom, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) console.log("dy", dy, dy * graphZoom, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) - // if ( // ((dx < 0 || xTranslation < 0) && // Math.abs(xTranslation) * graphZoom >= @@ -320,6 +319,10 @@ export var drawGraph = function (workbook) { ) { return false; } + + if (dPadMove && yTranslation < 0 && dy < 0 && Math.abs(yTranslation + dy) > flexibleContainer.y) { + return false + } if (dy > 0 && flexibleContainer.height + @@ -540,7 +543,7 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { - if (exportBoundsMoveDragY(graphZoom, moveWidth, moveHeight)) { + if (exportBoundsMoveDrag(graphZoom, moveWidth, moveHeight, true)) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); updateZoomContainerInfo(); console.log("new yTranslation value", yTranslation) From b83e744e112f5618ab5a87f13b16348300ded94d Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 18 Mar 2024 21:59:02 -0700 Subject: [PATCH 085/150] can stay within x borders when drag or move at 100%, now going to work on other zoom levels --- web-client/public/js/graph.js | 63 +++++++++++++++++++++-------------- 1 file changed, 38 insertions(+), 25 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index a7ecbb53..85efe145 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -272,32 +272,45 @@ export var drawGraph = function (workbook) { .split("(")[1].split(",")[1].split(")")[0]); }; - // TODO: issue with this, might also have to do with boundaries of graph and clamping - // does not allow flexbox to go outside of container when move or drag, have to incorporate into tick somehow? - // NEED TO USE PREVIOUS POSITION - // let prevUpwardMoveViolated = false - // issue where if drag graph and then move with arrows, exceed bounds, has something to do with yTranslation since for some reason the old value is kept - // when use cursor, top and bottom bound are shifted up by same amount function exportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { updateZoomContainerInfo(); - // console.log("dx", dx, dx * graphZoom, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) - console.log("dy", dy, dy * graphZoom, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) - // if ( - // ((dx < 0 || xTranslation < 0) && - // Math.abs(xTranslation) * graphZoom >= - // Math.floor(flexibleContainer.x) + dx * graphZoom && - // !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx * graphZoom)) || - // (dx > 0 && - // flexibleContainer.width + flexibleContainer.x + xTranslation + dx * graphZoom >= - // width / graphZoom) - // ) { - // return false; - // } - - // TODO: this handles left border, but the graph still goes through the left edge - // console.log(!(Math.abs(xTranslation) < flexibleContainer.x), !(Math.abs(xTranslation) * graphZoom - flexibleContainer.x > dx)); - - // this allows to move up and down from bottom border, but goes through top border + console.log("dx", dx, dx * graphZoom, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) + // console.log("dy", dy, dy * graphZoom, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) + // TODO: take away hardcoded 5 and use BOUNDARY_MARGIN instead + if ( + (flexibleContainer.x <= 5 || xTranslation < 0) && + Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) && + (dx < 0 || + (dx > 0 && + Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) + dx)) + ) { + console.log("2nd x statement false") + return false; + } + + if ( + dPadMove && + xTranslation < 0 && + dx < 0 && + Math.abs(xTranslation + dx) > flexibleContainer.x + ) { + console.log("3rd x statement false") + return false; + } + + if ( + dx > 0 && + flexibleContainer.width + + flexibleContainer.x + + xTranslation + + dx * graphZoom >= + width / graphZoom + ) { + console.log("4th x statement false") + return false; + } + + // Y-axis boundaries if ( dy < 0 && Math.abs(yTranslation) * graphZoom > Math.floor(flexibleContainer.y) + dy * graphZoom @@ -310,6 +323,7 @@ export var drawGraph = function (workbook) { return false; } + // TODO: take away hardcoded 5 and use BOUNDARY_MARGIN instead if ((flexibleContainer.y <= 5 || yTranslation < 0) && Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) && @@ -330,7 +344,6 @@ export var drawGraph = function (workbook) { yTranslation + dy * graphZoom >= height / graphZoom) { - console.log("downward movement returning false") return false } From 5a064d8886b333599e6c25c09b5ea62f8529673b Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 18 Mar 2024 22:36:08 -0700 Subject: [PATCH 086/150] fixed issue of graph locking on left border when zoomed in --- web-client/public/js/graph.js | 62 +++++++++++++++++------------------ 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 85efe145..030e776e 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -176,12 +176,11 @@ export var drawGraph = function (workbook) { scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } - // if (adaptive || (!adaptive && flexRectInBounds(graphZoom) && exportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy))) { if ( adaptive || (!adaptive && flexRectInBounds(graphZoom) && - exportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy, false)) + viewportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy, false)) ) { zoom.translateBy( zoomContainer, @@ -272,47 +271,52 @@ export var drawGraph = function (workbook) { .split("(")[1].split(",")[1].split(")")[0]); }; - function exportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { + function viewportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { updateZoomContainerInfo(); - console.log("dx", dx, dx * graphZoom, "flexibleContainer.x", flexibleContainer.x, "xTranslation", xTranslation, "viewport width", width) + console.log("dx", dx, dx * graphZoom, "flexContainer.x", flexibleContainer.x, "flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "viewport width", width) // console.log("dy", dy, dy * graphZoom, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) - // TODO: take away hardcoded 5 and use BOUNDARY_MARGIN instead - if ( - (flexibleContainer.x <= 5 || xTranslation < 0) && - Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) && + // left border + if (xTranslation < 0 && + Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) * graphZoom && (dx < 0 || (dx > 0 && - Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) + dx)) + Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) * graphZoom + dx * graphZoom)) ) { - console.log("2nd x statement false") + console.log("1st x statement false") return false; } - + + //dPad movement when moving left if ( dPadMove && xTranslation < 0 && dx < 0 && - Math.abs(xTranslation + dx) > flexibleContainer.x + Math.abs(xTranslation + dx) > flexibleContainer.x * graphZoom ) { console.log("3rd x statement false") return false; } - if ( - dx > 0 && - flexibleContainer.width + - flexibleContainer.x + - xTranslation + - dx * graphZoom >= - width / graphZoom - ) { - console.log("4th x statement false") - return false; + // right border + if (graphZoom >= 1) { + if (dx > 0 && + flexibleContainer.width + + flexibleContainer.x + + xTranslation + + dx * graphZoom >= + width / graphZoom + ) { + console.log("4th x statement false") + return false; + } + } else { + } + // Y-axis boundaries - if ( - dy < 0 && Math.abs(yTranslation) * graphZoom > + // moving up, prevents from graph locking at bottom of viewport + if (dy < 0 && Math.abs(yTranslation) * graphZoom > Math.floor(flexibleContainer.y) + dy * graphZoom && !( @@ -323,9 +327,7 @@ export var drawGraph = function (workbook) { return false; } - // TODO: take away hardcoded 5 and use BOUNDARY_MARGIN instead - if ((flexibleContainer.y <= 5 || - yTranslation < 0) && + if (yTranslation < 0 && Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) && (dy < 0 || (dy > 0 && @@ -556,10 +558,8 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { - if (exportBoundsMoveDrag(graphZoom, moveWidth, moveHeight, true)) { + if (viewportBoundsMoveDrag(graphZoom, moveWidth, moveHeight, true)) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); - updateZoomContainerInfo(); - console.log("new yTranslation value", yTranslation) } } } @@ -1530,7 +1530,7 @@ export var drawGraph = function (workbook) { function flexRectLimitBounds() { // limit flexContainer from exceeding bounding box - // TODO: add 5 so never hit edges exactly + // TODO: add 5 so flexibleContainerRect stays within BOUNDARY_MARGIN, remove hardcoded value later if (flexibleContainer) { // x left bound if (flexibleContainer.x < 0) { From b78c7789af605acd8becf6eff3b04ab9682a8225 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 18 Mar 2024 22:48:37 -0700 Subject: [PATCH 087/150] temporary solution for maintaining right boundary --- web-client/public/js/graph.js | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 030e776e..7a571e6c 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -310,6 +310,18 @@ export var drawGraph = function (workbook) { return false; } } else { + // this is somewhat of a solution, still a white gap sometimes + if ( + dx > 0 && + (flexibleContainer.width + + flexibleContainer.x + + xTranslation + + dx * graphZoom) + flexibleContainer.x * graphZoom >= + width / graphZoom + ) { + console.log("4th x statement false"); + return false; + } } From 7d306be02ce817f52e4a9fc2b3a9ed4bb1eb3670 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 20 Mar 2024 19:05:24 -0700 Subject: [PATCH 088/150] =?UTF-8?q?Issue=20#1083.=20Worked=20with=20Dondi?= =?UTF-8?q?=20to=20understand=20the=20borders=20of=20viewport,=20so=20now?= =?UTF-8?q?=20stay=20within=20borders=20for=20all=20zoom=20values=20?= =?UTF-8?q?=F0=9F=98=84?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- web-client/public/js/graph.js | 62 ++++++++++------------------------- 1 file changed, 18 insertions(+), 44 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 7a571e6c..eee894ce 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -273,8 +273,6 @@ export var drawGraph = function (workbook) { function viewportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { updateZoomContainerInfo(); - console.log("dx", dx, dx * graphZoom, "flexContainer.x", flexibleContainer.x, "flexContainer.width", flexibleContainer.width, "xTranslation", xTranslation, "viewport width", width) - // console.log("dy", dy, dy * graphZoom, "flexibleContainer.y", flexibleContainer.y, "yTranslation", yTranslation, "viewport height", height) // left border if (xTranslation < 0 && Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) * graphZoom && @@ -298,36 +296,12 @@ export var drawGraph = function (workbook) { } // right border - if (graphZoom >= 1) { - if (dx > 0 && - flexibleContainer.width + - flexibleContainer.x + - xTranslation + - dx * graphZoom >= - width / graphZoom - ) { - console.log("4th x statement false") - return false; - } - } else { - // this is somewhat of a solution, still a white gap sometimes - if ( - dx > 0 && - (flexibleContainer.width + - flexibleContainer.x + - xTranslation + - dx * graphZoom) + flexibleContainer.x * graphZoom >= - width / graphZoom - ) { - console.log("4th x statement false"); - return false; - } - + if (xTranslation + dx > width - (graphZoom * flexibleContainer.width + graphZoom * flexibleContainer.x)) { + return false } - // Y-axis boundaries - // moving up, prevents from graph locking at bottom of viewport + // when moving graph up, prevents from graph from locking at bottom of viewport if (dy < 0 && Math.abs(yTranslation) * graphZoom > Math.floor(flexibleContainer.y) + dy * graphZoom && @@ -336,31 +310,33 @@ export var drawGraph = function (workbook) { dy * graphZoom ) ) { - return false; + console.log("first y statement false") + return false; } + // prevents graph from going through top border if (yTranslation < 0 && - Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) && + Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) * graphZoom && (dy < 0 || (dy > 0 && - Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) + dy )) + Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) + dy * graphZoom)) ) { - return false; + console.log("second y statement false") + return false; } + // moving up with dPad if (dPadMove && yTranslation < 0 && dy < 0 && Math.abs(yTranslation + dy) > flexibleContainer.y) { + console.log("third y statement false") return false } - if (dy > 0 && - flexibleContainer.height + - flexibleContainer.y + - yTranslation + - dy * graphZoom >= - height / graphZoom) { + // bottom border + if (yTranslation + dy > height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { + console.log("hard coded y statement retuning false") return false } - + return true }; @@ -370,10 +346,9 @@ export var drawGraph = function (workbook) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); } var container = zoomContainer; - // graphZoom is current zoom of - graphZoom = zoomScale; if (adaptive || (!adaptive && flexRectInBounds(graphZoom))) { zoom.scaleTo(container, zoomScale); + graphZoom = zoomScale } }; @@ -383,7 +358,7 @@ export var drawGraph = function (workbook) { let zoomScaleSliderLeft; let zoomScaleSliderRight; let prevGrnstateZoomVal; - let centerXCoord; + // let centerXCoord; const updateAppBasedOnZoomValue = () => { let zoomDisplay; @@ -420,7 +395,6 @@ export var drawGraph = function (workbook) { if (!adaptive) { center(); updateZoomContainerInfo(); - centerXCoord = xTranslation } $(ZOOM_SLIDER).val( From 7fd41b413d83081dfac6fc44a5b62e149e8df3f0 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 20 Mar 2024 19:26:10 -0700 Subject: [PATCH 089/150] fixed an x calculation, but sometimes graph goes through left border if move graph too fast --- web-client/public/js/graph.js | 23 ++++------------------- 1 file changed, 4 insertions(+), 19 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index eee894ce..c3c2d944 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -275,12 +275,10 @@ export var drawGraph = function (workbook) { updateZoomContainerInfo(); // left border if (xTranslation < 0 && - Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) * graphZoom && - (dx < 0 || - (dx > 0 && - Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) * graphZoom + dx * graphZoom)) - ) { - console.log("1st x statement false") + Math.abs(xTranslation) >= + Math.floor(flexibleContainer.x) * graphZoom + dx * graphZoom) + { + console.log("1st x statement false"); return false; } @@ -301,19 +299,6 @@ export var drawGraph = function (workbook) { } // Y-axis boundaries - // when moving graph up, prevents from graph from locking at bottom of viewport - if (dy < 0 && Math.abs(yTranslation) * graphZoom > - Math.floor(flexibleContainer.y) + dy * graphZoom - && - !( - Math.abs(yTranslation) * graphZoom - flexibleContainer.y > - dy * graphZoom - ) - ) { - console.log("first y statement false") - return false; - } - // prevents graph from going through top border if (yTranslation < 0 && Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) * graphZoom && From a63bca77a4c77ae875e26c0aad7c9866d0198596 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Thu, 21 Mar 2024 13:56:46 -0700 Subject: [PATCH 090/150] Adding files to update protein-protein-interaction database --- .../scripts/filter_genes.py | 133 ++++++++++++++++++ .../scripts/loader_update.py | 132 +++++++++++++++++ 2 files changed, 265 insertions(+) create mode 100644 database/protein-protein-database/scripts/filter_genes.py create mode 100644 database/protein-protein-database/scripts/loader_update.py diff --git a/database/protein-protein-database/scripts/filter_genes.py b/database/protein-protein-database/scripts/filter_genes.py new file mode 100644 index 00000000..df717a93 --- /dev/null +++ b/database/protein-protein-database/scripts/filter_genes.py @@ -0,0 +1,133 @@ +import os +import csv +import psycopg2 +from sqlalchemy import create_engine +from sqlalchemy import text + +PROCESSED_GENES = "../script-results/processed-loader-files/gene.csv" +PROCESSED_PROTEIN = "../script-results/processed-loader-files/protein.csv" +MISSING_GENE_DESTINATION = '../script-results/processed-loader-files/missing-genes.csv' +UPDATE_GENE_DESTINATION = '../script-results/processed-loader-files/update-genes.csv' +MISSING_PROTEIN_DESTINATION = '../script-results/processed-loader-files/missing-proteins.csv' +UPDATE_PROTEIN_DESTINATION = '../script-results/processed-loader-files/update-proteins.csv' + +def get_all_genes_proteins(): + # Create envrionment variable for db url + db = create_engine(os.environ['DB_URL']) + + with db.connect() as connection: + result_set = connection.execute(text("SELECT * FROM protein_protein_interactions.gene")) + + genes_record = result_set.fetchall() + + db_genes = {} + for gene in genes_record: + print(gene) + # key = (gene_id, taxon_id) + key = (gene[0], gene[3]) + # values = (display_gene_id, species) + value = (gene[1], gene[2]) + db_genes[key] = value + + # Collect proteins + result_set = connection.execute(text("SELECT * FROM protein_protein_interactions.protein")) + proteins_record = result_set.fetchall() + + db_proteins = {} + for protein in proteins_record: + # Key = (gene_systematic_name, taxon_id) + key = (protein[1], protein[5]) + # value = (standard_name, length, molecular_weight, PI) + value = (protein[0], protein[2], protein[3], protein[4]) + db_proteins[key] = value + + return db_genes, db_proteins + +db_genes, db_proteins = get_all_genes_proteins() # Format [(display_gene_id, gene_id), ...] and [(gene_systematic_name, ), ...] + +print("Genes", db_genes) +print("Protein", db_proteins) + +genes_to_update = {} +missing_genes = {} + +print(f'Processing file {PROCESSED_GENES}') +with open(PROCESSED_GENES, 'r+', encoding="UTF-8") as f: + i = 0 + reader = csv.reader(f) + for row in reader: + if i != 0: + row = row[0].split('\t') + gene_id = row[0] + display_gene_id = row[1] + species = row[2] + taxon_id = row[3] + key = (gene_id, taxon_id) + value = (display_gene_id, species) + if key not in db_genes: + missing_genes[key] = value + print(f'Gene {display_gene_id} not found in the database') + elif db_genes[key] != value: + print("db_genes[key]", db_genes[key]) + print("value", value) + # the value is not the same, let's update + genes_to_update[key] = value + i+=1 + +print(f'Creating missing-genes.csv\n') +gene_file = open(MISSING_GENE_DESTINATION, 'w') +headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' +gene_file.write(f'{headers}\n') +for gene in missing_genes: + gene_file.write(f'{gene[0]}\t{missing_genes[gene][0]}\t{missing_genes[gene][1]}\t{gene[1]}\n') +gene_file.close() + +print(f'Creating update-genes.csv\n') +gene_file = open(UPDATE_GENE_DESTINATION, 'w') +headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' +gene_file.write(f'{headers}\n') +for gene in genes_to_update: + gene_file.write(f'{gene[0]}\t{genes_to_update[gene][0]}\t{genes_to_update[gene][1]}\t{gene[1]}\n') +gene_file.close() + +missing_proteins = {} +proteins_to_update = {} + +print(f"Processing file {PROCESSED_PROTEIN}") +with open(PROCESSED_PROTEIN, 'r+', encoding="UTF-8") as f: + i = 0 + reader = csv.reader(f) + for row in reader: + if i != 0: + row = row[0].split('\t') + standard_name = row[0] + gene_systematic_name = row[1] + length = float(row[2]) if row[2] != "None" else 0 + molecular_weight = float(row[3]) if row[3] != "None" else 0 + pi = float(row[4]) if row[4] != "None" else 0 + taxon_id = row[5] + key = (gene_systematic_name, taxon_id) + value = (standard_name, length, molecular_weight, pi) + if key not in db_proteins: + missing_proteins[key] = value + elif db_proteins[key] != value: + print("Protein", db_proteins[key]) + print("Value", value) + proteins_to_update[key] = value + i+=1 + +print(f'Creating missing-proteins.csv\n') +protein_file = open(MISSING_PROTEIN_DESTINATION, 'w') +headers = f'Standard Name\tGene Systematic Name\tLength\t Molecular Weight\tPI\tTaxon ID' +protein_file.write(f'{headers}\n') +for protein in missing_proteins: + protein_file.write(f'{missing_proteins[protein][0]}\t{[protein][0]}\t{missing_proteins[protein][1]}\t{missing_proteins[protein][2]}\t{missing_proteins[protein][3]}\t{protein[1]}\n') +protein_file.close() + +print(f'Creating update-proteins.csv\n') +protein_file = open(UPDATE_PROTEIN_DESTINATION, 'w') +headers = f'Standard Name\tGene Systematic Name\tLength\t Molecular Weight\tPI\tTaxon ID' +protein_file.write(f'{headers}\n') +for protein in proteins_to_update: + protein_file.write(f'{proteins_to_update[protein][0]}\t{[protein][0]}\t{proteins_to_update[protein][1]}\t{proteins_to_update[protein][2]}\t{proteins_to_update[protein][3]}\t{protein[1]}\n') +protein_file.close() \ No newline at end of file diff --git a/database/protein-protein-database/scripts/loader_update.py b/database/protein-protein-database/scripts/loader_update.py new file mode 100644 index 00000000..5630da56 --- /dev/null +++ b/database/protein-protein-database/scripts/loader_update.py @@ -0,0 +1,132 @@ +import csv + +""" +This function Loads Protein Protein Interactions Data Sources into the database +""" + +MISSING_GENE_DESTINATION = '../script-results/processed-loader-files/missing-genes.csv' +UPDATE_GENE_DESTINATION = '../script-results/processed-loader-files/update-genes.csv' +MISSING_PROTEIN_DESTINATION = '../script-results/processed-loader-files/missing-proteins.csv' +UPDATE_PROTEIN_DESTINATION = '../script-results/processed-loader-files/update-proteins.csv' +def LOAD_SOURCES(): + print('COPY protein_protein_interactions.source (time_stamp, source, display_name) FROM stdin;') + NETWORK_DATA_SOURCE = '../script-results/processed-loader-files/source.csv' + with open(NETWORK_DATA_SOURCE, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + time_stamp = r[0] + source = r[1] + display_name = r[2] + print(f'{time_stamp}\t{source}\t{display_name}') + row_num += 1 + print('\\.') + +""" +This function Loads Gene ID Mapping into the database +""" +def LOAD_GENES(): + print('COPY protein_protein_interactions.gene (gene_id, display_gene_id, species, taxon_id) FROM stdin;') + with open(MISSING_GENE_DESTINATION, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + gene_id = r[0] + display_gene_id= r[1] + species = r[2] + taxon_id = r[3] + print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}') + row_num += 1 + print('\\.') + +""" +This Updates to Gene ID Mapping into the database +""" +def UPDATE_GENES(): + print('BEGIN;') + with open(UPDATE_GENE_DESTINATION, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + gene_id = r[0] + display_gene_id= r[1] + print(f"UPDATE protein_protein_interactions.gene\nSET display_gene_id = '{display_gene_id}'\nWHERE gene_id = '{gene_id}';") + row_num += 1 + print('COMMIT;') + +""" +This function Loads Gene ID Mapping into the database +""" +def LOAD_PROTEINS(): + print('COPY protein_protein_interactions.protein (standard_name, gene_systematic_name, length, molecular_weight, PI, taxon_id) FROM stdin;') + with open(MISSING_PROTEIN_DESTINATION, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + taxon_id =559292 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + standard_name = r[0] + gene_name= r[1] + length = r[2] if r[2] != "None" else 0 + molecular_weight = r[3] if r[3] != "None" else 0 + pi = r[4] if r[4] != "None" else 0 + taxon_id = r[5] + print(f'{standard_name}\t{gene_name}\t{length}\t{molecular_weight}\t{pi}\t{taxon_id}') + row_num += 1 + print('\\.') + +""" +This Updates to Protein ID Mapping into the database +""" +def UPDATE_PROTEINS(): + print('BEGIN;') + with open(UPDATE_PROTEIN_DESTINATION, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + standard_name = r[0] + gene_name= r[1] + length = r[2] if r[2] != "None" else 0 + molecular_weight = r[3] if r[3] != "None" else 0 + pi = r[4] if r[4] != "None" else 0 + print(f"UPDATE protein_protein_interactions.gene\nSET standard_name = '{standard_name}', length = {length}, molecular_weight = {molecular_weight}, PI = {pi}\nWHERE gene_systematic_name = '{gene_name}';") + row_num += 1 + print('COMMIT;') + +""" +This function Loads the Network Matrix of physical interactions into the database +""" +def LOAD_PHYSICAL_INTERACTIONS(): + print('COPY protein_protein_interactions.physical_interactions (protein1, protein2, interaction_detection_methods_identifier, experiment_name, time_stamp, source) FROM stdin;') + NETWORK_SOURCE = '../script-results/processed-loader-files/physical_interaction_no_dupe.csv' + with open(NETWORK_SOURCE, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + protein1 = r[0] + protein2= r[1] + idmi = r[2] + exp_name = r[3] + timestamp = r[4] + source = r[5] + print(f'{protein1}\t{protein2}\t{idmi}\t{exp_name}\t{timestamp}\t{source}') + row_num += 1 + print('\\.') + +# LOAD_SOURCES() +UPDATE_GENES() +UPDATE_PROTEINS() +LOAD_GENES() +LOAD_PROTEINS() +# LOAD_PHYSICAL_INTERACTIONS() \ No newline at end of file From 045100830a6361b06e99d8adcd43658e0638c6d9 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Thu, 21 Mar 2024 20:20:47 -0700 Subject: [PATCH 091/150] Create a Utils class in utils file to handle loading data to database for network-database and protein-protein-database --- .../network-database/scripts/constants.py | 7 + .../scripts/generate_new_network_version.py | 2 +- database/network-database/scripts/loader.py | 28 ++-- .../scripts/loader_updates.py | 105 ++----------- .../scripts/constants.py | 12 ++ .../scripts/filter_genes.py | 30 ++-- .../scripts/loader.py | 102 +------------ .../scripts/loader_update.py | 141 ++---------------- 8 files changed, 76 insertions(+), 351 deletions(-) create mode 100644 database/network-database/scripts/constants.py create mode 100644 database/protein-protein-database/scripts/constants.py diff --git a/database/network-database/scripts/constants.py b/database/network-database/scripts/constants.py new file mode 100644 index 00000000..2f856fee --- /dev/null +++ b/database/network-database/scripts/constants.py @@ -0,0 +1,7 @@ +class Constants: + NETWORK_DATA_SOURCE = 'network-database/script-results/processed-loader-files/source.csv' + DATABASE_NAMESPACE = "gene_regulatory_network_testing" + NETWORK_SOURCE = 'network-database/script-results/processed-loader-files/network.csv' + GENE_SOURCE = 'network-database/script-results/processed-loader-files/gene.csv' + GENE_UPDATE_DESTINATION = 'network-database/script-results/processed-loader-files/gene_update.csv' + \ No newline at end of file diff --git a/database/network-database/scripts/generate_new_network_version.py b/database/network-database/scripts/generate_new_network_version.py index fcd5487c..4bf1702b 100644 --- a/database/network-database/scripts/generate_new_network_version.py +++ b/database/network-database/scripts/generate_new_network_version.py @@ -17,7 +17,7 @@ def get_all_genes(): with db.connect() as connection: result_set = connection.execute( f""" - SELECT display_gene_id, gene_id FROM gene_regulatory_network.gene; + SELECT display_gene_id, gene_id FROM gene_regulatory_network.gene """) result = result_set.fetchall() return list(result) diff --git a/database/network-database/scripts/loader.py b/database/network-database/scripts/loader.py index 932352ef..7996f877 100644 --- a/database/network-database/scripts/loader.py +++ b/database/network-database/scripts/loader.py @@ -1,5 +1,10 @@ import csv import re +import sys + +sys.path.insert(1, '../database') +from constants import * +from utils import * # Usage # python3 loader.py | psql postgresql://localhost/postgres """ @@ -11,13 +16,13 @@ directly into a database command line utility such as `psql`. """ -""" +"""x This function Loads Network Data Sources into the database """ -def LOAD_SOURCES(): +def load_sources(): print('COPY gene_regulatory_network.source (time_stamp, source, display_name) FROM stdin;') - NETWORK_DATA_SOURCE = '../script-results/processed-loader-files/source.csv' - with open(NETWORK_DATA_SOURCE, 'r+') as f: + # NETWORK_DATA_SOURCE = '../script-results/processed-loader-files/source.csv' + with open(Constants.NETWORK_DATA_SOURCE, 'r+') as f: reader = csv.reader(f) row_num = 0 for row in reader: @@ -34,7 +39,7 @@ def LOAD_SOURCES(): """ This function Loads Gene ID Mapping into the database """ -def LOAD_GENES(): +def load_genes(): print('COPY gene_regulatory_network.gene (gene_id, display_gene_id, species, taxon_id, regulator) FROM stdin;') GENE_SOURCE = '../script-results/processed-loader-files/gene.csv' with open(GENE_SOURCE, 'r+') as f: @@ -56,7 +61,7 @@ def LOAD_GENES(): """ This function Loads the Network Matrix into the database """ -def LOAD_NETWORK(): +def load_network(): print('COPY gene_regulatory_network.network (regulator_gene_id, target_gene_id, taxon_id, time_stamp, source) FROM stdin;') NETWORK_SOURCE = '../script-results/processed-loader-files/network.csv' with open(NETWORK_SOURCE, 'r+') as f: @@ -74,6 +79,11 @@ def LOAD_NETWORK(): row_num += 1 print('\\.') -LOAD_SOURCES() -LOAD_GENES() -LOAD_NETWORK() +# load_sources() +Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) + +# load_genes() +Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, False) + +# load_network() +Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, False) diff --git a/database/network-database/scripts/loader_updates.py b/database/network-database/scripts/loader_updates.py index 7d25fa00..c31b79e9 100644 --- a/database/network-database/scripts/loader_updates.py +++ b/database/network-database/scripts/loader_updates.py @@ -1,99 +1,12 @@ -import csv -import re +import sys +sys.path.insert(1, '../database') +from constants import * +from utils import * + # Usage # python3 loader.py | psql postgresql://localhost/postgres -""" -This program generates direct SQL statements from the source files in order -to populate a relational database with those files’ data. - -By taking the approach of emitting SQL statements directly, we bypass the need to import -some kind of database library for the loading process, instead passing the statements -directly into a database command line utility such as `psql`. -""" - -""" -This function Loads Network Data Sources into the database -""" -def LOAD_SOURCES(): - print('COPY gene_regulatory_network.source (time_stamp, source, display_name) FROM stdin;') - NETWORK_DATA_SOURCE = '../script-results/processed-loader-files/source.csv' - with open(NETWORK_DATA_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - time_stamp = r[0] - source = r[1] - display_name = r[2] - print(f'{time_stamp}\t{source}\t{display_name}') - row_num += 1 - print('\\.') - - -""" -This function Loads Gene ID Mapping into the database -""" -def LOAD_GENES(): - print('COPY gene_regulatory_network.gene (gene_id, display_gene_id, species, taxon_id, regulator) FROM stdin;') - GENE_SOURCE = '../script-results/processed-loader-files/gene.csv' - with open(GENE_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - gene_id = r[0] - display_gene_id= r[1] - species = r[2] - taxon_id = r[3] - regulator = r[4] - print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}\t{regulator}') - row_num += 1 - print('\\.') - -""" -This Updates to Gene ID Mapping into the database -""" -def UPDATE_GENES(): - print('BEGIN;') - GENE_SOURCE = '../script-results/processed-loader-files/gene_update.csv' - with open(GENE_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - gene_id = r[0] - display_gene_id= r[1] - regulator = r[2] - print(f"UPDATE gene_regulatory_network.gene\nSET display_gene_id = '{display_gene_id}', regulator={regulator}\nWHERE gene_id = '{gene_id}';") - row_num += 1 - print('COMMIT;') - -""" -This function Loads the Network Matrix into the database -""" -def LOAD_NETWORK(): - print('COPY gene_regulatory_network.network (regulator_gene_id, target_gene_id, taxon_id, time_stamp, source) FROM stdin;') - NETWORK_SOURCE = '../script-results/processed-loader-files/network.csv' - with open(NETWORK_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - regulator_gene_id = r[0] - target_gene_id= r[1] - taxon_id = r[2] - time_stamp = r[3] - source = r[4] - print(f'{regulator_gene_id}\t{target_gene_id}\t{taxon_id}\t{time_stamp}\t{source}') - row_num += 1 - print('\\.') - -UPDATE_GENES() -LOAD_SOURCES() -LOAD_GENES() -LOAD_NETWORK() +Utils.update_genes(Constants.GENE_UPDATE_DESTINATION, Constants.DATABASE_NAMESPACE, False) +Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) +Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, False) +Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, False) diff --git a/database/protein-protein-database/scripts/constants.py b/database/protein-protein-database/scripts/constants.py new file mode 100644 index 00000000..b38d47e9 --- /dev/null +++ b/database/protein-protein-database/scripts/constants.py @@ -0,0 +1,12 @@ +class Constants: + PROCESSED_GENES = "protein-protein-database/script-results/processed-loader-files/gene.csv" + PROCESSED_PROTEIN = "protein-protein-database/script-results/processed-loader-files/protein.csv" + MISSING_GENE_DESTINATION = 'protein-protein-database/script-results/processed-loader-files/missing-genes.csv' + UPDATE_GENE_DESTINATION = 'protein-protein-database/script-results/processed-loader-files/update-genes.csv' + MISSING_PROTEIN_DESTINATION = 'protein-protein-database/script-results/processed-loader-files/missing-proteins.csv' + UPDATE_PROTEIN_DESTINATION = 'protein-protein-database/script-results/processed-loader-files/update-proteins.csv' + NETWORK_DATA_SOURCE = 'protein-protein-database/script-results/processed-loader-files/source.csv' + GENE_SOURCE = 'protein-protein-database/script-results/processed-loader-files/gene.csv' + PROTEIN_SOURCE = 'protein-protein-database/script-results/processed-loader-files/protein.csv' + NETWORK_SOURCE = 'protein-protein-database/script-results/processed-loader-files/physical_interaction_no_dupe.csv' + DATABASE_NAMESPACE = "protein_protein_interactions_testing" \ No newline at end of file diff --git a/database/protein-protein-database/scripts/filter_genes.py b/database/protein-protein-database/scripts/filter_genes.py index df717a93..efdd772b 100644 --- a/database/protein-protein-database/scripts/filter_genes.py +++ b/database/protein-protein-database/scripts/filter_genes.py @@ -3,20 +3,14 @@ import psycopg2 from sqlalchemy import create_engine from sqlalchemy import text - -PROCESSED_GENES = "../script-results/processed-loader-files/gene.csv" -PROCESSED_PROTEIN = "../script-results/processed-loader-files/protein.csv" -MISSING_GENE_DESTINATION = '../script-results/processed-loader-files/missing-genes.csv' -UPDATE_GENE_DESTINATION = '../script-results/processed-loader-files/update-genes.csv' -MISSING_PROTEIN_DESTINATION = '../script-results/processed-loader-files/missing-proteins.csv' -UPDATE_PROTEIN_DESTINATION = '../script-results/processed-loader-files/update-proteins.csv' +from constants import * def get_all_genes_proteins(): # Create envrionment variable for db url db = create_engine(os.environ['DB_URL']) with db.connect() as connection: - result_set = connection.execute(text("SELECT * FROM protein_protein_interactions.gene")) + result_set = connection.execute(text(f"SELECT * FROM {Constants.DATABASE_NAMESPACE}.gene")) genes_record = result_set.fetchall() @@ -30,7 +24,7 @@ def get_all_genes_proteins(): db_genes[key] = value # Collect proteins - result_set = connection.execute(text("SELECT * FROM protein_protein_interactions.protein")) + result_set = connection.execute(text(f"SELECT * FROM {Constants.DATABASE_NAMESPACE}.protein")) proteins_record = result_set.fetchall() db_proteins = {} @@ -51,8 +45,8 @@ def get_all_genes_proteins(): genes_to_update = {} missing_genes = {} -print(f'Processing file {PROCESSED_GENES}') -with open(PROCESSED_GENES, 'r+', encoding="UTF-8") as f: +print(f'Processing file {Constants.PROCESSED_GENES}') +with open(Constants.PROCESSED_GENES, 'r+', encoding="UTF-8") as f: i = 0 reader = csv.reader(f) for row in reader: @@ -68,14 +62,12 @@ def get_all_genes_proteins(): missing_genes[key] = value print(f'Gene {display_gene_id} not found in the database') elif db_genes[key] != value: - print("db_genes[key]", db_genes[key]) - print("value", value) # the value is not the same, let's update genes_to_update[key] = value i+=1 print(f'Creating missing-genes.csv\n') -gene_file = open(MISSING_GENE_DESTINATION, 'w') +gene_file = open(Constants.MISSING_GENE_DESTINATION, 'w') headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' gene_file.write(f'{headers}\n') for gene in missing_genes: @@ -83,7 +75,7 @@ def get_all_genes_proteins(): gene_file.close() print(f'Creating update-genes.csv\n') -gene_file = open(UPDATE_GENE_DESTINATION, 'w') +gene_file = open(Constants.UPDATE_GENE_DESTINATION, 'w') headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' gene_file.write(f'{headers}\n') for gene in genes_to_update: @@ -93,8 +85,8 @@ def get_all_genes_proteins(): missing_proteins = {} proteins_to_update = {} -print(f"Processing file {PROCESSED_PROTEIN}") -with open(PROCESSED_PROTEIN, 'r+', encoding="UTF-8") as f: +print(f"Processing file {Constants.PROCESSED_PROTEIN}") +with open(Constants.PROCESSED_PROTEIN, 'r+', encoding="UTF-8") as f: i = 0 reader = csv.reader(f) for row in reader: @@ -117,7 +109,7 @@ def get_all_genes_proteins(): i+=1 print(f'Creating missing-proteins.csv\n') -protein_file = open(MISSING_PROTEIN_DESTINATION, 'w') +protein_file = open(Constants.MISSING_PROTEIN_DESTINATION, 'w') headers = f'Standard Name\tGene Systematic Name\tLength\t Molecular Weight\tPI\tTaxon ID' protein_file.write(f'{headers}\n') for protein in missing_proteins: @@ -125,7 +117,7 @@ def get_all_genes_proteins(): protein_file.close() print(f'Creating update-proteins.csv\n') -protein_file = open(UPDATE_PROTEIN_DESTINATION, 'w') +protein_file = open(Constants.UPDATE_PROTEIN_DESTINATION, 'w') headers = f'Standard Name\tGene Systematic Name\tLength\t Molecular Weight\tPI\tTaxon ID' protein_file.write(f'{headers}\n') for protein in proteins_to_update: diff --git a/database/protein-protein-database/scripts/loader.py b/database/protein-protein-database/scripts/loader.py index 27abb95e..99c9f94f 100644 --- a/database/protein-protein-database/scripts/loader.py +++ b/database/protein-protein-database/scripts/loader.py @@ -1,6 +1,7 @@ import csv - +from constants import * +from utils import * # Usage # python3 loader.py | psql postgresql://localhost/postgres """ @@ -12,98 +13,7 @@ directly into a database command line utility such as `psql`. """ -""" -This function Loads Protein-Protein Network Data Sources into the database -""" -def LOAD_SOURCES(): - print('COPY protein_protein_interactions.source (time_stamp, source, display_name) FROM stdin;') - NETWORK_DATA_SOURCE = '../script-results/processed-loader-files/source.csv' - with open(NETWORK_DATA_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - time_stamp = r[0] - source = r[1] - display_name = r[2] - print(f'{time_stamp}\t{source}\t{display_name}') - row_num += 1 - print('\\.') - -""" -This function Loads Gene ID Mapping into the database -""" -def LOAD_GENES(): - print('COPY protein_protein_interactions.gene (gene_id, display_gene_id, species, taxon_id) FROM stdin;') - GENE_SOURCE = '../script-results/processed-loader-files/gene.csv' - with open(GENE_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - gene_id = r[0] - display_gene_id= r[1] - species = r[2] - taxon_id = r[3] - print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}') - row_num += 1 - print('\\.') - -""" -This function Loads Protein ID Mapping into the database -""" -def LOAD_PROTEINS(): - print('COPY protein_protein_interactions.protein (standard_name, gene_systematic_name, length, molecular_weight, PI, taxon_id) FROM stdin;') - PROTEIN_SOURCE = '../script-results/processed-loader-files/protein.csv' - with open(PROTEIN_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - taxon_id =559292 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - standard_name = r[0] - gene_name= r[1] - length = r[2] if r[2] != "None" else 0 - molecular_weight = r[3] if r[3] != "None" else 0 - pi = r[4] if r[4] != "None" else 0 - taxon_id = r[5] - print(f'{standard_name}\t{gene_name}\t{length}\t{molecular_weight}\t{pi}\t{taxon_id}') - row_num += 1 - print('\\.') - -""" -This function Loads the Network Matrix of physical interactions into the database -""" -def LOAD_PHYSICAL_INTERACTIONS(): - print('COPY protein_protein_interactions.physical_interactions (protein1, protein2, interaction_detection_methods_identifier, experiment_name, time_stamp, source) FROM stdin;') - NETWORK_SOURCE = '../script-results/processed-loader-files/physical_interaction_no_dupe.csv' - with open(NETWORK_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - protein1 = r[0] - protein2= r[1] - idmi = r[2] - exp_name = r[3] - timestamp = r[4] - source = r[5] - print(f'{protein1}\t{protein2}\t{idmi}\t{exp_name}\t{timestamp}\t{source}') - row_num += 1 - print('\\.') - -def TRUNCATE_TABLES(): - # Truncate tables to remove existing data - print('TRUNCATE TABLE protein_protein_interactions.physical_interactions, protein_protein_interactions.protein, protein_protein_interactions.gene, protein_protein_interactions;') - -# Call the TRUNCATE_TABLES function before loading data -TRUNCATE_TABLES() - -LOAD_SOURCES() -LOAD_GENES() -LOAD_PROTEINS() -LOAD_PHYSICAL_INTERACTIONS() \ No newline at end of file +Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) +Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, True) +Utils.load_proteins(Constants.PROTEIN_SOURCE, Constants.DATABASE_NAMESPACE) +Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, True) \ No newline at end of file diff --git a/database/protein-protein-database/scripts/loader_update.py b/database/protein-protein-database/scripts/loader_update.py index 5630da56..0b0556bb 100644 --- a/database/protein-protein-database/scripts/loader_update.py +++ b/database/protein-protein-database/scripts/loader_update.py @@ -1,132 +1,13 @@ import csv +from constants import * +import sys -""" -This function Loads Protein Protein Interactions Data Sources into the database -""" - -MISSING_GENE_DESTINATION = '../script-results/processed-loader-files/missing-genes.csv' -UPDATE_GENE_DESTINATION = '../script-results/processed-loader-files/update-genes.csv' -MISSING_PROTEIN_DESTINATION = '../script-results/processed-loader-files/missing-proteins.csv' -UPDATE_PROTEIN_DESTINATION = '../script-results/processed-loader-files/update-proteins.csv' -def LOAD_SOURCES(): - print('COPY protein_protein_interactions.source (time_stamp, source, display_name) FROM stdin;') - NETWORK_DATA_SOURCE = '../script-results/processed-loader-files/source.csv' - with open(NETWORK_DATA_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - time_stamp = r[0] - source = r[1] - display_name = r[2] - print(f'{time_stamp}\t{source}\t{display_name}') - row_num += 1 - print('\\.') - -""" -This function Loads Gene ID Mapping into the database -""" -def LOAD_GENES(): - print('COPY protein_protein_interactions.gene (gene_id, display_gene_id, species, taxon_id) FROM stdin;') - with open(MISSING_GENE_DESTINATION, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - gene_id = r[0] - display_gene_id= r[1] - species = r[2] - taxon_id = r[3] - print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}') - row_num += 1 - print('\\.') - -""" -This Updates to Gene ID Mapping into the database -""" -def UPDATE_GENES(): - print('BEGIN;') - with open(UPDATE_GENE_DESTINATION, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - gene_id = r[0] - display_gene_id= r[1] - print(f"UPDATE protein_protein_interactions.gene\nSET display_gene_id = '{display_gene_id}'\nWHERE gene_id = '{gene_id}';") - row_num += 1 - print('COMMIT;') - -""" -This function Loads Gene ID Mapping into the database -""" -def LOAD_PROTEINS(): - print('COPY protein_protein_interactions.protein (standard_name, gene_systematic_name, length, molecular_weight, PI, taxon_id) FROM stdin;') - with open(MISSING_PROTEIN_DESTINATION, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - taxon_id =559292 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - standard_name = r[0] - gene_name= r[1] - length = r[2] if r[2] != "None" else 0 - molecular_weight = r[3] if r[3] != "None" else 0 - pi = r[4] if r[4] != "None" else 0 - taxon_id = r[5] - print(f'{standard_name}\t{gene_name}\t{length}\t{molecular_weight}\t{pi}\t{taxon_id}') - row_num += 1 - print('\\.') - -""" -This Updates to Protein ID Mapping into the database -""" -def UPDATE_PROTEINS(): - print('BEGIN;') - with open(UPDATE_PROTEIN_DESTINATION, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - standard_name = r[0] - gene_name= r[1] - length = r[2] if r[2] != "None" else 0 - molecular_weight = r[3] if r[3] != "None" else 0 - pi = r[4] if r[4] != "None" else 0 - print(f"UPDATE protein_protein_interactions.gene\nSET standard_name = '{standard_name}', length = {length}, molecular_weight = {molecular_weight}, PI = {pi}\nWHERE gene_systematic_name = '{gene_name}';") - row_num += 1 - print('COMMIT;') - -""" -This function Loads the Network Matrix of physical interactions into the database -""" -def LOAD_PHYSICAL_INTERACTIONS(): - print('COPY protein_protein_interactions.physical_interactions (protein1, protein2, interaction_detection_methods_identifier, experiment_name, time_stamp, source) FROM stdin;') - NETWORK_SOURCE = '../script-results/processed-loader-files/physical_interaction_no_dupe.csv' - with open(NETWORK_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - protein1 = r[0] - protein2= r[1] - idmi = r[2] - exp_name = r[3] - timestamp = r[4] - source = r[5] - print(f'{protein1}\t{protein2}\t{idmi}\t{exp_name}\t{timestamp}\t{source}') - row_num += 1 - print('\\.') - -# LOAD_SOURCES() -UPDATE_GENES() -UPDATE_PROTEINS() -LOAD_GENES() -LOAD_PROTEINS() -# LOAD_PHYSICAL_INTERACTIONS() \ No newline at end of file +sys.path.insert(1, '../database') +from utils import * + +Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) +Utils.update_genes(Constants.UPDATE_GENE_DESTINATION, Constants.DATABASE_NAMESPACE, True) +Utils.update_proteins(Constants.UPDATE_PROTEIN_DESTINATION, Constants.DATABASE_NAMESPACE) +Utils.load_genes(Constants.MISSING_GENE_DESTINATION, Constants.DATABASE_NAMESPACE, True) +Utils.load_proteins(Constants.MISSING_PROTEIN_DESTINATION, Constants.DATABASE_NAMESPACE, True) +Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, True) \ No newline at end of file From 0aa4d4656ef302c7f7d62a9764b03930ca7513b5 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 26 Mar 2024 10:11:45 -0700 Subject: [PATCH 092/150] Adding utils file to the codebase --- database/utils.py | 224 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 224 insertions(+) create mode 100644 database/utils.py diff --git a/database/utils.py b/database/utils.py new file mode 100644 index 00000000..78c5252d --- /dev/null +++ b/database/utils.py @@ -0,0 +1,224 @@ +import csv +import os + +class Utils: + """ + A class to define utility functions. The class contains functions to load sources, + genes, proteins and network data into the database. These functions generate direct + SQL statements from the source files in order to populate a relational database with + those files’ data. + + By taking the approach of emitting SQL statements directly, we bypass the need to import + some kind of database library for the loading process, instead passing the statements + directly into a database command line utility such as `psql`. + + ... + Attributes + ---------- + + Methods + ---------- + load_sources(source_path: str, database_namespace: str) + Load Sources into the database + load_genes(gene_path: str, database_namespace: str, is_protein: bool) + Load Gene ID Mapping into the database + load_proteins(protein_path: str, database_namespace: str) + Load Protein ID Mapping into the database + load_network(network_source_path: str, database_namespace: str, is_protein: bool) + Load Network Matrix into the database + update_genes(update_gene_path: str, database_namespace: str, is_protein: bool) + Update Gene ID Mapping into the database + update_proteins(update_protein_path: str, database_namespace: str) + Update Protein ID Mapping into the database + """ + + @classmethod + def load_sources(cls, source_path: str, database_namespace: str): + """ + Load Sources (time_stamp, source, display_name) into the database using the COPY command + + Parameters + ---------- + source_path : str + The path to the file containing the sources that want to add to the database + database_namespace : str + The database namespace i.e the schema name where the sources will be loaded + """ + print(f'COPY {database_namespace}.source (time_stamp, source, display_name) FROM stdin;') + with open(source_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + time_stamp = r[0] + source = r[1] + display_name = r[2] + print(f'{time_stamp}\t{source}\t{display_name}') + row_num += 1 + print('\\.') + + @classmethod + def load_genes(cls, gene_path: str, database_namespace: str, is_protein: bool): + """ + Load Gene ID Mapping into the database using the COPY command + + Parameters + ---------- + gene_path : str + The path to the file containing the gene data that want to add to the database + database_namespace: str + The database namespace i.e the schema name where the gene data will be loaded + is_protein : bool + A boolean value to check if the schema is for protein_protein_interactions or gene_regulatory_network + """ + if is_protein: + print(f'COPY {database_namespace}.gene (gene_id, display_gene_id, species, taxon_id) FROM stdin;') + else: + print(f'COPY {database_namespace}.gene (gene_id, display_gene_id, species, taxon_id, regulator) FROM stdin;') + with open(gene_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + gene_id = r[0] + display_gene_id= r[1] + species = r[2] + taxon_id = r[3] + if not is_protein: + regulator = r[4] + print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}\t{regulator}') + else: + print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}') + row_num += 1 + print('\\.') + + @classmethod + def load_proteins(cls, protein_path: str, database_namespace: str): + """ + Load Protein ID Mapping into the database using the COPY command + + Parameters + ---------- + protein_path : str + The path to the file containing the protein data that want to add to the database + database_namespace : str + The database namespace i.e the schema name where the protein data will be loaded + """ + print(f'COPY {database_namespace}.protein (standard_name, gene_systematic_name, length, molecular_weight, PI, taxon_id) FROM stdin;') + with open(protein_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + standard_name = r[0] + gene_name= r[1] + length = r[2] if r[2] != "None" else 0 + molecular_weight = r[3] if r[3] != "None" else 0 + pi = r[4] if r[4] != "None" else 0 + taxon_id = r[5] + print(f'{standard_name}\t{gene_name}\t{length}\t{molecular_weight}\t{pi}\t{taxon_id}') + row_num += 1 + print('\\.') + + @classmethod + def load_network(cls, network_source_path: str, database_namespace: str, is_protein: bool): + """ + Load Network Matrix into the database using the COPY command + + Parameters + ---------- + network_source_path : str + The path to the file containing the network data that want to add to the database + database_namespace : str + The database namespace i.e the schema name where the network data will be loaded + is_protein : bool + A boolean value to check if the schema is for protein_protein_interactions or gene_regulatory_network + """ + if is_protein: + print(f'COPY {database_namespace}.physical_interactions (protein1, protein2, interaction_detection_methods_identifier, experiment_name, time_stamp, source) FROM stdin;'); + else: + print(f'COPY {database_namespace}.network (regulator_gene_id, target_gene_id, taxon_id, time_stamp, source) FROM stdin;') + with open(network_source_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + if is_protein: + protein1 = r[0] + protein2= r[1] + idmi = r[2] + exp_name = r[3] + timestamp = r[4] + source = r[5] + print(f'{protein1}\t{protein2}\t{idmi}\t{exp_name}\t{timestamp}\t{source}') + else: + regulator_gene_id = r[0] + target_gene_id= r[1] + taxon_id = r[2] + time_stamp = r[3] + source = r[4] + print(f'{regulator_gene_id}\t{target_gene_id}\t{taxon_id}\t{time_stamp}\t{source}') + row_num += 1 + print('\\.') + + @classmethod + def update_genes(cls, update_gene_path: str, database_namespace: str, is_protein: bool): + """ + Update Gene ID Mapping into the database + + Parameters + ---------- + update_gene_path : str + The path to the file containing the gene data that want to update in the database + database_namespace : str + The database namespace i.e the schema name where the gene data will be updated + is_protein : bool + A boolean value to check if the schema is for protein_protein_interactions or gene_regulatory_network + """ + print('BEGIN;') + with open(update_gene_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + gene_id = r[0] + display_gene_id= r[1] + if is_protein: + print(f"UPDATE {database_namespace}.gene\nSET display_gene_id = '{display_gene_id}'\nWHERE gene_id = '{gene_id}';") + else: + regulator = r[2] + print(f"UPDATE {database_namespace}.gene\nSET display_gene_id = '{display_gene_id}', regulator={regulator}\nWHERE gene_id = '{gene_id}';") + row_num += 1 + print('COMMIT;') + + @classmethod + def update_proteins(cls, update_protein_path: str, database_namespace: str): + """ + Update Protein ID Mapping into the database + + Args: + update_protein_path : str + The path to the file containing the protein data that want to update in the database + database_namespace : str + The database namespace i.e the schema name where the protein data will be updated + """ + print('BEGIN;') + with open(update_protein_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + standard_name = r[0] + gene_name= r[1] + length = r[2] if r[2] != "None" else 0 + molecular_weight = r[3] if r[3] != "None" else 0 + pi = r[4] if r[4] != "None" else 0 + print(f"UPDATE {database_namespace}.gene\nSET standard_name = '{standard_name}', length = {length}, molecular_weight = {molecular_weight}, PI = {pi}\nWHERE gene_systematic_name = '{gene_name}';") + row_num += 1 + print('COMMIT;') \ No newline at end of file From a0a761c67403804571bd65b6cd266a5e46c699a3 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Wed, 27 Mar 2024 10:46:48 -0700 Subject: [PATCH 093/150] Adding named parameter for any method have boolean parameter #1089 --- database/network-database/scripts/loader.py | 67 +------------------ .../scripts/loader_updates.py | 6 +- .../scripts/loader.py | 4 +- .../scripts/loader_update.py | 8 +-- 4 files changed, 11 insertions(+), 74 deletions(-) diff --git a/database/network-database/scripts/loader.py b/database/network-database/scripts/loader.py index 7996f877..346e0dee 100644 --- a/database/network-database/scripts/loader.py +++ b/database/network-database/scripts/loader.py @@ -16,74 +16,11 @@ directly into a database command line utility such as `psql`. """ -"""x -This function Loads Network Data Sources into the database -""" -def load_sources(): - print('COPY gene_regulatory_network.source (time_stamp, source, display_name) FROM stdin;') - # NETWORK_DATA_SOURCE = '../script-results/processed-loader-files/source.csv' - with open(Constants.NETWORK_DATA_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - time_stamp = r[0] - source = r[1] - display_name = r[2] - print(f'{time_stamp}\t{source}\t{display_name}') - row_num += 1 - print('\\.') - - -""" -This function Loads Gene ID Mapping into the database -""" -def load_genes(): - print('COPY gene_regulatory_network.gene (gene_id, display_gene_id, species, taxon_id, regulator) FROM stdin;') - GENE_SOURCE = '../script-results/processed-loader-files/gene.csv' - with open(GENE_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - gene_id = r[0] - display_gene_id= r[1] - species = r[2] - taxon_id = r[3] - regulator = r[4] - print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}\t{regulator}') - row_num += 1 - print('\\.') - - -""" -This function Loads the Network Matrix into the database -""" -def load_network(): - print('COPY gene_regulatory_network.network (regulator_gene_id, target_gene_id, taxon_id, time_stamp, source) FROM stdin;') - NETWORK_SOURCE = '../script-results/processed-loader-files/network.csv' - with open(NETWORK_SOURCE, 'r+') as f: - reader = csv.reader(f) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - regulator_gene_id = r[0] - target_gene_id= r[1] - taxon_id = r[2] - time_stamp = r[3] - source = r[4] - print(f'{regulator_gene_id}\t{target_gene_id}\t{taxon_id}\t{time_stamp}\t{source}') - row_num += 1 - print('\\.') - # load_sources() Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) # load_genes() -Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, False) +Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) # load_network() -Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, False) +Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) diff --git a/database/network-database/scripts/loader_updates.py b/database/network-database/scripts/loader_updates.py index c31b79e9..532c6583 100644 --- a/database/network-database/scripts/loader_updates.py +++ b/database/network-database/scripts/loader_updates.py @@ -6,7 +6,7 @@ # Usage # python3 loader.py | psql postgresql://localhost/postgres -Utils.update_genes(Constants.GENE_UPDATE_DESTINATION, Constants.DATABASE_NAMESPACE, False) +Utils.update_genes(Constants.GENE_UPDATE_DESTINATION, Constants.DATABASE_NAMESPACE, is_protein=False) Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, False) -Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, False) +Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) +Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) diff --git a/database/protein-protein-database/scripts/loader.py b/database/protein-protein-database/scripts/loader.py index 99c9f94f..05e04df6 100644 --- a/database/protein-protein-database/scripts/loader.py +++ b/database/protein-protein-database/scripts/loader.py @@ -14,6 +14,6 @@ """ Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, True) +Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE,is_protein=True) Utils.load_proteins(Constants.PROTEIN_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, True) \ No newline at end of file +Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE,is_protein=True) \ No newline at end of file diff --git a/database/protein-protein-database/scripts/loader_update.py b/database/protein-protein-database/scripts/loader_update.py index 0b0556bb..f0266419 100644 --- a/database/protein-protein-database/scripts/loader_update.py +++ b/database/protein-protein-database/scripts/loader_update.py @@ -6,8 +6,8 @@ from utils import * Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.update_genes(Constants.UPDATE_GENE_DESTINATION, Constants.DATABASE_NAMESPACE, True) +Utils.update_genes(Constants.UPDATE_GENE_DESTINATION, Constants.DATABASE_NAMESPACE, is_protein=True) Utils.update_proteins(Constants.UPDATE_PROTEIN_DESTINATION, Constants.DATABASE_NAMESPACE) -Utils.load_genes(Constants.MISSING_GENE_DESTINATION, Constants.DATABASE_NAMESPACE, True) -Utils.load_proteins(Constants.MISSING_PROTEIN_DESTINATION, Constants.DATABASE_NAMESPACE, True) -Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, True) \ No newline at end of file +Utils.load_genes(Constants.MISSING_GENE_DESTINATION, Constants.DATABASE_NAMESPACE, is_protein=True) +Utils.load_proteins(Constants.MISSING_PROTEIN_DESTINATION, Constants.DATABASE_NAMESPACE) +Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=True) \ No newline at end of file From 1d70ac4586d70fe60abc57d0e97cfc1cc6a4326b Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 30 Mar 2024 01:10:06 -0700 Subject: [PATCH 094/150] can now bound by the left boundary, still having trouble with the right. Also cleaned up some comments --- web-client/public/js/graph.js | 92 ++++++++++++++++++++++------------- 1 file changed, 59 insertions(+), 33 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index c3c2d944..c0106268 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -306,22 +306,19 @@ export var drawGraph = function (workbook) { (dy > 0 && Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) + dy * graphZoom)) ) { - console.log("second y statement false") return false; } // moving up with dPad if (dPadMove && yTranslation < 0 && dy < 0 && Math.abs(yTranslation + dy) > flexibleContainer.y) { - console.log("third y statement false") return false } // bottom border if (yTranslation + dy > height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { - console.log("hard coded y statement retuning false") return false } - + return true }; @@ -1467,7 +1464,6 @@ export var drawGraph = function (workbook) { } } }); - const xValuesNodes = nodes.map((node) => node.x); const yValuesNodes = nodes.map((node) => node.y); @@ -1489,7 +1485,7 @@ export var drawGraph = function (workbook) { if (flexibleContainer) { updateZoomContainerInfo(); if (flexibleContainer.width * zoomValue > width ) { - console.log("width out of bounds") + console.log("width out of bounds", flexibleContainer.x, flexibleContainer.y) return false; } else if (flexibleContainer.height * zoomValue > height) { console.log("height out of bounds") @@ -1499,27 +1495,34 @@ export var drawGraph = function (workbook) { return true } - function flexRectLimitBounds() { - // limit flexContainer from exceeding bounding box - // TODO: add 5 so flexibleContainerRect stays within BOUNDARY_MARGIN, remove hardcoded value later - if (flexibleContainer) { - // x left bound - if (flexibleContainer.x < 0) { - flexibleContainer.x = 0 + 5; - } - // x right bound - if (flexibleContainer.width > width - flexibleContainer.x - 5) { - flexibleContainer.width = width - flexibleContainer.x - 5; - } - // y top bound - if (flexibleContainer.y < 0) { - flexibleContainer.y = 0 + 5; - } - // y bottom bound - if (flexibleContainer.height > height - flexibleContainer.y - 5) { - flexibleContainer.height = height - flexibleContainer.y - 5; - } + function flexRectLimitBounds( + BOUNDARY_MARGIN_X_L, + BOUNDARY_MARGIN_X_R + ) { + // limit flexContainer from exceeding bounding box + // TODO: add 5 so flexibleContainerRect stays within BOUNDARY_MARGIN, remove hardcoded value later + if (flexibleContainer) { + // x left bound + if (flexibleContainer.x < 0) { + flexibleContainer.x = BOUNDARY_MARGIN_X_L; + } + // x right bound + if ( + flexibleContainer.width > + width - flexibleContainer.x - BOUNDARY_MARGIN_X_R + ) { + flexibleContainer.width = + width - flexibleContainer.x - BOUNDARY_MARGIN_X_R; + } + // y top bound + if (flexibleContainer.y < 0) { + flexibleContainer.y = 0 + 5; } + // y bottom bound + if (flexibleContainer.height > height - flexibleContainer.y - 5) { + flexibleContainer.height = height - flexibleContainer.y - 5; + } + } } // Tick only runs while the graph physics are still running. @@ -1542,9 +1545,31 @@ export var drawGraph = function (workbook) { // let BOUNDARY_MARGIN_X_LEFT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation <= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; // let BOUNDARY_MARGIN_X_RIGHT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation >= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; + // let BOUNDARY_MARGIN_Y = adaptive? BOUNDARY_MARGIN: graphZoom >= 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; - let BOUNDARY_MARGIN_X_LEFT = BOUNDARY_MARGIN - let BOUNDARY_MARGIN_X_RIGHT = BOUNDARY_MARGIN + // Left and right boundary margins: + let BOUNDARY_MARGIN_X_L = BOUNDARY_MARGIN; + let BOUNDARY_MARGIN_X_R = BOUNDARY_MARGIN; + if (!adaptive && flexibleContainer && graphZoom >= 1) { + + if ( + Math.abs(xTranslation) > + Math.floor(flexibleContainer.x) * graphZoom + ) { + BOUNDARY_MARGIN_X_L = Math.abs(xTranslation); + } + if ( + xTranslation > + $container.width() - + (graphZoom * flexibleContainer.width + + graphZoom * flexibleContainer.x) + ) { + console.log(flexibleContainer.x + flexibleContainer.width, xTranslation) + BOUNDARY_MARGIN_X_R = Math.abs(xTranslation); + } + } + // must be equal to the left border of exportContainer * graphZoom, right? + // export container - exportContainer * graphZoom and then take into account xTranslation for margin let BOUNDARY_MARGIN_Y = BOUNDARY_MARGIN var SELF_REFERRING_Y_OFFSET = 6; var MAX_WIDTH = 5000; @@ -1553,7 +1578,7 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(); - flexRectLimitBounds(); + flexRectLimitBounds(BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_X_L); flexibleContainerRect .attr("x", flexibleContainer.x) @@ -1561,6 +1586,7 @@ export var drawGraph = function (workbook) { .attr("width", flexibleContainer.width) .attr("height", flexibleContainer.height); } + // this controls movement and position of nodes, clamps the nodes to boundary try { @@ -1573,11 +1599,11 @@ export var drawGraph = function (workbook) { // a stack overflow link to look at: https://stackoverflow.com/questions/26781129/d3-v2-prevent-zooming-and-panning-chart-outside-viewport // could also look at this: https://observablehq.com/@john-guerra/force-directed-adjusted // and look at this too: https://www.w3.org/TR/SVG/coords.html - var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X_RIGHT - selfReferringEdgeWidth; + var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X_R - selfReferringEdgeWidth; // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentXPos = Math.max(BOUNDARY_MARGIN_X_LEFT, Math.min(rightBoundary, d.x)); - if (adaptive && width < MAX_WIDTH && - (currentXPos === BOUNDARY_MARGIN_X_LEFT || currentXPos === rightBoundary)) { + var currentXPos = Math.max(BOUNDARY_MARGIN_X_L, Math.min(rightBoundary, d.x)); + if (width < MAX_WIDTH && + (currentXPos === BOUNDARY_MARGIN_X_L || currentXPos === rightBoundary)) { if (!d3.select(this).classed("fixed")) { width += OFFSET_VALUE; boundingBoxContainer.attr("width", width); From ef0eccee0d45c53785155053e516bd6acd3cbd8b Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 30 Mar 2024 01:53:20 -0700 Subject: [PATCH 095/150] can now get nodes to stay in top border of graph, but edges exceed top of graph --- web-client/public/js/graph.js | 31 +++++++++++++++---------------- 1 file changed, 15 insertions(+), 16 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index c0106268..e572b311 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1540,22 +1540,17 @@ export var drawGraph = function (workbook) { }; let BOUNDARY_MARGIN = 5; - // xTranslation > 0 -> moved to the left? wo right boundary hidden, left is too short - // let BOUNDARY_MARGIN_X_LEFT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation <= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; - // let BOUNDARY_MARGIN_X_LEFT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation <= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; - - // let BOUNDARY_MARGIN_X_RIGHT = adaptive ? BOUNDARY_MARGIN : graphZoom >= 1 && xTranslation >= centerXCoord ? Math.abs(xTranslation) * graphZoom: BOUNDARY_MARGIN; - - // let BOUNDARY_MARGIN_Y = adaptive? BOUNDARY_MARGIN: graphZoom >= 1 ? Math.abs(yTranslation) * graphZoom: BOUNDARY_MARGIN; // Left and right boundary margins: let BOUNDARY_MARGIN_X_L = BOUNDARY_MARGIN; let BOUNDARY_MARGIN_X_R = BOUNDARY_MARGIN; + let BOUNDARY_MARGIN_Y = BOUNDARY_MARGIN; if (!adaptive && flexibleContainer && graphZoom >= 1) { if ( Math.abs(xTranslation) > Math.floor(flexibleContainer.x) * graphZoom ) { + // bouncing behavior because for some reason 15 pixels too far to the right BOUNDARY_MARGIN_X_L = Math.abs(xTranslation); } if ( @@ -1564,13 +1559,16 @@ export var drawGraph = function (workbook) { (graphZoom * flexibleContainer.width + graphZoom * flexibleContainer.x) ) { - console.log(flexibleContainer.x + flexibleContainer.width, xTranslation) BOUNDARY_MARGIN_X_R = Math.abs(xTranslation); + console.log("BOUNDARY_MARGIN_X_R", BOUNDARY_MARGIN_X_R, flexibleContainer.x + flexibleContainer.width) + } + if ( + Math.abs(yTranslation) > + Math.floor(flexibleContainer.y) * graphZoom + ) { + BOUNDARY_MARGIN_Y = Math.abs(yTranslation); } } - // must be equal to the left border of exportContainer * graphZoom, right? - // export container - exportContainer * graphZoom and then take into account xTranslation for margin - let BOUNDARY_MARGIN_Y = BOUNDARY_MARGIN var SELF_REFERRING_Y_OFFSET = 6; var MAX_WIDTH = 5000; var MAX_HEIGHT = 5000; @@ -1600,11 +1598,12 @@ export var drawGraph = function (workbook) { // could also look at this: https://observablehq.com/@john-guerra/force-directed-adjusted // and look at this too: https://www.w3.org/TR/SVG/coords.html var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X_R - selfReferringEdgeWidth; + console.log("rightBoundary", rightBoundary, width, d.textWidth, BOUNDARY_MARGIN_X_R, selfReferringEdgeWidth) // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentXPos = Math.max(BOUNDARY_MARGIN_X_L, Math.min(rightBoundary, d.x)); if (width < MAX_WIDTH && (currentXPos === BOUNDARY_MARGIN_X_L || currentXPos === rightBoundary)) { - if (!d3.select(this).classed("fixed")) { + // if (!d3.select(this).classed("fixed")) { width += OFFSET_VALUE; boundingBoxContainer.attr("width", width); @@ -1620,7 +1619,7 @@ export var drawGraph = function (workbook) { .attr("x", function (d) { return d.x; }); - } + // } } return d.x = currentXPos; }).attr("y", function (d) { @@ -1630,9 +1629,9 @@ export var drawGraph = function (workbook) { var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN_Y - selfReferringEdgeHeight; // currentYPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentYPos = Math.max(BOUNDARY_MARGIN_Y, Math.min(bottomBoundary, d.y)); - if (adaptive && height < MAX_HEIGHT && + if (height < MAX_HEIGHT && (currentYPos === BOUNDARY_MARGIN_Y || currentYPos === bottomBoundary)) { - if (!d3.select(this).classed("fixed")) { + // if (!d3.select(this).classed("fixed")) { height += OFFSET_VALUE; boundingBoxContainer.attr("height", height); link @@ -1646,7 +1645,7 @@ export var drawGraph = function (workbook) { node.attr("y", function (d) { return d.y; }); - } + // } } return d.y = currentYPos; }).attr("transform", function (d) { From 4bd948dcd228e1bf8f534ef26ab876068bc3ec68 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 30 Mar 2024 19:35:36 -0700 Subject: [PATCH 096/150] Issue #1081. Fixed styling of Node navbar menu so that consistent with the rest of the navbar when disabled. This required some custom css styling and selecting in the grnsight.styl file, and I had to reference the div #node-coloring-navbar-options in upload.pug --- web-client/public/stylesheets/grnsight.styl | 43 ++++++++++++++++----- web-client/views/upload.pug | 2 +- 2 files changed, 35 insertions(+), 10 deletions(-) diff --git a/web-client/public/stylesheets/grnsight.styl b/web-client/public/stylesheets/grnsight.styl index 94f51503..33afd7c2 100644 --- a/web-client/public/stylesheets/grnsight.styl +++ b/web-client/public/stylesheets/grnsight.styl @@ -163,8 +163,9 @@ nav.navbar.navbar-default font-size: 12px display: inline-block -.dropdown-menu > li > a:hover +.dropdown-menu > li > a:hover, .dropdown-menu > #node-coloring-navbar-options > li > a:hover background-color: #dfebe5 + text-decoration: none; #undoResetButton margin-top: 5px @@ -246,7 +247,7 @@ nav.navbar.navbar-default .dropdown-submenu position:relative -.dropdown-submenu>.dropdown-menu +.dropdown-submenu>.dropdown-menu, .dropdown-menu > #node-coloring-navbar-options dropdown-submenu top:0 left:100% margin-top:-6px @@ -255,10 +256,13 @@ nav.navbar.navbar-default -moz-border-radius:0 6px 6px 6px border-radius:0 6px 6px 6px -.dropdown-submenu:hover>.dropdown-menu, #node-coloring-navbar-options>.dropdown-submenu:hover>.dropdown-menu +.dropdown-submenu:hover>.dropdown-menu, #node-coloring-navbar-options .dropdown-submenu:hover>.dropdown-menu display:block -.dropdown-submenu>a:after, #node-coloring-navbar-options>.dropdown-submenu:hover>a:after +.dropdown-submenu:hover>.dropdown-menu, #node-coloring-navbar-options .disabled:hover>.dropdown-menu + display:none + +.dropdown-submenu>a:after display:block content:" " float:right @@ -271,25 +275,46 @@ nav.navbar.navbar-default margin-top:5px margin-right:-10px -.dropdown-submenu:hover>a:after, #node-coloring-navbar-options>.dropdown-submenu:hover>a:after +.dropdown-submenu:hover>a:after border-left-color:#ffffff -.dropdown-submenu.pull-left, #node-coloring-navbar-options>.dropdown-submenu.pull-left +#node-coloring-navbar-options>li>a + display: block; + padding: 3px 20px; + clear: both; + font-weight: 400; + line-height: 1.42857143; + color: #333; + white-space: nowrap; + +#node-coloring-navbar-options>.disabled>a, #node-coloring-navbar-options + color: #999; + cursor: not-allowed; + text-decoration: none; + aria-disabled: true; + +.dropdown-menu > #node-coloring-navbar-options > .disabled > a:hover + background-color: #FFFFFF; + +.dropdown-submenu.pull-left, #node-coloring-navbar-options .dropdown-submenu.pull-left float:none -.dropdown-submenu.pull-left>.dropdown-menu, #node-coloring-navbar-options>.dropdown-submenu.pull-left>.dropdown-menu +#node-coloring-navbar-options + cursor: pointer + +.dropdown-submenu.pull-left>.dropdown-menu, .dropdown-submenu.pull-left, .dropdown-menu #node-coloring-navbar-options .dropdown-submenu.pull-left left:-100% margin-left:10px -webkit-border-radius:6px 0 6px 6px -moz-border-radius:6px 0 6px 6px border-radius:6px 0 6px 6px -.dropdown a.with-input +.dropdown a.with-input, #node-coloring-navbar-options a.with-input display:flex align-items:center user-select:none -.dropdown a.with-input>*:last-child +.dropdown a.with-input>*:last-child, #node-coloring-navbar-options a.with-input > *:last-child margin-left:auto // Graph statistics styling is due to absolute position and size of grnsight-container diff --git a/web-client/views/upload.pug b/web-client/views/upload.pug index f3230144..7132c0bd 100644 --- a/web-client/views/upload.pug +++ b/web-client/views/upload.pug @@ -118,7 +118,7 @@ html a(href='#' id='node-coloring-toggle-menu' class='nodeColoringToggle') span(class='glyphicon') |   Enable Node Coloring - div(id='node-coloring-navbar-options') + div(id='node-coloring-navbar-options' class='disabled') li(class='divider') li(class='node-coloring-menu dropdown-submenu disabled') a(href='#') From 38243850ea1a67ff6347a4dd44cd4b6712bc30a6 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 1 Apr 2024 18:24:40 -0700 Subject: [PATCH 097/150] Issue #1081. Removing unnecessary console logs --- web-client/public/js/update-app.js | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/web-client/public/js/update-app.js b/web-client/public/js/update-app.js index 8225a1b1..6874503d 100644 --- a/web-client/public/js/update-app.js +++ b/web-client/public/js/update-app.js @@ -878,7 +878,6 @@ export const updateApp = grnState => { $(NODE_COLORING_SIDEBAR_BODY).removeClass("hidden"); $(NODE_COLORING_MENU).removeClass("hidden"); $(NODE_COLORING_NAVBAR_OPTIONS).removeClass("hidden"); - console.log("node coloring menus shown") if (grnState.database.expressionDatasets.includes(grnState.nodeColoring.topDataset) && grnState.workbook.expression[grnState.nodeColoring.topDataset] === undefined) { if ($(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked")) { @@ -939,9 +938,7 @@ export const updateApp = grnState => { $(NODE_COLORING_SIDEBAR_BODY).addClass("hidden"); $(NODE_COLORING_MENU).addClass("disabled"); $(NODE_COLORING_NAVBAR_OPTIONS).addClass("hidden"); - $(`${NODE_COLORING_TOGGLE_MENU} span`).removeClass("glyphicon-ok"); - - console.log("node coloring hidden") + $(`${NODE_COLORING_TOGGLE_MENU} span`).removeClass("glyphicon-ok"); $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", false); } From 37706669f616e1e83c20c65cd9cd97690e694310 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Mon, 1 Apr 2024 18:34:27 -0700 Subject: [PATCH 098/150] Issue #1081. Passing all tests and lint --- web-client/public/js/update-app.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web-client/public/js/update-app.js b/web-client/public/js/update-app.js index 6874503d..48797d7a 100644 --- a/web-client/public/js/update-app.js +++ b/web-client/public/js/update-app.js @@ -938,7 +938,7 @@ export const updateApp = grnState => { $(NODE_COLORING_SIDEBAR_BODY).addClass("hidden"); $(NODE_COLORING_MENU).addClass("disabled"); $(NODE_COLORING_NAVBAR_OPTIONS).addClass("hidden"); - $(`${NODE_COLORING_TOGGLE_MENU} span`).removeClass("glyphicon-ok"); + $(`${NODE_COLORING_TOGGLE_MENU} span`).removeClass("glyphicon-ok"); $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", false); } From 7bdd970a358c19a45e86b45774cfe1948a8834d2 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 2 Apr 2024 13:53:11 -0700 Subject: [PATCH 099/150] Issue #1081. Export Data and Export Image options were not displaying due to some css styling that I added, so I adjusted styling so only select the #node-coloring-navbar-options --- web-client/public/stylesheets/grnsight.styl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/web-client/public/stylesheets/grnsight.styl b/web-client/public/stylesheets/grnsight.styl index 33afd7c2..2d67b5db 100644 --- a/web-client/public/stylesheets/grnsight.styl +++ b/web-client/public/stylesheets/grnsight.styl @@ -256,10 +256,10 @@ nav.navbar.navbar-default -moz-border-radius:0 6px 6px 6px border-radius:0 6px 6px 6px -.dropdown-submenu:hover>.dropdown-menu, #node-coloring-navbar-options .dropdown-submenu:hover>.dropdown-menu +#node-coloring-navbar-options .dropdown-submenu:hover>.dropdown-menu display:block -.dropdown-submenu:hover>.dropdown-menu, #node-coloring-navbar-options .disabled:hover>.dropdown-menu +#node-coloring-navbar-options .disabled:hover>.dropdown-menu display:none .dropdown-submenu>a:after From c29fe8cbe6aaa71c5524afb849ad7cae973c274a Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 2 Apr 2024 14:11:53 -0700 Subject: [PATCH 100/150] Issue #1081. Adding back line I accidentally deleted in last commit, export data and image options display now --- web-client/public/stylesheets/grnsight.styl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web-client/public/stylesheets/grnsight.styl b/web-client/public/stylesheets/grnsight.styl index 2d67b5db..885b7e19 100644 --- a/web-client/public/stylesheets/grnsight.styl +++ b/web-client/public/stylesheets/grnsight.styl @@ -256,7 +256,7 @@ nav.navbar.navbar-default -moz-border-radius:0 6px 6px 6px border-radius:0 6px 6px 6px -#node-coloring-navbar-options .dropdown-submenu:hover>.dropdown-menu +.dropdown-submenu:hover>.dropdown-menu, #node-coloring-navbar-options .dropdown-submenu:hover>.dropdown-menu display:block #node-coloring-navbar-options .disabled:hover>.dropdown-menu From f96cc53948bfa622ea9170907046d71866fc6293 Mon Sep 17 00:00:00 2001 From: Cecilia Zaragoza <105010308+ceciliazaragoza@users.noreply.github.com> Date: Tue, 2 Apr 2024 14:53:02 -0700 Subject: [PATCH 101/150] Version Bump 7.0.14 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 93012c73..c89a274f 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "grnsight", - "version": "7.0.13", + "version": "7.0.14", "description": "Web app and service for visualizing models of gene regulatory networks", "directories": { "test": "test" From 37f84c0a2ea453a38684316be87c7258d4746865 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 3 Apr 2024 17:38:50 -0700 Subject: [PATCH 102/150] Issue #1083. The left and right clamping border are consistently too far to the right, and sometimes nodes exceed right clamping border by a large amount if the node is and not being dragged by user. left clamping border seems to be working as expected other than that, though, and can drag graph as long as have room to move left and right --- web-client/public/js/graph.js | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 3fc991d0..698f41bf 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1486,7 +1486,7 @@ export var drawGraph = function (workbook) { if (flexibleContainer) { updateZoomContainerInfo(); if (flexibleContainer.width * zoomValue > width ) { - console.log("width out of bounds", flexibleContainer.x, flexibleContainer.y) + console.log("width out of bounds") return false; } else if (flexibleContainer.height * zoomValue > height) { console.log("height out of bounds") @@ -1599,12 +1599,12 @@ export var drawGraph = function (workbook) { // could also look at this: https://observablehq.com/@john-guerra/force-directed-adjusted // and look at this too: https://www.w3.org/TR/SVG/coords.html var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X_R - selfReferringEdgeWidth; - console.log("rightBoundary", rightBoundary, width, d.textWidth, BOUNDARY_MARGIN_X_R, selfReferringEdgeWidth) + // console.log("rightBoundary", rightBoundary, width, d.textWidth, BOUNDARY_MARGIN_X_R, selfReferringEdgeWidth) // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentXPos = Math.max(BOUNDARY_MARGIN_X_L, Math.min(rightBoundary, d.x)); - if (width < MAX_WIDTH && + if (adaptive && width < MAX_WIDTH && (currentXPos === BOUNDARY_MARGIN_X_L || currentXPos === rightBoundary)) { - // if (!d3.select(this).classed("fixed")) { + if (!d3.select(this).classed("fixed")) { width += OFFSET_VALUE; boundingBoxContainer.attr("width", width); @@ -1620,7 +1620,7 @@ export var drawGraph = function (workbook) { .attr("x", function (d) { return d.x; }); - // } + } } return d.x = currentXPos; }).attr("y", function (d) { @@ -1630,9 +1630,9 @@ export var drawGraph = function (workbook) { var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN_Y - selfReferringEdgeHeight; // currentYPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentYPos = Math.max(BOUNDARY_MARGIN_Y, Math.min(bottomBoundary, d.y)); - if (height < MAX_HEIGHT && + if (adaptive && height < MAX_HEIGHT && (currentYPos === BOUNDARY_MARGIN_Y || currentYPos === bottomBoundary)) { - // if (!d3.select(this).classed("fixed")) { + if (!d3.select(this).classed("fixed")) { height += OFFSET_VALUE; boundingBoxContainer.attr("height", height); link @@ -1646,7 +1646,7 @@ export var drawGraph = function (workbook) { node.attr("y", function (d) { return d.y; }); - // } + } } return d.y = currentYPos; }).attr("transform", function (d) { From eb85936e65b10f1b24fec717ce01d1d2f2200e86 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 6 Apr 2024 12:57:46 -0700 Subject: [PATCH 103/150] Issue #1083. Trying to resolve flexiBox being larger than the positions of the nodes, so commenting out code and trying to isolate issue by loading smaller graph with 3 nodes from database --- web-client/public/js/graph.js | 106 ++++++++++++++++++---------------- 1 file changed, 56 insertions(+), 50 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 698f41bf..daee126d 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -279,7 +279,6 @@ export var drawGraph = function (workbook) { Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) * graphZoom + dx * graphZoom) { - console.log("1st x statement false"); return false; } @@ -290,7 +289,6 @@ export var drawGraph = function (workbook) { dx < 0 && Math.abs(xTranslation + dx) > flexibleContainer.x * graphZoom ) { - console.log("3rd x statement false") return false; } @@ -341,7 +339,7 @@ export var drawGraph = function (workbook) { let zoomScaleSliderLeft; let zoomScaleSliderRight; let prevGrnstateZoomVal; - // let centerXCoord; + let centerXCoord; const updateAppBasedOnZoomValue = () => { let zoomDisplay; @@ -378,6 +376,7 @@ export var drawGraph = function (workbook) { if (!adaptive) { center(); updateZoomContainerInfo(); + centerXCoord = xTranslation } $(ZOOM_SLIDER).val( @@ -1438,46 +1437,45 @@ export var drawGraph = function (workbook) { let xValuesPaths = [] let yValuesPaths = [] - link.selectAll("path").each( function(pathData) { - if (pathData.source) { - // Log the "d" attribute for each path - const controlPoints = d3.select(this).attr("d"); - if (controlPoints) { - if (controlPoints.includes("A")) { - const splitSpaces = controlPoints.split(" "); - const controlPointXY = splitSpaces[2].split(",") - const controlPointX = controlPointXY[0]; - const controlPointY = controlPointXY[1]; - xValuesPaths.push(parseFloat(controlPointX)) - yValuesPaths.push(parseFloat(controlPointY)) - } - else if (controlPoints.includes("C")) { - const splitC = controlPoints.split("C"); - - splitC[1].split(",").forEach((coordinates) => { - const splitSpaces = coordinates.split(" "); - const xValue = splitSpaces[splitSpaces.length - 2]; - const yValue = splitSpaces[splitSpaces.length - 1]; - xValuesPaths.push(parseFloat(xValue)); - yValuesPaths.push(parseFloat(yValue)); - }); - } - } - } - }); + // link.selectAll("path").each( function(pathData) { + // if (pathData.source) { + // // Log the "d" attribute for each path + // const controlPoints = d3.select(this).attr("d"); + // if (controlPoints) { + // if (controlPoints.includes("A")) { + // const splitSpaces = controlPoints.split(" "); + // const controlPointXY = splitSpaces[2].split(",") + // const controlPointX = controlPointXY[0]; + // const controlPointY = controlPointXY[1]; + // xValuesPaths.push(parseFloat(controlPointX)) + // yValuesPaths.push(parseFloat(controlPointY)) + // } + // else if (controlPoints.includes("C")) { + // const splitC = controlPoints.split("C"); + + // splitC[1].split(",").forEach((coordinates) => { + // const splitSpaces = coordinates.split(" "); + // const xValue = splitSpaces[splitSpaces.length - 2]; + // const yValue = splitSpaces[splitSpaces.length - 1]; + // xValuesPaths.push(parseFloat(xValue)); + // yValuesPaths.push(parseFloat(yValue)); + // }); + // } + // } + // } + // }); const xValuesNodes = nodes.map((node) => node.x); const yValuesNodes = nodes.map((node) => node.y); - const xValues = xValuesPaths.concat(xValuesNodes); - const yValues = yValuesPaths.concat(yValuesNodes); + // const xValues = xValuesPaths.concat(xValuesNodes); + // const yValues = yValuesPaths.concat(yValuesNodes); - const minX = Math.min(...xValues); - const minY = Math.min(...yValues); + const minX = Math.min(...xValuesNodes); + const minY = Math.min(...yValuesNodes); - const maxX = Math.max(...xValues) + nodeWidth; - const maxY = Math.max(...yValues) + nodeHeight; + const maxX = Math.max(...xValuesNodes) + nodeWidth; + const maxY = Math.max(...yValuesNodes) + nodeHeight; - // console.log("minX", minX, "minY", minY, "width", maxX - minX, "height", maxY - minY); return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } @@ -1498,30 +1496,38 @@ export var drawGraph = function (workbook) { function flexRectLimitBounds( BOUNDARY_MARGIN_X_L, - BOUNDARY_MARGIN_X_R + BOUNDARY_MARGIN_X_R, + BOUNDARY_MARGIN_Y ) { // limit flexContainer from exceeding bounding box // TODO: add 5 so flexibleContainerRect stays within BOUNDARY_MARGIN, remove hardcoded value later if (flexibleContainer) { // x left bound - if (flexibleContainer.x < 0) { - flexibleContainer.x = BOUNDARY_MARGIN_X_L; + if (flexibleContainer.x < BOUNDARY_MARGIN_X_L) { + // flexibleContainer.x = BOUNDARY_MARGIN_X_L; + console.log("left boundary exceeds", BOUNDARY_MARGIN_X_L); } // x right bound if ( - flexibleContainer.width > - width - flexibleContainer.x - BOUNDARY_MARGIN_X_R + (graphZoom * flexibleContainer.width + + graphZoom * flexibleContainer.x) > $container.width() * graphZoom - BOUNDARY_MARGIN_X_R ) { - flexibleContainer.width = - width - flexibleContainer.x - BOUNDARY_MARGIN_X_R; + // flexibleContainer.width = $container.width() - flexibleContainer.width - BOUNDARY_MARGIN_X_R; + console.log( + "right boundary exceeds", + BOUNDARY_MARGIN_X_R, + $container.width() - + (graphZoom * flexibleContainer.width + + graphZoom * flexibleContainer.x) + ); } // y top bound - if (flexibleContainer.y < 0) { - flexibleContainer.y = 0 + 5; + if (flexibleContainer.y < BOUNDARY_MARGIN_Y) { + flexibleContainer.y = BOUNDARY_MARGIN_Y; } // y bottom bound - if (flexibleContainer.height > height - flexibleContainer.y - 5) { - flexibleContainer.height = height - flexibleContainer.y - 5; + if (flexibleContainer.height > height - flexibleContainer.y) { + flexibleContainer.height = height - flexibleContainer.y; } } } @@ -1561,7 +1567,6 @@ export var drawGraph = function (workbook) { graphZoom * flexibleContainer.x) ) { BOUNDARY_MARGIN_X_R = Math.abs(xTranslation); - console.log("BOUNDARY_MARGIN_X_R", BOUNDARY_MARGIN_X_R, flexibleContainer.x + flexibleContainer.width) } if ( Math.abs(yTranslation) > @@ -1577,13 +1582,14 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(); - flexRectLimitBounds(BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_X_L); + flexRectLimitBounds(BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_Y); flexibleContainerRect .attr("x", flexibleContainer.x) .attr("y", flexibleContainer.y) .attr("width", flexibleContainer.width) .attr("height", flexibleContainer.height); + // console.log(flexibleContainer.x, flexibleContainer.width) } From 4a4d28f36c141edc6d09685895758726e4b13925 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 6 Apr 2024 14:03:55 -0700 Subject: [PATCH 104/150] added elemtn temporarily in navbar to view all flexibleContainer info. had to adjust value of flexibleContainer.x in calcFlexiBox, not in flexRectLimitBounds. now will work on adjusting right boundary --- web-client/public/js/graph.js | 78 +++++++++++++++++++---------------- web-client/views/upload.pug | 5 ++- 2 files changed, 47 insertions(+), 36 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index daee126d..147494d8 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1427,7 +1427,7 @@ export var drawGraph = function (workbook) { }; // there is too much whitespace in flexiContainer - function calcFlexiBox () { + function calcFlexiBox (BOUNDARY_MARGIN_X_L) { const nodes = simulation.nodes() let nodeWidth = 0; if (nodes.length > 0) { @@ -1470,12 +1470,15 @@ export var drawGraph = function (workbook) { // const xValues = xValuesPaths.concat(xValuesNodes); // const yValues = yValuesPaths.concat(yValuesNodes); - const minX = Math.min(...xValuesNodes); + let minX = Math.min(...xValuesNodes); const minY = Math.min(...yValuesNodes); const maxX = Math.max(...xValuesNodes) + nodeWidth; const maxY = Math.max(...yValuesNodes) + nodeHeight; + // handle left x boundary to not be less than 0 + console.log("left boundary", BOUNDARY_MARGIN_X_L) + minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } @@ -1502,11 +1505,6 @@ export var drawGraph = function (workbook) { // limit flexContainer from exceeding bounding box // TODO: add 5 so flexibleContainerRect stays within BOUNDARY_MARGIN, remove hardcoded value later if (flexibleContainer) { - // x left bound - if (flexibleContainer.x < BOUNDARY_MARGIN_X_L) { - // flexibleContainer.x = BOUNDARY_MARGIN_X_L; - console.log("left boundary exceeds", BOUNDARY_MARGIN_X_L); - } // x right bound if ( (graphZoom * flexibleContainer.width + @@ -1529,6 +1527,16 @@ export var drawGraph = function (workbook) { if (flexibleContainer.height > height - flexibleContainer.y) { flexibleContainer.height = height - flexibleContainer.y; } + + const flexDimensions = `flex.x + ${flexibleContainer.x} + flex.width + ${flexibleContainer.width} + flex.y + ${flexibleContainer.y} + flex.height + ${flexibleContainer.height}`; + $("#flexiBox-dimensions").text(flexDimensions); } } @@ -1551,44 +1559,44 @@ export var drawGraph = function (workbook) { let BOUNDARY_MARGIN_X_L = BOUNDARY_MARGIN; let BOUNDARY_MARGIN_X_R = BOUNDARY_MARGIN; let BOUNDARY_MARGIN_Y = BOUNDARY_MARGIN; - if (!adaptive && flexibleContainer && graphZoom >= 1) { + // if (!adaptive && flexibleContainer && graphZoom >= 1) { + // if ( + // Math.abs(xTranslation) > + // Math.floor(flexibleContainer.x) * graphZoom + // ) { + // // bouncing behavior because for some reason 15 pixels too far to the right + // BOUNDARY_MARGIN_X_L = Math.abs(xTranslation); + // } + // if ( + // xTranslation > + // $container.width() - + // (graphZoom * flexibleContainer.width + + // graphZoom * flexibleContainer.x) + // ) { + // BOUNDARY_MARGIN_X_R = Math.abs(xTranslation); + // } + // if ( + // Math.abs(yTranslation) > + // Math.floor(flexibleContainer.y) * graphZoom + // ) { + // BOUNDARY_MARGIN_Y = Math.abs(yTranslation); + // } - if ( - Math.abs(xTranslation) > - Math.floor(flexibleContainer.x) * graphZoom - ) { - // bouncing behavior because for some reason 15 pixels too far to the right - BOUNDARY_MARGIN_X_L = Math.abs(xTranslation); - } - if ( - xTranslation > - $container.width() - - (graphZoom * flexibleContainer.width + - graphZoom * flexibleContainer.x) - ) { - BOUNDARY_MARGIN_X_R = Math.abs(xTranslation); - } - if ( - Math.abs(yTranslation) > - Math.floor(flexibleContainer.y) * graphZoom - ) { - BOUNDARY_MARGIN_Y = Math.abs(yTranslation); - } - } + // } var SELF_REFERRING_Y_OFFSET = 6; var MAX_WIDTH = 5000; var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; if (!adaptive) { - flexibleContainer = calcFlexiBox(); + flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L); flexRectLimitBounds(BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_Y); flexibleContainerRect - .attr("x", flexibleContainer.x) - .attr("y", flexibleContainer.y) - .attr("width", flexibleContainer.width) - .attr("height", flexibleContainer.height); + .attr("x", flexibleContainer.x) + .attr("y", flexibleContainer.y) + .attr("width", flexibleContainer.width) + .attr("height", flexibleContainer.height); // console.log(flexibleContainer.x, flexibleContainer.width) } diff --git a/web-client/views/upload.pug b/web-client/views/upload.pug index 7132c0bd..b7bbf70c 100644 --- a/web-client/views/upload.pug +++ b/web-client/views/upload.pug @@ -285,10 +285,13 @@ html include components/demo.pug li a(href='#' id='fileName') + li + a(href='#' id='flexiBox-dimensions') ul(class='nav navbar-nav navbar-right graph-metadata-container') li(class='navbar-text text-right') small(id='graph-metadata') - + + div(class='container') div(class='grnsight-container' data-iframe-width data-iframe-height) div(class='scale-and-scroll') From 352d21734cf8e6917415ffbc1f13da323e419e78 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 6 Apr 2024 14:26:01 -0700 Subject: [PATCH 105/150] Now correctly limit flexibleContainer to not exceed right boundary, just had to add logic to ensure max X did not exceed .width() --- web-client/public/js/graph.js | 36 +++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 147494d8..96cfaf4e 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1427,7 +1427,7 @@ export var drawGraph = function (workbook) { }; // there is too much whitespace in flexiContainer - function calcFlexiBox (BOUNDARY_MARGIN_X_L) { + function calcFlexiBox (BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R) { const nodes = simulation.nodes() let nodeWidth = 0; if (nodes.length > 0) { @@ -1471,14 +1471,15 @@ export var drawGraph = function (workbook) { // const yValues = yValuesPaths.concat(yValuesNodes); let minX = Math.min(...xValuesNodes); - const minY = Math.min(...yValuesNodes); + let minY = Math.min(...yValuesNodes); - const maxX = Math.max(...xValuesNodes) + nodeWidth; - const maxY = Math.max(...yValuesNodes) + nodeHeight; + let maxX = Math.max(...xValuesNodes) + nodeWidth; + let maxY = Math.max(...yValuesNodes) + nodeHeight; - // handle left x boundary to not be less than 0 - console.log("left boundary", BOUNDARY_MARGIN_X_L) + // handle left x and y boundaries to not exceed BOUNDARY_MARGIN minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; + // TODO: probably need to factor in graphZoom + maxX = maxX > $container.width() ? $container.width() - BOUNDARY_MARGIN_X_R : maxX; return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } @@ -1527,16 +1528,6 @@ export var drawGraph = function (workbook) { if (flexibleContainer.height > height - flexibleContainer.y) { flexibleContainer.height = height - flexibleContainer.y; } - - const flexDimensions = `flex.x - ${flexibleContainer.x} - flex.width - ${flexibleContainer.width} - flex.y - ${flexibleContainer.y} - flex.height - ${flexibleContainer.height}`; - $("#flexiBox-dimensions").text(flexDimensions); } } @@ -1589,8 +1580,17 @@ export var drawGraph = function (workbook) { var OFFSET_VALUE = 5; if (!adaptive) { - flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L); - flexRectLimitBounds(BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_Y); + flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R); + + const flexDimensions = `flex.x + ${flexibleContainer.x} + flex.width + ${flexibleContainer.width} + flex.y + ${flexibleContainer.y} + flex.height + ${flexibleContainer.height}`; + $("#flexiBox-dimensions").text(flexDimensions); flexibleContainerRect .attr("x", flexibleContainer.x) From f6ef5ac57505c61a3e50c8fc39329da25abc86d9 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 6 Apr 2024 14:30:15 -0700 Subject: [PATCH 106/150] Issue #1083. Now limit top and bottom boundaries. Need to add more logic to ensure that all borders are accurate according to graphZoom --- web-client/public/js/graph.js | 25 ++++++------------------- 1 file changed, 6 insertions(+), 19 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 96cfaf4e..b8bfda96 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1427,7 +1427,7 @@ export var drawGraph = function (workbook) { }; // there is too much whitespace in flexiContainer - function calcFlexiBox (BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R) { + function calcFlexiBox (BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y) { const nodes = simulation.nodes() let nodeWidth = 0; if (nodes.length > 0) { @@ -1471,15 +1471,17 @@ export var drawGraph = function (workbook) { // const yValues = yValuesPaths.concat(yValuesNodes); let minX = Math.min(...xValuesNodes); - let minY = Math.min(...yValuesNodes); - let maxX = Math.max(...xValuesNodes) + nodeWidth; + + let minY = Math.min(...yValuesNodes); let maxY = Math.max(...yValuesNodes) + nodeHeight; // handle left x and y boundaries to not exceed BOUNDARY_MARGIN minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; // TODO: probably need to factor in graphZoom maxX = maxX > $container.width() ? $container.width() - BOUNDARY_MARGIN_X_R : maxX; + minY = minY < BOUNDARY_MARGIN_Y ? BOUNDARY_MARGIN_Y : minY; + maxY = maxY > $container.height() ? $container.height() - BOUNDARY_MARGIN_Y : maxY; return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; } @@ -1506,20 +1508,6 @@ export var drawGraph = function (workbook) { // limit flexContainer from exceeding bounding box // TODO: add 5 so flexibleContainerRect stays within BOUNDARY_MARGIN, remove hardcoded value later if (flexibleContainer) { - // x right bound - if ( - (graphZoom * flexibleContainer.width + - graphZoom * flexibleContainer.x) > $container.width() * graphZoom - BOUNDARY_MARGIN_X_R - ) { - // flexibleContainer.width = $container.width() - flexibleContainer.width - BOUNDARY_MARGIN_X_R; - console.log( - "right boundary exceeds", - BOUNDARY_MARGIN_X_R, - $container.width() - - (graphZoom * flexibleContainer.width + - graphZoom * flexibleContainer.x) - ); - } // y top bound if (flexibleContainer.y < BOUNDARY_MARGIN_Y) { flexibleContainer.y = BOUNDARY_MARGIN_Y; @@ -1580,8 +1568,7 @@ export var drawGraph = function (workbook) { var OFFSET_VALUE = 5; if (!adaptive) { - flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R); - + flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y); const flexDimensions = `flex.x ${flexibleContainer.x} flex.width From 9bf4ff9ee6fcd615aaed1a7720b3aadf1875bcdf Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sat, 6 Apr 2024 21:56:16 -0700 Subject: [PATCH 107/150] can now correctly clamp the left and right borders of graph without any extra whitespace --- web-client/public/js/graph.js | 132 +++++++++++++++++----------------- 1 file changed, 66 insertions(+), 66 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index b8bfda96..8b89f070 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -278,10 +278,10 @@ export var drawGraph = function (workbook) { if (xTranslation < 0 && Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) * graphZoom + dx * graphZoom) - { - return false; + { + return false; } - + //dPad movement when moving left if ( dPadMove && @@ -289,7 +289,7 @@ export var drawGraph = function (workbook) { dx < 0 && Math.abs(xTranslation + dx) > flexibleContainer.x * graphZoom ) { - return false; + return false; } // right border @@ -340,6 +340,7 @@ export var drawGraph = function (workbook) { let zoomScaleSliderRight; let prevGrnstateZoomVal; let centerXCoord; + let centerYCoord; const updateAppBasedOnZoomValue = () => { let zoomDisplay; @@ -376,7 +377,8 @@ export var drawGraph = function (workbook) { if (!adaptive) { center(); updateZoomContainerInfo(); - centerXCoord = xTranslation + centerXCoord = xTranslation; + centerYCoord = yTranslation; } $(ZOOM_SLIDER).val( @@ -1427,7 +1429,7 @@ export var drawGraph = function (workbook) { }; // there is too much whitespace in flexiContainer - function calcFlexiBox (BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y) { + function calcFlexiBox (BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B) { const nodes = simulation.nodes() let nodeWidth = 0; if (nodes.length > 0) { @@ -1480,9 +1482,9 @@ export var drawGraph = function (workbook) { minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; // TODO: probably need to factor in graphZoom maxX = maxX > $container.width() ? $container.width() - BOUNDARY_MARGIN_X_R : maxX; - minY = minY < BOUNDARY_MARGIN_Y ? BOUNDARY_MARGIN_Y : minY; - maxY = maxY > $container.height() ? $container.height() - BOUNDARY_MARGIN_Y : maxY; - return {x: minX, y: minY, width: maxX - minX, height: maxY - minY}; + minY = minY < BOUNDARY_MARGIN_Y_T ? BOUNDARY_MARGIN_Y_T : minY; + maxY = maxY > $container.height() ? $container.height() - BOUNDARY_MARGIN_Y_B : maxY; + return {x: minX, y: minY, width: maxX - minX, height: maxY - minY, maxX: maxX, maxY: maxY}; } // this checks if zoomInValue is in bounds when zoom in and out @@ -1500,25 +1502,6 @@ export var drawGraph = function (workbook) { return true } - function flexRectLimitBounds( - BOUNDARY_MARGIN_X_L, - BOUNDARY_MARGIN_X_R, - BOUNDARY_MARGIN_Y - ) { - // limit flexContainer from exceeding bounding box - // TODO: add 5 so flexibleContainerRect stays within BOUNDARY_MARGIN, remove hardcoded value later - if (flexibleContainer) { - // y top bound - if (flexibleContainer.y < BOUNDARY_MARGIN_Y) { - flexibleContainer.y = BOUNDARY_MARGIN_Y; - } - // y bottom bound - if (flexibleContainer.height > height - flexibleContainer.y) { - flexibleContainer.height = height - flexibleContainer.y; - } - } - } - // Tick only runs while the graph physics are still running. // (I.e. when the graph is completely relaxed, tick stops running.) function tick () { @@ -1537,46 +1520,64 @@ export var drawGraph = function (workbook) { // Left and right boundary margins: let BOUNDARY_MARGIN_X_L = BOUNDARY_MARGIN; let BOUNDARY_MARGIN_X_R = BOUNDARY_MARGIN; - let BOUNDARY_MARGIN_Y = BOUNDARY_MARGIN; - // if (!adaptive && flexibleContainer && graphZoom >= 1) { - // if ( - // Math.abs(xTranslation) > - // Math.floor(flexibleContainer.x) * graphZoom - // ) { - // // bouncing behavior because for some reason 15 pixels too far to the right - // BOUNDARY_MARGIN_X_L = Math.abs(xTranslation); - // } - // if ( - // xTranslation > - // $container.width() - - // (graphZoom * flexibleContainer.width + - // graphZoom * flexibleContainer.x) - // ) { - // BOUNDARY_MARGIN_X_R = Math.abs(xTranslation); - // } - // if ( - // Math.abs(yTranslation) > - // Math.floor(flexibleContainer.y) * graphZoom - // ) { - // BOUNDARY_MARGIN_Y = Math.abs(yTranslation); - // } - - // } + // top and bottom boundary margins: + let BOUNDARY_MARGIN_Y_T = BOUNDARY_MARGIN; + let BOUNDARY_MARGIN_Y_B = BOUNDARY_MARGIN; + if (!adaptive && flexibleContainer && graphZoom >= 1) { + if (Math.abs(xTranslation) >= + Math.floor(flexibleContainer.x) * graphZoom + ) { + BOUNDARY_MARGIN_X_L = Math.abs(xTranslation) / graphZoom; + } + if ( + xTranslation > + $container.width() - + (graphZoom * flexibleContainer.width + + graphZoom * flexibleContainer.x) + ) { + console.log("right bound violated"); + BOUNDARY_MARGIN_X_R = Math.abs(xTranslation) / graphZoom; + } + if ( + Math.abs(yTranslation) >= + Math.floor(flexibleContainer.y) * graphZoom + ) { + // console.log("top bound violated") + // BOUNDARY_MARGIN_Y_T = Math.abs(xTranslation); + } + + if (yTranslation >= height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { + // console.log("bottom bound violated") + // BOUNDARY_MARGIN_Y_B = Math.abs(xTranslation); + } + } + var SELF_REFERRING_Y_OFFSET = 6; var MAX_WIDTH = 5000; var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; if (!adaptive) { - flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y); - const flexDimensions = `flex.x - ${flexibleContainer.x} - flex.width - ${flexibleContainer.width} - flex.y - ${flexibleContainer.y} - flex.height - ${flexibleContainer.height}`; + flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B); + const flexDimensions = `xTrnslt + ${Math.round(xTranslation)} + yTrnslt + ${Math.round(yTranslation)} + flx.x + ${Math.round(flexibleContainer.x)} + flx.w + ${Math.round(flexibleContainer.width)} + flx.y + ${Math.round(flexibleContainer.y)} + flx.h + ${Math.round(flexibleContainer.height)} + + boundX + ${Math.round(BOUNDARY_MARGIN_X_L)} + ${Math.round(BOUNDARY_MARGIN_X_R)} + boundY + ${Math.round(BOUNDARY_MARGIN_Y_T)} + ${Math.round(BOUNDARY_MARGIN_Y_B)}`; $("#flexiBox-dimensions").text(flexDimensions); flexibleContainerRect @@ -1584,7 +1585,6 @@ export var drawGraph = function (workbook) { .attr("y", flexibleContainer.y) .attr("width", flexibleContainer.width) .attr("height", flexibleContainer.height); - // console.log(flexibleContainer.x, flexibleContainer.width) } @@ -1628,11 +1628,11 @@ export var drawGraph = function (workbook) { var selfReferringEdge = getSelfReferringEdge(d); var selfReferringEdgeHeight = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + SELF_REFERRING_Y_OFFSET + 0.5 : 0); - var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN_Y - selfReferringEdgeHeight; + var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN_Y_B - selfReferringEdgeHeight; // currentYPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentYPos = Math.max(BOUNDARY_MARGIN_Y, Math.min(bottomBoundary, d.y)); + var currentYPos = Math.max(BOUNDARY_MARGIN_Y_T, Math.min(bottomBoundary, d.y)); if (adaptive && height < MAX_HEIGHT && - (currentYPos === BOUNDARY_MARGIN_Y || currentYPos === bottomBoundary)) { + (currentYPos === BOUNDARY_MARGIN_Y_T || currentYPos === bottomBoundary)) { if (!d3.select(this).classed("fixed")) { height += OFFSET_VALUE; boundingBoxContainer.attr("height", height); From f9b17f7215217845037620b386db8d22e7c4c121 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sun, 7 Apr 2024 01:15:49 -0700 Subject: [PATCH 108/150] Issue #1083. Borders are too wide when move graph to left or right, especially for the right bound. Also need to alter bounds so that clamp graph correctly when zoomed out too --- web-client/public/js/graph.js | 47 +++++++++++++++++++++++------------ 1 file changed, 31 insertions(+), 16 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 8b89f070..175962ca 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1527,17 +1527,28 @@ export var drawGraph = function (workbook) { if (Math.abs(xTranslation) >= Math.floor(flexibleContainer.x) * graphZoom ) { + console.log("left bound violated") BOUNDARY_MARGIN_X_L = Math.abs(xTranslation) / graphZoom; } + console.log($container.width() - + (graphZoom * flexibleContainer.width + + graphZoom * flexibleContainer.x)) if ( - xTranslation > + xTranslation >= $container.width() - (graphZoom * flexibleContainer.width + graphZoom * flexibleContainer.x) ) { - console.log("right bound violated"); - BOUNDARY_MARGIN_X_R = Math.abs(xTranslation) / graphZoom; - } + console.log("right bound violated"); + if (flexibleContainer.x * graphZoom < $container.width() / graphZoom / 2){ + BOUNDARY_MARGIN_X_R = + $container.width() - + (graphZoom * flexibleContainer.width + + graphZoom * flexibleContainer.x); + } else { + BOUNDARY_MARGIN_X_R = Math.abs(xTranslation) / graphZoom; + } + } if ( Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) * graphZoom @@ -1559,25 +1570,29 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B); + /* + yTrnslt + ${Math.round(yTranslation)} + flx.y + ${Math.round(flexibleContainer.y)} + flx.h + ${Math.round(flexibleContainer.height)} + boundY + ${Math.round(BOUNDARY_MARGIN_Y_T)} + ${Math.round(BOUNDARY_MARGIN_Y_B)}*/ const flexDimensions = `xTrnslt ${Math.round(xTranslation)} - yTrnslt - ${Math.round(yTranslation)} flx.x ${Math.round(flexibleContainer.x)} flx.w ${Math.round(flexibleContainer.width)} - flx.y - ${Math.round(flexibleContainer.y)} - flx.h - ${Math.round(flexibleContainer.height)} - + flx.x+flx.w + ${Math.round(flexibleContainer.x + flexibleContainer.width)} + flxx+w scaled + ${Math.round((flexibleContainer.x + flexibleContainer.width) * graphZoom) } boundX ${Math.round(BOUNDARY_MARGIN_X_L)} - ${Math.round(BOUNDARY_MARGIN_X_R)} - boundY - ${Math.round(BOUNDARY_MARGIN_Y_T)} - ${Math.round(BOUNDARY_MARGIN_Y_B)}`; + ${Math.round(BOUNDARY_MARGIN_X_R)}`; $("#flexiBox-dimensions").text(flexDimensions); flexibleContainerRect @@ -1600,7 +1615,7 @@ export var drawGraph = function (workbook) { // could also look at this: https://observablehq.com/@john-guerra/force-directed-adjusted // and look at this too: https://www.w3.org/TR/SVG/coords.html var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X_R - selfReferringEdgeWidth; - // console.log("rightBoundary", rightBoundary, width, d.textWidth, BOUNDARY_MARGIN_X_R, selfReferringEdgeWidth) + // console.log("rightBoundary", rightBoundary) // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentXPos = Math.max(BOUNDARY_MARGIN_X_L, Math.min(rightBoundary, d.x)); if (adaptive && width < MAX_WIDTH && From 9e7b43702b979f110bdb8861397a95b6800af535 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 9 Apr 2024 00:52:05 -0700 Subject: [PATCH 109/150] #1106 fixing off-by-one column issue. Previously the first column was cols regulator/rows targetETR1. Fix by adding \t to the header --- database/network-database/scripts/generate_network.py | 2 +- .../network-database/scripts/generate_new_network_version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/database/network-database/scripts/generate_network.py b/database/network-database/scripts/generate_network.py index fa0e1f94..b745b153 100644 --- a/database/network-database/scripts/generate_network.py +++ b/database/network-database/scripts/generate_network.py @@ -115,7 +115,7 @@ def createMatrix(fileName: str): statusMessage: str = 'Creating REGULATORS TO TARGETS MATRIX\n' if fileName == REGULATORS_TO_TARGETS_MATRIX else 'Creating REGULATORS TO REGULATORS MATRIX\n' print(statusMessage) regulator_to_target_file = open(fileName, 'w') - headers = "cols regulators/rows targets" + headers = "cols regulators/rows targets\t" headers += '\t'.join(regulators_list) regulator_to_target_file.write(f'{headers}\n') for target in targets: diff --git a/database/network-database/scripts/generate_new_network_version.py b/database/network-database/scripts/generate_new_network_version.py index 4bf1702b..14f8dae5 100644 --- a/database/network-database/scripts/generate_new_network_version.py +++ b/database/network-database/scripts/generate_new_network_version.py @@ -131,7 +131,7 @@ def createMatrix(fileName: str): statusMessage: str = 'Creating REGULATORS TO TARGETS MATRIX\n' if fileName == REGULATORS_TO_TARGETS_MATRIX else 'Creating REGULATORS TO REGULATORS MATRIX\n' print(statusMessage) regulator_to_target_file = open(fileName, 'w') - headers = "cols regulators/rows targets" + headers = "cols regulators/rows targets\t" headers += '\t'.join(regulators_list) regulator_to_target_file.write(f'{headers}\n') for target in targets: From 5d7c5be7c74630ad76052b50ec68abd581545a47 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Mon, 15 Apr 2024 23:23:21 -0700 Subject: [PATCH 110/150] Adding a separate method to load network gene, load protein gene, update network gene, and update protein gene, making load_genes and update_genes to be private --- database/network-database/scripts/loader_updates.py | 2 +- database/protein-protein-database/scripts/loader.py | 6 +++++- database/utils.py | 8 ++++++++ 3 files changed, 14 insertions(+), 2 deletions(-) diff --git a/database/network-database/scripts/loader_updates.py b/database/network-database/scripts/loader_updates.py index 532c6583..b5ab9219 100644 --- a/database/network-database/scripts/loader_updates.py +++ b/database/network-database/scripts/loader_updates.py @@ -8,5 +8,5 @@ Utils.update_genes(Constants.GENE_UPDATE_DESTINATION, Constants.DATABASE_NAMESPACE, is_protein=False) Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) +Utils.load_network_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE) Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) diff --git a/database/protein-protein-database/scripts/loader.py b/database/protein-protein-database/scripts/loader.py index 05e04df6..bfb0680d 100644 --- a/database/protein-protein-database/scripts/loader.py +++ b/database/protein-protein-database/scripts/loader.py @@ -1,7 +1,11 @@ import csv from constants import * + +import sys +sys.path.insert(1, '../database') from utils import * + # Usage # python3 loader.py | psql postgresql://localhost/postgres """ @@ -14,6 +18,6 @@ """ Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE,is_protein=True) +Utils.load_protein_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE) Utils.load_proteins(Constants.PROTEIN_SOURCE, Constants.DATABASE_NAMESPACE) Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE,is_protein=True) \ No newline at end of file diff --git a/database/utils.py b/database/utils.py index 78c5252d..22944875 100644 --- a/database/utils.py +++ b/database/utils.py @@ -57,6 +57,14 @@ def load_sources(cls, source_path: str, database_namespace: str): print(f'{time_stamp}\t{source}\t{display_name}') row_num += 1 print('\\.') + + @classmethod + def load_network_genes(cls, gene_path: str, database_namespace: str): + cls.load_genes(gene_path, database_namespace, is_protein = False) + + @classmethod + def load_protein_genes(cls, gene_path: str, database_namespace: str): + cls.load_genes(gene_path, database_namespace, is_protein = True) @classmethod def load_genes(cls, gene_path: str, database_namespace: str, is_protein: bool): From 455b36f7235867ce5dfd515665e9b40e76ab2eae Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Mon, 15 Apr 2024 23:26:15 -0700 Subject: [PATCH 111/150] The last commit didn't add the changes for update, update that method in this commit --- .../network-database/scripts/loader_updates.py | 2 +- .../scripts/loader_update.py | 2 +- database/utils.py | 16 ++++++++++++---- 3 files changed, 14 insertions(+), 6 deletions(-) diff --git a/database/network-database/scripts/loader_updates.py b/database/network-database/scripts/loader_updates.py index b5ab9219..c470d7d3 100644 --- a/database/network-database/scripts/loader_updates.py +++ b/database/network-database/scripts/loader_updates.py @@ -6,7 +6,7 @@ # Usage # python3 loader.py | psql postgresql://localhost/postgres -Utils.update_genes(Constants.GENE_UPDATE_DESTINATION, Constants.DATABASE_NAMESPACE, is_protein=False) +Utils.update__network_genes(Constants.GENE_UPDATE_DESTINATION, Constants.DATABASE_NAMESPACE) Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) Utils.load_network_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE) Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) diff --git a/database/protein-protein-database/scripts/loader_update.py b/database/protein-protein-database/scripts/loader_update.py index f0266419..11afe912 100644 --- a/database/protein-protein-database/scripts/loader_update.py +++ b/database/protein-protein-database/scripts/loader_update.py @@ -6,7 +6,7 @@ from utils import * Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.update_genes(Constants.UPDATE_GENE_DESTINATION, Constants.DATABASE_NAMESPACE, is_protein=True) +Utils.update_protein_genes(Constants.UPDATE_GENE_DESTINATION, Constants.DATABASE_NAMESPACE) Utils.update_proteins(Constants.UPDATE_PROTEIN_DESTINATION, Constants.DATABASE_NAMESPACE) Utils.load_genes(Constants.MISSING_GENE_DESTINATION, Constants.DATABASE_NAMESPACE, is_protein=True) Utils.load_proteins(Constants.MISSING_PROTEIN_DESTINATION, Constants.DATABASE_NAMESPACE) diff --git a/database/utils.py b/database/utils.py index 22944875..bb79f30f 100644 --- a/database/utils.py +++ b/database/utils.py @@ -60,14 +60,14 @@ def load_sources(cls, source_path: str, database_namespace: str): @classmethod def load_network_genes(cls, gene_path: str, database_namespace: str): - cls.load_genes(gene_path, database_namespace, is_protein = False) + cls._load_genes(gene_path, database_namespace, is_protein = False) @classmethod def load_protein_genes(cls, gene_path: str, database_namespace: str): - cls.load_genes(gene_path, database_namespace, is_protein = True) + cls._load_genes(gene_path, database_namespace, is_protein = True) @classmethod - def load_genes(cls, gene_path: str, database_namespace: str, is_protein: bool): + def _load_genes(cls, gene_path: str, database_namespace: str, is_protein: bool): """ Load Gene ID Mapping into the database using the COPY command @@ -172,9 +172,17 @@ def load_network(cls, network_source_path: str, database_namespace: str, is_prot print(f'{regulator_gene_id}\t{target_gene_id}\t{taxon_id}\t{time_stamp}\t{source}') row_num += 1 print('\\.') + + @classmethod + def update_network_genes(cls, gene_path: str, database_namespace: str): + cls._update_genes(gene_path, database_namespace, is_protein = False) + + @classmethod + def update_protein_genes(cls, gene_path: str, database_namespace: str): + cls._update_genes(gene_path, database_namespace, is_protein = True) @classmethod - def update_genes(cls, update_gene_path: str, database_namespace: str, is_protein: bool): + def _update_genes(cls, update_gene_path: str, database_namespace: str, is_protein: bool): """ Update Gene ID Mapping into the database From 9c02aa7d6074778b602398482b6fb36b9f0e326d Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 16 Apr 2024 02:18:13 -0700 Subject: [PATCH 112/150] #1106 Adding scripts to create a union gene file in combine_all_genes.py. Adding all populating data to database in loader.py. Need to work on Readme file to update the command in the next commit, and fixing update scripts --- database/combine_all_genes.py | 116 ++++++++++++++++++++++++++ database/loader.py | 41 +++++++++ database/utils.py | 151 +++++++++++++++++++++++++++++++--- 3 files changed, 297 insertions(+), 11 deletions(-) create mode 100644 database/combine_all_genes.py create mode 100644 database/loader.py diff --git a/database/combine_all_genes.py b/database/combine_all_genes.py new file mode 100644 index 00000000..f74c7d66 --- /dev/null +++ b/database/combine_all_genes.py @@ -0,0 +1,116 @@ +# get all the genes from all files + +NETWORK_GENE_SOURCE = "network-database/script-results/processed-loader-files/gene.csv" +PROTEIN_GENE_SOURCE = "protein-protein-database/script-results/processed-loader-files/gene.csv" +EXPRESSION_GENE_SOURCE = "expression-database/script-results/processed-expression/genes.csv" + +# all_genes = {} +# with open(NETWORK_GENE_SOURCE, 'r') as network_gene_file: +# network_gene_file.readline() +# for line in network_gene_file: +# gene_id, display_gene_id, species, taxon_id, regulator = line.strip().split('\t') +# all_genes[display_gene_id] = gene_id + +import csv + + +# Function to read genes from a CSV file into a set +def read_genes_from_csv(file_path): + genes = set() + with open(file_path, 'r') as file: + reader = csv.reader(file) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + genes.add(r[0]) + row_num += 1 + return genes + +# # Function to read gene information from a CSV file into a dictionary +# def read_gene_info_from_csv(file_path): +# gene_info = {} +# with open(file_path, 'r') as file: +# reader = csv.reader(file) +# row_num = 0 +# for row in reader: +# if row_num != 0: +# r= ','.join(row).split('\t') +# gene_info[r[0]] = { +# 'Display Gene ID': r[1], +# 'Species': r[2], +# 'Taxon': r[3], +# 'Regulator': r[4] +# } +# row_num += 1 +# return gene_info + +def read_gene_info_from_csv(file_path): + gene_info = {} + with open(file_path, 'r') as file: + reader = csv.reader(file) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + if len(r) == 4: + r.append('False') + gene_info[r[0]] = { + 'Display Gene ID': r[1], + 'Species': r[2], + 'Taxon': r[3], + 'Regulator': r[4] + } + row_num += 1 + return gene_info + + +# File paths for the three source files +protein_protein_interactions_file = 'protein_protein_interactions.csv' +network_table_file = 'network_table.csv' +expression_table_file = 'expression_table.csv' + +# Read genes from each source file into sets +protein_genes = read_genes_from_csv(PROTEIN_GENE_SOURCE) +network_genes = read_genes_from_csv(NETWORK_GENE_SOURCE) +expression_genes = read_genes_from_csv(EXPRESSION_GENE_SOURCE) + +# Determine the missing genes from protein table and expression table compared to network table genes. If a gene is missing, set its regulator status to False +missing_genes_from_protein = protein_genes - network_genes +missing_genes_from_expression = expression_genes - network_genes +missing_genes = missing_genes_from_protein.union(missing_genes_from_expression) + +# Create a union set containing all unique genes +all_genes = protein_genes.union(network_genes, expression_genes) + +# Create a dictionary to store regulator status for each gene +gene_regulator_status = {gene: False for gene in all_genes} + +# Update regulator status for missing genes +for gene in missing_genes: + gene_regulator_status[gene] = False # Set to False as per requirement + +# Read gene information from each source file into dictionaries +protein_gene_info = read_gene_info_from_csv(PROTEIN_GENE_SOURCE) +network_gene_info = read_gene_info_from_csv(NETWORK_GENE_SOURCE) +expression_gene_info = read_gene_info_from_csv(EXPRESSION_GENE_SOURCE) + +union_genes_info = {} +for gene_id in all_genes: + gene_info = {} + if gene_id in network_gene_info: + gene_info = network_gene_info[gene_id] + elif gene_id in protein_gene_info: + gene_info = protein_gene_info[gene_id] + elif gene_id in expression_gene_info: + gene_info = expression_gene_info[gene_id] + union_genes_info[gene_id] = gene_info + +union_file_path = 'union_genes.csv' +with open(union_file_path, 'w', newline='') as union_file: + headers = ['Gene ID', 'Display Gene ID', 'Species', 'Taxon', 'Regulator'] + union_file.write('\t'.join(headers) + '\n') + + for gene_id, gene_info in union_genes_info.items(): + row_data = [gene_id, gene_info['Display Gene ID'], gene_info['Species'], gene_info['Taxon'], gene_info['Regulator']] + union_file.write('\t'.join(row_data) + '\n') diff --git a/database/loader.py b/database/loader.py new file mode 100644 index 00000000..a9c3793c --- /dev/null +++ b/database/loader.py @@ -0,0 +1,41 @@ +import csv +from utils import * + +# python3 loader.py | psql postgresql://localhost/postgres + +GENE_DATA_DIRECTORY = 'union_genes.csv' +# Network data source file path +# Constants name: NETWORK__DATA_DIRECTORY +NETWORK_DATABASE_NAMESPACE = 'gene_regulatory_network_testing' +NETWORK_SOURCE_TABLE_DATA_DIRECTORY = 'network-database/script-results/processed-loader-files/source.csv' +NETWORK_NETWORK_TABLE_DATA_DIRECTORY = 'network-database/script-results/processed-loader-files/network.csv' + +Utils.load_sources(NETWORK_SOURCE_TABLE_DATA_DIRECTORY, NETWORK_DATABASE_NAMESPACE) +Utils.load_network_genes(GENE_DATA_DIRECTORY, NETWORK_DATABASE_NAMESPACE) +Utils.load_network_network(NETWORK_NETWORK_TABLE_DATA_DIRECTORY, NETWORK_DATABASE_NAMESPACE) + +# Protein-protein-interactions +PROTEIN_DATABASE_NAMESPACE = 'protein_protein_interactions_testing' +PROTEIN_SOURCE_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/source.csv' +PROTEIN_NETWORK_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/physical_interaction_no_dupe.csv' +PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/protein.csv' + +Utils.load_sources(PROTEIN_SOURCE_TABLE_DATA_DIRECTORY, PROTEIN_DATABASE_NAMESPACE) +Utils.load_protein_genes(GENE_DATA_DIRECTORY, PROTEIN_DATABASE_NAMESPACE) +Utils.load_proteins(PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY, PROTEIN_DATABASE_NAMESPACE) +Utils.load_protein_network(PROTEIN_NETWORK_TABLE_DATA_DIRECTORY, PROTEIN_DATABASE_NAMESPACE) + +# Expression data +EXPRESISON_DATABASE_NAMESPACE = 'gene_expression_testing' +EXPRESSION_REFS_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/refs.csv' +EXPRESSION_METADATA_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-metadata.csv' +EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-data.csv' +EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/production-rates.csv' +EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/degradation-rates.csv' + +Utils.load_refs(EXPRESSION_REFS_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) +Utils.load_expression_genes(GENE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) +Utils.load_expression_metadata(EXPRESSION_METADATA_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) +Utils.load_expression_data(EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) +Utils.load_production_rates(EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) +Utils.load_degradation_rates(EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) \ No newline at end of file diff --git a/database/utils.py b/database/utils.py index bb79f30f..369edd73 100644 --- a/database/utils.py +++ b/database/utils.py @@ -60,14 +60,18 @@ def load_sources(cls, source_path: str, database_namespace: str): @classmethod def load_network_genes(cls, gene_path: str, database_namespace: str): - cls._load_genes(gene_path, database_namespace, is_protein = False) + cls._load_genes(gene_path, database_namespace, is_network = True) @classmethod def load_protein_genes(cls, gene_path: str, database_namespace: str): - cls._load_genes(gene_path, database_namespace, is_protein = True) + cls._load_genes(gene_path, database_namespace, is_network = False) + + @classmethod + def load_expression_genes(cls, gene_path: str, database_namespace: str): + cls._load_genes(gene_path, database_namespace, is_network = False) @classmethod - def _load_genes(cls, gene_path: str, database_namespace: str, is_protein: bool): + def _load_genes(cls, gene_path: str, database_namespace: str, is_network: bool): """ Load Gene ID Mapping into the database using the COPY command @@ -77,13 +81,13 @@ def _load_genes(cls, gene_path: str, database_namespace: str, is_protein: bool): The path to the file containing the gene data that want to add to the database database_namespace: str The database namespace i.e the schema name where the gene data will be loaded - is_protein : bool - A boolean value to check if the schema is for protein_protein_interactions or gene_regulatory_network + is_network : bool + A boolean value to check if the schema is for gene_regulatory_network """ - if is_protein: - print(f'COPY {database_namespace}.gene (gene_id, display_gene_id, species, taxon_id) FROM stdin;') - else: + if is_network: print(f'COPY {database_namespace}.gene (gene_id, display_gene_id, species, taxon_id, regulator) FROM stdin;') + else: + print(f'COPY {database_namespace}.gene (gene_id, display_gene_id, species, taxon_id) FROM stdin;') with open(gene_path, 'r+') as f: reader = csv.reader(f) row_num = 0 @@ -94,7 +98,7 @@ def _load_genes(cls, gene_path: str, database_namespace: str, is_protein: bool): display_gene_id= r[1] species = r[2] taxon_id = r[3] - if not is_protein: + if is_network: regulator = r[4] print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}\t{regulator}') else: @@ -132,7 +136,15 @@ def load_proteins(cls, protein_path: str, database_namespace: str): print('\\.') @classmethod - def load_network(cls, network_source_path: str, database_namespace: str, is_protein: bool): + def load_protein_network(cls, network_source_path: str, database_namespace: str): + cls._load_network(network_source_path, database_namespace, is_protein = True) + + @classmethod + def load_network_network(cls, network_source_path: str, database_namespace: str): + cls._load_network(network_source_path, database_namespace, is_protein = False) + + @classmethod + def _load_network(cls, network_source_path: str, database_namespace: str, is_protein: bool): """ Load Network Matrix into the database using the COPY command @@ -237,4 +249,121 @@ def update_proteins(cls, update_protein_path: str, database_namespace: str): pi = r[4] if r[4] != "None" else 0 print(f"UPDATE {database_namespace}.gene\nSET standard_name = '{standard_name}', length = {length}, molecular_weight = {molecular_weight}, PI = {pi}\nWHERE gene_systematic_name = '{gene_name}';") row_num += 1 - print('COMMIT;') \ No newline at end of file + print('COMMIT;') + + # The following functions are for expression database specifically + """ + This program Loads Refs into the database + """ + @classmethod + def load_refs(cls, refs_path: str, database_namespace: str): + print(f'COPY {database_namespace}.ref (pubmed_id, authors, publication_year, title, doi, ncbi_geo_id) FROM stdin;') + with open(refs_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + pubmed_id = r[0] + authors = r[1] + publication_year = r[2] + title = r[3] + doi = r[4] + ncbi_geo_id = r[5] + print(f'{pubmed_id}\t{authors}\t{publication_year}\t{title}\t{doi}\t{ncbi_geo_id}') + row_num += 1 + print('\\.') + + """ + This program Loads Expression Metadata into the database + """ + @classmethod + def load_expression_metadata(cls, expression_metadata_path: str, database_namespace: str): + print(f'COPY {database_namespace}.expression_metadata (ncbi_geo_id, pubmed_id, control_yeast_strain, treatment_yeast_strain, control, treatment, concentration_value, concentration_unit, time_value, time_unit, number_of_replicates, expression_table) FROM stdin;') + with open(expression_metadata_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + ncbi_geo_id = r[0] + pubmed_id =r[1] + control_yeast_strain = r[2] + treatment_yeast_strain = r[3] + control = r[4] + treatment = r[5] + concentration_value = float(r[6]) + concentration_unit = r[7] + time_value = float(r[8]) + time_unit = r[9] + number_of_replicates = int(r[10]) + expression_table = r[11] + + print(f'{ncbi_geo_id}\t{pubmed_id}\t{control_yeast_strain}\t{treatment_yeast_strain}\t{control}\t{treatment}\t{concentration_value}\t{concentration_unit}\t{time_value}\t{time_unit}\t{number_of_replicates}\t{expression_table}') + row_num += 1 + print('\\.') + """ + This program Loads Expression Data into the database + """ + @classmethod + def load_expression_data(cls, expression_data_path: str, database_namespace: str): + print(f'COPY {database_namespace}.expression (gene_id, taxon_id, sort_index, sample_id, expression, time_point, dataset) FROM stdin;') + with open(expression_data_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + gene_id = r[0] + taxon_id = r[1] + sort_index = int(r[2]) + sample_id = r[3] + expression = float(r[4]) if r[4] != "" else "NaN" + + time_point = float(r[5]) + data_set = r[6] + print(f'{gene_id}\t{taxon_id}\t{sort_index}\t{sample_id}\t{expression}\t{time_point}\t{data_set}') + row_num += 1 + print('\\.') + + """ + This program Loads Production Rates into the database + """ + @classmethod + def load_production_rates(cls, production_rates_path: str, database_namespace: str): + print(f'COPY {database_namespace}.production_rate (gene_id, taxon_id, ncbi_geo_id, pubmed_id, production_rate) FROM stdin;') + with open(production_rates_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + gene_id = r[0] + taxon_id = r[1] + ncbi_geo_id = r[2] + pubmed_id = r[3] + production_rate = float(r[4]) if r[4] != "" else "NaN" + print(f'{gene_id}\t{taxon_id}\t{ncbi_geo_id}\t{pubmed_id}\t{production_rate}') + row_num += 1 + print('\\.') + + """ + This program Loads Degradation Rates into the database + """ + @classmethod + def load_degradation_rates(cls, degradation_rates_path: str, database_namespace: str): + print(f'COPY {database_namespace}.degradation_rate (gene_id, taxon_id, ncbi_geo_id, pubmed_id, degradation_rate) FROM stdin;') + with open(degradation_rates_path, 'r+') as f: + reader = csv.reader(f) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + gene_id = r[0] + taxon_id = r[1] + ncbi_geo_id = r[2] + pubmed_id = r[3] + degradation_rate = float(r[4]) if r[4] != "" else "NaN" + print(f'{gene_id}\t{taxon_id}\t{ncbi_geo_id}\t{pubmed_id}\t{degradation_rate}') + row_num += 1 + print('\\.') \ No newline at end of file From 786c18ae605f55dfed1a7d9e6be0f4b0dfc176ef Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 16 Apr 2024 02:20:44 -0700 Subject: [PATCH 113/150] #1106 delete commented code --- database/combine_all_genes.py | 25 ------------------------- 1 file changed, 25 deletions(-) diff --git a/database/combine_all_genes.py b/database/combine_all_genes.py index f74c7d66..1b130e1f 100644 --- a/database/combine_all_genes.py +++ b/database/combine_all_genes.py @@ -4,13 +4,6 @@ PROTEIN_GENE_SOURCE = "protein-protein-database/script-results/processed-loader-files/gene.csv" EXPRESSION_GENE_SOURCE = "expression-database/script-results/processed-expression/genes.csv" -# all_genes = {} -# with open(NETWORK_GENE_SOURCE, 'r') as network_gene_file: -# network_gene_file.readline() -# for line in network_gene_file: -# gene_id, display_gene_id, species, taxon_id, regulator = line.strip().split('\t') -# all_genes[display_gene_id] = gene_id - import csv @@ -27,24 +20,6 @@ def read_genes_from_csv(file_path): row_num += 1 return genes -# # Function to read gene information from a CSV file into a dictionary -# def read_gene_info_from_csv(file_path): -# gene_info = {} -# with open(file_path, 'r') as file: -# reader = csv.reader(file) -# row_num = 0 -# for row in reader: -# if row_num != 0: -# r= ','.join(row).split('\t') -# gene_info[r[0]] = { -# 'Display Gene ID': r[1], -# 'Species': r[2], -# 'Taxon': r[3], -# 'Regulator': r[4] -# } -# row_num += 1 -# return gene_info - def read_gene_info_from_csv(file_path): gene_info = {} with open(file_path, 'r') as file: From 699106f30072dc17fc5bf8c2a621bf5d478d439a Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 16 Apr 2024 02:23:50 -0700 Subject: [PATCH 114/150] Delete unnessary code that I forgot to comment out --- database/combine_all_genes.py | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/database/combine_all_genes.py b/database/combine_all_genes.py index 1b130e1f..e3b67fa1 100644 --- a/database/combine_all_genes.py +++ b/database/combine_all_genes.py @@ -6,7 +6,6 @@ import csv - # Function to read genes from a CSV file into a set def read_genes_from_csv(file_path): genes = set() @@ -39,7 +38,6 @@ def read_gene_info_from_csv(file_path): row_num += 1 return gene_info - # File paths for the three source files protein_protein_interactions_file = 'protein_protein_interactions.csv' network_table_file = 'network_table.csv' @@ -50,20 +48,8 @@ def read_gene_info_from_csv(file_path): network_genes = read_genes_from_csv(NETWORK_GENE_SOURCE) expression_genes = read_genes_from_csv(EXPRESSION_GENE_SOURCE) -# Determine the missing genes from protein table and expression table compared to network table genes. If a gene is missing, set its regulator status to False -missing_genes_from_protein = protein_genes - network_genes -missing_genes_from_expression = expression_genes - network_genes -missing_genes = missing_genes_from_protein.union(missing_genes_from_expression) - # Create a union set containing all unique genes all_genes = protein_genes.union(network_genes, expression_genes) - -# Create a dictionary to store regulator status for each gene -gene_regulator_status = {gene: False for gene in all_genes} - -# Update regulator status for missing genes -for gene in missing_genes: - gene_regulator_status[gene] = False # Set to False as per requirement # Read gene information from each source file into dictionaries protein_gene_info = read_gene_info_from_csv(PROTEIN_GENE_SOURCE) From ae1225386d06936dc74168f3d436dc557aa03799 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 09:59:19 -0700 Subject: [PATCH 115/150] Can manually change the size of the boundingRectangle, but cannot get it to match the borders of the viewport consistently. May consider restructuring graph so that bounding is jus the viewport svg itself --- web-client/public/js/graph.js | 57 +++++++++++++++++++++++++---------- 1 file changed, 41 insertions(+), 16 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 175962ca..aa572f2a 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -219,13 +219,13 @@ export var drawGraph = function (workbook) { // This rectangle catches all of the mousewheel and pan events, without letting // them bubble up to the body. - boundingBoxContainer.append("rect") + var boundingBoxRect = boundingBoxContainer.append("rect") .attr("width", width) .attr("height", height) .style("fill", "none") .style("pointer-events", "all") .attr("stroke", "none" ) - .append("g"); + .attr("id", "boundingBoxRect"); var flexibleContainerRect = boundingBoxContainer.append("rect") .attr("class", "boundingBox") @@ -241,6 +241,7 @@ export var drawGraph = function (workbook) { svg.style("pointer-events", "all").call(zoomDrag) .style("font-family", "sans-serif"); + // this allows zoomContainer to be zoomed, dragged function zoomed () { zoomContainer.attr("transform", d3.event.transform); } @@ -261,15 +262,28 @@ export var drawGraph = function (workbook) { let yTranslation = 0; let flexibleContainer = null; + function getXTranslation() { + return xTranslation; + } + function updateZoomContainerInfo() { // transform attribute of zoomContainer contains translation info about graph - xTranslation = parseFloat(zoomContainer - .attr("transform") - .split("(")[1].split(",")[0]); + if (zoomContainer.attr("transform")) { + xTranslation = parseFloat( + zoomContainer + .attr("transform") + .split("(")[1] + .split(",")[0] + ); - yTranslation = parseFloat(zoomContainer - .attr("transform") - .split("(")[1].split(",")[1].split(")")[0]); + yTranslation = parseFloat( + zoomContainer + .attr("transform") + .split("(")[1] + .split(",")[1] + .split(")")[0] + ); + } }; function viewportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { @@ -328,8 +342,13 @@ export var drawGraph = function (workbook) { } var container = zoomContainer; if (adaptive || (!adaptive && flexRectInBounds(graphZoom))) { - zoom.scaleTo(container, zoomScale); - graphZoom = zoomScale + zoom.scaleTo(container, zoomScale); + console.log( + "zoomContainer transform", + zoomContainer.attr("transform") + ); + // boundingBoxContainer.attr("transform", zoomContainer.attr("transform") * (1/scale)); + graphZoom = zoomScale; } }; @@ -1528,11 +1547,11 @@ export var drawGraph = function (workbook) { Math.floor(flexibleContainer.x) * graphZoom ) { console.log("left bound violated") - BOUNDARY_MARGIN_X_L = Math.abs(xTranslation) / graphZoom; + BOUNDARY_MARGIN_X_L = -xTranslation / graphZoom; } - console.log($container.width() - - (graphZoom * flexibleContainer.width + - graphZoom * flexibleContainer.x)) + // console.log($container.width() - + // (graphZoom * flexibleContainer.width + + // graphZoom * flexibleContainer.x)) if ( xTranslation >= $container.width() - @@ -1554,12 +1573,12 @@ export var drawGraph = function (workbook) { Math.floor(flexibleContainer.y) * graphZoom ) { // console.log("top bound violated") - // BOUNDARY_MARGIN_Y_T = Math.abs(xTranslation); + BOUNDARY_MARGIN_Y_T = Math.abs(xTranslation); } if (yTranslation >= height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { // console.log("bottom bound violated") - // BOUNDARY_MARGIN_Y_B = Math.abs(xTranslation); + BOUNDARY_MARGIN_Y_B = Math.abs(xTranslation); } } @@ -1600,6 +1619,12 @@ export var drawGraph = function (workbook) { .attr("y", flexibleContainer.y) .attr("width", flexibleContainer.width) .attr("height", flexibleContainer.height); + + boundingBoxRect + .attr("x", -xTranslation) + .attr("width", width / graphZoom - BOUNDARY_MARGIN_X_R) + .attr("y", -yTranslation) + .attr("height", height / graphZoom - BOUNDARY_MARGIN_X_R); } From 7480cbb60b985e052e852403884690225c0fb306 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 10:50:14 -0700 Subject: [PATCH 116/150] Issue #1083. Now the boundingBoxRect is close to the borders when zoom in and out, but when zoom out to the max and zoom in to the max the boundingBoxRect, so need to make sure that the calculation is consistent. Will also work towards making the borders be the boundingBoxRect values as well --- web-client/public/js/graph.js | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index aa572f2a..8f42c7a2 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1549,9 +1549,6 @@ export var drawGraph = function (workbook) { console.log("left bound violated") BOUNDARY_MARGIN_X_L = -xTranslation / graphZoom; } - // console.log($container.width() - - // (graphZoom * flexibleContainer.width + - // graphZoom * flexibleContainer.x)) if ( xTranslation >= $container.width() - @@ -1621,12 +1618,11 @@ export var drawGraph = function (workbook) { .attr("height", flexibleContainer.height); boundingBoxRect - .attr("x", -xTranslation) + .attr("x", -xTranslation / graphZoom + BOUNDARY_MARGIN_X_L / 2) .attr("width", width / graphZoom - BOUNDARY_MARGIN_X_R) - .attr("y", -yTranslation) - .attr("height", height / graphZoom - BOUNDARY_MARGIN_X_R); + .attr("y", -yTranslation / graphZoom + BOUNDARY_MARGIN_Y_T) + .attr("height", height / graphZoom - BOUNDARY_MARGIN_Y_B / 2); } - // this controls movement and position of nodes, clamps the nodes to boundary try { From 8e2b394d1e88f755b4166e711f41e35769657071 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 11:07:05 -0700 Subject: [PATCH 117/150] Issue #1083 fixing top and bottom borders to be evenly close to the viewport edges --- web-client/public/js/graph.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 8f42c7a2..a6613269 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1620,8 +1620,8 @@ export var drawGraph = function (workbook) { boundingBoxRect .attr("x", -xTranslation / graphZoom + BOUNDARY_MARGIN_X_L / 2) .attr("width", width / graphZoom - BOUNDARY_MARGIN_X_R) - .attr("y", -yTranslation / graphZoom + BOUNDARY_MARGIN_Y_T) - .attr("height", height / graphZoom - BOUNDARY_MARGIN_Y_B / 2); + .attr("y", -yTranslation / graphZoom + BOUNDARY_MARGIN_Y_T / 2) + .attr("height", height / graphZoom - BOUNDARY_MARGIN_Y_B); } // this controls movement and position of nodes, clamps the nodes to boundary From d458c043d1ab41277d18828329c01db2fd335954 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 16:24:06 -0700 Subject: [PATCH 118/150] Issue #1083. Left and Top viewport borders are bounding at all zoom levels. Need to work on right and bottom borders since they are too large --- web-client/public/js/graph.js | 122 ++++++++++++++++++---------------- 1 file changed, 64 insertions(+), 58 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index a6613269..be63efe3 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -288,6 +288,13 @@ export var drawGraph = function (workbook) { function viewportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { updateZoomContainerInfo(); + //TODO: need to call calcFlexiBox here so that updates even when tick isn't running because nodes aren't moving + // flexibleContainer = calcFlexiBox( + // BOUNDARY_MARGIN_X_L, + // BOUNDARY_MARGIN_X_R, + // BOUNDARY_MARGIN_Y_T, + // BOUNDARY_MARGIN_Y_B + // ); // left border if (xTranslation < 0 && Math.abs(xTranslation) >= @@ -343,11 +350,6 @@ export var drawGraph = function (workbook) { var container = zoomContainer; if (adaptive || (!adaptive && flexRectInBounds(graphZoom))) { zoom.scaleTo(container, zoomScale); - console.log( - "zoomContainer transform", - zoomContainer.attr("transform") - ); - // boundingBoxContainer.attr("transform", zoomContainer.attr("transform") * (1/scale)); graphZoom = zoomScale; } }; @@ -1449,6 +1451,7 @@ export var drawGraph = function (workbook) { // there is too much whitespace in flexiContainer function calcFlexiBox (BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B) { + console.log("calc flexi box run") const nodes = simulation.nodes() let nodeWidth = 0; if (nodes.length > 0) { @@ -1542,41 +1545,26 @@ export var drawGraph = function (workbook) { // top and bottom boundary margins: let BOUNDARY_MARGIN_Y_T = BOUNDARY_MARGIN; let BOUNDARY_MARGIN_Y_B = BOUNDARY_MARGIN; - if (!adaptive && flexibleContainer && graphZoom >= 1) { - if (Math.abs(xTranslation) >= - Math.floor(flexibleContainer.x) * graphZoom - ) { - console.log("left bound violated") - BOUNDARY_MARGIN_X_L = -xTranslation / graphZoom; - } - if ( - xTranslation >= - $container.width() - - (graphZoom * flexibleContainer.width + - graphZoom * flexibleContainer.x) - ) { - console.log("right bound violated"); - if (flexibleContainer.x * graphZoom < $container.width() / graphZoom / 2){ - BOUNDARY_MARGIN_X_R = - $container.width() - - (graphZoom * flexibleContainer.width + - graphZoom * flexibleContainer.x); - } else { - BOUNDARY_MARGIN_X_R = Math.abs(xTranslation) / graphZoom; - } - } - if ( - Math.abs(yTranslation) >= - Math.floor(flexibleContainer.y) * graphZoom - ) { - // console.log("top bound violated") - BOUNDARY_MARGIN_Y_T = Math.abs(xTranslation); - } - - if (yTranslation >= height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { + if (!adaptive && flexibleContainer) { + BOUNDARY_MARGIN_X_L = -xTranslation / graphZoom + BOUNDARY_MARGIN / 2; + // if ( + // xTranslation >= + // $container.width() - + // (graphZoom * flexibleContainer.width + + // graphZoom * flexibleContainer.x) + // ) { + // console.log("right bound violated"); + // if (flexibleContainer.x * graphZoom < $container.width() / graphZoom / 2){ + BOUNDARY_MARGIN_X_R = width / graphZoom - BOUNDARY_MARGIN; + // } else { + // BOUNDARY_MARGIN_X_R = Math.abs(xTranslation) / graphZoom; + // } + // } + BOUNDARY_MARGIN_Y_T = -yTranslation / graphZoom + BOUNDARY_MARGIN / 2; + // if (yTranslation >= height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { // console.log("bottom bound violated") - BOUNDARY_MARGIN_Y_B = Math.abs(xTranslation); - } + BOUNDARY_MARGIN_Y_B = height / graphZoom - BOUNDARY_MARGIN; + // } } var SELF_REFERRING_Y_OFFSET = 6; @@ -1587,28 +1575,40 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B); /* - yTrnslt + xTrnslt + ${Math.round(xTranslation)} + flx.x + ${Math.round(flexibleContainer.x)} + flx.w + ${Math.round(flexibleContainer.width)} + flx.x+flx.w + ${Math.round(flexibleContainer.x + flexibleContainer.width)} + flxx+w scaled + ${Math.round( + (flexibleContainer.x + flexibleContainer.width) * graphZoom + )} + boundX + ${Math.round(BOUNDARY_MARGIN_X_L)} + ${Math.round(BOUNDARY_MARGIN_X_R)} + */ + const flexDimensions = ` + yTrnslt ${Math.round(yTranslation)} - flx.y + flx.y ${Math.round(flexibleContainer.y)} flx.h ${Math.round(flexibleContainer.height)} - boundY + boundY ${Math.round(BOUNDARY_MARGIN_Y_T)} - ${Math.round(BOUNDARY_MARGIN_Y_B)}*/ - const flexDimensions = `xTrnslt - ${Math.round(xTranslation)} + ${Math.round(BOUNDARY_MARGIN_Y_B)} flx.x ${Math.round(flexibleContainer.x)} flx.w ${Math.round(flexibleContainer.width)} - flx.x+flx.w - ${Math.round(flexibleContainer.x + flexibleContainer.width)} - flxx+w scaled - ${Math.round((flexibleContainer.x + flexibleContainer.width) * graphZoom) } boundX ${Math.round(BOUNDARY_MARGIN_X_L)} - ${Math.round(BOUNDARY_MARGIN_X_R)}`; + ${Math.round(BOUNDARY_MARGIN_X_R)} + `; $("#flexiBox-dimensions").text(flexDimensions); flexibleContainerRect @@ -1618,10 +1618,10 @@ export var drawGraph = function (workbook) { .attr("height", flexibleContainer.height); boundingBoxRect - .attr("x", -xTranslation / graphZoom + BOUNDARY_MARGIN_X_L / 2) - .attr("width", width / graphZoom - BOUNDARY_MARGIN_X_R) - .attr("y", -yTranslation / graphZoom + BOUNDARY_MARGIN_Y_T / 2) - .attr("height", height / graphZoom - BOUNDARY_MARGIN_Y_B); + .attr("x", -xTranslation / graphZoom + BOUNDARY_MARGIN / 2) + .attr("width", width / graphZoom - BOUNDARY_MARGIN) + .attr("y", -yTranslation / graphZoom + BOUNDARY_MARGIN / 2) + .attr("height", height / graphZoom - BOUNDARY_MARGIN); } // this controls movement and position of nodes, clamps the nodes to boundary @@ -1635,12 +1635,14 @@ export var drawGraph = function (workbook) { // a stack overflow link to look at: https://stackoverflow.com/questions/26781129/d3-v2-prevent-zooming-and-panning-chart-outside-viewport // could also look at this: https://observablehq.com/@john-guerra/force-directed-adjusted // and look at this too: https://www.w3.org/TR/SVG/coords.html - var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN_X_R - selfReferringEdgeWidth; - // console.log("rightBoundary", rightBoundary) - // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds + var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN - selfReferringEdgeWidth; + if (!adaptive) { + rightBoundary = -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + width / graphZoom - BOUNDARY_MARGIN; + } + // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentXPos = Math.max(BOUNDARY_MARGIN_X_L, Math.min(rightBoundary, d.x)); if (adaptive && width < MAX_WIDTH && - (currentXPos === BOUNDARY_MARGIN_X_L || currentXPos === rightBoundary)) { + (currentXPos === BOUNDARY_MARGIN || currentXPos === rightBoundary)) { if (!d3.select(this).classed("fixed")) { width += OFFSET_VALUE; boundingBoxContainer.attr("width", width); @@ -1665,8 +1667,12 @@ export var drawGraph = function (workbook) { var selfReferringEdgeHeight = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + SELF_REFERRING_Y_OFFSET + 0.5 : 0); var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN_Y_B - selfReferringEdgeHeight; + if (!adaptive) { + bottomBoundary = -yTranslation / graphZoom + BOUNDARY_MARGIN / 2 + height / graphZoom - BOUNDARY_MARGIN; + } // currentYPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentYPos = Math.max(BOUNDARY_MARGIN_Y_T, Math.min(bottomBoundary, d.y)); + if (adaptive && height < MAX_HEIGHT && (currentYPos === BOUNDARY_MARGIN_Y_T || currentYPos === bottomBoundary)) { if (!d3.select(this).classed("fixed")) { From 749cf2855179968db3f67a5ec37ea98476cb9751 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 16:47:53 -0700 Subject: [PATCH 119/150] Issue #1083. Now experiencing issue where flexContainerRect will get a negative height or width. probably has to do with the negative x and y values the graph can have now --- web-client/public/js/graph.js | 35 ++++++++++++++++++++++++----------- 1 file changed, 24 insertions(+), 11 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index be63efe3..597f36f5 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -13,6 +13,7 @@ import { ZOOM_ADAPTIVE_MAX_SCALE, NETWORK_GRN_MODE } from "./constants"; +import { max } from "moment"; /* globals d3 */ /* eslint-disable no-use-before-define, func-style */ @@ -1506,7 +1507,20 @@ export var drawGraph = function (workbook) { maxX = maxX > $container.width() ? $container.width() - BOUNDARY_MARGIN_X_R : maxX; minY = minY < BOUNDARY_MARGIN_Y_T ? BOUNDARY_MARGIN_Y_T : minY; maxY = maxY > $container.height() ? $container.height() - BOUNDARY_MARGIN_Y_B : maxY; - return {x: minX, y: minY, width: maxX - minX, height: maxY - minY, maxX: maxX, maxY: maxY}; + // console.log("flexi box width and height", maxX - minX, "maxX", maxX, "minX", minX, "maxY - minY", maxY - minY, "maxY", maxY, "minY", minY) + let width = 1234; + if (maxX < 0 && minX < 0) { + width = Math.abs(maxX) - Math.abs(minX); + } else { + width = maxX - minX; + } + let height = 1234; + if (maxY < 0 && minY < 0) { + height = Math.abs(maxY) - Math.abs(minY); + } else { + height = maxY - minY; + } + return {x: minX, y: minY, maxX: maxX, maxY: maxY, width: width, height: height}; } // this checks if zoomInValue is in bounds when zoom in and out @@ -1590,9 +1604,7 @@ export var drawGraph = function (workbook) { boundX ${Math.round(BOUNDARY_MARGIN_X_L)} ${Math.round(BOUNDARY_MARGIN_X_R)} - */ - const flexDimensions = ` - yTrnslt + yTrnslt ${Math.round(yTranslation)} flx.y ${Math.round(flexibleContainer.y)} @@ -1601,13 +1613,14 @@ export var drawGraph = function (workbook) { boundY ${Math.round(BOUNDARY_MARGIN_Y_T)} ${Math.round(BOUNDARY_MARGIN_Y_B)} - flx.x - ${Math.round(flexibleContainer.x)} - flx.w - ${Math.round(flexibleContainer.width)} - boundX - ${Math.round(BOUNDARY_MARGIN_X_L)} - ${Math.round(BOUNDARY_MARGIN_X_R)} + */ + const flexDimensions = ` + width ${Math.round(flexibleContainerRect.attr("width"))} + x ${Math.round(flexibleContainerRect.attr("x"))} + maxX ${Math.round(flexibleContainer.maxX)} + height ${Math.round(flexibleContainerRect.attr("height"))} + y ${Math.round(flexibleContainerRect.attr("y"))} + maxY ${Math.round(flexibleContainer.maxY)} `; $("#flexiBox-dimensions").text(flexDimensions); From 69e79d45787578a23bfa57f0d7c361c1347086c6 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 18:23:37 -0700 Subject: [PATCH 120/150] Issue #1083. Graph is restricted to viewport bounds! The left, right, top, and bottom bounds restrict the graph to viewport, and when the graph is moved, all of the borders clamp the graph as well --- web-client/public/js/graph.js | 38 ++++++++++++++++++++++++----------- 1 file changed, 26 insertions(+), 12 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 597f36f5..a3c3d2fa 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1452,7 +1452,7 @@ export var drawGraph = function (workbook) { // there is too much whitespace in flexiContainer function calcFlexiBox (BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B) { - console.log("calc flexi box run") + // console.log("calc flexi box run") const nodes = simulation.nodes() let nodeWidth = 0; if (nodes.length > 0) { @@ -1504,9 +1504,10 @@ export var drawGraph = function (workbook) { // handle left x and y boundaries to not exceed BOUNDARY_MARGIN minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; // TODO: probably need to factor in graphZoom - maxX = maxX > $container.width() ? $container.width() - BOUNDARY_MARGIN_X_R : maxX; + // maxX = maxX > $container.width() ? $container.width() - BOUNDARY_MARGIN_X_R : maxX; minY = minY < BOUNDARY_MARGIN_Y_T ? BOUNDARY_MARGIN_Y_T : minY; - maxY = maxY > $container.height() ? $container.height() - BOUNDARY_MARGIN_Y_B : maxY; + // maxY = maxY > $container.height() ? $container.height() - BOUNDARY_MARGIN_Y_B : maxY; + // console.log("flexi box width and height", maxX - minX, "maxX", maxX, "minX", minX, "maxY - minY", maxY - minY, "maxY", maxY, "minY", minY) let width = 1234; if (maxX < 0 && minX < 0) { @@ -1570,15 +1571,8 @@ export var drawGraph = function (workbook) { // console.log("right bound violated"); // if (flexibleContainer.x * graphZoom < $container.width() / graphZoom / 2){ BOUNDARY_MARGIN_X_R = width / graphZoom - BOUNDARY_MARGIN; - // } else { - // BOUNDARY_MARGIN_X_R = Math.abs(xTranslation) / graphZoom; - // } - // } BOUNDARY_MARGIN_Y_T = -yTranslation / graphZoom + BOUNDARY_MARGIN / 2; - // if (yTranslation >= height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { - // console.log("bottom bound violated") BOUNDARY_MARGIN_Y_B = height / graphZoom - BOUNDARY_MARGIN; - // } } var SELF_REFERRING_Y_OFFSET = 6; @@ -1618,9 +1612,15 @@ export var drawGraph = function (workbook) { width ${Math.round(flexibleContainerRect.attr("width"))} x ${Math.round(flexibleContainerRect.attr("x"))} maxX ${Math.round(flexibleContainer.maxX)} + boundX + ${Math.round(BOUNDARY_MARGIN_X_L)} + ${Math.round(BOUNDARY_MARGIN_X_R)} height ${Math.round(flexibleContainerRect.attr("height"))} y ${Math.round(flexibleContainerRect.attr("y"))} maxY ${Math.round(flexibleContainer.maxY)} + boundY + ${Math.round(BOUNDARY_MARGIN_Y_T)} + ${Math.round(BOUNDARY_MARGIN_Y_B)} `; $("#flexiBox-dimensions").text(flexDimensions); @@ -1833,8 +1833,22 @@ export var drawGraph = function (workbook) { } function dragged (d) { - d.fx = d3.event.x; - d.fy = d3.event.y; + console.log(d, "d.fx", d3.event.x, "d.fy", d3.event.y) + if (!adaptive) { + if (d3.event.x + d.textWidth <= (-xTranslation / graphZoom + 5/2) + (width / graphZoom) - 5) { + d.fx = d3.event.x; + } else { + d.fx = (-xTranslation / graphZoom + 5/2) + (width / graphZoom) - 5 - d.textWidth; + } + if (d3.event.y + nodeHeight<= -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5) { + d.fy = d3.event.y; + } else { + d.fy = -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5 - nodeHeight; + } + } else { + d.fx = d3.event.x; + d.fy = d3.event.y; + } } grnState.simulation = simulation; From fdb61dc36de2f6109e3a253bdedf68f169d36f11 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 19:06:09 -0700 Subject: [PATCH 121/150] Issue #1083. Cleaning up comments and adjusting rightBoundary and bottomBoundary to take the textWidth and nodeHeight into account as well as the selfReferringEdgeWidth and selfReferringEdgeHeight --- web-client/public/js/graph.js | 78 ++++++++++------------------------- 1 file changed, 21 insertions(+), 57 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index a3c3d2fa..12c47ba8 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1450,9 +1450,7 @@ export var drawGraph = function (workbook) { } }; - // there is too much whitespace in flexiContainer function calcFlexiBox (BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B) { - // console.log("calc flexi box run") const nodes = simulation.nodes() let nodeWidth = 0; if (nodes.length > 0) { @@ -1501,30 +1499,22 @@ export var drawGraph = function (workbook) { let minY = Math.min(...yValuesNodes); let maxY = Math.max(...yValuesNodes) + nodeHeight; - // handle left x and y boundaries to not exceed BOUNDARY_MARGIN + // handle left x and top y boundaries to not exceed BOUNDARY_MARGIN minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; - // TODO: probably need to factor in graphZoom - // maxX = maxX > $container.width() ? $container.width() - BOUNDARY_MARGIN_X_R : maxX; minY = minY < BOUNDARY_MARGIN_Y_T ? BOUNDARY_MARGIN_Y_T : minY; - // maxY = maxY > $container.height() ? $container.height() - BOUNDARY_MARGIN_Y_B : maxY; - - // console.log("flexi box width and height", maxX - minX, "maxX", maxX, "minX", minX, "maxY - minY", maxY - minY, "maxY", maxY, "minY", minY) - let width = 1234; + let width = maxX - minX; if (maxX < 0 && minX < 0) { width = Math.abs(maxX) - Math.abs(minX); - } else { - width = maxX - minX; - } - let height = 1234; + } + + let height = maxY - minY; if (maxY < 0 && minY < 0) { height = Math.abs(maxY) - Math.abs(minY); - } else { - height = maxY - minY; } return {x: minX, y: minY, maxX: maxX, maxY: maxY, width: width, height: height}; } - // this checks if zoomInValue is in bounds when zoom in and out + // this checks if zoomValue is in bounds when zoom in and out function flexRectInBounds(zoomValue) { if (flexibleContainer) { updateZoomContainerInfo(); @@ -1562,14 +1552,6 @@ export var drawGraph = function (workbook) { let BOUNDARY_MARGIN_Y_B = BOUNDARY_MARGIN; if (!adaptive && flexibleContainer) { BOUNDARY_MARGIN_X_L = -xTranslation / graphZoom + BOUNDARY_MARGIN / 2; - // if ( - // xTranslation >= - // $container.width() - - // (graphZoom * flexibleContainer.width + - // graphZoom * flexibleContainer.x) - // ) { - // console.log("right bound violated"); - // if (flexibleContainer.x * graphZoom < $container.width() / graphZoom / 2){ BOUNDARY_MARGIN_X_R = width / graphZoom - BOUNDARY_MARGIN; BOUNDARY_MARGIN_Y_T = -yTranslation / graphZoom + BOUNDARY_MARGIN / 2; BOUNDARY_MARGIN_Y_B = height / graphZoom - BOUNDARY_MARGIN; @@ -1582,32 +1564,6 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B); - /* - xTrnslt - ${Math.round(xTranslation)} - flx.x - ${Math.round(flexibleContainer.x)} - flx.w - ${Math.round(flexibleContainer.width)} - flx.x+flx.w - ${Math.round(flexibleContainer.x + flexibleContainer.width)} - flxx+w scaled - ${Math.round( - (flexibleContainer.x + flexibleContainer.width) * graphZoom - )} - boundX - ${Math.round(BOUNDARY_MARGIN_X_L)} - ${Math.round(BOUNDARY_MARGIN_X_R)} - yTrnslt - ${Math.round(yTranslation)} - flx.y - ${Math.round(flexibleContainer.y)} - flx.h - ${Math.round(flexibleContainer.height)} - boundY - ${Math.round(BOUNDARY_MARGIN_Y_T)} - ${Math.round(BOUNDARY_MARGIN_Y_B)} - */ const flexDimensions = ` width ${Math.round(flexibleContainerRect.attr("width"))} x ${Math.round(flexibleContainerRect.attr("x"))} @@ -1644,15 +1600,17 @@ export var drawGraph = function (workbook) { var selfReferringEdgeWidth = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + 2 : 0); - // this creates too much whitespace, want it to be the BOUNDARY_MARGIN_X when can see right side of borerbox - // a stack overflow link to look at: https://stackoverflow.com/questions/26781129/d3-v2-prevent-zooming-and-panning-chart-outside-viewport - // could also look at this: https://observablehq.com/@john-guerra/force-directed-adjusted - // and look at this too: https://www.w3.org/TR/SVG/coords.html var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN - selfReferringEdgeWidth; if (!adaptive) { - rightBoundary = -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + width / graphZoom - BOUNDARY_MARGIN; + rightBoundary = + -xTranslation / graphZoom + + BOUNDARY_MARGIN / 2 + + width / graphZoom - + BOUNDARY_MARGIN - + (d.textWidth + OFFSET_VALUE) - + selfReferringEdgeWidth; } - // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds + // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentXPos = Math.max(BOUNDARY_MARGIN_X_L, Math.min(rightBoundary, d.x)); if (adaptive && width < MAX_WIDTH && (currentXPos === BOUNDARY_MARGIN || currentXPos === rightBoundary)) { @@ -1681,7 +1639,13 @@ export var drawGraph = function (workbook) { selfReferringEdge.strokeWidth + SELF_REFERRING_Y_OFFSET + 0.5 : 0); var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN_Y_B - selfReferringEdgeHeight; if (!adaptive) { - bottomBoundary = -yTranslation / graphZoom + BOUNDARY_MARGIN / 2 + height / graphZoom - BOUNDARY_MARGIN; + bottomBoundary = + -yTranslation / graphZoom + + BOUNDARY_MARGIN / 2 + + height / graphZoom - + BOUNDARY_MARGIN - + nodeHeight - + selfReferringEdgeHeight; } // currentYPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds var currentYPos = Math.max(BOUNDARY_MARGIN_Y_T, Math.min(bottomBoundary, d.y)); From 3341c506125b0b04982243c99b7b72979d42b5b0 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 20:10:29 -0700 Subject: [PATCH 122/150] Issue #1083. Deleting more console logs and adding checks in calcFlexiBox to ensure that the flexbox does not exceed the bounds. need to take the edges into account for flexiBox --- web-client/public/js/graph.js | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 12c47ba8..4d2fbbf8 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1502,16 +1502,27 @@ export var drawGraph = function (workbook) { // handle left x and top y boundaries to not exceed BOUNDARY_MARGIN minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; minY = minY < BOUNDARY_MARGIN_Y_T ? BOUNDARY_MARGIN_Y_T : minY; - let width = maxX - minX; + + maxX = + maxX > -xTranslation / graphZoom + 5 / 2 + width / graphZoom - 5 + ? -xTranslation / graphZoom + 5 / 2 + width / graphZoom - 5 + : maxX; + + maxY = + maxY > -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5 + ? -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5 + : maxY; + + let flexiBoxWidth = maxX - minX; if (maxX < 0 && minX < 0) { - width = Math.abs(maxX) - Math.abs(minX); + flexiBoxWidth = Math.abs(maxX) - Math.abs(minX); } - let height = maxY - minY; + let flexiBoxHeight = maxY - minY; if (maxY < 0 && minY < 0) { - height = Math.abs(maxY) - Math.abs(minY); + flexiBoxHeight = Math.abs(maxY) - Math.abs(minY); } - return {x: minX, y: minY, maxX: maxX, maxY: maxY, width: width, height: height}; + return {x: minX, y: minY, maxX: maxX, maxY: maxY, width: flexiBoxWidth, height: flexiBoxHeight}; } // this checks if zoomValue is in bounds when zoom in and out @@ -1519,10 +1530,8 @@ export var drawGraph = function (workbook) { if (flexibleContainer) { updateZoomContainerInfo(); if (flexibleContainer.width * zoomValue > width ) { - console.log("width out of bounds") return false; } else if (flexibleContainer.height * zoomValue > height) { - console.log("height out of bounds") return false; } } @@ -1797,14 +1806,13 @@ export var drawGraph = function (workbook) { } function dragged (d) { - console.log(d, "d.fx", d3.event.x, "d.fy", d3.event.y) if (!adaptive) { if (d3.event.x + d.textWidth <= (-xTranslation / graphZoom + 5/2) + (width / graphZoom) - 5) { d.fx = d3.event.x; } else { d.fx = (-xTranslation / graphZoom + 5/2) + (width / graphZoom) - 5 - d.textWidth; } - if (d3.event.y + nodeHeight<= -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5) { + if (d3.event.y + nodeHeight <= -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5) { d.fy = d3.event.y; } else { d.fy = -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5 - nodeHeight; From 83b6a5809f438af70c252fead45d7fd7345b0fe4 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 20:47:04 -0700 Subject: [PATCH 123/150] Issue #1083. Cleaning up comments, console logs and making calculations for left and top boundaries a function. for some reason now graph exceeds left side of viewport so need to see why that is happening --- web-client/public/js/graph.js | 138 ++++++++++++++++------------------ 1 file changed, 66 insertions(+), 72 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 4d2fbbf8..7df93574 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -179,9 +179,9 @@ export var drawGraph = function (workbook) { } if ( - adaptive || - (!adaptive && - flexRectInBounds(graphZoom) && + adaptive || + (!adaptive && + flexZoomInBounds(graphZoom) && viewportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy, false)) ) { zoom.translateBy( @@ -289,13 +289,7 @@ export var drawGraph = function (workbook) { function viewportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { updateZoomContainerInfo(); - //TODO: need to call calcFlexiBox here so that updates even when tick isn't running because nodes aren't moving - // flexibleContainer = calcFlexiBox( - // BOUNDARY_MARGIN_X_L, - // BOUNDARY_MARGIN_X_R, - // BOUNDARY_MARGIN_Y_T, - // BOUNDARY_MARGIN_Y_B - // ); + flexibleContainer = calcFlexiBox() // left border if (xTranslation < 0 && Math.abs(xTranslation) >= @@ -349,7 +343,7 @@ export var drawGraph = function (workbook) { $container.removeClass(CURSOR_CLASSES).addClass("cursorGrab"); } var container = zoomContainer; - if (adaptive || (!adaptive && flexRectInBounds(graphZoom))) { + if (adaptive || (!adaptive && flexZoomInBounds(graphZoom))) { zoom.scaleTo(container, zoomScale); graphZoom = zoomScale; } @@ -369,7 +363,7 @@ export var drawGraph = function (workbook) { if (adaptive) { zoomDisplay = grnState.zoomValue - } else if (!adaptive && flexRectInBounds((grnState.zoomValue <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)(grnState.zoomValue)) ) { + } else if (!adaptive && flexZoomInBounds((grnState.zoomValue <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)(grnState.zoomValue)) ) { zoomDisplay = grnState.zoomValue; } else { grnState.zoomValue = prevGrnstateZoomVal; @@ -392,10 +386,8 @@ export var drawGraph = function (workbook) { $(ZOOM_INPUT).val(finalDisplay); } - // This controls actual movement of slider - if (adaptive || (!adaptive && flexRectInBounds(calcGraphZoom))) { - // TODO: don't really want to center anymore for zooming since don't care if see bounding box anymore - // if don't center, then get issue of zooming into the box since not inside the width of the viewport + // This controls movement of slider and is where the zoomSlider can be restricted + if (adaptive || (!adaptive && flexZoomInBounds(calcGraphZoom))) { if (!adaptive) { center(); updateZoomContainerInfo(); @@ -1450,7 +1442,8 @@ export var drawGraph = function (workbook) { } }; - function calcFlexiBox (BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B) { + const BOUNDARY_MARGIN = 5; + function calcFlexiBox () { const nodes = simulation.nodes() let nodeWidth = 0; if (nodes.length > 0) { @@ -1500,17 +1493,19 @@ export var drawGraph = function (workbook) { let maxY = Math.max(...yValuesNodes) + nodeHeight; // handle left x and top y boundaries to not exceed BOUNDARY_MARGIN + const BOUNDARY_MARGIN_X_L = getBOUNDARY_MARGIN_X_L(); + const BOUNDARY_MARGIN_Y_T = getBOUNDARY_MARGIN_Y_T(); minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; minY = minY < BOUNDARY_MARGIN_Y_T ? BOUNDARY_MARGIN_Y_T : minY; maxX = - maxX > -xTranslation / graphZoom + 5 / 2 + width / graphZoom - 5 - ? -xTranslation / graphZoom + 5 / 2 + width / graphZoom - 5 + maxX > -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + width / graphZoom - BOUNDARY_MARGIN + ? -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + width / graphZoom - BOUNDARY_MARGIN : maxX; maxY = - maxY > -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5 - ? -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5 + maxY > -yTranslation / graphZoom + BOUNDARY_MARGIN / 2 + height / graphZoom - BOUNDARY_MARGIN + ? -yTranslation / graphZoom + BOUNDARY_MARGIN / 2 + height / graphZoom - BOUNDARY_MARGIN : maxY; let flexiBoxWidth = maxX - minX; @@ -1522,13 +1517,21 @@ export var drawGraph = function (workbook) { if (maxY < 0 && minY < 0) { flexiBoxHeight = Math.abs(maxY) - Math.abs(minY); } + + boundingBoxRect + .attr("x", -xTranslation / graphZoom + BOUNDARY_MARGIN / 2) + .attr("width", width / graphZoom - BOUNDARY_MARGIN) + .attr("y", -yTranslation / graphZoom + BOUNDARY_MARGIN / 2) + .attr("height", height / graphZoom - BOUNDARY_MARGIN); + return {x: minX, y: minY, maxX: maxX, maxY: maxY, width: flexiBoxWidth, height: flexiBoxHeight}; } // this checks if zoomValue is in bounds when zoom in and out - function flexRectInBounds(zoomValue) { + function flexZoomInBounds(zoomValue) { if (flexibleContainer) { updateZoomContainerInfo(); + flexibleContainer = calcFlexiBox(); if (flexibleContainer.width * zoomValue > width ) { return false; } else if (flexibleContainer.height * zoomValue > height) { @@ -1538,6 +1541,16 @@ export var drawGraph = function (workbook) { return true } + // only calculate Left and Top boundary margins because calculate rightboundary and bottomboundary in tick + function getBOUNDARY_MARGIN_X_L() { + return !adaptive && flexibleContainer ? -xTranslation / graphZoom + BOUNDARY_MARGIN / 2: BOUNDARY_MARGIN; + } + + function getBOUNDARY_MARGIN_Y_T() { + return !adaptive && flexibleContainer ? - yTranslation / graphZoom + BOUNDARY_MARGIN / 2 : BOUNDARY_MARGIN; + ; + } + // Tick only runs while the graph physics are still running. // (I.e. when the graph is completely relaxed, tick stops running.) function tick () { @@ -1552,54 +1565,32 @@ export var drawGraph = function (workbook) { return edge ? 17 + (getEdgeThickness(edge) / 2) : 0; }; - let BOUNDARY_MARGIN = 5; - // Left and right boundary margins: - let BOUNDARY_MARGIN_X_L = BOUNDARY_MARGIN; - let BOUNDARY_MARGIN_X_R = BOUNDARY_MARGIN; - // top and bottom boundary margins: - let BOUNDARY_MARGIN_Y_T = BOUNDARY_MARGIN; - let BOUNDARY_MARGIN_Y_B = BOUNDARY_MARGIN; - if (!adaptive && flexibleContainer) { - BOUNDARY_MARGIN_X_L = -xTranslation / graphZoom + BOUNDARY_MARGIN / 2; - BOUNDARY_MARGIN_X_R = width / graphZoom - BOUNDARY_MARGIN; - BOUNDARY_MARGIN_Y_T = -yTranslation / graphZoom + BOUNDARY_MARGIN / 2; - BOUNDARY_MARGIN_Y_B = height / graphZoom - BOUNDARY_MARGIN; - } - var SELF_REFERRING_Y_OFFSET = 6; var MAX_WIDTH = 5000; var MAX_HEIGHT = 5000; var OFFSET_VALUE = 5; if (!adaptive) { - flexibleContainer = calcFlexiBox(BOUNDARY_MARGIN_X_L, BOUNDARY_MARGIN_X_R, BOUNDARY_MARGIN_Y_T, BOUNDARY_MARGIN_Y_B); + flexibleContainer = calcFlexiBox(); + const flexDimensions = ` width ${Math.round(flexibleContainerRect.attr("width"))} x ${Math.round(flexibleContainerRect.attr("x"))} maxX ${Math.round(flexibleContainer.maxX)} - boundX - ${Math.round(BOUNDARY_MARGIN_X_L)} - ${Math.round(BOUNDARY_MARGIN_X_R)} + height ${Math.round(flexibleContainerRect.attr("height"))} y ${Math.round(flexibleContainerRect.attr("y"))} maxY ${Math.round(flexibleContainer.maxY)} - boundY - ${Math.round(BOUNDARY_MARGIN_Y_T)} - ${Math.round(BOUNDARY_MARGIN_Y_B)} + `; $("#flexiBox-dimensions").text(flexDimensions); + flexibleContainerRect .attr("x", flexibleContainer.x) .attr("y", flexibleContainer.y) .attr("width", flexibleContainer.width) .attr("height", flexibleContainer.height); - - boundingBoxRect - .attr("x", -xTranslation / graphZoom + BOUNDARY_MARGIN / 2) - .attr("width", width / graphZoom - BOUNDARY_MARGIN) - .attr("y", -yTranslation / graphZoom + BOUNDARY_MARGIN / 2) - .attr("height", height / graphZoom - BOUNDARY_MARGIN); } // this controls movement and position of nodes, clamps the nodes to boundary @@ -1620,33 +1611,36 @@ export var drawGraph = function (workbook) { selfReferringEdgeWidth; } // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentXPos = Math.max(BOUNDARY_MARGIN_X_L, Math.min(rightBoundary, d.x)); - if (adaptive && width < MAX_WIDTH && - (currentXPos === BOUNDARY_MARGIN || currentXPos === rightBoundary)) { - if (!d3.select(this).classed("fixed")) { - width += OFFSET_VALUE; - boundingBoxContainer.attr("width", width); - - link - .attr("x1", function (d) { - return d.source.x; - }) - .attr("x2", function (d) { - return d.target.x; - }); - - node - .attr("x", function (d) { - return d.x; - }); - } + var currentXPos = Math.max(BOUNDARY_MARGIN, Math.min(rightBoundary, d.x)); + if ( + adaptive && + width < MAX_WIDTH && + (currentXPos === getBOUNDARY_MARGIN_X_L() || + currentXPos === rightBoundary) + ) { + if (!d3.select(this).classed("fixed")) { + width += OFFSET_VALUE; + boundingBoxContainer.attr("width", width); + + link + .attr("x1", function(d) { + return d.source.x; + }) + .attr("x2", function(d) { + return d.target.x; + }); + + node.attr("x", function(d) { + return d.x; + }); + } } return d.x = currentXPos; }).attr("y", function (d) { var selfReferringEdge = getSelfReferringEdge(d); var selfReferringEdgeHeight = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + SELF_REFERRING_Y_OFFSET + 0.5 : 0); - var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN_Y_B - selfReferringEdgeHeight; + var bottomBoundary = height - nodeHeight - BOUNDARY_MARGIN - selfReferringEdgeHeight; if (!adaptive) { bottomBoundary = -yTranslation / graphZoom + @@ -1657,10 +1651,10 @@ export var drawGraph = function (workbook) { selfReferringEdgeHeight; } // currentYPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentYPos = Math.max(BOUNDARY_MARGIN_Y_T, Math.min(bottomBoundary, d.y)); + var currentYPos = Math.max(getBOUNDARY_MARGIN_Y_T(), Math.min(bottomBoundary, d.y)); if (adaptive && height < MAX_HEIGHT && - (currentYPos === BOUNDARY_MARGIN_Y_T || currentYPos === bottomBoundary)) { + (currentYPos === getBOUNDARY_MARGIN_Y_T() || currentYPos === bottomBoundary)) { if (!d3.select(this).classed("fixed")) { height += OFFSET_VALUE; boundingBoxContainer.attr("height", height); From f502b11ed5b7d1226372c38b6edc8484f2b504cb Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 16 Apr 2024 21:15:47 -0700 Subject: [PATCH 124/150] Issue #1083. Fixed problem with exceeding left border. It was because I was using BOUNDARY_MARGIN and not BOUNDARY_MARGIN_X_L in tick --- web-client/public/js/graph.js | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 7df93574..13ea7e78 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -1577,11 +1577,9 @@ export var drawGraph = function (workbook) { width ${Math.round(flexibleContainerRect.attr("width"))} x ${Math.round(flexibleContainerRect.attr("x"))} maxX ${Math.round(flexibleContainer.maxX)} - height ${Math.round(flexibleContainerRect.attr("height"))} y ${Math.round(flexibleContainerRect.attr("y"))} maxY ${Math.round(flexibleContainer.maxY)} - `; $("#flexiBox-dimensions").text(flexDimensions); @@ -1611,7 +1609,7 @@ export var drawGraph = function (workbook) { selfReferringEdgeWidth; } // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentXPos = Math.max(BOUNDARY_MARGIN, Math.min(rightBoundary, d.x)); + var currentXPos = Math.max(getBOUNDARY_MARGIN_X_L(), Math.min(rightBoundary, d.x)); if ( adaptive && width < MAX_WIDTH && From e0f61ccb4214bb56b5fd02bbea35feea65011543 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 17 Apr 2024 18:57:21 -0700 Subject: [PATCH 125/150] Issue #1083. Removing stroke color from boundingBoxRect and flexBoxRect. Also removing comments and extra spaces. Also moved viewportBoundsMoveDrag so next to the other flexibleContainer functions --- web-client/public/js/graph.js | 35 +++++++---------------------------- web-client/views/upload.pug | 2 -- 2 files changed, 7 insertions(+), 30 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 13ea7e78..f7ecf824 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -230,8 +230,6 @@ export var drawGraph = function (workbook) { var flexibleContainerRect = boundingBoxContainer.append("rect") .attr("class", "boundingBox") - .attr("stroke", "black") - .attr("stroke-width", 1) .attr("fill", "none") .attr("id", "flexibleContainerRect"); @@ -263,10 +261,6 @@ export var drawGraph = function (workbook) { let yTranslation = 0; let flexibleContainer = null; - function getXTranslation() { - return xTranslation; - } - function updateZoomContainerInfo() { // transform attribute of zoomContainer contains translation info about graph if (zoomContainer.attr("transform")) { @@ -355,12 +349,11 @@ export var drawGraph = function (workbook) { let zoomScaleSliderLeft; let zoomScaleSliderRight; let prevGrnstateZoomVal; - let centerXCoord; - let centerYCoord; const updateAppBasedOnZoomValue = () => { let zoomDisplay; + // If the zoom value is out of bounds, reset it to the previous value. if (adaptive) { zoomDisplay = grnState.zoomValue } else if (!adaptive && flexZoomInBounds((grnState.zoomValue <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)(grnState.zoomValue)) ) { @@ -391,8 +384,6 @@ export var drawGraph = function (workbook) { if (!adaptive) { center(); updateZoomContainerInfo(); - centerXCoord = xTranslation; - centerYCoord = yTranslation; } $(ZOOM_SLIDER).val( @@ -507,11 +498,10 @@ export var drawGraph = function (workbook) { width = $container.width(); height = $container.height(); // put a border with a gray stroke around the original container size - d3.select("rect").attr("stroke", "#9A9A9A") - .attr("width", width) - .attr("height", height); + d3.select("rect") + .attr("width", width) + .attr("height", height); $(".boundingBox").attr("width", width).attr("height", height); - d3.select("#flexibleContainerRect").attr("stroke", "black"); center(); } updateAppBasedOnZoomValue(); // Update zoom value within bounds @@ -1497,7 +1487,7 @@ export var drawGraph = function (workbook) { const BOUNDARY_MARGIN_Y_T = getBOUNDARY_MARGIN_Y_T(); minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; minY = minY < BOUNDARY_MARGIN_Y_T ? BOUNDARY_MARGIN_Y_T : minY; - + maxX = maxX > -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + width / graphZoom - BOUNDARY_MARGIN ? -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + width / graphZoom - BOUNDARY_MARGIN @@ -1511,7 +1501,7 @@ export var drawGraph = function (workbook) { let flexiBoxWidth = maxX - minX; if (maxX < 0 && minX < 0) { flexiBoxWidth = Math.abs(maxX) - Math.abs(minX); - } + } let flexiBoxHeight = maxY - minY; if (maxY < 0 && minY < 0) { @@ -1538,7 +1528,7 @@ export var drawGraph = function (workbook) { return false; } } - return true + return true; } // only calculate Left and Top boundary margins because calculate rightboundary and bottomboundary in tick @@ -1573,17 +1563,6 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(); - const flexDimensions = ` - width ${Math.round(flexibleContainerRect.attr("width"))} - x ${Math.round(flexibleContainerRect.attr("x"))} - maxX ${Math.round(flexibleContainer.maxX)} - height ${Math.round(flexibleContainerRect.attr("height"))} - y ${Math.round(flexibleContainerRect.attr("y"))} - maxY ${Math.round(flexibleContainer.maxY)} - `; - $("#flexiBox-dimensions").text(flexDimensions); - - flexibleContainerRect .attr("x", flexibleContainer.x) .attr("y", flexibleContainer.y) diff --git a/web-client/views/upload.pug b/web-client/views/upload.pug index b7bbf70c..1f1b0558 100644 --- a/web-client/views/upload.pug +++ b/web-client/views/upload.pug @@ -285,8 +285,6 @@ html include components/demo.pug li a(href='#' id='fileName') - li - a(href='#' id='flexiBox-dimensions') ul(class='nav navbar-nav navbar-right graph-metadata-container') li(class='navbar-text text-right') small(id='graph-metadata') From ed1707955582800dff416837cf302916cef9d49f Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 17 Apr 2024 18:57:42 -0700 Subject: [PATCH 126/150] Issue #1083. Removing stroke color from boundingBoxRect and flexBoxRect. Also removing comments and extra spaces. Also moved viewportBoundsMoveDrag so next to the other flexibleContainer functions --- web-client/public/js/graph.js | 100 +++++++++++++++++----------------- 1 file changed, 50 insertions(+), 50 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index f7ecf824..3fa73984 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -281,56 +281,6 @@ export var drawGraph = function (workbook) { } }; - function viewportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { - updateZoomContainerInfo(); - flexibleContainer = calcFlexiBox() - // left border - if (xTranslation < 0 && - Math.abs(xTranslation) >= - Math.floor(flexibleContainer.x) * graphZoom + dx * graphZoom) - { - return false; - } - - //dPad movement when moving left - if ( - dPadMove && - xTranslation < 0 && - dx < 0 && - Math.abs(xTranslation + dx) > flexibleContainer.x * graphZoom - ) { - return false; - } - - // right border - if (xTranslation + dx > width - (graphZoom * flexibleContainer.width + graphZoom * flexibleContainer.x)) { - return false - } - - // Y-axis boundaries - // prevents graph from going through top border - if (yTranslation < 0 && - Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) * graphZoom && - (dy < 0 || - (dy > 0 && - Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) + dy * graphZoom)) - ) { - return false; - } - - // moving up with dPad - if (dPadMove && yTranslation < 0 && dy < 0 && Math.abs(yTranslation + dy) > flexibleContainer.y) { - return false - } - - // bottom border - if (yTranslation + dy > height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { - return false - } - - return true - }; - // controls reading movement of zoomSlider and scaling graph to that zoomScale const setGraphZoom = zoomScale => { if (zoomScale < MIDDLE_SCALE) { @@ -1433,6 +1383,56 @@ export var drawGraph = function (workbook) { }; const BOUNDARY_MARGIN = 5; + function viewportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { + updateZoomContainerInfo(); + flexibleContainer = calcFlexiBox() + // left border + if (xTranslation < 0 && + Math.abs(xTranslation) >= + Math.floor(flexibleContainer.x) * graphZoom + dx * graphZoom) + { + return false; + } + + //dPad movement when moving left + if ( + dPadMove && + xTranslation < 0 && + dx < 0 && + Math.abs(xTranslation + dx) > flexibleContainer.x * graphZoom + ) { + return false; + } + + // right border + if (xTranslation + dx > width - (graphZoom * flexibleContainer.width + graphZoom * flexibleContainer.x)) { + return false + } + + // Y-axis boundaries + // prevents graph from going through top border + if (yTranslation < 0 && + Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) * graphZoom && + (dy < 0 || + (dy > 0 && + Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) + dy * graphZoom)) + ) { + return false; + } + + // moving up with dPad + if (dPadMove && yTranslation < 0 && dy < 0 && Math.abs(yTranslation + dy) > flexibleContainer.y) { + return false + } + + // bottom border + if (yTranslation + dy > height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { + return false + } + + return true + }; + function calcFlexiBox () { const nodes = simulation.nodes() let nodeWidth = 0; From 948eca8019a2d31611d48b06014207d5d712ddd8 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 17 Apr 2024 21:33:45 -0700 Subject: [PATCH 127/150] Issue #1083. There was an edge case where if the nodes were not moving, then the nodes would be able to exceed the viewport bounds when dragged. I changed the viewportBoundsMoveDrag to check that the viewport is in bounds when dragged and now the nodes are always in bounds --- web-client/public/js/graph.js | 136 ++++++++++++++-------------------- 1 file changed, 55 insertions(+), 81 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 3fa73984..2d2d4f07 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -178,17 +178,15 @@ export var drawGraph = function (workbook) { scale = 1 / +(string.match(/scale\(([^\)]+)\)/)[1]); } - if ( - adaptive || - (!adaptive && + if (adaptive || (!adaptive && flexZoomInBounds(graphZoom) && - viewportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy, false)) + viewportBoundsMoveDrag(graphZoom, d3.event.dx, d3.event.dy)) ) { - zoom.translateBy( - zoomContainer, - scale * (d3.event.x - zoomDragPrevX), - scale * (d3.event.y - zoomDragPrevY) - ); + zoom.translateBy( + zoomContainer, + scale * (d3.event.x - zoomDragPrevX), + scale * (d3.event.y - zoomDragPrevY) + ); } zoomDragPrevX = d3.event.x; zoomDragPrevY = d3.event.y; @@ -482,7 +480,7 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { - if (viewportBoundsMoveDrag(graphZoom, moveWidth, moveHeight, true)) { + if (viewportBoundsMoveDrag(graphZoom, moveWidth, moveHeight)) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } } @@ -1383,51 +1381,37 @@ export var drawGraph = function (workbook) { }; const BOUNDARY_MARGIN = 5; - function viewportBoundsMoveDrag(graphZoom, dx, dy, dPadMove) { + // TODO: take off dPadMove + function viewportBoundsMoveDrag(graphZoom, dx, dy) { updateZoomContainerInfo(); - flexibleContainer = calcFlexiBox() - // left border - if (xTranslation < 0 && - Math.abs(xTranslation) >= - Math.floor(flexibleContainer.x) * graphZoom + dx * graphZoom) - { - return false; - } + flexibleContainer = calcFlexiBox(); - //dPad movement when moving left if ( - dPadMove && - xTranslation < 0 && - dx < 0 && - Math.abs(xTranslation + dx) > flexibleContainer.x * graphZoom + flexibleContainer.x + flexibleContainer.width + dx >= + -xTranslation / graphZoom + + BOUNDARY_MARGIN / 2 + + width / graphZoom - + BOUNDARY_MARGIN ) { return false; } - // right border - if (xTranslation + dx > width - (graphZoom * flexibleContainer.width + graphZoom * flexibleContainer.x)) { - return false - } - - // Y-axis boundaries - // prevents graph from going through top border - if (yTranslation < 0 && - Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) * graphZoom && - (dy < 0 || - (dy > 0 && - Math.abs(yTranslation) >= Math.floor(flexibleContainer.y) + dy * graphZoom)) - ) { + if (flexibleContainer.x + dx <= getBOUNDARY_MARGIN_X_L()) { return false; } - // moving up with dPad - if (dPadMove && yTranslation < 0 && dy < 0 && Math.abs(yTranslation + dy) > flexibleContainer.y) { + if ( + flexibleContainer.y + flexibleContainer.height + dy >= + -yTranslation / graphZoom + + BOUNDARY_MARGIN / 2 + + height / graphZoom - + BOUNDARY_MARGIN + ) { return false } - // bottom border - if (yTranslation + dy > height - (graphZoom * flexibleContainer.height + graphZoom * flexibleContainer.y)) { - return false + if (flexibleContainer.y + dy <= getBOUNDARY_MARGIN_Y_T()) { + return false; } return true @@ -1440,42 +1424,9 @@ export var drawGraph = function (workbook) { nodeWidth = nodes[0].textWidth + 8; } - let xValuesPaths = [] - let yValuesPaths = [] - - // link.selectAll("path").each( function(pathData) { - // if (pathData.source) { - // // Log the "d" attribute for each path - // const controlPoints = d3.select(this).attr("d"); - // if (controlPoints) { - // if (controlPoints.includes("A")) { - // const splitSpaces = controlPoints.split(" "); - // const controlPointXY = splitSpaces[2].split(",") - // const controlPointX = controlPointXY[0]; - // const controlPointY = controlPointXY[1]; - // xValuesPaths.push(parseFloat(controlPointX)) - // yValuesPaths.push(parseFloat(controlPointY)) - // } - // else if (controlPoints.includes("C")) { - // const splitC = controlPoints.split("C"); - - // splitC[1].split(",").forEach((coordinates) => { - // const splitSpaces = coordinates.split(" "); - // const xValue = splitSpaces[splitSpaces.length - 2]; - // const yValue = splitSpaces[splitSpaces.length - 1]; - // xValuesPaths.push(parseFloat(xValue)); - // yValuesPaths.push(parseFloat(yValue)); - // }); - // } - // } - // } - // }); const xValuesNodes = nodes.map((node) => node.x); const yValuesNodes = nodes.map((node) => node.y); - // const xValues = xValuesPaths.concat(xValuesNodes); - // const yValues = yValuesPaths.concat(yValuesNodes); - let minX = Math.min(...xValuesNodes); let maxX = Math.max(...xValuesNodes) + nodeWidth; @@ -1681,7 +1632,6 @@ export var drawGraph = function (workbook) { var ADDITIONAL_SHIFT = 0.07; var END_POINT_ADJUSTMENT = 1.2; - // Self edge. if (x1 === x2 && y1 === y2) { // Move the position of the loop. @@ -1778,15 +1728,39 @@ export var drawGraph = function (workbook) { function dragged (d) { if (!adaptive) { - if (d3.event.x + d.textWidth <= (-xTranslation / graphZoom + 5/2) + (width / graphZoom) - 5) { + // prevents nodes from being dragged outside of right boundary + if ( + d3.event.x + d.textWidth <= + -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + + width / graphZoom - + BOUNDARY_MARGIN + ) { d.fx = d3.event.x; } else { - d.fx = (-xTranslation / graphZoom + 5/2) + (width / graphZoom) - 5 - d.textWidth; + d.fx = + -xTranslation / graphZoom + + BOUNDARY_MARGIN / 2 + + width / graphZoom - + BOUNDARY_MARGIN - + d.textWidth; } - if (d3.event.y + nodeHeight <= -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5) { - d.fy = d3.event.y; + + // prevent nodes from being dragged out of bottom boundary + if ( + d3.event.y + nodeHeight <= + -yTranslation / graphZoom + + BOUNDARY_MARGIN / 2 + + height / graphZoom - + BOUNDARY_MARGIN + ) { + d.fy = d3.event.y; } else { - d.fy = -yTranslation / graphZoom + 5 / 2 + height / graphZoom - 5 - nodeHeight; + d.fy = + -yTranslation / graphZoom + + BOUNDARY_MARGIN / 2 + + height / graphZoom - + BOUNDARY_MARGIN - + nodeHeight; } } else { d.fx = d3.event.x; From 35fece7a35d47e2fcc748884c75e20451248dfe8 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 17 Apr 2024 22:22:40 -0700 Subject: [PATCH 128/150] Issue #1083. Passing all lint. Had to change variable name get_BOUNDARY_MARGIN_X_L to getLeftXBoundaryMargin and same for get_BOUNDARY_MARGIN_Y_T. Made comments more descriptive and adjust dimensions of flexiBox in calcFlexiBox --- web-client/public/js/graph.js | 144 ++++++++++++++++++---------------- 1 file changed, 76 insertions(+), 68 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 2d2d4f07..4a6661f6 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -13,7 +13,6 @@ import { ZOOM_ADAPTIVE_MAX_SCALE, NETWORK_GRN_MODE } from "./constants"; -import { max } from "moment"; /* globals d3 */ /* eslint-disable no-use-before-define, func-style */ @@ -257,9 +256,8 @@ export var drawGraph = function (workbook) { let xTranslation = 0; let yTranslation = 0; - let flexibleContainer = null; - function updateZoomContainerInfo() { + function updateZoomContainerInfo () { // transform attribute of zoomContainer contains translation info about graph if (zoomContainer.attr("transform")) { xTranslation = parseFloat( @@ -277,7 +275,7 @@ export var drawGraph = function (workbook) { .split(")")[0] ); } - }; + } // controls reading movement of zoomSlider and scaling graph to that zoomScale const setGraphZoom = zoomScale => { @@ -286,8 +284,8 @@ export var drawGraph = function (workbook) { } var container = zoomContainer; if (adaptive || (!adaptive && flexZoomInBounds(graphZoom))) { - zoom.scaleTo(container, zoomScale); - graphZoom = zoomScale; + zoom.scaleTo(container, zoomScale); + graphZoom = zoomScale; } }; @@ -303,8 +301,15 @@ export var drawGraph = function (workbook) { // If the zoom value is out of bounds, reset it to the previous value. if (adaptive) { - zoomDisplay = grnState.zoomValue - } else if (!adaptive && flexZoomInBounds((grnState.zoomValue <= ZOOM_DISPLAY_MIDDLE ? zoomScaleLeft : zoomScaleRight)(grnState.zoomValue)) ) { + zoomDisplay = grnState.zoomValue; + } else if ( + !adaptive && + flexZoomInBounds( + (grnState.zoomValue <= ZOOM_DISPLAY_MIDDLE + ? zoomScaleLeft + : zoomScaleRight)(grnState.zoomValue) + ) + ) { zoomDisplay = grnState.zoomValue; } else { grnState.zoomValue = prevGrnstateZoomVal; @@ -330,6 +335,7 @@ export var drawGraph = function (workbook) { // This controls movement of slider and is where the zoomSlider can be restricted if (adaptive || (!adaptive && flexZoomInBounds(calcGraphZoom))) { if (!adaptive) { + // Recenter graph when zooming to ensure that graph stays in viewport center(); updateZoomContainerInfo(); } @@ -431,7 +437,7 @@ export var drawGraph = function (workbook) { $("input[name=viewport]").removeProp("checked"); adaptive = true; d3.select("rect").attr("stroke", "none"); - d3.select("#flexibleContainerRect").attr("stroke", "none") + d3.select("#flexibleContainerRect").attr("stroke", "none"); center(); } else { $("#restrict-graph-to-viewport span").addClass("glyphicon-ok"); @@ -445,7 +451,6 @@ export var drawGraph = function (workbook) { } width = $container.width(); height = $container.height(); - // put a border with a gray stroke around the original container size d3.select("rect") .attr("width", width) .attr("height", height); @@ -463,8 +468,8 @@ export var drawGraph = function (workbook) { d3.selectAll("input[name=viewport]").on("change", function () { var fixed = $(this).prop("checked"); restrictGraphToViewport(fixed); - // refresh the graph so that nodes and paths are restricted - tick() + // Refresh the graph so that nodes and paths are adjusted to fit in viewport when restrictd to viewport + tick(); }); function center () { @@ -473,14 +478,14 @@ export var drawGraph = function (workbook) { zoom.translateTo(zoomContainer, viewportWidth / 2, viewportHeight / 2); } - // move: moves graph with D-pad + // move: Moves graph with D-pad function move (direction) { var moveWidth = direction === "left" ? -50 : direction === "right" ? 50 : 0; var moveHeight = direction === "up" ? -50 : direction === "down" ? 50 : 0; if (adaptive) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { - if (viewportBoundsMoveDrag(graphZoom, moveWidth, moveHeight)) { + if ((graphZoom, moveWidth, moveHeight)) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } } @@ -1381,13 +1386,14 @@ export var drawGraph = function (workbook) { }; const BOUNDARY_MARGIN = 5; - // TODO: take off dPadMove - function viewportBoundsMoveDrag(graphZoom, dx, dy) { + let flexibleContainer = null; + + function viewportBoundsMoveDrag (graphZoom, dx, dy) { updateZoomContainerInfo(); flexibleContainer = calcFlexiBox(); if ( - flexibleContainer.x + flexibleContainer.width + dx >= + flexibleContainer.x + flexibleContainer.width + dx >= -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + width / graphZoom - @@ -1396,7 +1402,7 @@ export var drawGraph = function (workbook) { return false; } - if (flexibleContainer.x + dx <= getBOUNDARY_MARGIN_X_L()) { + if (flexibleContainer.x + dx <= getLeftXBoundaryMargin()) { return false; } @@ -1407,18 +1413,18 @@ export var drawGraph = function (workbook) { height / graphZoom - BOUNDARY_MARGIN ) { - return false + return false; } - if (flexibleContainer.y + dy <= getBOUNDARY_MARGIN_Y_T()) { + if (flexibleContainer.y + dy <= getTopYBoundaryMargin()) { return false; } - return true - }; - + return true; + } + function calcFlexiBox () { - const nodes = simulation.nodes() + const nodes = simulation.nodes(); let nodeWidth = 0; if (nodes.length > 0) { nodeWidth = nodes[0].textWidth + 8; @@ -1433,9 +1439,9 @@ export var drawGraph = function (workbook) { let minY = Math.min(...yValuesNodes); let maxY = Math.max(...yValuesNodes) + nodeHeight; - // handle left x and top y boundaries to not exceed BOUNDARY_MARGIN - const BOUNDARY_MARGIN_X_L = getBOUNDARY_MARGIN_X_L(); - const BOUNDARY_MARGIN_Y_T = getBOUNDARY_MARGIN_Y_T(); + // Handle left x and top y boundaries to not exceed graph BOUNDARY_MARGINs + const BOUNDARY_MARGIN_X_L = getLeftXBoundaryMargin(); + const BOUNDARY_MARGIN_Y_T = getTopYBoundaryMargin(); minX = minX < BOUNDARY_MARGIN_X_L ? BOUNDARY_MARGIN_X_L : minX; minY = minY < BOUNDARY_MARGIN_Y_T ? BOUNDARY_MARGIN_Y_T : minY; @@ -1465,11 +1471,16 @@ export var drawGraph = function (workbook) { .attr("y", -yTranslation / graphZoom + BOUNDARY_MARGIN / 2) .attr("height", height / graphZoom - BOUNDARY_MARGIN); + flexibleContainerRect + .attr("x", minX) + .attr("y", minY) + .attr("width", flexiBoxWidth) + .attr("height", flexiBoxHeight); return {x: minX, y: minY, maxX: maxX, maxY: maxY, width: flexiBoxWidth, height: flexiBoxHeight}; } // this checks if zoomValue is in bounds when zoom in and out - function flexZoomInBounds(zoomValue) { + function flexZoomInBounds (zoomValue) { if (flexibleContainer) { updateZoomContainerInfo(); flexibleContainer = calcFlexiBox(); @@ -1482,14 +1493,13 @@ export var drawGraph = function (workbook) { return true; } - // only calculate Left and Top boundary margins because calculate rightboundary and bottomboundary in tick - function getBOUNDARY_MARGIN_X_L() { - return !adaptive && flexibleContainer ? -xTranslation / graphZoom + BOUNDARY_MARGIN / 2: BOUNDARY_MARGIN; + // Only calculate Left and Top boundary margins because calculate rightboundary and bottomboundary in tick + function getLeftXBoundaryMargin () { + return !adaptive && flexibleContainer ? -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 : BOUNDARY_MARGIN; } - function getBOUNDARY_MARGIN_Y_T() { - return !adaptive && flexibleContainer ? - yTranslation / graphZoom + BOUNDARY_MARGIN / 2 : BOUNDARY_MARGIN; - ; + function getTopYBoundaryMargin () { + return !adaptive && flexibleContainer ? -yTranslation / graphZoom + BOUNDARY_MARGIN / 2 : BOUNDARY_MARGIN; } // Tick only runs while the graph physics are still running. @@ -1513,12 +1523,6 @@ export var drawGraph = function (workbook) { if (!adaptive) { flexibleContainer = calcFlexiBox(); - - flexibleContainerRect - .attr("x", flexibleContainer.x) - .attr("y", flexibleContainer.y) - .attr("width", flexibleContainer.width) - .attr("height", flexibleContainer.height); } // this controls movement and position of nodes, clamps the nodes to boundary @@ -1528,7 +1532,7 @@ export var drawGraph = function (workbook) { var selfReferringEdgeWidth = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) + selfReferringEdge.strokeWidth + 2 : 0); - var rightBoundary = width -(d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN - selfReferringEdgeWidth; + var rightBoundary = width - (d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN - selfReferringEdgeWidth; if (!adaptive) { rightBoundary = -xTranslation / graphZoom + @@ -1539,29 +1543,29 @@ export var drawGraph = function (workbook) { selfReferringEdgeWidth; } // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentXPos = Math.max(getBOUNDARY_MARGIN_X_L(), Math.min(rightBoundary, d.x)); + var currentXPos = Math.max(getLeftXBoundaryMargin(), Math.min(rightBoundary, d.x)); if ( adaptive && width < MAX_WIDTH && - (currentXPos === getBOUNDARY_MARGIN_X_L() || + (currentXPos === getLeftXBoundaryMargin() || currentXPos === rightBoundary) ) { - if (!d3.select(this).classed("fixed")) { - width += OFFSET_VALUE; - boundingBoxContainer.attr("width", width); - - link - .attr("x1", function(d) { - return d.source.x; - }) - .attr("x2", function(d) { - return d.target.x; - }); - - node.attr("x", function(d) { - return d.x; - }); - } + if (!d3.select(this).classed("fixed")) { + width += OFFSET_VALUE; + boundingBoxContainer.attr("width", width); + + link + .attr("x1", function (d) { + return d.source.x; + }) + .attr("x2", function (d) { + return d.target.x; + }); + + node.attr("x", function (d) { + return d.x; + }); + } } return d.x = currentXPos; }).attr("y", function (d) { @@ -1579,10 +1583,10 @@ export var drawGraph = function (workbook) { selfReferringEdgeHeight; } // currentYPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds - var currentYPos = Math.max(getBOUNDARY_MARGIN_Y_T(), Math.min(bottomBoundary, d.y)); + var currentYPos = Math.max(getTopYBoundaryMargin(), Math.min(bottomBoundary, d.y)); if (adaptive && height < MAX_HEIGHT && - (currentYPos === getBOUNDARY_MARGIN_Y_T() || currentYPos === bottomBoundary)) { + (currentYPos === getTopYBoundaryMargin() || currentYPos === bottomBoundary)) { if (!d3.select(this).classed("fixed")) { height += OFFSET_VALUE; boundingBoxContainer.attr("height", height); @@ -1728,11 +1732,14 @@ export var drawGraph = function (workbook) { function dragged (d) { if (!adaptive) { + /* fx and fy stands for fixed x and y which is when node is fixed to a position or + to prevent tick from adjusting position of node + */ // prevents nodes from being dragged outside of right boundary if ( - d3.event.x + d.textWidth <= - -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + - width / graphZoom - + d3.event.x + d.textWidth <= + -xTranslation / graphZoom + BOUNDARY_MARGIN / 2 + + width / graphZoom - BOUNDARY_MARGIN ) { d.fx = d3.event.x; @@ -1747,15 +1754,16 @@ export var drawGraph = function (workbook) { // prevent nodes from being dragged out of bottom boundary if ( - d3.event.y + nodeHeight <= - -yTranslation / graphZoom + + d3.event.y + nodeHeight <= + -yTranslation / graphZoom + BOUNDARY_MARGIN / 2 + height / graphZoom - BOUNDARY_MARGIN ) { - d.fy = d3.event.y; + // fy stands for fixed y + d.fy = d3.event.y; } else { - d.fy = + d.fy = -yTranslation / graphZoom + BOUNDARY_MARGIN / 2 + height / graphZoom - From 41aced49cec5078d576438e5d2970b901503ae22 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Wed, 17 Apr 2024 22:33:34 -0700 Subject: [PATCH 129/150] Issue #1083. Removing extra line spacing from upload.pug --- web-client/views/upload.pug | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/web-client/views/upload.pug b/web-client/views/upload.pug index 1f1b0558..7132c0bd 100644 --- a/web-client/views/upload.pug +++ b/web-client/views/upload.pug @@ -288,8 +288,7 @@ html ul(class='nav navbar-nav navbar-right graph-metadata-container') li(class='navbar-text text-right') small(id='graph-metadata') - - + div(class='container') div(class='grnsight-container' data-iframe-width data-iframe-height) div(class='scale-and-scroll') From a95de0c6bc17302f01d33e8cb70b86e7535d948f Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Thu, 18 Apr 2024 00:05:46 -0700 Subject: [PATCH 130/150] Issue #1083. Fixed behavior where could not view graph is switched between graphs when restrictToViewport was checked. To fix had to move flexibleContainer variable earlier in code --- web-client/public/js/graph.js | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 4a6661f6..7adc4322 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -295,6 +295,7 @@ export var drawGraph = function (workbook) { let zoomScaleSliderLeft; let zoomScaleSliderRight; let prevGrnstateZoomVal; + let flexibleContainer = null; const updateAppBasedOnZoomValue = () => { let zoomDisplay; @@ -436,8 +437,7 @@ export var drawGraph = function (workbook) { $("#restrict-graph-to-viewport span").removeClass("glyphicon-ok"); $("input[name=viewport]").removeProp("checked"); adaptive = true; - d3.select("rect").attr("stroke", "none"); - d3.select("#flexibleContainerRect").attr("stroke", "none"); + flexibleContainer = null; center(); } else { $("#restrict-graph-to-viewport span").addClass("glyphicon-ok"); @@ -1386,7 +1386,6 @@ export var drawGraph = function (workbook) { }; const BOUNDARY_MARGIN = 5; - let flexibleContainer = null; function viewportBoundsMoveDrag (graphZoom, dx, dy) { updateZoomContainerInfo(); @@ -1479,7 +1478,7 @@ export var drawGraph = function (workbook) { return {x: minX, y: minY, maxX: maxX, maxY: maxY, width: flexiBoxWidth, height: flexiBoxHeight}; } - // this checks if zoomValue is in bounds when zoom in and out + // Checks if zoomValue is in bounds when zoom in and out function flexZoomInBounds (zoomValue) { if (flexibleContainer) { updateZoomContainerInfo(); From 242c1ab4028c2685107e05933b643393fea5f906 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Sun, 21 Apr 2024 22:09:12 -0700 Subject: [PATCH 131/150] Issue #1083. Updating parseFloat to Number according to feedback and deleting unnecessary comment with StackOverflow link since that link ended up not being used --- web-client/public/js/graph.js | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 7adc4322..6b069590 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -35,8 +35,6 @@ import { * updateFunction being set when needed. */ -// Stack overflow link for trying to create a box containing the graph: -// https://stackoverflow.com/questions/47544041/how-to-visualize-groups-of-nodes-in-a-d3-force-directed-graph-layout let mutationCallback = null; const resizeObserver = new MutationObserver((mutationsList, observer) => { if (typeof(mutationCallback) === "function") { @@ -260,14 +258,14 @@ export var drawGraph = function (workbook) { function updateZoomContainerInfo () { // transform attribute of zoomContainer contains translation info about graph if (zoomContainer.attr("transform")) { - xTranslation = parseFloat( + xTranslation = Number( zoomContainer .attr("transform") .split("(")[1] .split(",")[0] ); - yTranslation = parseFloat( + yTranslation = Number( zoomContainer .attr("transform") .split("(")[1] From 4cf1a07b54cef6c5585fbab54edc4cdc084070bf Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Mon, 22 Apr 2024 23:54:01 -0700 Subject: [PATCH 132/150] #1106 Make create_union_file a Utils method for reuse so for loader_update, can create a union missing_gene and update_gene files. The code for loader_update will be in later commit. --- database/combine_all_genes.py | 77 ----------------------------------- database/loader.py | 9 ++++ database/utils.py | 47 ++++++++++++++++++++- 3 files changed, 55 insertions(+), 78 deletions(-) delete mode 100644 database/combine_all_genes.py diff --git a/database/combine_all_genes.py b/database/combine_all_genes.py deleted file mode 100644 index e3b67fa1..00000000 --- a/database/combine_all_genes.py +++ /dev/null @@ -1,77 +0,0 @@ -# get all the genes from all files - -NETWORK_GENE_SOURCE = "network-database/script-results/processed-loader-files/gene.csv" -PROTEIN_GENE_SOURCE = "protein-protein-database/script-results/processed-loader-files/gene.csv" -EXPRESSION_GENE_SOURCE = "expression-database/script-results/processed-expression/genes.csv" - -import csv - -# Function to read genes from a CSV file into a set -def read_genes_from_csv(file_path): - genes = set() - with open(file_path, 'r') as file: - reader = csv.reader(file) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - genes.add(r[0]) - row_num += 1 - return genes - -def read_gene_info_from_csv(file_path): - gene_info = {} - with open(file_path, 'r') as file: - reader = csv.reader(file) - row_num = 0 - for row in reader: - if row_num != 0: - r= ','.join(row).split('\t') - if len(r) == 4: - r.append('False') - gene_info[r[0]] = { - 'Display Gene ID': r[1], - 'Species': r[2], - 'Taxon': r[3], - 'Regulator': r[4] - } - row_num += 1 - return gene_info - -# File paths for the three source files -protein_protein_interactions_file = 'protein_protein_interactions.csv' -network_table_file = 'network_table.csv' -expression_table_file = 'expression_table.csv' - -# Read genes from each source file into sets -protein_genes = read_genes_from_csv(PROTEIN_GENE_SOURCE) -network_genes = read_genes_from_csv(NETWORK_GENE_SOURCE) -expression_genes = read_genes_from_csv(EXPRESSION_GENE_SOURCE) - -# Create a union set containing all unique genes -all_genes = protein_genes.union(network_genes, expression_genes) - -# Read gene information from each source file into dictionaries -protein_gene_info = read_gene_info_from_csv(PROTEIN_GENE_SOURCE) -network_gene_info = read_gene_info_from_csv(NETWORK_GENE_SOURCE) -expression_gene_info = read_gene_info_from_csv(EXPRESSION_GENE_SOURCE) - -union_genes_info = {} -for gene_id in all_genes: - gene_info = {} - if gene_id in network_gene_info: - gene_info = network_gene_info[gene_id] - elif gene_id in protein_gene_info: - gene_info = protein_gene_info[gene_id] - elif gene_id in expression_gene_info: - gene_info = expression_gene_info[gene_id] - union_genes_info[gene_id] = gene_info - -union_file_path = 'union_genes.csv' -with open(union_file_path, 'w', newline='') as union_file: - headers = ['Gene ID', 'Display Gene ID', 'Species', 'Taxon', 'Regulator'] - union_file.write('\t'.join(headers) + '\n') - - for gene_id, gene_info in union_genes_info.items(): - row_data = [gene_id, gene_info['Display Gene ID'], gene_info['Species'], gene_info['Taxon'], gene_info['Regulator']] - union_file.write('\t'.join(row_data) + '\n') diff --git a/database/loader.py b/database/loader.py index a9c3793c..f49fb442 100644 --- a/database/loader.py +++ b/database/loader.py @@ -3,7 +3,16 @@ # python3 loader.py | psql postgresql://localhost/postgres +# Get union gene data + +# Gene data source file path +NETWORK_GENE_SOURCE = "network-database/script-results/processed-loader-files/gene.csv" +PROTEIN_GENE_SOURCE = "protein-protein-database/script-results/processed-loader-files/gene.csv" +EXPRESSION_GENE_SOURCE = "expression-database/script-results/processed-expression/genes.csv" + GENE_DATA_DIRECTORY = 'union_genes.csv' +Utils.create_union_file([EXPRESSION_GENE_SOURCE, PROTEIN_GENE_SOURCE, NETWORK_GENE_SOURCE], GENE_DATA_DIRECTORY) + # Network data source file path # Constants name: NETWORK__DATA_DIRECTORY NETWORK_DATABASE_NAMESPACE = 'gene_regulatory_network_testing' diff --git a/database/utils.py b/database/utils.py index 369edd73..c9b332e4 100644 --- a/database/utils.py +++ b/database/utils.py @@ -366,4 +366,49 @@ def load_degradation_rates(cls, degradation_rates_path: str, database_namespace: degradation_rate = float(r[4]) if r[4] != "" else "NaN" print(f'{gene_id}\t{taxon_id}\t{ncbi_geo_id}\t{pubmed_id}\t{degradation_rate}') row_num += 1 - print('\\.') \ No newline at end of file + print('\\.') + + @classmethod + def _read_gene_info_from_csv(cls, file_path): + gene_info = {} + with open(file_path, 'r') as file: + reader = csv.reader(file) + row_num = 0 + for row in reader: + if row_num != 0: + r= ','.join(row).split('\t') + if len(r) == 4: + r.append('False') + if r[1] == 'None': + r[1] = r[0] + gene_info[r[0]] = { + 'Display Gene ID': r[1], + 'Species': r[2], + 'Taxon': r[3], + 'Regulator': r[4] + } + row_num += 1 + return gene_info + + @classmethod + def create_union_file(cls, file_paths, output_file_path): + """ + Create a union file containing all unique genes from all input files. + + Args: + file_paths (List[str]): a list of file paths to read genes from (should list network genes file path at the end) because it can overwrite the regulator status of the gene + output_file_path (str): the file path to write the union genes to + """ + all_gene_info = {} + + for file_path in file_paths: + gene_info = cls._read_gene_info_from_csv(file_path) + all_gene_info.update(gene_info) + + with open(output_file_path, 'w', newline='') as union_file: + headers = ['Gene ID', 'Display Gene ID', 'Species', 'Taxon', 'Regulator'] + union_file.write('\t'.join(headers) + '\n') + + for gene_id, gene_info in all_gene_info.items(): + row_data = [gene_id, gene_info['Display Gene ID'], gene_info['Species'], gene_info['Taxon'], gene_info['Regulator']] + union_file.write('\t'.join(row_data) + '\n') \ No newline at end of file From 8d4dde07697d058510c1a3812f56df394fdd286d Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 23 Apr 2024 00:06:25 -0700 Subject: [PATCH 133/150] #1106 Create constants.py file to contain all file path directory --- database/constants.py | 26 ++++++++++++++++++++ database/loader.py | 56 +++++++++++++------------------------------ 2 files changed, 42 insertions(+), 40 deletions(-) create mode 100644 database/constants.py diff --git a/database/constants.py b/database/constants.py new file mode 100644 index 00000000..3a1a03ee --- /dev/null +++ b/database/constants.py @@ -0,0 +1,26 @@ +class Constants: + # Gene data source file path + NETWORK_GENE_SOURCE = "network-database/script-results/processed-loader-files/gene.csv" + PROTEIN_GENE_SOURCE = "protein-protein-database/script-results/processed-loader-files/gene.csv" + EXPRESSION_GENE_SOURCE = "expression-database/script-results/processed-expression/genes.csv" + + GENE_DATA_DIRECTORY = 'union_genes.csv' + + # Constants name: NETWORK__DATA_DIRECTORY + NETWORK_DATABASE_NAMESPACE = 'gene_regulatory_network_testing' + NETWORK_SOURCE_TABLE_DATA_DIRECTORY = 'network-database/script-results/processed-loader-files/source.csv' + NETWORK_NETWORK_TABLE_DATA_DIRECTORY = 'network-database/script-results/processed-loader-files/network.csv' + + # Protein-protein-interactions + PROTEIN_DATABASE_NAMESPACE = 'protein_protein_interactions_testing' + PROTEIN_SOURCE_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/source.csv' + PROTEIN_NETWORK_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/physical_interaction_no_dupe.csv' + PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/protein.csv' + + # Expression data + EXPRESISON_DATABASE_NAMESPACE = 'gene_expression_testing' + EXPRESSION_REFS_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/refs.csv' + EXPRESSION_METADATA_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-metadata.csv' + EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-data.csv' + EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/production-rates.csv' + EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/degradation-rates.csv' \ No newline at end of file diff --git a/database/loader.py b/database/loader.py index f49fb442..64a51954 100644 --- a/database/loader.py +++ b/database/loader.py @@ -1,50 +1,26 @@ import csv from utils import * - +from constants import Constants # python3 loader.py | psql postgresql://localhost/postgres # Get union gene data +Utils.create_union_file([Constants.EXPRESSION_GENE_SOURCE, Constants.PROTEIN_GENE_SOURCE, Constants.NETWORK_GENE_SOURCE], Constants.GENE_DATA_DIRECTORY) -# Gene data source file path -NETWORK_GENE_SOURCE = "network-database/script-results/processed-loader-files/gene.csv" -PROTEIN_GENE_SOURCE = "protein-protein-database/script-results/processed-loader-files/gene.csv" -EXPRESSION_GENE_SOURCE = "expression-database/script-results/processed-expression/genes.csv" - -GENE_DATA_DIRECTORY = 'union_genes.csv' -Utils.create_union_file([EXPRESSION_GENE_SOURCE, PROTEIN_GENE_SOURCE, NETWORK_GENE_SOURCE], GENE_DATA_DIRECTORY) - -# Network data source file path -# Constants name: NETWORK__DATA_DIRECTORY -NETWORK_DATABASE_NAMESPACE = 'gene_regulatory_network_testing' -NETWORK_SOURCE_TABLE_DATA_DIRECTORY = 'network-database/script-results/processed-loader-files/source.csv' -NETWORK_NETWORK_TABLE_DATA_DIRECTORY = 'network-database/script-results/processed-loader-files/network.csv' - -Utils.load_sources(NETWORK_SOURCE_TABLE_DATA_DIRECTORY, NETWORK_DATABASE_NAMESPACE) -Utils.load_network_genes(GENE_DATA_DIRECTORY, NETWORK_DATABASE_NAMESPACE) -Utils.load_network_network(NETWORK_NETWORK_TABLE_DATA_DIRECTORY, NETWORK_DATABASE_NAMESPACE) +# Regulatory Network +Utils.load_sources(Constants.NETWORK_SOURCE_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) +Utils.load_network_genes(Constants.GENE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) +Utils.load_network_network(Constants.NETWORK_NETWORK_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) # Protein-protein-interactions -PROTEIN_DATABASE_NAMESPACE = 'protein_protein_interactions_testing' -PROTEIN_SOURCE_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/source.csv' -PROTEIN_NETWORK_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/physical_interaction_no_dupe.csv' -PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/protein.csv' - -Utils.load_sources(PROTEIN_SOURCE_TABLE_DATA_DIRECTORY, PROTEIN_DATABASE_NAMESPACE) -Utils.load_protein_genes(GENE_DATA_DIRECTORY, PROTEIN_DATABASE_NAMESPACE) -Utils.load_proteins(PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY, PROTEIN_DATABASE_NAMESPACE) -Utils.load_protein_network(PROTEIN_NETWORK_TABLE_DATA_DIRECTORY, PROTEIN_DATABASE_NAMESPACE) +Utils.load_sources(Constants.PROTEIN_SOURCE_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.load_protein_genes(Constants.GENE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.load_proteins(Constants.PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.load_protein_network(Constants.PROTEIN_NETWORK_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) # Expression data -EXPRESISON_DATABASE_NAMESPACE = 'gene_expression_testing' -EXPRESSION_REFS_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/refs.csv' -EXPRESSION_METADATA_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-metadata.csv' -EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-data.csv' -EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/production-rates.csv' -EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/degradation-rates.csv' - -Utils.load_refs(EXPRESSION_REFS_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) -Utils.load_expression_genes(GENE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) -Utils.load_expression_metadata(EXPRESSION_METADATA_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) -Utils.load_expression_data(EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) -Utils.load_production_rates(EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) -Utils.load_degradation_rates(EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY, EXPRESISON_DATABASE_NAMESPACE) \ No newline at end of file +Utils.load_refs(Constants.EXPRESSION_REFS_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) +Utils.load_expression_genes(Constants.GENE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) +Utils.load_expression_metadata(Constants.EXPRESSION_METADATA_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) +Utils.load_expression_data(Constants.EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) +Utils.load_production_rates(Constants.EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) +Utils.load_degradation_rates(Constants.EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) \ No newline at end of file From 315710f6752efe543ed477be6f83f8def2cb507f Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 23 Apr 2024 02:08:03 -0700 Subject: [PATCH 134/150] #1106 Adding a combine filter_update.py file to find all missing genes, updated genes, misisng protein, updated proteins for both network and protein-protein interactions table --- database/constants.py | 22 ++++++- database/filter_update.py | 127 ++++++++++++++++++++++++++++++++++++++ database/loader_update.py | 22 +++++++ 3 files changed, 168 insertions(+), 3 deletions(-) create mode 100644 database/filter_update.py create mode 100644 database/loader_update.py diff --git a/database/constants.py b/database/constants.py index 3a1a03ee..8e2ca0b1 100644 --- a/database/constants.py +++ b/database/constants.py @@ -1,15 +1,22 @@ class Constants: + NETWORK_FOLDER_PATH = 'network-database' + PROTEIN_FOLDER_PATH = 'protein-protein-database' + EXPRESSION_FOLDER_PATH = 'expression-database' + # Gene data source file path NETWORK_GENE_SOURCE = "network-database/script-results/processed-loader-files/gene.csv" PROTEIN_GENE_SOURCE = "protein-protein-database/script-results/processed-loader-files/gene.csv" EXPRESSION_GENE_SOURCE = "expression-database/script-results/processed-expression/genes.csv" + # Union gene data GENE_DATA_DIRECTORY = 'union_genes.csv' + MISSING_GENE_UNION_DIRECTORY = 'union-missing-genes.csv' + UPDATE_GENE_UNION_DIRECTORY = 'union-update-genes.csv' # Constants name: NETWORK__DATA_DIRECTORY NETWORK_DATABASE_NAMESPACE = 'gene_regulatory_network_testing' - NETWORK_SOURCE_TABLE_DATA_DIRECTORY = 'network-database/script-results/processed-loader-files/source.csv' - NETWORK_NETWORK_TABLE_DATA_DIRECTORY = 'network-database/script-results/processed-loader-files/network.csv' + NETWORK_SOURCE_TABLE_DATA_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/source.csv' + NETWORK_NETWORK_TABLE_DATA_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/network.csv' # Protein-protein-interactions PROTEIN_DATABASE_NAMESPACE = 'protein_protein_interactions_testing' @@ -23,4 +30,13 @@ class Constants: EXPRESSION_METADATA_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-metadata.csv' EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-data.csv' EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/production-rates.csv' - EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/degradation-rates.csv' \ No newline at end of file + EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/degradation-rates.csv' + + # Paths for update files + PROTEIN_MISSING_GENE_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/missing-genes.csv' + PROTEIN_UPDATE_GENE_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/update-genes.csv' + PROTEIN_MISSING_PROTEIN_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/missing-proteins.csv' + PROTEIN_UPDATE_PROTEIN_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/update-proteins.csv' + + NETWORK_MISSING_GENE_DIRECTORY = 'network-database/script-results/processed-loader-files/missing-genes.csv' + NETWORK_UPDATE_GENE_DIRECTORY = 'network-database/script-results/processed-loader-files/update-genes.csv' \ No newline at end of file diff --git a/database/filter_update.py b/database/filter_update.py new file mode 100644 index 00000000..2cf959a3 --- /dev/null +++ b/database/filter_update.py @@ -0,0 +1,127 @@ +import os +import csv +from sqlalchemy import create_engine +from sqlalchemy import text +from constants import Constants + +def get_all_data_from_database_table(database_namespace, table_name): + db = create_engine(os.environ['DB_URL']) + with db.connect() as connection: + result_set = connection.execute(text(f"SELECT * FROM {database_namespace}.{table_name}")) + return result_set.fetchall() + +def get_all_genes(database_namespace): + gene_records = get_all_data_from_database_table(database_namespace, "gene") + genes = {} + for gene in gene_records: + key = (gene[0], gene[3]) + if len(gene) > 4: + value = (gene[1], gene[2], gene[4]) + else: + value = (gene[1], gene[2]) + genes[key] = value + return genes + +def get_all_network_genes(): + return get_all_genes(Constants.NETWORK_DATABASE_NAMESPACE) + +def get_all_protein_genes(): + return get_all_genes(Constants.PROTEIN_DATABASE_NAMESPACE) + +def get_all_proteins(): + protein_records = get_all_data_from_database_table(Constants.PROTEIN_DATABASE_NAMESPACE, "protein") + proteins = {} + for protein in protein_records: + key = (protein[1], protein[5]) + value = (protein[0], protein[2], protein[3], protein[4]) + proteins[key] = value + return proteins + +def processing_gene_file(file_path, db_genes, is_protein=True): + print(f'Processing file {file_path}') + missing_genes = {} + genes_to_update = {} + with open(file_path, 'r+', encoding="UTF-8") as f: + i = 0 + reader = csv.reader(f) + for row in reader: + if i != 0: + row = row[0].split('\t') + gene_id = row[0] + display_gene_id = row[1] + species = row[2] + taxon_id = row[3] + key = (gene_id, taxon_id) + if (is_protein): + value = (display_gene_id, species) + else: + regulator = row[4].capitalize() + value = (display_gene_id, species, regulator) + if key not in db_genes: + missing_genes[key] = value + elif db_genes[key][0] != display_gene_id: + # the value is not the same, let's update + if display_gene_id != "None": + genes_to_update[key] = value + i+=1 + return missing_genes, genes_to_update + +def processing_protein_file(file_path, db_proteins): + print(f'Processing file {file_path}') + missing_proteins = {} + proteins_to_update = {} + with open(file_path, 'r+', encoding="UTF-8") as f: + i = 0 + reader = csv.reader(f) + for row in reader: + if i != 0: + row = row[0].split('\t') + standard_name = row[0] + gene_systematic_name = row[1] + length = float(row[2]) if row[2] != "None" else 0 + molecular_weight = float(row[3]) if row[3] != "None" else 0 + pi = float(row[4]) if row[4] != "None" else 0 + taxon_id = row[5] + key = (gene_systematic_name, taxon_id) + value = (standard_name, length, molecular_weight, pi) + if key not in db_proteins: + missing_proteins[key] = value + elif db_proteins[key] != value: + proteins_to_update[key] = value + i+=1 + return missing_proteins, proteins_to_update + +def create_gene_file(file_path, headers, data, is_protein=True): + print(f'Creating {file_path}\n') + gene_file = open(file_path, 'w') + gene_file.write(f'{headers}\n') + for gene in data: + if is_protein: + gene_file.write(f'{gene[0]}\t{data[gene][0]}\t{data[gene][1]}\t{gene[1]}\n') + else: + gene_file.write(f'{gene[0]}\t{data[gene][0]}\t{data[gene][1]}\t{gene[1]}\t{data[gene][2]}\n') + gene_file.close() + +def create_protein_file(file_path, data): + print(f'Creating {file_path}\n') + protein_file = open(file_path, 'w') + headers = f'Standard Name\tGene Systematic Name\tLength\tMolecular Weight\tPI\tTaxon ID' + protein_file.write(f'{headers}\n') + for protein in data: + protein_file.write(f'{data[protein][0]}\t{[protein][0]}\t{data[protein][1]}\t{data[protein][2]}\t{data[protein][3]}\t{protein[1]}\n') + protein_file.close() + +# Processing gene files +protein_headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' +network_headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID\tRegulator' +network_db_genes = get_all_network_genes() +protein_db_genes = get_all_protein_genes() +protein_missing_genes, protein_genes_to_update = processing_gene_file(Constants.PROTEIN_GENE_SOURCE, protein_db_genes) +network_missing_genes, network_genes_to_update = processing_gene_file(Constants.NETWORK_GENE_SOURCE, network_db_genes, is_protein=False) +missing_proteins, proteins_to_update = processing_protein_file(Constants.PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY, get_all_proteins()) +create_gene_file(Constants.NETWORK_MISSING_GENE_DIRECTORY, network_headers, network_missing_genes, is_protein=False) +create_gene_file(Constants.PROTEIN_MISSING_GENE_DIRECTORY, protein_headers, protein_missing_genes) +create_gene_file(Constants.NETWORK_UPDATE_GENE_DIRECTORY, network_headers, network_genes_to_update, is_protein=False) +create_gene_file(Constants.PROTEIN_UPDATE_GENE_DIRECTORY, protein_headers, protein_genes_to_update) +create_protein_file(Constants.PROTEIN_MISSING_PROTEIN_DIRECTORY, missing_proteins) +create_protein_file(Constants.PROTEIN_UPDATE_PROTEIN_DIRECTORY, proteins_to_update) \ No newline at end of file diff --git a/database/loader_update.py b/database/loader_update.py new file mode 100644 index 00000000..6cd38c3d --- /dev/null +++ b/database/loader_update.py @@ -0,0 +1,22 @@ +from constants import Constants +from utils import Utils + +# Get missing union gene data +Utils.create_union_file([Constants.PROTEIN_MISSING_GENE_DIRECTORY, Constants.NETWORK_MISSING_GENE_DIRECTORY], Constants.MISSING_GENE_UNION_DIRECTORY) + +# Get update union gene data +Utils.create_union_file([Constants.PROTEIN_UPDATE_GENE_DIRECTORY, Constants.NETWORK_UPDATE_GENE_DIRECTORY], Constants.UPDATE_GENE_UNION_DIRECTORY) + +# Proteins +Utils.load_sources(Constants.PROTEIN_SOURCE_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.update_protein_genes(Constants.UPDATE_GENE_UNION_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.update_proteins(Constants.PROTEIN_UPDATE_PROTEIN_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.load_genes(Constants.MISSING_GENE_UNION_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE, is_protein=True) +Utils.load_proteins(Constants.PROTEIN_MISSING_PROTEIN_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.load_network(Constants.PROTEIN_NETWORK_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE, is_protein=True) + +# Network +Utils.load_sources(Constants.NETWORK_SOURCE_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) +Utils.update_network_genes(Constants.UPDATE_GENE_UNION_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) +Utils.load_network_genes(Constants.MISSING_GENE_UNION_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) +Utils.load_network_network(Constants.NETWORK_NETWORK_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) \ No newline at end of file From 46c077b40aef60015f87b9f6f742f272b64dc534 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 23 Apr 2024 02:32:57 -0700 Subject: [PATCH 135/150] #1106 Modify the path to store union-gene-data --- database/constants.py | 25 +++++++++++++------------ database/loader.py | 4 ++++ database/loader_update.py | 4 ++++ 3 files changed, 21 insertions(+), 12 deletions(-) diff --git a/database/constants.py b/database/constants.py index 8e2ca0b1..45bb52a8 100644 --- a/database/constants.py +++ b/database/constants.py @@ -2,6 +2,7 @@ class Constants: NETWORK_FOLDER_PATH = 'network-database' PROTEIN_FOLDER_PATH = 'protein-protein-database' EXPRESSION_FOLDER_PATH = 'expression-database' + UNION_GENE_FOLDER_PATH = 'union-gene-data/' # Gene data source file path NETWORK_GENE_SOURCE = "network-database/script-results/processed-loader-files/gene.csv" @@ -9,9 +10,9 @@ class Constants: EXPRESSION_GENE_SOURCE = "expression-database/script-results/processed-expression/genes.csv" # Union gene data - GENE_DATA_DIRECTORY = 'union_genes.csv' - MISSING_GENE_UNION_DIRECTORY = 'union-missing-genes.csv' - UPDATE_GENE_UNION_DIRECTORY = 'union-update-genes.csv' + GENE_DATA_DIRECTORY = UNION_GENE_FOLDER_PATH + 'union_genes.csv' + MISSING_GENE_UNION_DIRECTORY = UNION_GENE_FOLDER_PATH + 'union-missing-genes.csv' + UPDATE_GENE_UNION_DIRECTORY = UNION_GENE_FOLDER_PATH + 'union-update-genes.csv' # Constants name: NETWORK__DATA_DIRECTORY NETWORK_DATABASE_NAMESPACE = 'gene_regulatory_network_testing' @@ -20,9 +21,9 @@ class Constants: # Protein-protein-interactions PROTEIN_DATABASE_NAMESPACE = 'protein_protein_interactions_testing' - PROTEIN_SOURCE_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/source.csv' - PROTEIN_NETWORK_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/physical_interaction_no_dupe.csv' - PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/protein.csv' + PROTEIN_SOURCE_TABLE_DATA_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/source.csv' + PROTEIN_NETWORK_TABLE_DATA_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/physical_interaction_no_dupe.csv' + PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/protein.csv' # Expression data EXPRESISON_DATABASE_NAMESPACE = 'gene_expression_testing' @@ -33,10 +34,10 @@ class Constants: EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/degradation-rates.csv' # Paths for update files - PROTEIN_MISSING_GENE_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/missing-genes.csv' - PROTEIN_UPDATE_GENE_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/update-genes.csv' - PROTEIN_MISSING_PROTEIN_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/missing-proteins.csv' - PROTEIN_UPDATE_PROTEIN_DIRECTORY = 'protein-protein-database/script-results/processed-loader-files/update-proteins.csv' + PROTEIN_MISSING_GENE_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/missing-genes.csv' + PROTEIN_UPDATE_GENE_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/update-genes.csv' + PROTEIN_MISSING_PROTEIN_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/missing-proteins.csv' + PROTEIN_UPDATE_PROTEIN_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/update-proteins.csv' - NETWORK_MISSING_GENE_DIRECTORY = 'network-database/script-results/processed-loader-files/missing-genes.csv' - NETWORK_UPDATE_GENE_DIRECTORY = 'network-database/script-results/processed-loader-files/update-genes.csv' \ No newline at end of file + NETWORK_MISSING_GENE_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/missing-genes.csv' + NETWORK_UPDATE_GENE_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/update-genes.csv' \ No newline at end of file diff --git a/database/loader.py b/database/loader.py index 64a51954..522c5d59 100644 --- a/database/loader.py +++ b/database/loader.py @@ -2,7 +2,11 @@ from utils import * from constants import Constants # python3 loader.py | psql postgresql://localhost/postgres +import os +if not os.path.exists('union-gene-data'): + os.makedirs('union-gene-data') + # Get union gene data Utils.create_union_file([Constants.EXPRESSION_GENE_SOURCE, Constants.PROTEIN_GENE_SOURCE, Constants.NETWORK_GENE_SOURCE], Constants.GENE_DATA_DIRECTORY) diff --git a/database/loader_update.py b/database/loader_update.py index 6cd38c3d..df03daa0 100644 --- a/database/loader_update.py +++ b/database/loader_update.py @@ -1,6 +1,10 @@ from constants import Constants from utils import Utils +import os +if not os.path.exists('union-gene-data'): + os.makedirs('union-gene-data') + # Get missing union gene data Utils.create_union_file([Constants.PROTEIN_MISSING_GENE_DIRECTORY, Constants.NETWORK_MISSING_GENE_DIRECTORY], Constants.MISSING_GENE_UNION_DIRECTORY) From d1be504317ee33aa1bda3ccbbdad5192ef77e5cb Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 23 Apr 2024 02:37:16 -0700 Subject: [PATCH 136/150] #1106 delete unused files --- .../network-database/scripts/constants.py | 7 - .../network-database/scripts/filter_genes.py | 76 ----------- database/network-database/scripts/loader.py | 26 ---- .../scripts/loader_updates.py | 12 -- .../scripts/constants.py | 12 -- .../scripts/filter_genes.py | 125 ------------------ .../scripts/loader.py | 23 ---- .../scripts/loader_update.py | 13 -- 8 files changed, 294 deletions(-) delete mode 100644 database/network-database/scripts/constants.py delete mode 100644 database/network-database/scripts/filter_genes.py delete mode 100644 database/network-database/scripts/loader.py delete mode 100644 database/network-database/scripts/loader_updates.py delete mode 100644 database/protein-protein-database/scripts/constants.py delete mode 100644 database/protein-protein-database/scripts/filter_genes.py delete mode 100644 database/protein-protein-database/scripts/loader.py delete mode 100644 database/protein-protein-database/scripts/loader_update.py diff --git a/database/network-database/scripts/constants.py b/database/network-database/scripts/constants.py deleted file mode 100644 index 2f856fee..00000000 --- a/database/network-database/scripts/constants.py +++ /dev/null @@ -1,7 +0,0 @@ -class Constants: - NETWORK_DATA_SOURCE = 'network-database/script-results/processed-loader-files/source.csv' - DATABASE_NAMESPACE = "gene_regulatory_network_testing" - NETWORK_SOURCE = 'network-database/script-results/processed-loader-files/network.csv' - GENE_SOURCE = 'network-database/script-results/processed-loader-files/gene.csv' - GENE_UPDATE_DESTINATION = 'network-database/script-results/processed-loader-files/gene_update.csv' - \ No newline at end of file diff --git a/database/network-database/scripts/filter_genes.py b/database/network-database/scripts/filter_genes.py deleted file mode 100644 index ffb727e6..00000000 --- a/database/network-database/scripts/filter_genes.py +++ /dev/null @@ -1,76 +0,0 @@ -import psycopg2 -import csv -import os - -PROCESSED_GENES = "../script-results/processed-loader-files/gene.csv" -MISSING_GENE_DESTINATION = '../script-results/processed-loader-files/missing-genes.csv' -UPDATE_GENE_DESTINATION = '../script-results/processed-loader-files/update-genes.csv' - -try: - connection = psycopg2.connect(user="postgres", - password="", - host="grnsight2.cfimp3lu6uob.us-west-1.rds.amazonaws.com", - port="5432", - database="postgres") - cursor = connection.cursor() - postgreSQL_select_Query = "select * from gene_regulatory_network.gene" - - cursor.execute(postgreSQL_select_Query) - print("Selecting rows from gene table using cursor.fetchall") - gene_records = cursor.fetchall() - - db_genes = {} - missing_genes = {} - genes_to_update = {} - for gene in gene_records: - # key = (gene_id, taxon_id) - key = (gene[0], gene[3]) - value = {"display_gene_id": gene[1], "species": gene[2], "regulator": gene[4]} - db_genes[key] = value - - print(f'Processing file {PROCESSED_GENES}') - with open(PROCESSED_GENES, 'r+', encoding="UTF-8") as f: - i = 0 - reader = csv.reader(f) - for row in reader: - if i != 0: - row = row[0].split('\t') - gene_id = row[0] - display_gene_id = row[1] - species = row[2] - taxon_id = row[3] - regulator = row[4] - key = (gene_id, taxon_id) - value = {"display_gene_id": display_gene_id , "species": species, "regulator": regulator} - if key not in db_genes: - missing_genes[key] = value - elif db_genes[key]["display_gene_id"] != display_gene_id: - # the display gene id got updated, so lets update our db to account for that - genes_to_update[key] = value - i+=1 - - print(f'Creating missing-genes.csv\n') - gene_file = open(MISSING_GENE_DESTINATION, 'w') - headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID\tRegulator' - gene_file.write(f'{headers}\n') - for gene in missing_genes: - gene_file.write(f'{gene[0]}\t{missing_genes[gene]["display_gene_id"]}\t{missing_genes[gene]["species"]}\t{gene[1]}\t{missing_genes[gene]["regulator"]}\n') - gene_file.close() - - print(f'Creating update-genes.csv\n') - gene_file = open(UPDATE_GENE_DESTINATION, 'w') - headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID\tRegulator' - gene_file.write(f'{headers}\n') - for gene in genes_to_update: - gene_file.write(f'{gene[0]}\t{genes_to_update[gene]["display_gene_id"]}\t{genes_to_update[gene]["species"]}\t{gene[1]}\t{genes_to_update[gene]["regulator"]}\n') - gene_file.close() - -except (Exception, psycopg2.Error) as error: - print("Error while fetching data from PostgreSQL", error) - -finally: - # closing database connection. - if connection: - cursor.close() - connection.close() - print("PostgreSQL connection is closed") \ No newline at end of file diff --git a/database/network-database/scripts/loader.py b/database/network-database/scripts/loader.py deleted file mode 100644 index 346e0dee..00000000 --- a/database/network-database/scripts/loader.py +++ /dev/null @@ -1,26 +0,0 @@ -import csv -import re -import sys - -sys.path.insert(1, '../database') -from constants import * -from utils import * -# Usage -# python3 loader.py | psql postgresql://localhost/postgres -""" -This program generates direct SQL statements from the source files in order -to populate a relational database with those files’ data. - -By taking the approach of emitting SQL statements directly, we bypass the need to import -some kind of database library for the loading process, instead passing the statements -directly into a database command line utility such as `psql`. -""" - -# load_sources() -Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) - -# load_genes() -Utils.load_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) - -# load_network() -Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) diff --git a/database/network-database/scripts/loader_updates.py b/database/network-database/scripts/loader_updates.py deleted file mode 100644 index c470d7d3..00000000 --- a/database/network-database/scripts/loader_updates.py +++ /dev/null @@ -1,12 +0,0 @@ -import sys -sys.path.insert(1, '../database') -from constants import * -from utils import * - -# Usage -# python3 loader.py | psql postgresql://localhost/postgres - -Utils.update__network_genes(Constants.GENE_UPDATE_DESTINATION, Constants.DATABASE_NAMESPACE) -Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_network_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=False) diff --git a/database/protein-protein-database/scripts/constants.py b/database/protein-protein-database/scripts/constants.py deleted file mode 100644 index b38d47e9..00000000 --- a/database/protein-protein-database/scripts/constants.py +++ /dev/null @@ -1,12 +0,0 @@ -class Constants: - PROCESSED_GENES = "protein-protein-database/script-results/processed-loader-files/gene.csv" - PROCESSED_PROTEIN = "protein-protein-database/script-results/processed-loader-files/protein.csv" - MISSING_GENE_DESTINATION = 'protein-protein-database/script-results/processed-loader-files/missing-genes.csv' - UPDATE_GENE_DESTINATION = 'protein-protein-database/script-results/processed-loader-files/update-genes.csv' - MISSING_PROTEIN_DESTINATION = 'protein-protein-database/script-results/processed-loader-files/missing-proteins.csv' - UPDATE_PROTEIN_DESTINATION = 'protein-protein-database/script-results/processed-loader-files/update-proteins.csv' - NETWORK_DATA_SOURCE = 'protein-protein-database/script-results/processed-loader-files/source.csv' - GENE_SOURCE = 'protein-protein-database/script-results/processed-loader-files/gene.csv' - PROTEIN_SOURCE = 'protein-protein-database/script-results/processed-loader-files/protein.csv' - NETWORK_SOURCE = 'protein-protein-database/script-results/processed-loader-files/physical_interaction_no_dupe.csv' - DATABASE_NAMESPACE = "protein_protein_interactions_testing" \ No newline at end of file diff --git a/database/protein-protein-database/scripts/filter_genes.py b/database/protein-protein-database/scripts/filter_genes.py deleted file mode 100644 index efdd772b..00000000 --- a/database/protein-protein-database/scripts/filter_genes.py +++ /dev/null @@ -1,125 +0,0 @@ -import os -import csv -import psycopg2 -from sqlalchemy import create_engine -from sqlalchemy import text -from constants import * - -def get_all_genes_proteins(): - # Create envrionment variable for db url - db = create_engine(os.environ['DB_URL']) - - with db.connect() as connection: - result_set = connection.execute(text(f"SELECT * FROM {Constants.DATABASE_NAMESPACE}.gene")) - - genes_record = result_set.fetchall() - - db_genes = {} - for gene in genes_record: - print(gene) - # key = (gene_id, taxon_id) - key = (gene[0], gene[3]) - # values = (display_gene_id, species) - value = (gene[1], gene[2]) - db_genes[key] = value - - # Collect proteins - result_set = connection.execute(text(f"SELECT * FROM {Constants.DATABASE_NAMESPACE}.protein")) - proteins_record = result_set.fetchall() - - db_proteins = {} - for protein in proteins_record: - # Key = (gene_systematic_name, taxon_id) - key = (protein[1], protein[5]) - # value = (standard_name, length, molecular_weight, PI) - value = (protein[0], protein[2], protein[3], protein[4]) - db_proteins[key] = value - - return db_genes, db_proteins - -db_genes, db_proteins = get_all_genes_proteins() # Format [(display_gene_id, gene_id), ...] and [(gene_systematic_name, ), ...] - -print("Genes", db_genes) -print("Protein", db_proteins) - -genes_to_update = {} -missing_genes = {} - -print(f'Processing file {Constants.PROCESSED_GENES}') -with open(Constants.PROCESSED_GENES, 'r+', encoding="UTF-8") as f: - i = 0 - reader = csv.reader(f) - for row in reader: - if i != 0: - row = row[0].split('\t') - gene_id = row[0] - display_gene_id = row[1] - species = row[2] - taxon_id = row[3] - key = (gene_id, taxon_id) - value = (display_gene_id, species) - if key not in db_genes: - missing_genes[key] = value - print(f'Gene {display_gene_id} not found in the database') - elif db_genes[key] != value: - # the value is not the same, let's update - genes_to_update[key] = value - i+=1 - -print(f'Creating missing-genes.csv\n') -gene_file = open(Constants.MISSING_GENE_DESTINATION, 'w') -headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' -gene_file.write(f'{headers}\n') -for gene in missing_genes: - gene_file.write(f'{gene[0]}\t{missing_genes[gene][0]}\t{missing_genes[gene][1]}\t{gene[1]}\n') -gene_file.close() - -print(f'Creating update-genes.csv\n') -gene_file = open(Constants.UPDATE_GENE_DESTINATION, 'w') -headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' -gene_file.write(f'{headers}\n') -for gene in genes_to_update: - gene_file.write(f'{gene[0]}\t{genes_to_update[gene][0]}\t{genes_to_update[gene][1]}\t{gene[1]}\n') -gene_file.close() - -missing_proteins = {} -proteins_to_update = {} - -print(f"Processing file {Constants.PROCESSED_PROTEIN}") -with open(Constants.PROCESSED_PROTEIN, 'r+', encoding="UTF-8") as f: - i = 0 - reader = csv.reader(f) - for row in reader: - if i != 0: - row = row[0].split('\t') - standard_name = row[0] - gene_systematic_name = row[1] - length = float(row[2]) if row[2] != "None" else 0 - molecular_weight = float(row[3]) if row[3] != "None" else 0 - pi = float(row[4]) if row[4] != "None" else 0 - taxon_id = row[5] - key = (gene_systematic_name, taxon_id) - value = (standard_name, length, molecular_weight, pi) - if key not in db_proteins: - missing_proteins[key] = value - elif db_proteins[key] != value: - print("Protein", db_proteins[key]) - print("Value", value) - proteins_to_update[key] = value - i+=1 - -print(f'Creating missing-proteins.csv\n') -protein_file = open(Constants.MISSING_PROTEIN_DESTINATION, 'w') -headers = f'Standard Name\tGene Systematic Name\tLength\t Molecular Weight\tPI\tTaxon ID' -protein_file.write(f'{headers}\n') -for protein in missing_proteins: - protein_file.write(f'{missing_proteins[protein][0]}\t{[protein][0]}\t{missing_proteins[protein][1]}\t{missing_proteins[protein][2]}\t{missing_proteins[protein][3]}\t{protein[1]}\n') -protein_file.close() - -print(f'Creating update-proteins.csv\n') -protein_file = open(Constants.UPDATE_PROTEIN_DESTINATION, 'w') -headers = f'Standard Name\tGene Systematic Name\tLength\t Molecular Weight\tPI\tTaxon ID' -protein_file.write(f'{headers}\n') -for protein in proteins_to_update: - protein_file.write(f'{proteins_to_update[protein][0]}\t{[protein][0]}\t{proteins_to_update[protein][1]}\t{proteins_to_update[protein][2]}\t{proteins_to_update[protein][3]}\t{protein[1]}\n') -protein_file.close() \ No newline at end of file diff --git a/database/protein-protein-database/scripts/loader.py b/database/protein-protein-database/scripts/loader.py deleted file mode 100644 index bfb0680d..00000000 --- a/database/protein-protein-database/scripts/loader.py +++ /dev/null @@ -1,23 +0,0 @@ - -import csv -from constants import * - -import sys -sys.path.insert(1, '../database') -from utils import * - -# Usage -# python3 loader.py | psql postgresql://localhost/postgres -""" -This program generates direct SQL statements from the source files in order -to populate a relational database with those files’ data. - -By taking the approach of emitting SQL statements directly, we bypass the need to import -some kind of database library for the loading process, instead passing the statements -directly into a database command line utility such as `psql`. -""" - -Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_protein_genes(Constants.GENE_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_proteins(Constants.PROTEIN_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE,is_protein=True) \ No newline at end of file diff --git a/database/protein-protein-database/scripts/loader_update.py b/database/protein-protein-database/scripts/loader_update.py deleted file mode 100644 index 11afe912..00000000 --- a/database/protein-protein-database/scripts/loader_update.py +++ /dev/null @@ -1,13 +0,0 @@ -import csv -from constants import * -import sys - -sys.path.insert(1, '../database') -from utils import * - -Utils.load_sources(Constants.NETWORK_DATA_SOURCE, Constants.DATABASE_NAMESPACE) -Utils.update_protein_genes(Constants.UPDATE_GENE_DESTINATION, Constants.DATABASE_NAMESPACE) -Utils.update_proteins(Constants.UPDATE_PROTEIN_DESTINATION, Constants.DATABASE_NAMESPACE) -Utils.load_genes(Constants.MISSING_GENE_DESTINATION, Constants.DATABASE_NAMESPACE, is_protein=True) -Utils.load_proteins(Constants.MISSING_PROTEIN_DESTINATION, Constants.DATABASE_NAMESPACE) -Utils.load_network(Constants.NETWORK_SOURCE, Constants.DATABASE_NAMESPACE, is_protein=True) \ No newline at end of file From b9efb4d16df474b0d721085bfd7c180b1623d3b1 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 23 Apr 2024 03:19:57 -0700 Subject: [PATCH 137/150] #1106 Modify instructions on how to load data into database, and adding instructions on how to update database --- database/README.md | 256 ++++++++++++++++++++++++++------------------- 1 file changed, 150 insertions(+), 106 deletions(-) diff --git a/database/README.md b/database/README.md index fe3fa032..20731f19 100644 --- a/database/README.md +++ b/database/README.md @@ -1,36 +1,45 @@ # GRNsight Database + Here are the files pertaining to both the network and expression databases. Look within the README.md files of both folders for information pertinent to the schema that you intend to be using. + ## Setting up a local postgres GRNsight Database + 1. Installing PostgreSQL on your computer + - MacOS and Windows can follow these instructions on how to install postgreSQL. - - Install the software at this [link](https://www.postgresql.org/download/) + + - Install the software at this [link](https://www.postgresql.org/download/) - Initialize the database - - If your terminal emits a message that looks like `initdb --locale=C -E UTF-8 location-of-cluster` from Step 1B, then your installer has initialized a database for you. - - Open the terminal and type the command `initdb --locale=C -E UTF-8 location-of-cluster` - - "Cluster" is the PostgreSQL term for the file structure of a PostgreSQL database instance - - You will have to modify location-of-cluster to the folder name you want to store the database (you don't need to create a folder, the command will create the folder for you, just create the name) + - If your terminal emits a message that looks like `initdb --locale=C -E UTF-8 location-of-cluster` from Step 1B, then your installer has initialized a database for you. + - Open the terminal and type the command `initdb --locale=C -E UTF-8 location-of-cluster` + - "Cluster" is the PostgreSQL term for the file structure of a PostgreSQL database instance + - You will have to modify location-of-cluster to the folder name you want to store the database (you don't need to create a folder, the command will create the folder for you, just create the name) - Start and stop the server - Additionally, your installer may start the server for you upon installation (You can save this command for further reuse). - To start the server yourself run `pg_ctl start -D location-of-cluster` (You can save this command for further reuse). - To stop the server run `pg_ctl stop -D location-of-cluster`. - + - Linux users - - The MacOS and Windows instructions will _probably_ not work for you. You can try at your own risk to check. - - Linux users can try these [instructions](https://www.geeksforgeeks.org/install-postgresql-on-linux/) and that should work for you (...maybe...). If it doesn't try googling instructions with your specific operating system. Sorry! + + - The MacOS and Windows instructions will _probably_ not work for you. You can try at your own risk to check. + - Linux users can try these [instructions](https://www.geeksforgeeks.org/install-postgresql-on-linux/) and that should work for you (...maybe...). If it doesn't try googling instructions with your specific operating system. Sorry! + 2. Loading data to your database + 1. Adding the Schemas to your database. - 1. Go into your database using the following command: - + + 1. Go into your database using the following command: + ``` psql postgresql://localhost/postgres - ``` - - From there, create the schemas using the following commands: - + ``` + + From there, create the schemas using the following commands: + ``` CREATE SCHEMA gene_regulatory_network; ``` - + ``` CREATE SCHEMA gene_expression; ``` @@ -38,111 +47,146 @@ Here are the files pertaining to both the network and expression databases. Look ``` CREATE SCHEMA protein_protein_interactions; ``` - - Once they are created you can exit your database using the command `\q`. - 2. Once your schema's are created, you can add the table specifications using the following commands: - + + Once they are created you can exit your database using the command `\q`. + + 2. Once your schema's are created, you can add the table specifications using the following commands: + ``` psql -f /schema.sql postgresql://localhost/postgres ``` - + ``` psql -f /schema.sql postgresql://localhost/postgres ``` - + ``` psql -f /schema.sql postgresql://localhost/postgres ``` + Your database is now ready to accept expression and network data! - - 2. Loading the GRNsight Network Data to your local database - 1. GRNsight generates Network Data from SGD through YeastMine. In order to run the script that generates these Network files, you must pip3 install the dependencies used. If you get an error saying that a module doesn't exist, just run `pip3 install ` and it should fix the error. If the error persists and is found in a specific file on your machine, you might have to manually go into that file and alter the naming conventions of the dependencies that are used. _Note: So far this issue has only occured on Ubuntu 22.04.1, and certain MacOS versions so you might be lucky and not have to do it!_ - - ``` - pip3 install pandas requests intermine tzlocal - ``` - - Once the dependencies have been installed, you can run - ``` - cd - python3 generate_network.py - ``` - This will take a while to get all of the network data and generate all of the files. This will create a folder full of the processed files in `database/network-database/script-results`. - - *** Note: *** If you get an error similar to the following image where it references the in then you are one of the unlucky few who has to edit the intermine.py file directly. - - ![image](https://user-images.githubusercontent.com/21343072/213089777-dfe772bc-deca-4df7-816f-72703db24d1e.png) - - - Navigate the referenced file ( \/intermine/webservice.py ) - - - The try-catch block should look like this: - - - ![image](https://user-images.githubusercontent.com/21343072/213094796-c48f54da-b76c-4266-81fb-6aaef24a36c9.png) - - - Change it to the following, rerun the `generate_network.py` command and it should work! If it doesn't you may need to troubleshoot a bit further (´◕ ᵔ ◕`✿)*ᶜʳᶦᵉˢ*. - - - ![image](https://user-images.githubusercontent.com/21343072/213094984-bff2deb3-d26b-4809-83d6-6a6615b6e3cf.png) - - 2. Load the processed files into your database. - - ``` - cd - python3 loader.py | psql postgresql://localhost/postgres - ``` - - This should output a bunch of COPY print statements to your terminal. Once complete your database is now loaded with the network data. - - 3. Loading the GRNsight Expression Data to your local database - 1. Create a directory (aka folder) in the database/expression-database folder called `source-files`. - - ``` - mkdir /source-files - ``` - - 2. Download the _"Expression 2020"_ folder from Box located in `GRNsight > GRNsight Expression > Expression 2020` to your newly created `source-files` folder. Your the path should look like this: GRNsight > database > expression-database > source-files > Expression 2020 > [the actual csv and xlsx files are here!] - 3. Run the pre-processing script on the data. This will create a folder full of the processed files in `database/expression-database/script-results`. - - ``` - cd - python3 preprocessing.py - ``` - - 4. Load the processed files into your database. - - ``` - cd - python3 loader.py | psql postgresql://localhost/postgres - ``` - - This should output a bunch of COPY print statements to your terminal. Once complete your database is now loaded with the expression data. - 4. Loading the GRNsight Protein-Protein Interactions to your local database - 1. GRNsight generates Protein-Protein Interactions from SGD through YeastMine. In order to run the script that generates these Network files, you must pip3 install the dependencies used. These are the same dependencies used when creating the Network Database, so if you have completed step 2.2.1, then you should be fine. Once the dependencies have been installed, you can run - ``` - cd - python3 generate_protein_network.py - ``` - This will take a while {almost 2 hours (´◕ ᵔ ◕\`✿)*ᶜʳᶦᵉˢ*} to get all of the network data and generate all of the files. This will create a folder full of the processed files in `database/protein-protein-database/script-results`. - - 2. Once you have finished generating the loader files, you need to remove duplicate entries from the physical interactions file. The bash script (`remove_duplicates.sh`) does this for you. The resultant file (`no_dupe.csv`)will be generated in the script-results directory located in the sub-directory processed-loader-files. If your machine doesn't support bash shell scripts, then you have to make a new script that removes duplicate lines from a file and writes the results to a file. Sorry! - - Run the following: - ``` - chmod u+x remove_duplicates.sh - - ./remove_duplicates.sh - ``` - 3. Load the processed files into your database. Note: You may get an error saying that there was a duplicate protein. You have to manually check which protein was being inserted twice, go to the SGD website (or Yeastmine) and confirm the correct protein gene interaction. Currently this occurs with the protein 'Aad6p'. To fix it go to your protein.csv file and make sure that 'Aad6p' is paired with the gene 'YFL056C', and 'Aad16p' is paired with the gene 'YFL057C'. If any other issues arise, you must manually confirm on the SGD website. Sorry! - To load to local database + 2. Getting Data + + 1. Getting Data for Network + GRNsight generates Network Data from SGD through YeastMine. In order to run the script that generates these Network files, you must pip3 install the dependencies used. If you get an error saying that a module doesn't exist, just run `pip3 install ` and it should fix the error. If the error persists and is found in a specific file on your machine, you might have to manually go into that file and alter the naming conventions of the dependencies that are used. _Note: So far this issue has only occured on Ubuntu 22.04.1, and certain MacOS versions so you might be lucky and not have to do it!_ + ``` - python3 loader.py | psql postgresql://localhost/postgres + pip3 install pandas requests intermine tzlocal ``` - To load to production database + + Once the dependencies have been installed, you can run + ``` - python3 loader.py | psql + cd + python3 generate_network.py ``` - Once again, this should output a bunch of COPY print statements to your terminal. Once complete your database is now loaded with the expression data. - - + This will take a while to get all of the network data and generate all of the files. This will create a folder full of the processed files in `database/network-database/script-results`. + + **_ Note: _** If you get an error similar to the following image where it references the in then you are one of the unlucky few who has to edit the intermine.py file directly. + + ![image](https://user-images.githubusercontent.com/21343072/213089777-dfe772bc-deca-4df7-816f-72703db24d1e.png) + + - Navigate the referenced file ( \/intermine/webservice.py ) + - The try-catch block should look like this: + + - ![image](https://user-images.githubusercontent.com/21343072/213094796-c48f54da-b76c-4266-81fb-6aaef24a36c9.png) + - Change it to the following, rerun the `generate_network.py` command and it should work! If it doesn't you may need to troubleshoot a bit further (´◕ ᵔ ◕`✿)_ᶜʳᶦᵉˢ_. + + - ![image](https://user-images.githubusercontent.com/21343072/213094984-bff2deb3-d26b-4809-83d6-6a6615b6e3cf.png) + + 2. Getting Data for Expression + + 1. Create a directory (aka folder) in the database/expression-database folder called `source-files`. + + ``` + mkdir /source-files + ``` + + 2. Download the _"Expression 2020"_ folder from Box located in `GRNsight > GRNsight Expression > Expression 2020` to your newly created `source-files` folder. Your the path should look like this: GRNsight > database > expression-database > source-files > Expression 2020 > [the actual csv and xlsx files are here!] + 3. Run the pre-processing script on the data. This will create a folder full of the processed files in `database/expression-database/script-results`. + + ``` + cd + python3 preprocessing.py + ``` + + 3. Getting Data for Protein-Protein Interactions + + 1. GRNsight generates Protein-Protein Interactions from SGD through YeastMine. In order to run the script that generates these Network files, you must pip3 install the dependencies used. These are the same dependencies used when creating the Network Database, so if you have completed step 2.2.1, then you should be fine. Once the dependencies have been installed, you can run + + ``` + cd + python3 generate_protein_network.py + ``` + + This will take a while {almost 2 hours (´◕ ᵔ ◕\`✿)_ᶜʳᶦᵉˢ_} to get all of the network data and generate all of the files. This will create a folder full of the processed files in `database/protein-protein-database/script-results`. + + 2. Once you have finished generating the loader files, you need to remove duplicate entries from the physical interactions file. The bash script (`remove_duplicates.sh`) does this for you. The resultant file (`no_dupe.csv`)will be generated in the script-results directory located in the sub-directory processed-loader-files. If your machine doesn't support bash shell scripts, then you have to make a new script that removes duplicate lines from a file and writes the results to a file. Sorry! + + Run the following: + + ``` + chmod u+x remove_duplicates.sh + + ./remove_duplicates.sh + ``` + + 3. Loading all processed files into your local database + Need to run the script under `database` folder and run `loader.py`. The file contains scripts to collect union genes from expression, network, and protein-protein interactions. After that, the scripts populate all data from generated files in "Getting Data" section above into database. + + ``` + cd + ``` + + To load to local database + + ``` + python3 loader.py | psql postgresql://localhost/postgres + ``` + + To load to production database + + ``` + python3 loader.py | psql + ``` + + This should output a bunch of COPY print statements to your terminal. Once complete your database is now loaded with the expression, network, and protein-protein interactions data. + +## Instructions for Updating Database + +1. Getting new data + + 1. Generate a new network from Yeastmine using the script `generate_network.py` inside `network-database` folder. + ``` + cd + python3 generate_network.py + ``` + 2. Generate a new Protein-Protein Interactions from SGD using Yeastmine + + ``` + cd + python3 generate_protein_network.py + ``` + + 3. Filter all the missing genes, and updated genes in both Network and Protein-Protein Interactions. Also you need to filter the missing protein, and updated proteins in Protein-Protein Interactions. Everything is done in `filter_update.py`. The script will access the database get all of the genes stored within. From there it will generate a csv file of all genes that are missing from your database, and all genes that have updated their display name (standard like name). + + ``` + cd + ``` + 3. Continue setting up in the [Initial Setup Wiki page](https://github.com/dondi/GRNsight/wiki/Initial-Setup) From b0e3cf67b4a17eb043a84cb3d168e3a011666c37 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 23 Apr 2024 03:22:05 -0700 Subject: [PATCH 138/150] #1106 remove all the testing namespace --- database/constants.py | 6 +++--- database/network-database/schema.sql | 4 ++-- database/protein-protein-database/schema.sql | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/database/constants.py b/database/constants.py index 45bb52a8..8623f593 100644 --- a/database/constants.py +++ b/database/constants.py @@ -15,18 +15,18 @@ class Constants: UPDATE_GENE_UNION_DIRECTORY = UNION_GENE_FOLDER_PATH + 'union-update-genes.csv' # Constants name: NETWORK__DATA_DIRECTORY - NETWORK_DATABASE_NAMESPACE = 'gene_regulatory_network_testing' + NETWORK_DATABASE_NAMESPACE = 'gene_regulatory_network' NETWORK_SOURCE_TABLE_DATA_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/source.csv' NETWORK_NETWORK_TABLE_DATA_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/network.csv' # Protein-protein-interactions - PROTEIN_DATABASE_NAMESPACE = 'protein_protein_interactions_testing' + PROTEIN_DATABASE_NAMESPACE = 'protein_protein_interactions' PROTEIN_SOURCE_TABLE_DATA_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/source.csv' PROTEIN_NETWORK_TABLE_DATA_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/physical_interaction_no_dupe.csv' PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/protein.csv' # Expression data - EXPRESISON_DATABASE_NAMESPACE = 'gene_expression_testing' + EXPRESISON_DATABASE_NAMESPACE = 'gene_expression' EXPRESSION_REFS_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/refs.csv' EXPRESSION_METADATA_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-metadata.csv' EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-data.csv' diff --git a/database/network-database/schema.sql b/database/network-database/schema.sql index 377f845b..59a315ff 100644 --- a/database/network-database/schema.sql +++ b/database/network-database/schema.sql @@ -20,6 +20,6 @@ CREATE TABLE gene_regulatory_network.network ( time_stamp TIMESTAMP WITH TIME ZONE, source VARCHAR, FOREIGN KEY (regulator_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id), - FOREIGN KEY (target_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id), - FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network.source(time_stamp, source) + FOREIGN KEY (target_gene_id, taxon_id) REFERENCES gene_regulatory_network_testing.gene(gene_id, taxon_id), + FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network_testing.source(time_stamp, source) ); \ No newline at end of file diff --git a/database/protein-protein-database/schema.sql b/database/protein-protein-database/schema.sql index a2f43a94..922bfac2 100644 --- a/database/protein-protein-database/schema.sql +++ b/database/protein-protein-database/schema.sql @@ -20,7 +20,7 @@ CREATE TABLE protein_protein_interactions.protein ( molecular_weight FLOAT, PI FLOAT, taxon_id VARCHAR, - FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions.gene(gene_id, taxon_id) + FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions_testing.gene(gene_id, taxon_id) ); CREATE TABLE protein_protein_interactions.physical_interactions ( @@ -30,8 +30,8 @@ CREATE TABLE protein_protein_interactions.physical_interactions ( experiment_name VARCHAR, time_stamp TIMESTAMP WITH TIME ZONE, source VARCHAR, - FOREIGN KEY (protein1) REFERENCES protein_protein_interactions.protein(standard_name), - FOREIGN KEY (protein2) REFERENCES protein_protein_interactions.protein(standard_name), - FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions.source(time_stamp, source), + FOREIGN KEY (protein1) REFERENCES protein_protein_interactions_testing.protein(standard_name), + FOREIGN KEY (protein2) REFERENCES protein_protein_interactions_testing.protein(standard_name), + FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions_testing.source(time_stamp, source), CONSTRAINT unique_physical_interaction UNIQUE (protein1, protein2, interaction_detection_methods_identifier, experiment_name, time_stamp, source) ); From 6dc0eaa53d60753d60c94f5a83614143a2e95ff2 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 23 Apr 2024 03:32:47 -0700 Subject: [PATCH 139/150] #1106 Adding update to expression gene table --- database/loader_update.py | 5 ++++- database/utils.py | 4 ++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/database/loader_update.py b/database/loader_update.py index df03daa0..2983528b 100644 --- a/database/loader_update.py +++ b/database/loader_update.py @@ -23,4 +23,7 @@ Utils.load_sources(Constants.NETWORK_SOURCE_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) Utils.update_network_genes(Constants.UPDATE_GENE_UNION_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) Utils.load_network_genes(Constants.MISSING_GENE_UNION_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.load_network_network(Constants.NETWORK_NETWORK_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) \ No newline at end of file +Utils.load_network_network(Constants.NETWORK_NETWORK_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) + +# Expression +Utils.update_expression_genes(Constants.UPDATE_GENE_UNION_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) \ No newline at end of file diff --git a/database/utils.py b/database/utils.py index c9b332e4..d37a680d 100644 --- a/database/utils.py +++ b/database/utils.py @@ -192,6 +192,10 @@ def update_network_genes(cls, gene_path: str, database_namespace: str): @classmethod def update_protein_genes(cls, gene_path: str, database_namespace: str): cls._update_genes(gene_path, database_namespace, is_protein = True) + + @classmethod + def update_expression_genes(cls, gene_path: str, database_namespace: str): + cls._update_genes(gene_path, database_namespace, is_protein = False) @classmethod def _update_genes(cls, update_gene_path: str, database_namespace: str, is_protein: bool): From a5efaa0e2f28a49e345f7a9d540f806f6dd1c3f1 Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 23 Apr 2024 08:39:46 -0700 Subject: [PATCH 140/150] Issue #1083. In move function did not call function properly so the graph was not restricting viewport with Dpad. Fixed by calling viewportBoundsMoveDrag(graphZoom, moveWidth, moveHeight) instead of just (graphZoom, moveWidth, moveHeight) that did not have function name --- web-client/public/js/graph.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 6b069590..5e1b507a 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -483,8 +483,8 @@ export var drawGraph = function (workbook) { if (adaptive) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { - if ((graphZoom, moveWidth, moveHeight)) { - zoom.translateBy(zoomContainer, moveWidth, moveHeight); + if (viewportBoundsMoveDrag(graphZoom, moveWidth, moveHeight)) { + zoom.translateBy(zoomContainer, moveWidth, moveHeight); } } } From 4ebe78f5a6fe436ae552d9e34df405be6683c9ad Mon Sep 17 00:00:00 2001 From: ceciliazaragoza Date: Tue, 23 Apr 2024 08:42:50 -0700 Subject: [PATCH 141/150] Issue #1083. Passing all lint and test --- web-client/public/js/graph.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js index 5e1b507a..0f58821e 100644 --- a/web-client/public/js/graph.js +++ b/web-client/public/js/graph.js @@ -484,7 +484,7 @@ export var drawGraph = function (workbook) { zoom.translateBy(zoomContainer, moveWidth, moveHeight); } else if (!adaptive) { if (viewportBoundsMoveDrag(graphZoom, moveWidth, moveHeight)) { - zoom.translateBy(zoomContainer, moveWidth, moveHeight); + zoom.translateBy(zoomContainer, moveWidth, moveHeight); } } } From deac16ccafbe441519955b72ac8163c837003b59 Mon Sep 17 00:00:00 2001 From: Cecilia Zaragoza <105010308+ceciliazaragoza@users.noreply.github.com> Date: Tue, 23 Apr 2024 10:27:37 -0700 Subject: [PATCH 142/150] Version Bump 7.0.15 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index c89a274f..ab494d07 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "grnsight", - "version": "7.0.14", + "version": "7.0.15", "description": "Web app and service for visualizing models of gene regulatory networks", "directories": { "test": "test" From 8652b3308fc28d9f611a178d6169483a21d0bf89 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Tue, 23 Apr 2024 11:38:02 -0700 Subject: [PATCH 143/150] Changing the gene source directory to use the old gene files, instead of using union genes. The code for union genes can just leave it there for now --- database/loader.py | 6 +++--- database/loader_update.py | 15 ++++++--------- 2 files changed, 9 insertions(+), 12 deletions(-) diff --git a/database/loader.py b/database/loader.py index 522c5d59..51fb64d9 100644 --- a/database/loader.py +++ b/database/loader.py @@ -12,18 +12,18 @@ # Regulatory Network Utils.load_sources(Constants.NETWORK_SOURCE_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.load_network_genes(Constants.GENE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) +Utils.load_network_genes(Constants.NETWORK_GENE_SOURCE, Constants.NETWORK_DATABASE_NAMESPACE) Utils.load_network_network(Constants.NETWORK_NETWORK_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) # Protein-protein-interactions Utils.load_sources(Constants.PROTEIN_SOURCE_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.load_protein_genes(Constants.GENE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.load_protein_genes(Constants.PROTEIN_GENE_SOURCE, Constants.PROTEIN_DATABASE_NAMESPACE) Utils.load_proteins(Constants.PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) Utils.load_protein_network(Constants.PROTEIN_NETWORK_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) # Expression data Utils.load_refs(Constants.EXPRESSION_REFS_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) -Utils.load_expression_genes(Constants.GENE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) +Utils.load_expression_genes(Constants.EXPRESSION_GENE_SOURCE, Constants.EXPRESISON_DATABASE_NAMESPACE) Utils.load_expression_metadata(Constants.EXPRESSION_METADATA_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) Utils.load_expression_data(Constants.EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) Utils.load_production_rates(Constants.EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) diff --git a/database/loader_update.py b/database/loader_update.py index 2983528b..5ad1b862 100644 --- a/database/loader_update.py +++ b/database/loader_update.py @@ -13,17 +13,14 @@ # Proteins Utils.load_sources(Constants.PROTEIN_SOURCE_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.update_protein_genes(Constants.UPDATE_GENE_UNION_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.update_protein_genes(Constants.PROTEIN_UPDATE_GENE_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) Utils.update_proteins(Constants.PROTEIN_UPDATE_PROTEIN_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.load_genes(Constants.MISSING_GENE_UNION_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE, is_protein=True) +Utils.load_protein_genes(Constants.PROTEIN_MISSING_GENE_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) Utils.load_proteins(Constants.PROTEIN_MISSING_PROTEIN_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.load_network(Constants.PROTEIN_NETWORK_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE, is_protein=True) +Utils.load_protein_network(Constants.PROTEIN_NETWORK_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) # Network Utils.load_sources(Constants.NETWORK_SOURCE_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.update_network_genes(Constants.UPDATE_GENE_UNION_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.load_network_genes(Constants.MISSING_GENE_UNION_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.load_network_network(Constants.NETWORK_NETWORK_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) - -# Expression -Utils.update_expression_genes(Constants.UPDATE_GENE_UNION_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) \ No newline at end of file +Utils.update_network_genes(Constants.NETWORK_UPDATE_GENE_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) +Utils.load_network_genes(Constants.NETWORK_MISSING_GENE_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) +Utils.load_network_network(Constants.NETWORK_NETWORK_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) \ No newline at end of file From 17e05a37f12abe21575b073382305a377e07767c Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Wed, 24 Apr 2024 00:35:04 -0700 Subject: [PATCH 144/150] Fixing the naming --- database/constants.py | 47 ++++++++++++++--------------- database/filter_update.py | 63 +++++++++++++++++++++++---------------- database/loader.py | 16 +++++----- database/loader_update.py | 28 ++++++++--------- database/utils.py | 30 +++++++++---------- 5 files changed, 97 insertions(+), 87 deletions(-) diff --git a/database/constants.py b/database/constants.py index 8623f593..cc2d6cc8 100644 --- a/database/constants.py +++ b/database/constants.py @@ -1,13 +1,13 @@ class Constants: - NETWORK_FOLDER_PATH = 'network-database' - PROTEIN_FOLDER_PATH = 'protein-protein-database' + GRN_FOLDER_PATH = 'network-database' + PPI_FOLDER_PATH = 'protein-protein-database' EXPRESSION_FOLDER_PATH = 'expression-database' UNION_GENE_FOLDER_PATH = 'union-gene-data/' # Gene data source file path - NETWORK_GENE_SOURCE = "network-database/script-results/processed-loader-files/gene.csv" - PROTEIN_GENE_SOURCE = "protein-protein-database/script-results/processed-loader-files/gene.csv" - EXPRESSION_GENE_SOURCE = "expression-database/script-results/processed-expression/genes.csv" + GRN_GENE_SOURCE = GRN_FOLDER_PATH + "/script-results/processed-loader-files/gene.csv" + PPI_GENE_SOURCE = PPI_FOLDER_PATH + "/script-results/processed-loader-files/gene.csv" + EXPRESSION_GENE_SOURCE = EXPRESSION_FOLDER_PATH + "/script-results/processed-expression/genes.csv" # Union gene data GENE_DATA_DIRECTORY = UNION_GENE_FOLDER_PATH + 'union_genes.csv' @@ -15,29 +15,28 @@ class Constants: UPDATE_GENE_UNION_DIRECTORY = UNION_GENE_FOLDER_PATH + 'union-update-genes.csv' # Constants name: NETWORK__DATA_DIRECTORY - NETWORK_DATABASE_NAMESPACE = 'gene_regulatory_network' - NETWORK_SOURCE_TABLE_DATA_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/source.csv' - NETWORK_NETWORK_TABLE_DATA_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/network.csv' + GRN_DATABASE_NAMESPACE = 'gene_regulatory_network' + GRN_SOURCE_TABLE_DATA_DIRECTORY = GRN_FOLDER_PATH + '/script-results/processed-loader-files/source.csv' + GRN_NETWORK_TABLE_DATA_DIRECTORY = GRN_FOLDER_PATH + '/script-results/processed-loader-files/network.csv' # Protein-protein-interactions - PROTEIN_DATABASE_NAMESPACE = 'protein_protein_interactions' - PROTEIN_SOURCE_TABLE_DATA_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/source.csv' - PROTEIN_NETWORK_TABLE_DATA_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/physical_interaction_no_dupe.csv' - PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/protein.csv' + PPI_DATABASE_NAMESPACE = 'protein_protein_interactions' + PPI_SOURCE_TABLE_DATA_DIRECTORY = PPI_FOLDER_PATH + '/script-results/processed-loader-files/source.csv' + PPI_NETWORK_TABLE_DATA_DIRECTORY = PPI_FOLDER_PATH + '/script-results/processed-loader-files/physical_interaction_no_dupe.csv' + PPI_PROTEIN_TABLE_DATA_DIRECTORY = PPI_FOLDER_PATH + '/script-results/processed-loader-files/protein.csv' # Expression data EXPRESISON_DATABASE_NAMESPACE = 'gene_expression' - EXPRESSION_REFS_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/refs.csv' - EXPRESSION_METADATA_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-metadata.csv' - EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/expression-data.csv' - EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/production-rates.csv' - EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY = 'expression-database/script-results/processed-expression/degradation-rates.csv' + EXPRESSION_REFS_TABLE_DATA_DIRECTORY = EXPRESSION_FOLDER_PATH + '/script-results/processed-expression/refs.csv' + EXPRESSION_METADATA_TABLE_DATA_DIRECTORY = EXPRESSION_FOLDER_PATH + '/script-results/processed-expression/expression-metadata.csv' + EXPRESSION_EXPRESSION_TABLE_DATA_DIRECTORY = EXPRESSION_FOLDER_PATH + '/script-results/processed-expression/expression-data.csv' + EXPRESSION_PRODUCTION_RATE_TABLE_DATA_DIRECTORY = EXPRESSION_FOLDER_PATH + '/script-results/processed-expression/production-rates.csv' + EXPRESSION_DEGRADATION_RATE_TABLE_DATA_DIRECTORY = EXPRESSION_FOLDER_PATH + '/script-results/processed-expression/degradation-rates.csv' # Paths for update files - PROTEIN_MISSING_GENE_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/missing-genes.csv' - PROTEIN_UPDATE_GENE_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/update-genes.csv' - PROTEIN_MISSING_PROTEIN_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/missing-proteins.csv' - PROTEIN_UPDATE_PROTEIN_DIRECTORY = PROTEIN_FOLDER_PATH + '/script-results/processed-loader-files/update-proteins.csv' - - NETWORK_MISSING_GENE_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/missing-genes.csv' - NETWORK_UPDATE_GENE_DIRECTORY = NETWORK_FOLDER_PATH + '/script-results/processed-loader-files/update-genes.csv' \ No newline at end of file + PPI_MISSING_GENE_DIRECTORY = PPI_FOLDER_PATH + '/script-results/processed-loader-files/missing-genes.csv' + PPI_UPDATE_GENE_DIRECTORY = PPI_FOLDER_PATH + '/script-results/processed-loader-files/update-genes.csv' + PPI_MISSING_PROTEIN_DIRECTORY = PPI_FOLDER_PATH + '/script-results/processed-loader-files/missing-proteins.csv' + PPI_UPDATE_PROTEIN_DIRECTORY = PPI_FOLDER_PATH + '/script-results/processed-loader-files/update-proteins.csv' + GRN_MISSING_GENE_DIRECTORY = GRN_FOLDER_PATH + '/script-results/processed-loader-files/missing-genes.csv' + GRN_UPDATE_GENE_DIRECTORY = GRN_FOLDER_PATH + '/script-results/processed-loader-files/update-genes.csv' \ No newline at end of file diff --git a/database/filter_update.py b/database/filter_update.py index 2cf959a3..7e3b91bf 100644 --- a/database/filter_update.py +++ b/database/filter_update.py @@ -4,6 +4,9 @@ from sqlalchemy import text from constants import Constants +PROTEIN_GENE_HEADER = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' +GRN_GENE_HEADER = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID\tRegulator' + def get_all_data_from_database_table(database_namespace, table_name): db = create_engine(os.environ['DB_URL']) with db.connect() as connection: @@ -22,14 +25,14 @@ def get_all_genes(database_namespace): genes[key] = value return genes -def get_all_network_genes(): - return get_all_genes(Constants.NETWORK_DATABASE_NAMESPACE) +def get_all_grn_genes(): + return get_all_genes(Constants.GRN_DATABASE_NAMESPACE) -def get_all_protein_genes(): - return get_all_genes(Constants.PROTEIN_DATABASE_NAMESPACE) +def get_all_ppi_genes(): + return get_all_genes(Constants.PPI_DATABASE_NAMESPACE) def get_all_proteins(): - protein_records = get_all_data_from_database_table(Constants.PROTEIN_DATABASE_NAMESPACE, "protein") + protein_records = get_all_data_from_database_table(Constants.PPI_DATABASE_NAMESPACE, "protein") proteins = {} for protein in protein_records: key = (protein[1], protein[5]) @@ -37,7 +40,13 @@ def get_all_proteins(): proteins[key] = value return proteins -def processing_gene_file(file_path, db_genes, is_protein=True): +def processing_grn_gene_file(): + _processing_gene_file(Constants.GRN_GENE_SOURCE, get_all_grn_genes(), is_protein=False) + +def processing_ppi_gene_file(): + _processing_gene_file(Constants.PPI_GENE_SOURCE, get_all_ppi_genes()) + +def _processing_gene_file(file_path, db_genes, is_protein=True): print(f'Processing file {file_path}') missing_genes = {} genes_to_update = {} @@ -68,8 +77,8 @@ def processing_gene_file(file_path, db_genes, is_protein=True): def processing_protein_file(file_path, db_proteins): print(f'Processing file {file_path}') - missing_proteins = {} - proteins_to_update = {} + ppi_missing_proteins = {} + ppi_proteins_to_update = {} with open(file_path, 'r+', encoding="UTF-8") as f: i = 0 reader = csv.reader(f) @@ -85,13 +94,19 @@ def processing_protein_file(file_path, db_proteins): key = (gene_systematic_name, taxon_id) value = (standard_name, length, molecular_weight, pi) if key not in db_proteins: - missing_proteins[key] = value + ppi_missing_proteins[key] = value elif db_proteins[key] != value: - proteins_to_update[key] = value + ppi_proteins_to_update[key] = value i+=1 - return missing_proteins, proteins_to_update + return ppi_missing_proteins, ppi_proteins_to_update + +def create_grn_gene_file(file_path, data): + _create_gene_file(file_path, GRN_GENE_HEADER, data, is_protein=False) + +def create_ppi_gene_file(file_path, data): + _create_gene_file(file_path, PROTEIN_GENE_HEADER, data) -def create_gene_file(file_path, headers, data, is_protein=True): +def _create_gene_file(file_path, headers, data, is_protein=True): print(f'Creating {file_path}\n') gene_file = open(file_path, 'w') gene_file.write(f'{headers}\n') @@ -102,7 +117,7 @@ def create_gene_file(file_path, headers, data, is_protein=True): gene_file.write(f'{gene[0]}\t{data[gene][0]}\t{data[gene][1]}\t{gene[1]}\t{data[gene][2]}\n') gene_file.close() -def create_protein_file(file_path, data): +def create_ppi_protein_file(file_path, data): print(f'Creating {file_path}\n') protein_file = open(file_path, 'w') headers = f'Standard Name\tGene Systematic Name\tLength\tMolecular Weight\tPI\tTaxon ID' @@ -112,16 +127,12 @@ def create_protein_file(file_path, data): protein_file.close() # Processing gene files -protein_headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' -network_headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID\tRegulator' -network_db_genes = get_all_network_genes() -protein_db_genes = get_all_protein_genes() -protein_missing_genes, protein_genes_to_update = processing_gene_file(Constants.PROTEIN_GENE_SOURCE, protein_db_genes) -network_missing_genes, network_genes_to_update = processing_gene_file(Constants.NETWORK_GENE_SOURCE, network_db_genes, is_protein=False) -missing_proteins, proteins_to_update = processing_protein_file(Constants.PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY, get_all_proteins()) -create_gene_file(Constants.NETWORK_MISSING_GENE_DIRECTORY, network_headers, network_missing_genes, is_protein=False) -create_gene_file(Constants.PROTEIN_MISSING_GENE_DIRECTORY, protein_headers, protein_missing_genes) -create_gene_file(Constants.NETWORK_UPDATE_GENE_DIRECTORY, network_headers, network_genes_to_update, is_protein=False) -create_gene_file(Constants.PROTEIN_UPDATE_GENE_DIRECTORY, protein_headers, protein_genes_to_update) -create_protein_file(Constants.PROTEIN_MISSING_PROTEIN_DIRECTORY, missing_proteins) -create_protein_file(Constants.PROTEIN_UPDATE_PROTEIN_DIRECTORY, proteins_to_update) \ No newline at end of file +ppi_missing_genes, ppi_genes_to_update = processing_ppi_gene_file() +grn_missing_genes, grn_genes_to_update = processing_grn_gene_file() +ppi_missing_proteins, ppi_proteins_to_update = processing_protein_file(Constants.PPI_PROTEIN_TABLE_DATA_DIRECTORY, get_all_proteins()) +create_grn_gene_file(Constants.GRN_MISSING_GENE_DIRECTORY, grn_missing_genes) +create_grn_gene_file(Constants.GRN_UPDATE_GENE_DIRECTORY, grn_genes_to_update) +create_ppi_gene_file(Constants.PPI_MISSING_GENE_DIRECTORY, ppi_missing_genes) +create_ppi_gene_file(Constants.PPI_UPDATE_GENE_DIRECTORY, ppi_genes_to_update) +create_ppi_protein_file(Constants.PPI_MISSING_PROTEIN_DIRECTORY, ppi_missing_proteins) +create_ppi_protein_file(Constants.PPI_UPDATE_PROTEIN_DIRECTORY, ppi_proteins_to_update) \ No newline at end of file diff --git a/database/loader.py b/database/loader.py index 51fb64d9..50fede12 100644 --- a/database/loader.py +++ b/database/loader.py @@ -8,18 +8,18 @@ os.makedirs('union-gene-data') # Get union gene data -Utils.create_union_file([Constants.EXPRESSION_GENE_SOURCE, Constants.PROTEIN_GENE_SOURCE, Constants.NETWORK_GENE_SOURCE], Constants.GENE_DATA_DIRECTORY) +Utils.create_union_file([Constants.EXPRESSION_GENE_SOURCE, Constants.PPI_GENE_SOURCE, Constants.GRN_GENE_SOURCE], Constants.GENE_DATA_DIRECTORY) # Regulatory Network -Utils.load_sources(Constants.NETWORK_SOURCE_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.load_network_genes(Constants.NETWORK_GENE_SOURCE, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.load_network_network(Constants.NETWORK_NETWORK_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) +Utils.load_sources(Constants.GRN_SOURCE_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) +Utils.load_grn_genes(Constants.GRN_GENE_SOURCE, Constants.GRN_DATABASE_NAMESPACE) +Utils.load_grn_network(Constants.GRN_NETWORK_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) # Protein-protein-interactions -Utils.load_sources(Constants.PROTEIN_SOURCE_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.load_protein_genes(Constants.PROTEIN_GENE_SOURCE, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.load_proteins(Constants.PROTEIN_PROTEIN_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.load_protein_network(Constants.PROTEIN_NETWORK_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +Utils.load_sources(Constants.PPI_SOURCE_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) +Utils.load_ppi_genes(Constants.PPI_GENE_SOURCE, Constants.PPI_DATABASE_NAMESPACE) +Utils.load_proteins(Constants.PPI_PROTEIN_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) +Utils.load_ppi_network(Constants.PPI_NETWORK_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) # Expression data Utils.load_refs(Constants.EXPRESSION_REFS_TABLE_DATA_DIRECTORY, Constants.EXPRESISON_DATABASE_NAMESPACE) diff --git a/database/loader_update.py b/database/loader_update.py index 5ad1b862..615f7211 100644 --- a/database/loader_update.py +++ b/database/loader_update.py @@ -6,21 +6,21 @@ os.makedirs('union-gene-data') # Get missing union gene data -Utils.create_union_file([Constants.PROTEIN_MISSING_GENE_DIRECTORY, Constants.NETWORK_MISSING_GENE_DIRECTORY], Constants.MISSING_GENE_UNION_DIRECTORY) +Utils.create_union_file([Constants.PPI_MISSING_GENE_DIRECTORY, Constants.GRN_MISSING_GENE_DIRECTORY], Constants.MISSING_GENE_UNION_DIRECTORY) # Get update union gene data -Utils.create_union_file([Constants.PROTEIN_UPDATE_GENE_DIRECTORY, Constants.NETWORK_UPDATE_GENE_DIRECTORY], Constants.UPDATE_GENE_UNION_DIRECTORY) +Utils.create_union_file([Constants.PPI_UPDATE_GENE_DIRECTORY, Constants.GRN_UPDATE_GENE_DIRECTORY], Constants.UPDATE_GENE_UNION_DIRECTORY) -# Proteins -Utils.load_sources(Constants.PROTEIN_SOURCE_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.update_protein_genes(Constants.PROTEIN_UPDATE_GENE_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.update_proteins(Constants.PROTEIN_UPDATE_PROTEIN_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.load_protein_genes(Constants.PROTEIN_MISSING_GENE_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.load_proteins(Constants.PROTEIN_MISSING_PROTEIN_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) -Utils.load_protein_network(Constants.PROTEIN_NETWORK_TABLE_DATA_DIRECTORY, Constants.PROTEIN_DATABASE_NAMESPACE) +# PPI +Utils.load_sources(Constants.PPI_SOURCE_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) +Utils.update_ppi_genes(Constants.PPI_UPDATE_GENE_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) +Utils.update_ppi_proteins(Constants.PPI_UPDATE_PROTEIN_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) +Utils.load_ppi_genes(Constants.PPI_MISSING_GENE_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) +Utils.load_proteins(Constants.PPI_MISSING_PROTEIN_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) +Utils.load_ppi_network(Constants.PPI_NETWORK_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) -# Network -Utils.load_sources(Constants.NETWORK_SOURCE_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.update_network_genes(Constants.NETWORK_UPDATE_GENE_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.load_network_genes(Constants.NETWORK_MISSING_GENE_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) -Utils.load_network_network(Constants.NETWORK_NETWORK_TABLE_DATA_DIRECTORY, Constants.NETWORK_DATABASE_NAMESPACE) \ No newline at end of file +# GRN +Utils.load_sources(Constants.GRN_SOURCE_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) +Utils.update_grn_genes(Constants.GRN_UPDATE_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) +Utils.load_grn_genes(Constants.GRN_MISSING_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) +Utils.load_grn_network(Constants.GRN_NETWORK_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) \ No newline at end of file diff --git a/database/utils.py b/database/utils.py index d37a680d..06493829 100644 --- a/database/utils.py +++ b/database/utils.py @@ -28,7 +28,7 @@ class Utils: Load Network Matrix into the database update_genes(update_gene_path: str, database_namespace: str, is_protein: bool) Update Gene ID Mapping into the database - update_proteins(update_protein_path: str, database_namespace: str) + update_ppi_proteins(update_protein_path: str, database_namespace: str) Update Protein ID Mapping into the database """ @@ -59,19 +59,19 @@ def load_sources(cls, source_path: str, database_namespace: str): print('\\.') @classmethod - def load_network_genes(cls, gene_path: str, database_namespace: str): - cls._load_genes(gene_path, database_namespace, is_network = True) + def load_grn_genes(cls, gene_path: str, database_namespace: str): + cls._load_genes(gene_path, database_namespace, is_grn = True) @classmethod - def load_protein_genes(cls, gene_path: str, database_namespace: str): - cls._load_genes(gene_path, database_namespace, is_network = False) + def load_ppi_genes(cls, gene_path: str, database_namespace: str): + cls._load_genes(gene_path, database_namespace, is_grn = False) @classmethod def load_expression_genes(cls, gene_path: str, database_namespace: str): - cls._load_genes(gene_path, database_namespace, is_network = False) + cls._load_genes(gene_path, database_namespace, is_grn = False) @classmethod - def _load_genes(cls, gene_path: str, database_namespace: str, is_network: bool): + def _load_genes(cls, gene_path: str, database_namespace: str, is_grn: bool): """ Load Gene ID Mapping into the database using the COPY command @@ -81,10 +81,10 @@ def _load_genes(cls, gene_path: str, database_namespace: str, is_network: bool): The path to the file containing the gene data that want to add to the database database_namespace: str The database namespace i.e the schema name where the gene data will be loaded - is_network : bool + is_grn : bool A boolean value to check if the schema is for gene_regulatory_network """ - if is_network: + if is_grn: print(f'COPY {database_namespace}.gene (gene_id, display_gene_id, species, taxon_id, regulator) FROM stdin;') else: print(f'COPY {database_namespace}.gene (gene_id, display_gene_id, species, taxon_id) FROM stdin;') @@ -98,7 +98,7 @@ def _load_genes(cls, gene_path: str, database_namespace: str, is_network: bool): display_gene_id= r[1] species = r[2] taxon_id = r[3] - if is_network: + if is_grn: regulator = r[4] print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}\t{regulator}') else: @@ -136,11 +136,11 @@ def load_proteins(cls, protein_path: str, database_namespace: str): print('\\.') @classmethod - def load_protein_network(cls, network_source_path: str, database_namespace: str): + def load_ppi_network(cls, network_source_path: str, database_namespace: str): cls._load_network(network_source_path, database_namespace, is_protein = True) @classmethod - def load_network_network(cls, network_source_path: str, database_namespace: str): + def load_grn_network(cls, network_source_path: str, database_namespace: str): cls._load_network(network_source_path, database_namespace, is_protein = False) @classmethod @@ -186,11 +186,11 @@ def _load_network(cls, network_source_path: str, database_namespace: str, is_pro print('\\.') @classmethod - def update_network_genes(cls, gene_path: str, database_namespace: str): + def update_grn_genes(cls, gene_path: str, database_namespace: str): cls._update_genes(gene_path, database_namespace, is_protein = False) @classmethod - def update_protein_genes(cls, gene_path: str, database_namespace: str): + def update_ppi_genes(cls, gene_path: str, database_namespace: str): cls._update_genes(gene_path, database_namespace, is_protein = True) @classmethod @@ -229,7 +229,7 @@ def _update_genes(cls, update_gene_path: str, database_namespace: str, is_protei print('COMMIT;') @classmethod - def update_proteins(cls, update_protein_path: str, database_namespace: str): + def update_ppi_proteins(cls, update_protein_path: str, database_namespace: str): """ Update Protein ID Mapping into the database From f90180b91452104b77bd1aa112d0d876826cb682 Mon Sep 17 00:00:00 2001 From: dondi Date: Wed, 28 Aug 2024 11:32:36 -0700 Subject: [PATCH 145/150] Switch to new grnsight domain. --- server/config/config.js | 8 ++++---- web-client/config/config.js | 8 ++++---- web-client/public/js/iframe-coordination.js | 6 +++--- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/server/config/config.js b/server/config/config.js index 0df1ca13..cfaf9a38 100644 --- a/server/config/config.js +++ b/server/config/config.js @@ -17,10 +17,10 @@ module.exports = { }, production: { - host: "grnsight.cs.lmu.edu", + host: "grnsight.lmucs.org", port: 3000, url: "https://" + this.host + "/server", - corsOrigin: "//grnsight.cs.lmu.edu", + corsOrigin: "//grnsight.lmucs.org", root: rootPath, app: { name: "GRNsight" @@ -31,10 +31,10 @@ module.exports = { }, beta: { - host: "grnsight.cs.lmu.edu", + host: "grnsight.lmucs.org", port: 4000, url: "https://" + this.host + "/beta/server/", - corsOrigin: "//grnsight.cs.lmu.edu", + corsOrigin: "//grnsight.lmucs.org", root: rootPath, app: { name: "GRNsight" diff --git a/web-client/config/config.js b/web-client/config/config.js index 25480560..b14dacd0 100644 --- a/web-client/config/config.js +++ b/web-client/config/config.js @@ -14,24 +14,24 @@ module.exports = { }, production: { - host: "grnsight.cs.lmu.edu", + host: "grnsight.lmucs.org", port: 3001, url: "https://" + this.host + "/client", root: rootPath, app: { name: "GRNsight" }, - serviceRoot: "//grnsight.cs.lmu.edu/server" + serviceRoot: "//grnsight.lmucs.org/server" }, beta: { - host: "grnsight.cs.lmu.edu", + host: "grnsight.lmucs.org", port: 4001, url: "https://" + this.host + "/beta/client", root: rootPath, app: { name: "GRNsight" }, - serviceRoot: "//grnsight.cs.lmu.edu/beta/server" + serviceRoot: "//grnsight.lmucs.org/beta/server" } }; diff --git a/web-client/public/js/iframe-coordination.js b/web-client/public/js/iframe-coordination.js index 77517a92..a9aae3dd 100644 --- a/web-client/public/js/iframe-coordination.js +++ b/web-client/public/js/iframe-coordination.js @@ -11,7 +11,7 @@ * loaded into the web browser when this script executes. */ iFrameResize({ - checkOrigin: ["https://dondi.github.io", "https://grnsight.cs.lmu.edu"], + checkOrigin: ["https://dondi.github.io", "https://grnsight.lmucs.org"], widthCalculationMethod: "taggedElement", heightCalculationMethod: "taggedElement", sizeWidth: true, @@ -40,7 +40,7 @@ const sendDimensions = (destination, origin) => { }; window.addEventListener("message", event => { - if (event.origin.indexOf("https://grnsight.cs.lmu.edu") !== 0) { + if (event.origin.indexOf("https://grnsight.lmucs.org") !== 0) { // Ignore any message that did not originate from the GRNsight web client server. return; } @@ -51,5 +51,5 @@ window.addEventListener("message", event => { }); window.addEventListener("resize", () => sendDimensions( - document.querySelector("iframe.embedded-demo").contentWindow, "https://grnsight.cs.lmu.edu" + document.querySelector("iframe.embedded-demo").contentWindow, "https://grnsight.lmucs.org" )); From 3e158a240bec936d26a326cb53490c779ddad7e0 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Fri, 6 Sep 2024 00:23:07 -0700 Subject: [PATCH 146/150] Create a class to generate source data for both GRN and PPI. Refactor the code to increase readability --- database2/scripts/constants.py | 30 +++++++++++++++++++ .../scripts/data_generation/generator.py | 23 ++++++++++++++ .../data_generation/source_generator.py | 30 +++++++++++++++++++ 3 files changed, 83 insertions(+) create mode 100644 database2/scripts/constants.py create mode 100644 database2/scripts/data_generation/generator.py create mode 100644 database2/scripts/data_generation/source_generator.py diff --git a/database2/scripts/constants.py b/database2/scripts/constants.py new file mode 100644 index 00000000..cfbda6f1 --- /dev/null +++ b/database2/scripts/constants.py @@ -0,0 +1,30 @@ +class Constants: + + SERVICE_PATH = 'http://yeastmine.yeastgenome.org/yeastmine/service' + + # Gene Info + TAXON_ID = '559292' + SPECIES = 'Saccharomyces cerevisiae' + + # Source Info + SOURCE = 'YeastMine - Saccharomyces Genome Database' + SOURCE_DISPLAY_NAME = 'Yeastmine - SGD' + + + # gene data file path + GENE_FILE_PATH = '../script-results/gene/gene.csv' + MISSING_GENE_FILE_PATH = '../script-results/gene/missing-gene.csv' + UPDATE_GENE_FILE_PATH = '../script-results/gene/update-gene.csv' + + # protein data file path + PROTEIN_FILE_PATH = '../script-results/protein/protein.csv' + MISSING_PROTEIN_FILE_PATH = '../script-results/protein/missing-protein.csv' + UPDATE_PROTEIN_FILE_PATH = '../script-results/protein/update-protein.csv' + + # network file path + GRN_NETWORK_FILE_PATH = '../script-results/network/grn-network.csv' + PPI_NETWORK_FILE_PATH = '../script-results/network/ppi-network.csv' + + # source file path + GRN_SOURCE_FILE_PATH = '../script-results/source/grn-source.csv' + PPI_SOURCE_FILE_PATH = '../script-results/source/ppi-source.csv' \ No newline at end of file diff --git a/database2/scripts/data_generation/generator.py b/database2/scripts/data_generation/generator.py new file mode 100644 index 00000000..e9439a3c --- /dev/null +++ b/database2/scripts/data_generation/generator.py @@ -0,0 +1,23 @@ +import os +import sys +import datetime +from intermine.webservice import Service + +sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) + + +from constants import Constants + + +class Generator: + def __init__(self): + self.source = Constants.SOURCE + self.source_display_name = Constants.SOURCE_DISPLAY_NAME + self.timestamp = datetime.datetime.now(datetime.timezone.utc).replace(microsecond=0) + self.create_folder_paths() + pass + + def create_folder_paths(self): + if not os.path.exists('../script-results'): + os.makedirs('../script-results') + \ No newline at end of file diff --git a/database2/scripts/data_generation/source_generator.py b/database2/scripts/data_generation/source_generator.py new file mode 100644 index 00000000..25d5d019 --- /dev/null +++ b/database2/scripts/data_generation/source_generator.py @@ -0,0 +1,30 @@ +from generator import Generator +from constants import Constants +import os + +class SourceGenerator(Generator): + def __init__(self, source_file_destination: str): + super().__init__() + self.source_file_destination = source_file_destination + self.create_source_file() + + def create_folder_paths(self): + super().create_folder_paths() + if not os.path.exists('../script-results/source'): + os.makedirs('../script-results/source') + + def create_source_file(self): + source_file = open(self.source_file_destination, 'w') + headers = f'Timestamp\tSource\tDisplay Name\n{self.timestamp}\t{self.source}\t{self.source_display_name}' + source_file.write(f'{headers}\n') + source_file.close() + +class GRNSourceGenerator(SourceGenerator): + def __init__(self): + super().__init__(Constants.GRN_SOURCE_FILE_PATH) + +class PPISourceGenerator(SourceGenerator): + def __init__(self): + super().__init__(Constants.PPI_SOURCE_FILE_PATH) + +GRNSourceGenerator() \ No newline at end of file From 839b6f9c53f921fa4655fb1d4b44b4f7a1bf79c6 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Wed, 11 Sep 2024 15:17:24 -0700 Subject: [PATCH 147/150] Updating the script to create union genes from genes in the database and new genes downloaded from Yeastmine --- database/filter_update.py | 99 +++++++++++++++++++++++++-------------- database/loader_update.py | 50 ++++++++++++-------- 2 files changed, 94 insertions(+), 55 deletions(-) diff --git a/database/filter_update.py b/database/filter_update.py index 7e3b91bf..f49f7e89 100644 --- a/database/filter_update.py +++ b/database/filter_update.py @@ -3,18 +3,19 @@ from sqlalchemy import create_engine from sqlalchemy import text from constants import Constants +from utils import Utils PROTEIN_GENE_HEADER = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID' GRN_GENE_HEADER = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID\tRegulator' -def get_all_data_from_database_table(database_namespace, table_name): +def _get_all_data_from_database_table(database_namespace, table_name): db = create_engine(os.environ['DB_URL']) with db.connect() as connection: result_set = connection.execute(text(f"SELECT * FROM {database_namespace}.{table_name}")) return result_set.fetchall() -def get_all_genes(database_namespace): - gene_records = get_all_data_from_database_table(database_namespace, "gene") +def _get_all_db_genes(database_namespace): + gene_records = _get_all_data_from_database_table(database_namespace, "gene") genes = {} for gene in gene_records: key = (gene[0], gene[3]) @@ -25,14 +26,47 @@ def get_all_genes(database_namespace): genes[key] = value return genes -def get_all_grn_genes(): - return get_all_genes(Constants.GRN_DATABASE_NAMESPACE) +def _get_all_db_grn_genes(): + return _get_all_db_genes(Constants.GRN_DATABASE_NAMESPACE) -def get_all_ppi_genes(): - return get_all_genes(Constants.PPI_DATABASE_NAMESPACE) +def _get_all_db_ppi_genes(): + return _get_all_db_genes(Constants.PPI_DATABASE_NAMESPACE) + +def _get_all_genes(): + db_grn_genes = _get_all_db_grn_genes() + db_ppi_genes = _get_all_db_ppi_genes() + Utils.create_union_file([Constants.PPI_GENE_SOURCE, Constants.GRN_GENE_SOURCE], Constants.GENE_DATA_DIRECTORY) + genes = db_grn_genes + + for gene in db_ppi_genes: + if gene not in genes: + display_gene_id, species = db_ppi_genes[gene] + genes[gene] = [display_gene_id, species, False] + + with open(Constants.GENE_DATA_DIRECTORY, 'r+', encoding="UTF-8") as f: + i = 0 + reader = csv.reader(f) + for row in reader: + if i != 0: + row = row[0].split('\t') + gene_id = row[0] + display_gene_id = row[1] + species = row[2] + taxon_id = row[3] + regulator = row[4].capitalize() + key = (gene_id, taxon_id) + value = (display_gene_id, species, regulator) + if key not in genes: + genes[key] = value + elif genes[key][0] != display_gene_id: + if display_gene_id != "None": + genes[key] = value + i+=1 + return genes + def get_all_proteins(): - protein_records = get_all_data_from_database_table(Constants.PPI_DATABASE_NAMESPACE, "protein") + protein_records = _get_all_data_from_database_table(Constants.PPI_DATABASE_NAMESPACE, "protein") proteins = {} for protein in protein_records: key = (protein[1], protein[5]) @@ -41,38 +75,33 @@ def get_all_proteins(): return proteins def processing_grn_gene_file(): - _processing_gene_file(Constants.GRN_GENE_SOURCE, get_all_grn_genes(), is_protein=False) + return _processing_gene_file(_get_all_db_grn_genes(), is_protein=False) def processing_ppi_gene_file(): - _processing_gene_file(Constants.PPI_GENE_SOURCE, get_all_ppi_genes()) + return _processing_gene_file(_get_all_db_ppi_genes()) -def _processing_gene_file(file_path, db_genes, is_protein=True): - print(f'Processing file {file_path}') +def _processing_gene_file(db_genes, is_protein=True): + print(f'Processing gene') missing_genes = {} genes_to_update = {} - with open(file_path, 'r+', encoding="UTF-8") as f: - i = 0 - reader = csv.reader(f) - for row in reader: - if i != 0: - row = row[0].split('\t') - gene_id = row[0] - display_gene_id = row[1] - species = row[2] - taxon_id = row[3] - key = (gene_id, taxon_id) - if (is_protein): - value = (display_gene_id, species) + all_genes = _get_all_genes() + for gene in all_genes: + display_gene_id, species, regulator = all_genes[gene] + values_for_ppi = (display_gene_id, species) + values_for_grn = (display_gene_id, species, regulator) + if gene not in db_genes: + if is_protein: + missing_genes[gene] = values_for_ppi + else: + missing_genes[gene] = values_for_grn + elif gene in db_genes and db_genes[gene][0] != display_gene_id: + if db_genes[gene][0] != "None": + if is_protein: + genes_to_update[gene] = values_for_ppi else: - regulator = row[4].capitalize() - value = (display_gene_id, species, regulator) - if key not in db_genes: - missing_genes[key] = value - elif db_genes[key][0] != display_gene_id: - # the value is not the same, let's update - if display_gene_id != "None": - genes_to_update[key] = value - i+=1 + genes_to_update[gene] = values_for_grn + print("Missing genes", missing_genes) + print("Genes to update", genes_to_update) return missing_genes, genes_to_update def processing_protein_file(file_path, db_proteins): @@ -123,7 +152,7 @@ def create_ppi_protein_file(file_path, data): headers = f'Standard Name\tGene Systematic Name\tLength\tMolecular Weight\tPI\tTaxon ID' protein_file.write(f'{headers}\n') for protein in data: - protein_file.write(f'{data[protein][0]}\t{[protein][0]}\t{data[protein][1]}\t{data[protein][2]}\t{data[protein][3]}\t{protein[1]}\n') + protein_file.write(f'{data[protein][0]}\t{protein[0]}\t{data[protein][1]}\t{data[protein][2]}\t{data[protein][3]}\t{protein[1]}\n') protein_file.close() # Processing gene files diff --git a/database/loader_update.py b/database/loader_update.py index 615f7211..181e5ce1 100644 --- a/database/loader_update.py +++ b/database/loader_update.py @@ -1,26 +1,36 @@ +import argparse from constants import Constants from utils import Utils -import os -if not os.path.exists('union-gene-data'): - os.makedirs('union-gene-data') - -# Get missing union gene data -Utils.create_union_file([Constants.PPI_MISSING_GENE_DIRECTORY, Constants.GRN_MISSING_GENE_DIRECTORY], Constants.MISSING_GENE_UNION_DIRECTORY) +def load_grn_data_into_database(): + Utils.load_sources(Constants.GRN_SOURCE_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) + Utils.update_grn_genes(Constants.GRN_UPDATE_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) + Utils.load_grn_genes(Constants.GRN_MISSING_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) + Utils.load_grn_network(Constants.GRN_NETWORK_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) -# Get update union gene data -Utils.create_union_file([Constants.PPI_UPDATE_GENE_DIRECTORY, Constants.GRN_UPDATE_GENE_DIRECTORY], Constants.UPDATE_GENE_UNION_DIRECTORY) +def load_ppi_data_into_database(): + Utils.load_sources(Constants.PPI_SOURCE_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) + Utils.update_ppi_genes(Constants.PPI_UPDATE_GENE_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) + Utils.update_ppi_proteins(Constants.PPI_UPDATE_PROTEIN_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) + Utils.load_ppi_genes(Constants.PPI_MISSING_GENE_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) + Utils.load_proteins(Constants.PPI_MISSING_PROTEIN_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) + Utils.load_ppi_network(Constants.PPI_NETWORK_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) -# PPI -Utils.load_sources(Constants.PPI_SOURCE_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) -Utils.update_ppi_genes(Constants.PPI_UPDATE_GENE_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) -Utils.update_ppi_proteins(Constants.PPI_UPDATE_PROTEIN_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) -Utils.load_ppi_genes(Constants.PPI_MISSING_GENE_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) -Utils.load_proteins(Constants.PPI_MISSING_PROTEIN_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) -Utils.load_ppi_network(Constants.PPI_NETWORK_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) +def main(): + # Set up argument parsing + parser = argparse.ArgumentParser(description="Load data into database for GRN or PPI networks.") + parser.add_argument('--network', choices=['GRN', 'PPI'], required=True, help="Specify the network type to load data for") -# GRN -Utils.load_sources(Constants.GRN_SOURCE_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) -Utils.update_grn_genes(Constants.GRN_UPDATE_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) -Utils.load_grn_genes(Constants.GRN_MISSING_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) -Utils.load_grn_network(Constants.GRN_NETWORK_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) \ No newline at end of file + # Parse arguments + args = parser.parse_args() + + # Execute the relevant operations based on the argument + if args.network == 'GRN': + load_grn_data_into_database() + elif args.network == 'PPI': + load_ppi_data_into_database() + else: + print("Invalid network type. Please choose 'GRN' or 'PPI'.") + +if __name__ == "__main__": + main() From 4219ae3a807b307bd4988b23c71bc220a5091d39 Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Sun, 15 Sep 2024 22:46:57 -0700 Subject: [PATCH 148/150] #1077 Updating README.md and fixing updating GRN genes code to correctly update the regulator type and make sure to generate file path if not presented for union gene path --- database/README.md | 53 +++++++++++-------- database/filter_update.py | 7 +-- database/loader_update.py | 6 +-- database/utils.py | 2 +- database2/scripts/constants.py | 30 ----------- .../scripts/data_generation/generator.py | 23 -------- .../data_generation/source_generator.py | 30 ----------- 7 files changed, 38 insertions(+), 113 deletions(-) delete mode 100644 database2/scripts/constants.py delete mode 100644 database2/scripts/data_generation/generator.py delete mode 100644 database2/scripts/data_generation/source_generator.py diff --git a/database/README.md b/database/README.md index 20731f19..a11e8e51 100644 --- a/database/README.md +++ b/database/README.md @@ -156,37 +156,44 @@ Here are the files pertaining to both the network and expression databases. Look ## Instructions for Updating Database -1. Getting new data + 1. Getting new data + + 1. Generate a new network from Yeastmine using the script `generate_network.py` inside `network-database` folder. + ``` + cd + python3 generate_network.py + ``` + 2. Generate a new Protein-Protein Interactions from SGD using Yeastmine + + ``` + cd + python3 generate_protein_network.py + ``` + + 2. Filter all the missing genes, and updated genes in both Network and Protein-Protein Interactions. Also you need to filter the missing protein, and updated proteins in Protein-Protein Interactions. Everything is done in `filter_update.py`. The script will access the database get all of the genes stored within. From there it will generate a csv file of all genes that are missing from your database, and all genes that have updated their display name (standard like name). After running this script, you will see `missing-genes.csv`, `update-genes.csv` in `processed-loader-files` for both `network-database` and `protein-protein-database`, also `missing-protein.csv` and `update-protein.csv`. - 1. Generate a new network from Yeastmine using the script `generate_network.py` inside `network-database` folder. ``` - cd - python3 generate_network.py + cd + DB_URL="postgresql://[:]@
/" python3 filter_update.py ``` - 2. Generate a new Protein-Protein Interactions from SGD using Yeastmine + Ex: ``` - cd - python3 generate_protein_network.py + DB_URL="postgresql://postgres@localhost/postgres" python3 filter_update.py ``` + 3. Loading all the updates from Network or Protein-Protein Interactions to database. - 3. Filter all the missing genes, and updated genes in both Network and Protein-Protein Interactions. Also you need to filter the missing protein, and updated proteins in Protein-Protein Interactions. Everything is done in `filter_update.py`. The script will access the database get all of the genes stored within. From there it will generate a csv file of all genes that are missing from your database, and all genes that have updated their display name (standard like name). - - ``` - cd - ``` + ``` + python3 loader_update.py --network=[GRN|PPI]| psql + ``` -3. Continue setting up in the [Initial Setup Wiki page](https://github.com/dondi/GRNsight/wiki/Initial-Setup) +Continue setting up in the [Initial Setup Wiki page](https://github.com/dondi/GRNsight/wiki/Initial-Setup) diff --git a/database/filter_update.py b/database/filter_update.py index f49f7e89..8b929e5f 100644 --- a/database/filter_update.py +++ b/database/filter_update.py @@ -35,6 +35,9 @@ def _get_all_db_ppi_genes(): def _get_all_genes(): db_grn_genes = _get_all_db_grn_genes() db_ppi_genes = _get_all_db_ppi_genes() + + if not os.path.exists('union-gene-data'): + os.makedirs('union-gene-data') Utils.create_union_file([Constants.PPI_GENE_SOURCE, Constants.GRN_GENE_SOURCE], Constants.GENE_DATA_DIRECTORY) genes = db_grn_genes @@ -99,9 +102,7 @@ def _processing_gene_file(db_genes, is_protein=True): if is_protein: genes_to_update[gene] = values_for_ppi else: - genes_to_update[gene] = values_for_grn - print("Missing genes", missing_genes) - print("Genes to update", genes_to_update) + genes_to_update[gene] = values_for_grn return missing_genes, genes_to_update def processing_protein_file(file_path, db_proteins): diff --git a/database/loader_update.py b/database/loader_update.py index 181e5ce1..4d1bb6e8 100644 --- a/database/loader_update.py +++ b/database/loader_update.py @@ -3,10 +3,10 @@ from utils import Utils def load_grn_data_into_database(): - Utils.load_sources(Constants.GRN_SOURCE_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) + # Utils.load_sources(Constants.GRN_SOURCE_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) Utils.update_grn_genes(Constants.GRN_UPDATE_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) - Utils.load_grn_genes(Constants.GRN_MISSING_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) - Utils.load_grn_network(Constants.GRN_NETWORK_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) + # Utils.load_grn_genes(Constants.GRN_MISSING_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) + # Utils.load_grn_network(Constants.GRN_NETWORK_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) def load_ppi_data_into_database(): Utils.load_sources(Constants.PPI_SOURCE_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) diff --git a/database/utils.py b/database/utils.py index 06493829..871eb6e7 100644 --- a/database/utils.py +++ b/database/utils.py @@ -223,7 +223,7 @@ def _update_genes(cls, update_gene_path: str, database_namespace: str, is_protei if is_protein: print(f"UPDATE {database_namespace}.gene\nSET display_gene_id = '{display_gene_id}'\nWHERE gene_id = '{gene_id}';") else: - regulator = r[2] + regulator = r[4] print(f"UPDATE {database_namespace}.gene\nSET display_gene_id = '{display_gene_id}', regulator={regulator}\nWHERE gene_id = '{gene_id}';") row_num += 1 print('COMMIT;') diff --git a/database2/scripts/constants.py b/database2/scripts/constants.py deleted file mode 100644 index cfbda6f1..00000000 --- a/database2/scripts/constants.py +++ /dev/null @@ -1,30 +0,0 @@ -class Constants: - - SERVICE_PATH = 'http://yeastmine.yeastgenome.org/yeastmine/service' - - # Gene Info - TAXON_ID = '559292' - SPECIES = 'Saccharomyces cerevisiae' - - # Source Info - SOURCE = 'YeastMine - Saccharomyces Genome Database' - SOURCE_DISPLAY_NAME = 'Yeastmine - SGD' - - - # gene data file path - GENE_FILE_PATH = '../script-results/gene/gene.csv' - MISSING_GENE_FILE_PATH = '../script-results/gene/missing-gene.csv' - UPDATE_GENE_FILE_PATH = '../script-results/gene/update-gene.csv' - - # protein data file path - PROTEIN_FILE_PATH = '../script-results/protein/protein.csv' - MISSING_PROTEIN_FILE_PATH = '../script-results/protein/missing-protein.csv' - UPDATE_PROTEIN_FILE_PATH = '../script-results/protein/update-protein.csv' - - # network file path - GRN_NETWORK_FILE_PATH = '../script-results/network/grn-network.csv' - PPI_NETWORK_FILE_PATH = '../script-results/network/ppi-network.csv' - - # source file path - GRN_SOURCE_FILE_PATH = '../script-results/source/grn-source.csv' - PPI_SOURCE_FILE_PATH = '../script-results/source/ppi-source.csv' \ No newline at end of file diff --git a/database2/scripts/data_generation/generator.py b/database2/scripts/data_generation/generator.py deleted file mode 100644 index e9439a3c..00000000 --- a/database2/scripts/data_generation/generator.py +++ /dev/null @@ -1,23 +0,0 @@ -import os -import sys -import datetime -from intermine.webservice import Service - -sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) - - -from constants import Constants - - -class Generator: - def __init__(self): - self.source = Constants.SOURCE - self.source_display_name = Constants.SOURCE_DISPLAY_NAME - self.timestamp = datetime.datetime.now(datetime.timezone.utc).replace(microsecond=0) - self.create_folder_paths() - pass - - def create_folder_paths(self): - if not os.path.exists('../script-results'): - os.makedirs('../script-results') - \ No newline at end of file diff --git a/database2/scripts/data_generation/source_generator.py b/database2/scripts/data_generation/source_generator.py deleted file mode 100644 index 25d5d019..00000000 --- a/database2/scripts/data_generation/source_generator.py +++ /dev/null @@ -1,30 +0,0 @@ -from generator import Generator -from constants import Constants -import os - -class SourceGenerator(Generator): - def __init__(self, source_file_destination: str): - super().__init__() - self.source_file_destination = source_file_destination - self.create_source_file() - - def create_folder_paths(self): - super().create_folder_paths() - if not os.path.exists('../script-results/source'): - os.makedirs('../script-results/source') - - def create_source_file(self): - source_file = open(self.source_file_destination, 'w') - headers = f'Timestamp\tSource\tDisplay Name\n{self.timestamp}\t{self.source}\t{self.source_display_name}' - source_file.write(f'{headers}\n') - source_file.close() - -class GRNSourceGenerator(SourceGenerator): - def __init__(self): - super().__init__(Constants.GRN_SOURCE_FILE_PATH) - -class PPISourceGenerator(SourceGenerator): - def __init__(self): - super().__init__(Constants.PPI_SOURCE_FILE_PATH) - -GRNSourceGenerator() \ No newline at end of file From c05394809c795e0cb996792ec79fcc12753e4d4b Mon Sep 17 00:00:00 2001 From: ntran18 <108908370+ntran18@users.noreply.github.com> Date: Mon, 16 Sep 2024 19:31:13 -0700 Subject: [PATCH 149/150] Hotfix database - change the key of PPI from gene_systematic_name to standard_name --- database/filter_update.py | 10 +++++----- database/loader_update.py | 6 +++--- database/utils.py | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/database/filter_update.py b/database/filter_update.py index 8b929e5f..ab9a0d03 100644 --- a/database/filter_update.py +++ b/database/filter_update.py @@ -72,8 +72,8 @@ def get_all_proteins(): protein_records = _get_all_data_from_database_table(Constants.PPI_DATABASE_NAMESPACE, "protein") proteins = {} for protein in protein_records: - key = (protein[1], protein[5]) - value = (protein[0], protein[2], protein[3], protein[4]) + key = (protein[0], protein[5]) + value = (protein[1], protein[2], protein[3], protein[4]) proteins[key] = value return proteins @@ -121,8 +121,8 @@ def processing_protein_file(file_path, db_proteins): molecular_weight = float(row[3]) if row[3] != "None" else 0 pi = float(row[4]) if row[4] != "None" else 0 taxon_id = row[5] - key = (gene_systematic_name, taxon_id) - value = (standard_name, length, molecular_weight, pi) + key = (standard_name, taxon_id) + value = (gene_systematic_name, length, molecular_weight, pi) if key not in db_proteins: ppi_missing_proteins[key] = value elif db_proteins[key] != value: @@ -153,7 +153,7 @@ def create_ppi_protein_file(file_path, data): headers = f'Standard Name\tGene Systematic Name\tLength\tMolecular Weight\tPI\tTaxon ID' protein_file.write(f'{headers}\n') for protein in data: - protein_file.write(f'{data[protein][0]}\t{protein[0]}\t{data[protein][1]}\t{data[protein][2]}\t{data[protein][3]}\t{protein[1]}\n') + protein_file.write(f'{protein[0]}\t{data[protein][0]}\t{data[protein][1]}\t{data[protein][2]}\t{data[protein][3]}\t{protein[1]}\n') protein_file.close() # Processing gene files diff --git a/database/loader_update.py b/database/loader_update.py index 4d1bb6e8..181e5ce1 100644 --- a/database/loader_update.py +++ b/database/loader_update.py @@ -3,10 +3,10 @@ from utils import Utils def load_grn_data_into_database(): - # Utils.load_sources(Constants.GRN_SOURCE_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) + Utils.load_sources(Constants.GRN_SOURCE_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) Utils.update_grn_genes(Constants.GRN_UPDATE_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) - # Utils.load_grn_genes(Constants.GRN_MISSING_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) - # Utils.load_grn_network(Constants.GRN_NETWORK_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) + Utils.load_grn_genes(Constants.GRN_MISSING_GENE_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) + Utils.load_grn_network(Constants.GRN_NETWORK_TABLE_DATA_DIRECTORY, Constants.GRN_DATABASE_NAMESPACE) def load_ppi_data_into_database(): Utils.load_sources(Constants.PPI_SOURCE_TABLE_DATA_DIRECTORY, Constants.PPI_DATABASE_NAMESPACE) diff --git a/database/utils.py b/database/utils.py index 871eb6e7..9fc3128e 100644 --- a/database/utils.py +++ b/database/utils.py @@ -251,7 +251,7 @@ def update_ppi_proteins(cls, update_protein_path: str, database_namespace: str): length = r[2] if r[2] != "None" else 0 molecular_weight = r[3] if r[3] != "None" else 0 pi = r[4] if r[4] != "None" else 0 - print(f"UPDATE {database_namespace}.gene\nSET standard_name = '{standard_name}', length = {length}, molecular_weight = {molecular_weight}, PI = {pi}\nWHERE gene_systematic_name = '{gene_name}';") + print(f"UPDATE {database_namespace}.protein\nSET standard_name = '{standard_name}', length = {length}, molecular_weight = {molecular_weight}, PI = {pi}\nWHERE gene_systematic_name = '{gene_name}';") row_num += 1 print('COMMIT;') From feb269b3b65eba80dc462a4b5254032e818cccec Mon Sep 17 00:00:00 2001 From: dondi Date: Tue, 24 Sep 2024 11:23:02 -0700 Subject: [PATCH 150/150] Sync up version number. --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index ab494d07..ad68dba7 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "grnsight", - "version": "7.0.15", + "version": "7.1.0", "description": "Web app and service for visualizing models of gene regulatory networks", "directories": { "test": "test"