Merge branch 'brapi-V2.2' into 539-experimental-factors-added-to-study---add-new-fields-486

# Conflicts:
#	Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json

Author: Guy Davenport

Scripts/buildDocs.sh

@@ -27,7 +27,7 @@ echo
 echo
 echo "Build OpenAPI YAML files per domain: ./brapi_openapi.yaml"
 echo "Building  BrAPI-Core"
-python3 ./Scripts/buildOpenAPI.py "./Specification/BrAPI-Core/" "./Specification/Components/" "./Specification/BrAPI-Germplasm/" >> ./build/results/buildOpenAPIBrAPI-Coreesults.txt
+python3 ./Scripts/buildOpenAPI.py "./Specification/BrAPI-Core/" "./Specification/Components/" "./Specification/BrAPI-Germplasm/" >> ./build/results/buildOpenAPIBrAPI-CoreResults.txt
 echo "Building  BrAPI-Germplasm"
 python3 ./Scripts/buildOpenAPI.py "./Specification/BrAPI-Germplasm/" "./Specification/Components/" >> ./build/results/buildOpenAPIBrAPI-GermplasmResults.txt
 echo "Building  BrAPI-Phenotyping"

Scripts/buildOpenAPI.py

@@ -2,6 +2,8 @@
 
 # --------------------------------------------READ ME-------------------------------------------------------
 # Run this script to combine all the pieces of the the BrAPI specification into a single swagger file.
+# Example
+# > python3 ./Scripts/buildOpenAPI.py "./Specification/BrAPI-Core/" "./Specification/Components/"
 # ----------------------------------------------------------------------------------------------------------
 
 
@@ -63,7 +65,7 @@ def go(rootPaths, metaFilePath = './swaggerMetaData.yaml'):
     out['paths'].update(paths)
     out['components'].update(defin)
 
-    out = dereferenceAll.dereferenceAllOfClause(out, out)
+    # out = dereferenceAll.dereferenceAllOfClause(out, out)
 
     with open(outFilePath, 'w') as outfile:
         print(outFilePath)

Specification/BrAPI-Core/Lists/Lists_ListDbId_Data_POST.yaml

@@ -34,7 +34,7 @@ paths:
                   metadata:
                     $ref: '#/components/schemas/metadata'
                   result:
-                    $ref: '#/components/schemas/ListDetails'
+                    $ref: '#/components/schemas/List'
                 required:
                 - metadata
                 - result

Specification/BrAPI-Core/Lists/Lists_ListDbId_GET_PUT.yaml

@@ -70,7 +70,7 @@ components:
               metadata:
                 $ref: '#/components/schemas/metadata'
               result:
-                $ref: '#/components/schemas/ListDetails'
+                $ref: '#/components/schemas/List'
             required:
             - metadata
             - result

Specification/BrAPI-Core/Lists/Lists_ListDbId_Items_POST.yaml

@@ -36,7 +36,7 @@ paths:
                   metadata:
                     $ref: '#/components/schemas/metadata'
                   result:
-                    $ref: '#/components/schemas/ListDetails'
+                    $ref: '#/components/schemas/List'
                 required:
                 - metadata
                 - result

…rAPI-Core/Lists/Schemas/ListDetails.yaml …ation/BrAPI-Core/Lists/Schemas/List.yamlSpecification/BrAPI-Core/Lists/Schemas/ListDetails.yaml renamed to Specification/BrAPI-Core/Lists/Schemas/List.yaml Specification/BrAPI-Core/Lists/Schemas/ListDetails.yaml renamed to Specification/BrAPI-Core/Lists/Schemas/List.yaml

@@ -5,7 +5,7 @@ openapi: 3.0.0
 paths: {}
 components: 
   schemas:
-    ListDetails:
+    List:
       allOf:
       - $ref: '#/components/schemas/ListSummary'
       - $ref: '#/components/schemas/ListNewRequest'

Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json

@@ -30,6 +30,7 @@
                 }
             },
             "title": "OntologyTerm",
+            "description": "A pointer to an ontology used by a genomic reference",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

Specification/BrAPI-Schema/BrAPI-Common/Variable.json

@@ -132,6 +132,7 @@
                 "scale"
             ],
             "title": "Variable",
+            "description": "A unique combination of Trait, Method, and Scale to define a clear context for an Observation.",
             "type": "object",
             "brapi-metadata": {
                 "interface": true

Specification/BrAPI-Schema/BrAPI-Core/Contact.json

@@ -47,6 +47,7 @@
             ],
             "type": "object",
             "title": "Contact",
+            "description": "A persons contact information",
             "brapi-metadata": {
                 "primaryModel": false
             }

Specification/BrAPI-Schema/BrAPI-Core/DataLink.json

@@ -61,6 +61,7 @@
                 }
             },
             "title": "DataLink",
+            "description": "A link to extra data files associated with this study. Extra data could include notes, images, and reference data.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false