Merge branch 'master' into master

Author: alfredomp

README.md

@@ -1,2 +1,22 @@
 # SPINE-json-schema
 Public JSON schemas for SPINE
+
+
+# READ THIS BEFORE MAKING CHANGES
+If you make changes and tag this project make sure that the version of the ```package.json``` file is the same as the tagged version of the repository. This will allow the front-end of SPINE to ```npm install``` the correct version.
+
+# For SPINE developers
+- We have a version of the schema used in the SPINE project saved in a document in the database. All the documents in the database have to be compliant with this schema.
+- The front-end will generate the schema validator in a static way given that all the documents are in the same json schema version.
+- We need to provide migration scripts for the database for each change in the schema.
+
+## Procedure after changes
+  1. Update schema documents
+  1. Update the version of the ```package.json``` file
+  1. Commit, Pull Request, and Merge into the master branch
+  1. Tag this repository according to the version in the ```package.json``` file
+  1. In the SPINE repository change the version of this repository in the dependences in the ```package.json``` file
+  1. In SPINE project run ```npm install```
+  1. Create migration script for the database and save it the SPINE repository in the folder ```src/backedn/migrations_scripts/```. ***The migration script changes at least the document having the version of the json schema used.***
+  1. Create a release for SPINE project including migration instructions from previous releases. Please refer to the migration script in the commit messages.
+  

examples/annotationWorkflow/roi_notSubmitted.json

@@ -8,7 +8,7 @@
   "properties":{
     "implicit":{
       "implicitRelationWithRoi": "INSIDE",
-      "implicitGemetryPointer": "POINT",
+      "implicitGeometryPointer": "POINT",
       "roiProperties":{
         "worldCoordinates":{
           "x": 10.45,

package.json

@@ -0,0 +1,11 @@
+{
+  "name": "SPINE-json-schema",
+  "author": "Alfredo Morales Pinzon",
+  "license": "MIT",
+  "keywords": ["SPINE", "schema", "model", "json", "Image Processing", "pipelines", "workflow"],
+  "description": "Set of JSON schemas for the SPINE Virtual Laboratory",
+  "version": "1.0.0",
+  "dependencies": {
+    
+  }
+}

schemas/annotationTableData.schema.json

@@ -0,0 +1,56 @@
+{
+  "$id":"https://raw.githubusercontent.com/SPINEProject/SPINE-json-schema/master/schemas/annotationTableDefinition.schema.json",
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Annotation Table Data",
+  "description": "Schema an annotation table data",
+  "type": "object",
+  "properties": {
+    "lookAndFeel": {
+      "description": "References to other objects",
+      "type": "object",
+      "properties": {
+        "activeRoiId": {
+          "description":"ID of the active annotation",
+          "type":"string"
+        }
+      }
+    },
+    "reference": {
+      "description": "References to other objects",
+      "type": "object",
+      "properties": {
+        "annotationTableDefinitionId": {
+          "description":"ID of the annotation table definition",
+          "type":"string"
+        }
+      }
+    },
+    "data": {
+      "description": "The list of ROI and their annotations (content of the table)",
+      "type": "array",
+      "items": {
+        "type":"object"
+        "properties": {
+          "id": {
+            "description":"ID of the ROI",
+            "type":"string"
+          },
+          "roi": {
+            "type":"object",
+            "properties": {}
+          },
+          "annotations": {
+            "type":"object",
+            "patternProperties": {
+              ".*": {
+                "type": "object"
+              }
+            }
+          }
+        },
+        "required": ["id", "roi", "annotations"]
+      }
+    }
+  },
+  "required": ["lookAndFeel", "reference", "data"]
+  }

schemas/annotationTableDefinition.schema.json

@@ -0,0 +1,33 @@
+{
+  "$id":"https://raw.githubusercontent.com/SPINEProject/SPINE-json-schema/master/schemas/annotationTableDefinition.schema.json",
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Annotation Table Definition",
+  "description": "Schema an annotation table definition",
+  "type": "object",
+  "properties": {
+    "columns": {
+      "description": "Columns of the annotation table",
+      "type": "object",
+      "patternProperties" : {
+        ".*" : {
+          "properties": {
+            "type":{
+              "description":"Type of the column",
+              "type":"string"
+            },
+            "name": {
+              "description":"Name of the column",
+              "type":"string"
+            },
+            "value": {
+              "description":"Default value for the column",
+              "type":"string"
+            }
+          },
+          "required":["type", "name", "value"]
+        }
+      }
+    }
+  },
+  "required": ["columns"]
+  }

schemas/core.schema.json

@@ -44,7 +44,7 @@
       "type": "string",
       "enum": ["String","Number","imageFileInOut","imageEntityInOut",
         "auxiliaryImageFile","lookupTableInOut","roiInOut","annotationInOut",
-        "roiWithAnnotationsInOut"]
+        "roiWithAnnotationsInOut","annotationTableDefinitionInOut"]
     },
 
     "inputOutput": {
@@ -160,6 +160,40 @@
       ]
     },
 
+    "annotationTableDefinitionInOut": {
+      "$id": "#annotationTableDefinitionInOut",
+      "description": "Schema defining an annotation table definition as input output",
+      "allOf":[
+        {"$ref": "#/definitions/inputOutput_spine"},
+        {
+          "properties": {
+            "type":{
+              "type": "string",
+              "enum": ["annotationTableDefinitionInOut"]
+            }
+          },
+          "required": ["type"]
+        }
+      ]
+    },
+
+    "annotationTableDataInOut": {
+      "$id": "#annotationTableDataInOut",
+      "description": "Schema defining an annotation table data as input output",
+      "allOf":[
+        {"$ref": "#/definitions/inputOutput_spine"},
+        {
+          "properties": {
+            "type":{
+              "type": "string",
+              "enum": ["annotationTableDataInOut"]
+            }
+          },
+          "required": ["type"]
+        }
+      ]
+    },
+
     "lookupTableInOut_FileFormat": {
       "$id" : "#lookupTableInOut_Type",
       "description": "File format for lookup tables",
@@ -370,7 +404,9 @@
         {"$ref": "#/definitions/String"},
         {"$ref": "#/definitions/Number"},
         {"$ref": "#/definitions/imageFileInOut"},
-        {"$ref": "#/definitions/lookupTableInOut"}
+        {"$ref": "#/definitions/lookupTableInOut"},
+        {"$ref": "#/definitions/annotationTableDefinitionInOut"},
+        {"$ref": "#/definitions/annotationTableDataInOut"}
       ]
     }
 

schemas/roi.schema.json

@@ -138,7 +138,11 @@
                     "implicitGeometryPointer": {
                       "enum": ["POINT"]
                     },
-                    "roiProperties": {
+                    "
+          
+          
+          
+          ": {
                       "description": "Properties for a point in implicit pointer. If the implicitGemetryPointer is POINT.",
                       "type": "object",
                       "properties": {