Merge branch 'brapi-V2.2' into 9-1_entity_descriptions

Author: BrapiCoordinatorSelby

.github/workflows/generate-schema.yml

@@ -4,10 +4,37 @@ on:
   push:
   workflow_dispatch:
 jobs:
+  check:
+    runs-on: ubuntu-latest
+    outputs:
+      skip_job: ${{ steps.skip.outputs.skip_job }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Check last commit message
+        id: commit-message
+        run: |
+          echo "COMMIT_MESSAGE=$(git log -1 --pretty=format:'%s')" >> "$GITHUB_ENV"
+          echo "skip_job=false" >> "$GITHUB_OUTPUT"
+      - id: skip
+        name: Skip if automated push
+        if: contains(env.COMMIT_MESSAGE, 'Apply automatic changes')
+        run: |
+          echo "Automated commit detected - skipping job"
+          echo "skip_job=true" >> "$GITHUB_OUTPUT"
+
   generate:
     runs-on: ubuntu-latest
+    needs: check
+    if: needs.check.outputs.skip_job != 'true'
     steps:
-      - uses: actions/checkout@v4
+      - name: debug
+        run: echo ${{ needs.check.outputs.skip_job }}
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ssh-key: ${{ secrets.DEPLOY_KEY }}
       - name: Set up Docker Compose
         uses: docker/setup-compose-action@v1
       - name: Build and run the Docker image

Scripts/buildDocs.sh

@@ -11,48 +11,61 @@ mkdir -p ./build/results
 echo
 echo
 echo "Spell Check Run"
+echo "Spell checking BrAPI-Core"
 echo "BrAPI-Core" >> ./build/results/spellingResults.txt
 python3 ./Scripts/checkSpelling.py "./Specification/BrAPI-Core/" >> ./build/results/spellingResults.txt
+echo "Spell checking BrAPI-Germplasm"
 echo "BrAPI-Germplasm" >> ./build/results/spellingResults.txt
 python3 ./Scripts/checkSpelling.py "./Specification/BrAPI-Germplasm/" >> ./build/results/spellingResults.txt
+echo "Spell checking BrAPI-Phenotyping"
 echo "BrAPI-Phenotyping" >> ./build/results/spellingResults.txt
 python3 ./Scripts/checkSpelling.py "./Specification/BrAPI-Phenotyping/" >> ./build/results/spellingResults.txt
+echo "Spell checking BrAPI-Genotyping"
 echo "BrAPI-Genotyping" >> ./build/results/spellingResults.txt
 python3 ./Scripts/checkSpelling.py "./Specification/BrAPI-Genotyping/" >> ./build/results/spellingResults.txt
+echo "Spell checking Components"
 echo "Components" >> ./build/results/spellingResults.txt
 python3 ./Scripts/checkSpelling.py "./Specification/Components/" >> ./build/results/spellingResults.txt
 
 
 echo
 echo
 echo "Build OpenAPI YAML files per domain: ./brapi_openapi.yaml"
-echo "Building  BrAPI-Core"
+echo "Building BrAPI-Core"
 python3 ./Scripts/buildOpenAPI.py "./Specification/BrAPI-Core/" "./Specification/Components/" "./Specification/BrAPI-Germplasm/" >> ./build/results/buildOpenAPIBrAPI-CoreResults.txt
-echo "Building  BrAPI-Germplasm"
+echo "Building BrAPI-Germplasm"
 python3 ./Scripts/buildOpenAPI.py "./Specification/BrAPI-Germplasm/" "./Specification/Components/" >> ./build/results/buildOpenAPIBrAPI-GermplasmResults.txt
-echo "Building  BrAPI-Phenotyping"
+echo "Building BrAPI-Phenotyping"
 python3 ./Scripts/buildOpenAPI.py "./Specification/BrAPI-Phenotyping/" "./Specification/Components/" >> ./build/results/buildOpenAPIBrAPI-PhenotypingResults.txt
-echo "Building  BrAPI-Genotyping"
+echo "Building BrAPI-Genotyping"
 python3 ./Scripts/buildOpenAPI.py "./Specification/BrAPI-Genotyping/" "./Specification/Components/" "./Specification/BrAPI-Germplasm/" >> ./build/results/buildOpenAPIBrAPI-GenotypingResults.txt
 
 echo
 echo
-echo "Build README files for Bitbucket"
+echo "Build README files"
+echo "Building BrAPI-Core README files"
 echo "BrAPI-Core" >> ./build/results/buildREADMEBrAPI-CoreResults.txt
 python3 ./Scripts/buildReadMes.py "./Specification/BrAPI-Core/" >> ./build/results/buildREADMEBrAPI-CoreResults.txt
+echo "Building BrAPI-Germplasm README files"
 echo "BrAPI-Germplasm" >> ./build/results/buildREADMEBrAPI-GermplasmResults.txt
 python3 ./Scripts/buildReadMes.py "./Specification/BrAPI-Germplasm/" >> ./build/results/buildREADMEBrAPI-GermplasmResults.txt
+echo "Building BrAPI-Phenotyping README files"
 echo "BrAPI-Phenotyping" >> ./build/results/buildREADMEBrAPI-PhenotypingResults.txt
 python3 ./Scripts/buildReadMes.py "./Specification/BrAPI-Phenotyping/" >> ./build/results/buildREADMEBrAPI-PhenotypingResults.txt
+echo "Building BrAPI-Genotyping README files"
 echo "BrAPI-Genotyping" >> ./build/results/buildREADMEBrAPI-GenotypingResults.txt
 python3 ./Scripts/buildReadMes.py "./Specification/BrAPI-Genotyping/" >> ./build/results/buildREADMEBrAPI-GenotypingResults.txt
 
 echo
 echo
 echo "Build BluePrint MD file: ./brapi_blueprint.apib ./brapi_blueprint.apib.json"
+echo "Build BluePrint MD for BrAPI-Core"
 python3 ./Scripts/buildBlueprint.py -out "./Specification/BrAPI-Core/" -header "./Specification/BrAPI-Core/swaggerMetaData.yaml" -source "./Specification/BrAPI-Core/" >> ./build/results/buildBlueprintResults.txt
+echo "Build BluePrint MD for BrAPI-Germplasm"
 python3 ./Scripts/buildBlueprint.py -out "./Specification/BrAPI-Germplasm/" -header "./Specification/BrAPI-Germplasm/swaggerMetaData.yaml" -source "./Specification/BrAPI-Germplasm/" >> ./build/results/buildBlueprintResults.txt
+echo "Build BluePrint MD for BrAPI-Phenotyping"
 python3 ./Scripts/buildBlueprint.py -out "./Specification/BrAPI-Phenotyping/" -header "./Specification/BrAPI-Phenotyping/swaggerMetaData.yaml" -source "./Specification/BrAPI-Phenotyping/" >> ./build/results/buildBlueprintResults.txt
+echo "Build BluePrint MD for BrAPI-Genotyping"
 python3 ./Scripts/buildBlueprint.py -out "./Specification/BrAPI-Genotyping/" -header "./Specification/BrAPI-Genotyping/swaggerMetaData.yaml" -source "./Specification/BrAPI-Genotyping/" >> ./build/results/buildBlueprintResults.txt
 
 echo

Scripts/dereferenceAll.py

@@ -26,11 +26,13 @@ def dereferenceAll(obj, parent):
                     refObj = dereferenceAll(findRef(obj[fieldStr], parent), parent)
                     #refObj['title'] = refPath[-1]
                     obj = {**obj, **refObj}
+
                 elif(fieldStr == 'allOf'):
                     comboObj = {'properties': {}, 'type': 'object', 'required': []}
                     for item in obj[fieldStr]:
                         itemObj = dereferenceAll(item, parent)
-                        comboObj['properties'] = {**(comboObj['properties']), **(itemObj['properties'])}
+                        if 'properties' in itemObj:
+                            comboObj['properties'] = {**(comboObj['properties']), **(itemObj['properties'])}
                         if 'required' in itemObj:
                             comboObj['required'] = list(set(comboObj['required'] + itemObj['required']))
                         if 'title' in itemObj:
@@ -41,9 +43,10 @@ def dereferenceAll(obj, parent):
                             comboObj['example'] = itemObj['example']
                         if 'x-brapi-metadata' in itemObj:
                             comboObj['x-brapi-metadata'] = itemObj['x-brapi-metadata']
-                        
+                        if 'nullable' in itemObj:
+                            comboObj['nullable'] = itemObj['nullable']
                     obj = comboObj
-                else:
+                elif(fieldStr != 'nullable'):
                     obj[fieldStr] = dereferenceAll(obj[fieldStr], parent)
             if '$ref' in obj:
                 obj.pop('$ref')