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guydavenportGuy DavenportGuy Davenport
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649 merge generator changes into v2 2 fix the misplacement of a nullable tag and remove the out directory (#650)
* update CI * deleted out directory * fixed nullable * removed nullable for refs * removed nullable in wrong place * fixed indentation * improved logging * take into account nullable * take into account array in ref * correct as per https://stackoverflow.com/questions/40920441/how-to-specify-a-property-can-be-null-or-a-reference-with-swagger * Apply automatic changes * fixed ObservationTreatment link * Apply automatic changes --------- Co-authored-by: Guy Davenport <guy.davenport@partners.basf.com> Co-authored-by: Guy Davenport <daveneti@gmail.com> Co-authored-by: guydavenport <6523224+guydavenport@users.noreply.github.com>
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‎.github/workflows/generate-schema.yml‎

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

‎Scripts/buildDocs.sh‎

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

‎Scripts/dereferenceAll.py‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -26,11 +26,13 @@ def dereferenceAll(obj, parent):
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refObj = dereferenceAll(findRef(obj[fieldStr], parent), parent)
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#refObj['title'] = refPath[-1]
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obj = {**obj, **refObj}
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elif(fieldStr == 'allOf'):
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comboObj = {'properties': {}, 'type': 'object', 'required': []}
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for item in obj[fieldStr]:
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itemObj = dereferenceAll(item, parent)
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comboObj['properties'] = {**(comboObj['properties']), **(itemObj['properties'])}
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if 'properties' in itemObj:
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comboObj['properties'] = {**(comboObj['properties']), **(itemObj['properties'])}
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if 'required' in itemObj:
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comboObj['required'] = list(set(comboObj['required'] + itemObj['required']))
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if 'title' in itemObj:
@@ -41,9 +43,10 @@ def dereferenceAll(obj, parent):
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comboObj['example'] = itemObj['example']
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if 'x-brapi-metadata' in itemObj:
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comboObj['x-brapi-metadata'] = itemObj['x-brapi-metadata']
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if 'nullable' in itemObj:
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comboObj['nullable'] = itemObj['nullable']
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obj = comboObj
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else:
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elif(fieldStr != 'nullable'):
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obj[fieldStr] = dereferenceAll(obj[fieldStr], parent)
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if '$ref' in obj:
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obj.pop('$ref')

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