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Added function to create a framework for rapidly writing unit tests f…
…or the ETL.
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src/org/ohdsi/rabbitInAHat/ETLTestFrameWorkGenerator.java
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| /******************************************************************************* | ||
| * Copyright 2016 Observational Health Data Sciences and Informatics | ||
| * | ||
| * This file is part of WhiteRabbit | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| ******************************************************************************/ | ||
| package org.ohdsi.rabbitInAHat; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| import org.ohdsi.rabbitInAHat.dataModel.Database; | ||
| import org.ohdsi.rabbitInAHat.dataModel.ETL; | ||
| import org.ohdsi.rabbitInAHat.dataModel.Field; | ||
| import org.ohdsi.rabbitInAHat.dataModel.Table; | ||
| import org.ohdsi.utilities.StringUtilities; | ||
| import org.ohdsi.utilities.files.WriteTextFile; | ||
|
|
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| public class ETLTestFrameWorkGenerator { | ||
| public static void generate(ETL etl, String filename) { | ||
| List<String> r = generateRScript(etl); | ||
| WriteTextFile out = new WriteTextFile(filename); | ||
| for (String line : r) | ||
| out.writeln(line); | ||
| out.close(); | ||
| } | ||
|
|
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| private static List<String> generateRScript(ETL etl) { | ||
| List<String> r = new ArrayList<String>(); | ||
| createInitFunction(r, etl.getSourceDatabase()); | ||
| createDeclareTestFunction(r); | ||
| createAddFunctions(r, etl.getSourceDatabase()); | ||
| createExpectFunctions(r, false, etl.getTargetDatabase()); | ||
| createExpectFunctions(r, true, etl.getTargetDatabase()); | ||
| return r; | ||
| } | ||
|
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| private static void createDeclareTestFunction(List<String> r) { | ||
| r.add("declareTest <- function(id, description) {"); | ||
| r.add(" assign(\"testId\", id, envir = globalenv()) "); | ||
| r.add(" assign(\"testDescription\", description, envir = globalenv()) "); | ||
| r.add("}"); | ||
| r.add(""); | ||
| } | ||
|
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| private static void createExpectFunctions(List<String> r, boolean negation, Database database) { | ||
| for (Table table : database.getTables()) { | ||
| StringBuilder line = new StringBuilder(); | ||
| String rTableName = convertToRName(table.getName()); | ||
| String sqlTableName = convertToSqlName(table.getName()); | ||
| List<String> argDefs = new ArrayList<String>(); | ||
| List<String> testDefs = new ArrayList<String>(); | ||
| for (Field field : table.getFields()) { | ||
| String rFieldName = convertToRName(field.getName()); | ||
| String sqlFieldName = convertToSqlName(field.getName()); | ||
| argDefs.add(rFieldName); | ||
| testDefs.add(" if (!missing(" + rFieldName + ")) {"); | ||
| testDefs.add(" if (first) {"); | ||
| testDefs.add(" first <- FALSE"); | ||
| testDefs.add(" } else {"); | ||
| testDefs.add(" statement <- paste0(statement, \" AND\")"); | ||
| testDefs.add(" }"); | ||
| testDefs.add(" statement <- paste0(statement, \" " + sqlFieldName + " = '\", " + rFieldName + ",\"'\")"); | ||
| testDefs.add(" }"); | ||
| testDefs.add(""); | ||
| } | ||
|
|
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| if (negation) | ||
| line.append("expect_no_" + rTableName + " <- function("); | ||
| else | ||
| line.append("expect_" + rTableName + " <- function("); | ||
|
|
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| line.append(StringUtilities.join(argDefs, ", ")); | ||
| line.append(") {"); | ||
| r.add(line.toString()); | ||
|
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| line = new StringBuilder(); | ||
| line.append(" statement <- paste0(\"INSERT INTO test_results SELECT "); | ||
| line.append("\", get(\"testId\", envir = globalenv()), \" AS id, "); | ||
| line.append("'\", get(\"testDescription\", envir = globalenv()), \"' AS description, "); | ||
| line.append("'Expect " + table.getName() + "' AS test, "); | ||
| line.append("CASE WHEN(SELECT COUNT(*) FROM " + sqlTableName + " WHERE\")"); | ||
| r.add(line.toString()); | ||
|
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| r.add(" first <- TRUE"); | ||
|
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| r.addAll(testDefs); | ||
|
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| if (negation) | ||
| r.add(" statement <- paste0(statement, \") = 1 THEN 'FAIL' ELSE 'PASS' END AS status;\")"); | ||
| else | ||
| r.add(" statement <- paste0(statement, \") = 0 THEN 'FAIL' ELSE 'PASS' END AS status;\")"); | ||
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| r.add(" assign(\"testSql\", c(get(\"testSql\", envir = globalenv()), statement), envir = globalenv())"); | ||
| r.add(" invisible(statement)"); | ||
| r.add("}"); | ||
| r.add(""); | ||
| } | ||
| } | ||
|
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| private static String convertToSqlName(String name) { | ||
| if (name.contains(" ") || name.contains(".") || name.toLowerCase().equals("procedure")) | ||
| name = "[" + name + "]"; | ||
| return name; | ||
| } | ||
|
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| private static void createInitFunction(List<String> r, Database database) { | ||
| r.add("initFramework <- function() {"); | ||
| r.add(" insertSql <- c()"); | ||
| for (Table table : database.getTables()) { | ||
| String sqlTableName = convertToSqlName(table.getName()); | ||
| r.add(" insertSql <- c(insertSql, \"TRUNCATE TABLE " + sqlTableName + ";\")"); | ||
| } | ||
| r.add(" assign(\"insertSql\", insertSql, envir = globalenv())"); | ||
|
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| r.add(" testSql <- c()"); | ||
| r.add(" testSql <- c(testSql, \"IF OBJECT_ID('test_results', 'U') IS NOT NULL\")"); | ||
| r.add(" testSql <- c(testSql, \" DROP TABLE test_results;\")"); | ||
| r.add(" testSql <- c(testSql, \"\")"); | ||
| r.add(" testSql <- c(testSql, \"CREATE TABLE test_results (id INT, description VARCHAR(512), test VARCHAR(256), status VARCHAR(5));\")"); | ||
| r.add(" testSql <- c(testSql, \"\")"); | ||
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| r.add(" assign(\"testSql\", testSql, envir = globalenv()) "); | ||
| r.add(" assign(\"testId\", 1, envir = globalenv()) "); | ||
| r.add(" assign(\"testDescription\", \"\", envir = globalenv()) "); | ||
| r.add("}"); | ||
| r.add(""); | ||
| r.add("initFramework()"); | ||
| r.add(""); | ||
| } | ||
|
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| private static void createAddFunctions(List<String> r, Database database) { | ||
| for (Table table : database.getTables()) { | ||
| StringBuilder line = new StringBuilder(); | ||
| String rTableName = convertToRName(table.getName()); | ||
| String sqlTableName = convertToSqlName(table.getName()); | ||
| List<String> argDefs = new ArrayList<String>(); | ||
| List<String> insertLines = new ArrayList<String>(); | ||
| for (Field field : table.getFields()) { | ||
| String rFieldName = field.getName().replaceAll(" ", "_").replaceAll("-", "_"); | ||
| String sqlFieldName = convertToSqlName(field.getName()); | ||
| String defaultValue; | ||
| if (field.getValueCounts().length == 0) | ||
| defaultValue = ""; | ||
| else | ||
| defaultValue = field.getValueCounts()[0][0]; | ||
| if (defaultValue.equals("")) | ||
| argDefs.add(rFieldName + " = NULL"); | ||
| else | ||
| argDefs.add(rFieldName + " = \"" + defaultValue + "\""); | ||
|
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| insertLines.add(" if (!is.null(" + rFieldName + ")) {"); | ||
| insertLines.add(" insertFields <- c(insertFields, \"" + sqlFieldName + "\")"); | ||
| insertLines.add(" insertValues <- c(insertValues, " +rFieldName + ")"); | ||
| insertLines.add(" }"); | ||
| insertLines.add(""); | ||
| } | ||
|
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| line.append("add_" + rTableName + " <- function("); | ||
| line.append(StringUtilities.join(argDefs, ", ")); | ||
| line.append(") {"); | ||
| r.add(line.toString()); | ||
|
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| r.add(" insertFields <- c()"); | ||
| r.add(" insertValues <- c()"); | ||
| r.addAll(insertLines); | ||
|
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| line = new StringBuilder(); | ||
| line.append(" statement <- paste0(\"INSERT INTO " + sqlTableName + " (\", "); | ||
| line.append("paste(insertFields, collapse = \", \"), "); | ||
| line.append("\") VALUES ('\", "); | ||
| line.append("paste(insertValues, collapse = \"', '\"), "); | ||
| line.append("\"');\")"); | ||
| r.add(line.toString()); | ||
|
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| r.add(" assign(\"insertSql\", c(get(\"insertSql\", envir = globalenv()), statement), envir = globalenv())"); | ||
| r.add(" invisible(statement)"); | ||
| r.add("}"); | ||
| r.add(""); | ||
| } | ||
| } | ||
|
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| private static String convertToRName(String name) { | ||
| name = name.replaceAll(" ", "_").replaceAll("-", "_"); | ||
| return name; | ||
| } | ||
| } |
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8 changes: 3 additions & 5 deletions
8
src/org/ohdsi/rabbitInAHat/dataModel/TableCellLongTextRenderer.java
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