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Merge branch 'data-model-separation' into brapi-V2.1
2 parents 7a32fe9 + 75291cb commit bd60786

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‎.github/workflows/generate-schema.yml‎

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name: Java CI with Gradle
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on:
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push:
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workflow_dispatch:
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up JDK 21
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uses: actions/setup-java@v4
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with:
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java-version: '21'
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distribution: 'temurin'
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- name: Change wrapper permissions
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working-directory: ./generator/
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run: chmod +x ./gradlew
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- name: Validate
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working-directory: ./generator/
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run: ./gradlew validate
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- name: Generate OpenAPI, GraphQL and OWL
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working-directory: ./generator/
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run: ./gradlew generateAll
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- uses: stefanzweifel/git-auto-commit-action@v5

‎.gitignore‎

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.pydevproject
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.DS_Store
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.settings/
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.idea
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.vscode/
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.idea
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/_temp
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brapi_blueprint.apib
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brapi_openapi.yaml
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out.yaml
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Scripts/__pycache__/
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brapi_blueprint.apib.json
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/generator/.gradle/
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/generator/build

‎Scripts/buildERDData.py‎

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#! /usr/bin/env python
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import yaml
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import sys
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import json
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import dereferenceAll
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import os
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def buildERDDiagram(specPath):
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with open(specPath + '/brapi_openapi.yaml', "r") as stream:
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try:
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fullBrAPI = yaml.load(stream)
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stream.close()
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except yaml.YAMLError as exc:
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stream.close()
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classes = []
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if('components' in fullBrAPI):
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if('schemas' in fullBrAPI['components']):
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x = 0
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for schema in fullBrAPI['components']['schemas']:
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if('x-brapi-metadata' in fullBrAPI['components']['schemas'][schema] and fullBrAPI['components']['schemas'][schema]['x-brapi-metadata']['primaryModel']):
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schemaObj = fullBrAPI['components']['schemas'][schema]
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attributes = []
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if('properties' in schemaObj):
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attributes = list(schemaObj['properties'].keys())
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classObj = {'x': x, 'y':0, 'width': 150, 'classname': schema, 'attributes': attributes}
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x = x + 200
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classes.append(classObj)
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return classes
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def buildERDDiagramFile(specPath):
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fileContent = {}
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## For each BrAPI Module
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for module in next(os.walk(specPath))[1]:
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if module[:5] == 'BrAPI':
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print(specPath + module + '/')
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moduleObj = buildERDDiagram(specPath + module + '/')
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fileContent.update({module: moduleObj})
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fileName = specPath + '/ERDDiagram.json'
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with open(fileName, 'w') as outfile:
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json.dump(fileContent, outfile, indent=4, sort_keys=True)
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print("fileName - " + fileName)
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## Path to BrAPI spec repo. Should end in /Specification/
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rootPath = '.'
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if len(sys.argv) > 1 :
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rootPath = sys.argv[1];
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if rootPath[-1:] != '/':
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rootPath = rootPath + '/'
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buildERDDiagramFile(rootPath)

‎Scripts/buildJSONSchema2.py‎

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#! /usr/bin/env python
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import yaml
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import glob
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import sys
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import json
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import re
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import os
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from copy import deepcopy
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import dereferenceAll
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def buildJSONSchemas(parent, verbose):
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if 'schemas' in parent['components']:
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for schemaName in parent['components']['schemas']:
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if verbose:
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print('Data model: ' + schemaName)
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title = schemaName
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schema = parent['components']['schemas'][schemaName]
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module = ''
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if 'x-brapi-metadata' in schema:
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if 'primaryModel' in schema['x-brapi-metadata'] and schema['x-brapi-metadata']['primaryModel']:
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if verbose:
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print('-- Added')
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if 'title' in schema['x-brapi-metadata']:
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title = schema['x-brapi-metadata']['title']
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if 'module' in schema['x-brapi-metadata']:
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module = schema['x-brapi-metadata']['module']
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buildJSONSchema(schema, title, module, verbose)
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else:
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if verbose:
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print('-- Skipped')
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else:
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print("Error: no schemas found")
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def buildJSONSchema(schema, title, module, verbose):
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schema = fixSchema(schema)
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schemaObj = {
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"$schema": "http://json-schema.org/draft/2020-12/schema",
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"$id": "https://brapi.org/Specification/BrAPI-Schema/" + module + "/" + title +".json",
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"$defs": {
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title : {
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"title": title,
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"type": "object",
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"properties": schema["properties"]
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}
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}
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}
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if 'required' in schema:
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schemaObj['$defs'][title]['required'] = schema['required']
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filename = outPath + module + '/' + title + '.json'
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os.makedirs(os.path.dirname(filename), exist_ok=True)
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with open(filename, 'w') as outfile:
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json.dump(schemaObj, outfile, indent=4, sort_keys=True)
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def fixSchema(schema):
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schema = addMinItems(schema)
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schema = removeDeprecated(schema)
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schema = removeSwaggerTerms(schema)
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schema = fixStringFormats(schema)
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schema = allowNullFields(schema)
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# schema = addRequired(schema)
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schema = addRefs(schema)
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return schema
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def addRefs(parent):
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newParent = deepcopy(parent)
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if type(parent) is dict:
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if 'properties' in newParent:
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className = ''
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if 'x-brapi-metadata' in newParent:
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className = newParent['x-brapi-metadata']['title']
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for term in parent['properties']:
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if term.endswith('DbId') and (term.casefold() != (className + 'DbId').casefold()):
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oldTermDetails = newParent['properties'].pop(term)
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newTerm = term[:-4]
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newTermTitle = newTerm[0].upper() + newTerm[1:]
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if newTerm + 'Name' in newParent['properties']:
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newParent['properties'].pop(newTerm + 'Name')
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newParent['properties'][newTerm] = { '$ref': newTermTitle + '.json#/$defs/' + newTermTitle, 'description': oldTermDetails['description'], 'relationshipType': 'EDITME-to-one', 'referencedAttribute': className[0].lower() + className[1:] + 's' }
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elif term.endswith('DbIds') and (term.casefold() != (className + 'DbIds').casefold()):
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oldTermDetails = newParent['properties'].pop(term)
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newTerm = term[:-5]
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newTermTitle = newTerm[0].upper() + newTerm[1:]
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newParent['properties'][newTerm + 's'] = { 'items':{ '$ref': newTermTitle + '.json#/$defs/' + newTermTitle }, 'type': 'array', 'description': oldTermDetails['description'], 'relationshipType': 'EDITME-to-many', 'referencedAttribute': className[0].lower() + className[1:] + 's' }
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return newParent
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def addMinItems(parent):
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newParent = deepcopy(parent)
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if 'data' in newParent['properties']:
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newParent['properties']['data']['minItems'] = 1
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return newParent
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def removeDeprecated(parent):
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newParent = deepcopy(parent)
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if type(parent) is dict:
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for childKey in parent:
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child = parent[childKey]
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if type(child) is dict:
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if 'deprecated' in child and child['deprecated']:
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newParent.pop(childKey)
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else:
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newParent[childKey] = removeDeprecated(child)
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return newParent
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def addRequired(parent):
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newParent = deepcopy(parent)
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if type(newParent) is dict:
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if 'properties' in newParent:
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if 'required' in parent:
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newParent['required'] = list(newParent['properties'].keys());
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for childKey in newParent:
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newParent[childKey] = addRequired(newParent[childKey])
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return newParent
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def removeSwaggerTerms(parent):
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newParent = deepcopy(parent)
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if type(newParent) is dict:
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if 'example' in newParent:
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newParent.pop('example')
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if 'discriminator' in newParent:
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newParent.pop('discriminator')
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for childKey in newParent:
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newParent[childKey] = removeSwaggerTerms(newParent[childKey])
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elif type(newParent) is list:
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newList = []
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for item in newParent:
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newList.append(removeSwaggerTerms(item))
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newParent = newList
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return newParent
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def fixStringFormats(parent):
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newParent = deepcopy(parent)
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if type(parent) is dict:
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for childKey in parent:
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child = parent[childKey]
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if type(child) is dict:
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if 'format' in child and 'type' in child:
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if child['format'] != 'date-time' and child['format'] != 'uri':
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newParent[childKey].pop('format')
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else:
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newParent[childKey] = fixStringFormats(child)
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return newParent
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def allowNullFields(parent):
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newParent = deepcopy(parent)
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if type(parent) is dict:
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if 'properties' in parent:
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requiredFields = []
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if 'required' in parent:
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requiredFields = parent['required']
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for fieldName in parent['properties']:
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fieldObj = parent['properties'][fieldName]
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newParent['properties'][fieldName] = allowNullFields(fieldObj)
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if not fieldName in requiredFields:
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if 'enum' in fieldObj:
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newParent['properties'][fieldName]['enum'].append(None)
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types = ['null']
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if 'type' in fieldObj:
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types.append(fieldObj['type'])
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newParent['properties'][fieldName]['type'] = types
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else:
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for fieldName in parent:
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if type(parent[fieldName]) is dict:
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newParent[fieldName] = allowNullFields(parent[fieldName])
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return newParent
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outPath = './out/'
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yamlPath = './brapi_openapi.yaml'
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verbose = False
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verbose = '-v' in sys.argv
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if '-brapi' in sys.argv:
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bi = sys.argv.index('-brapi')
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yamlPath = sys.argv[bi + 1]
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if '-out' in sys.argv:
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ri = sys.argv.index('-out')
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outPath = sys.argv[ri + 1]
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if outPath[-1] != '/':
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outPath = outPath + '/'
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if verbose:
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print('input YAML file: ' + yamlPath)
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print('output directory: ' + outPath)
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parentFile = dereferenceAll.dereferenceBrAPI(yamlPath, verbose)
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buildJSONSchemas(parentFile, verbose)

‎Scripts/buildOpenAPI.py‎

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import yaml
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from yaml import Loader, Dumper, load, dump
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import glob
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import sys
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import os

‎Specification/BrAPI-Genotyping/VariantSets/Schemas/VariantSet.yaml‎

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x-brapi-metadata:
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primaryModel: true
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module: BrAPI-Genotyping
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title: Variant
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title: VariantSet
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description: A VariantSet is a collection of variants and variant calls intended to be analyzed together.
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required:
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- variantSetDbId

‎Specification/BrAPI-Germplasm/Germplasm/Schemas/BreedingMethod.yaml‎

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title: Breeding Method
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description: The techniques and protocol used to produce a Cross or Germplasm
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‎Specification/BrAPI-Schema/BrAPI-Common/AdditionalInfo.json‎

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{
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"$defs": {
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"AdditionalInfo": {
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"additionalProperties": {
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"type": "string"
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},
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"description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.",
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"title": "AdditionalInfo",
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"type": "object"
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}
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},
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"$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/AdditionalInfo.json",
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"$schema": "http://json-schema.org/draft/2020-12/schema"
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}

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

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{
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"$defs": {
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"Attribute": {
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"allOf": [
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{
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"$ref": "../BrAPI-Common/Variable.json#/$defs/Variable"
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},
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{
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"type": "object",
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"properties": {
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"attributeCategory": {
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"description": "General category for the attribute. very similar to Trait class.",
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"type": "string",
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"example": "Morphological"
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},
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"attributeDbId": {
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"description": "The ID which uniquely identifies this attribute within the given database server",
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"type": "string"
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},
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"attributeName": {
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"description": "A human readable name for this attribute",
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"type": "string",
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"example": "Plant Height 1"
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},
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"attributePUI": {
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"description": "The Permanent Unique Identifier of an Attribute, usually in the form of a URI",
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"type": "string",
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"example": "http://my-traits.com/trait/CO_123:0008012"
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},
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"attributeDescription": {
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"description": "A human readable description of this attribute",
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"type": "string",
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"example": "Height of the plant measured in meters by a tape"
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}
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},
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"required": [
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"attributeName"
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]
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}
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],
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"brapi-metadata": {
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"interface": true
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}
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}
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},
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"$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/Attribute.json",
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"$schema": "http://json-schema.org/draft/2020-12/schema"
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}

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