got library side working - still need to have parent working
This commit is contained in:
parent
79c69037dd
commit
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17
Pipfile
17
Pipfile
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@ -10,7 +10,6 @@ coverage = "*"
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[packages]
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[packages]
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alembic = "*"
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alembic = "*"
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connexion = {extras = ["swagger-ui"],version = "*"}
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coverage = "*"
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coverage = "*"
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docxtpl = "*"
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docxtpl = "*"
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flask = "*"
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flask = "*"
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@ -36,11 +35,8 @@ pyjwt = "*"
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python-dateutil = "*"
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python-dateutil = "*"
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recommonmark = "*"
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recommonmark = "*"
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requests = "*"
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requests = "*"
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sentry-sdk = {extras = ["flask"],version = "==0.14.4"}
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sphinx = "*"
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sphinx = "*"
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swagger-ui-bundle = "*"
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swagger-ui-bundle = "*"
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spiffworkflow = {git = "https://github.com/sartography/SpiffWorkflow.git"}
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# spiffworkflow = {editable = true, path = "./../SpiffWorkflow"}
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webtest = "*"
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webtest = "*"
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werkzeug = "*"
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werkzeug = "*"
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xlrd = "*"
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xlrd = "*"
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@ -50,4 +46,15 @@ python-levenshtein = "*"
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apscheduler = "*"
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apscheduler = "*"
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[requires]
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[requires]
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python_version = "3.8"
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python_version = "3.9"
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[packages.connexion]
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extras = [ "swagger-ui",]
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version = "*"
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[packages.sentry-sdk]
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extras = [ "flask",]
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version = "==0.14.4"
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[packages.spiffworkflow]
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git = "https://github.com/sartography/SpiffWorkflow.git"
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File diff suppressed because it is too large
Load Diff
79
crc/api.yml
79
crc/api.yml
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@ -426,6 +426,70 @@ paths:
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application/json:
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application/json:
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schema:
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schema:
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$ref: "#/components/schemas/WorkflowSpec"
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$ref: "#/components/schemas/WorkflowSpec"
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/workflow-specification/{spec_id}/libraries:
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parameters:
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- name: spec_id
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in: path
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required: true
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description: The unique id of an existing workflow specification.
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schema:
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type: string
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get:
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operationId: crc.api.workflow.get_workflow_specification_libraries
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summary: Returns all libraries that are enabled for a workflow spec
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tags:
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- Workflow Specifications
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responses:
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'200':
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description: Workflow specification.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/WorkflowSpec"
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/workflow-specification/{spec_id}/library/{library_id}:
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parameters:
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- name: spec_id
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in: path
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required: true
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description: The unique id of an existing workflow specification.
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schema:
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type: string
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- name: library_id
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in: path
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required: true
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description: The unique id of an existing library specification.
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schema:
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type: string
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post:
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operationId: crc.api.workflow.add_workflow_spec_library
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summary: Adds a library to a workflow spec
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tags:
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- Workflow Specifications
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responses:
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'200':
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description: Workflow specification.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/WorkflowSpec"
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delete:
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operationId: crc.api.workflow.drop_workflow_spec_library
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summary: Delete a library from a workflow
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tags:
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- Workflow Specifications
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responses:
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'200':
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description: Workflow specification.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/WorkflowSpec"
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/workflow-specification/{spec_id}:
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/workflow-specification/{spec_id}:
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parameters:
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parameters:
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- name: spec_id
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- name: spec_id
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@ -502,6 +566,21 @@ paths:
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type: array
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type: array
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items:
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items:
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$ref: "#/components/schemas/WorkflowSpec"
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$ref: "#/components/schemas/WorkflowSpec"
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/workflow-specification/libraries:
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get:
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operationId: crc.api.workflow.library_workflow_specs
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summary: Provides a list of workflow specifications that are considered libraries.
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tags:
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- Workflow Specifications
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responses:
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'200':
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description: A list of workflow specifications
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content:
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application/json:
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schema:
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type: array
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items:
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$ref: "#/components/schemas/WorkflowSpec"
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/workflow-specification/{spec_id}/validate:
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/workflow-specification/{spec_id}/validate:
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parameters:
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parameters:
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- name: spec_id
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- name: spec_id
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@ -10,7 +10,7 @@ from crc.models.study import StudyModel, WorkflowMetadata, StudyStatus
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from crc.models.task_event import TaskEventModel, TaskEvent, TaskEventSchema
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from crc.models.task_event import TaskEventModel, TaskEvent, TaskEventSchema
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from crc.models.user import UserModelSchema
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from crc.models.user import UserModelSchema
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from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, WorkflowSpecModel, WorkflowSpecCategoryModel, \
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from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, WorkflowSpecModel, WorkflowSpecCategoryModel, \
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WorkflowSpecCategoryModelSchema
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WorkflowSpecCategoryModelSchema, WorkflowLibraryModel, WorkflowLibraryModelSchema
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from crc.services.error_service import ValidationErrorService
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from crc.services.error_service import ValidationErrorService
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from crc.services.file_service import FileService
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from crc.services.file_service import FileService
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from crc.services.lookup_service import LookupService
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from crc.services.lookup_service import LookupService
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@ -22,7 +22,8 @@ from crc.services.workflow_service import WorkflowService
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def all_specifications():
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def all_specifications():
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schema = WorkflowSpecModelSchema(many=True)
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schema = WorkflowSpecModelSchema(many=True)
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return schema.dump(session.query(WorkflowSpecModel).all())
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return schema.dump(session.query(WorkflowSpecModel).filter((WorkflowSpecModel.library==False)|(
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WorkflowSpecModel.library==None)).all())
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def add_workflow_specification(body):
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def add_workflow_specification(body):
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@ -45,6 +46,50 @@ def get_workflow_specification(spec_id):
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return WorkflowSpecModelSchema().dump(spec)
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return WorkflowSpecModelSchema().dump(spec)
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def get_workflow_specification_libraries(spec_id):
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if spec_id is None:
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raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
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spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
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libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
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if spec is None:
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raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
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return WorkflowLibraryModelSchema(many=True).dump(libraries)
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def validate_spec_and_library(spec_id,library_id):
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if spec_id is None:
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raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
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if library_id is None:
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raise ApiError('unknown_spec', 'Please provide a valid Library Specification ID.')
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spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
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library: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=library_id).first()
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if spec is None:
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raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
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if library is None:
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raise ApiError('unknown_spec', 'The Library Specification "' + library_id + '" is not recognized.')
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if not library.library:
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raise ApiError('unknown_spec', 'Linked workflow spec is not a library.')
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def add_workflow_spec_library(spec_id,library_id):
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validate_spec_and_library(spec_id, library_id)
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libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
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libraryids = [x.library_spec_id for x in libraries]
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if library_id in libraryids:
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raise ApiError('unknown_spec', 'The Library Specification "' + spec_id + '" is already attached.')
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newlib = WorkflowLibraryModel()
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newlib.workflow_spec_id = spec_id
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newlib.library_spec_id = library_id
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session.add(newlib)
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session.commit()
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libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
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return WorkflowLibraryModelSchema(many=True).dump(libraries)
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def drop_workflow_spec_library(spec_id,library_id):
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validate_spec_and_library(spec_id, library_id)
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session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id,library_spec_id=library_id).delete()
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session.commit()
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libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
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return WorkflowLibraryModelSchema(many=True).dump(libraries)
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def validate_workflow_specification(spec_id, validate_study_id=None, test_until=None):
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def validate_workflow_specification(spec_id, validate_study_id=None, test_until=None):
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errors = {}
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errors = {}
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@ -118,6 +163,10 @@ def standalone_workflow_specs():
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specs = WorkflowService.get_standalone_workflow_specs()
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specs = WorkflowService.get_standalone_workflow_specs()
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return schema.dump(specs)
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return schema.dump(specs)
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def library_workflow_specs():
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schema = WorkflowSpecModelSchema(many=True)
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specs = WorkflowService.get_library_workflow_specs()
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return schema.dump(specs)
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def get_workflow(workflow_id, do_engine_steps=True):
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def get_workflow(workflow_id, do_engine_steps=True):
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"""Retrieve workflow based on workflow_id, and return it in the last saved State.
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"""Retrieve workflow based on workflow_id, and return it in the last saved State.
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@ -159,7 +159,6 @@ def create_or_update_local_spec(remote,workflow_spec_id):
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localcategory.name = specdict['category']['name']
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localcategory.name = specdict['category']['name']
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localcategory.display_name = specdict['category']['display_name']
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localcategory.display_name = specdict['category']['display_name']
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localcategory.display_order = specdict['category']['display_order']
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localcategory.display_order = specdict['category']['display_order']
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localcategory.library = False
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session.add(localcategory)
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session.add(localcategory)
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localspec.category = localcategory
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localspec.category = localcategory
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@ -1,7 +1,7 @@
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import enum
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import enum
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import marshmallow
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import marshmallow
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from marshmallow import EXCLUDE
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from marshmallow import EXCLUDE,fields
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from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
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from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
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from sqlalchemy import func
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from sqlalchemy import func
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@ -15,7 +15,6 @@ class WorkflowSpecCategoryModel(db.Model):
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name = db.Column(db.String)
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name = db.Column(db.String)
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display_name = db.Column(db.String)
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display_name = db.Column(db.String)
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display_order = db.Column(db.Integer)
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display_order = db.Column(db.Integer)
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library = db.Column(db.Boolean)
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class WorkflowSpecCategoryModelSchema(SQLAlchemyAutoSchema):
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class WorkflowSpecCategoryModelSchema(SQLAlchemyAutoSchema):
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include_relationships = True
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include_relationships = True
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class WorkflowSpecModel(db.Model):
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class WorkflowSpecModel(db.Model):
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__tablename__ = 'workflow_spec'
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__tablename__ = 'workflow_spec'
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id = db.Column(db.String, primary_key=True)
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id = db.Column(db.String, primary_key=True)
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category = db.relationship("WorkflowSpecCategoryModel")
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category = db.relationship("WorkflowSpecCategoryModel")
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is_master_spec = db.Column(db.Boolean, default=False)
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is_master_spec = db.Column(db.Boolean, default=False)
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standalone = db.Column(db.Boolean, default=False)
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standalone = db.Column(db.Boolean, default=False)
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library = db.Column(db.Boolean, default=False)
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class WorkflowLibraryModel(db.Model):
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__tablename__ = 'workflow_library'
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id = db.Column(db.Integer, primary_key=True)
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workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'), nullable=True)
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library_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'), nullable=True)
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workflow_side = db.relationship(WorkflowSpecModel,
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primaryjoin=workflow_spec_id==WorkflowSpecModel.id,
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backref='libraries')
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library = db.relationship(WorkflowSpecModel,primaryjoin=library_spec_id==WorkflowSpecModel.id,
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backref='referred_by')
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class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
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class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
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unknown = EXCLUDE
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unknown = EXCLUDE
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category = marshmallow.fields.Nested(WorkflowSpecCategoryModelSchema, dump_only=True)
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category = marshmallow.fields.Nested(WorkflowSpecCategoryModelSchema, dump_only=True)
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libraries = marshmallow.fields.Function(lambda obj: [{'id':x.library.id,
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'name':x.library.name,
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'display_name':x.library.display_name} for x in
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obj.libraries] )
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class WorkflowState(enum.Enum):
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class WorkflowState(enum.Enum):
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hidden = "hidden"
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hidden = "hidden"
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@ -79,6 +95,15 @@ class WorkflowSpecDependencyFile(db.Model):
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file_data = db.relationship(FileDataModel)
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file_data = db.relationship(FileDataModel)
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class WorkflowLibraryModelSchema(SQLAlchemyAutoSchema):
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class Meta:
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model = WorkflowLibraryModel
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load_instance = True
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include_relationships = True
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library = marshmallow.fields.Nested('WorkflowSpecModelSchema')
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class WorkflowModel(db.Model):
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class WorkflowModel(db.Model):
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__tablename__ = 'workflow'
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__tablename__ = 'workflow'
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id = db.Column(db.Integer, primary_key=True)
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id = db.Column(db.Integer, primary_key=True)
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@ -242,8 +242,7 @@ class StudyService(object):
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def get_categories():
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def get_categories():
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"""Returns a list of category objects, in the correct order."""
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"""Returns a list of category objects, in the correct order."""
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cat_models = db.session.query(WorkflowSpecCategoryModel) \
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cat_models = db.session.query(WorkflowSpecCategoryModel) \
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.order_by(WorkflowSpecCategoryModel.display_order) \
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.order_by(WorkflowSpecCategoryModel.display_order).all()
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.filter((WorkflowSpecCategoryModel.library == None)|(WorkflowSpecCategoryModel.library ==False)).all()
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categories = []
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categories = []
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for cat_model in cat_models:
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for cat_model in cat_models:
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categories.append(Category(cat_model))
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categories.append(Category(cat_model))
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@ -886,6 +886,11 @@ class WorkflowService(object):
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specs = db.session.query(WorkflowSpecModel).filter_by(standalone=True).all()
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specs = db.session.query(WorkflowSpecModel).filter_by(standalone=True).all()
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return specs
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return specs
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@staticmethod
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def get_library_workflow_specs():
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specs = db.session.query(WorkflowSpecModel).filter_by(library=True).all()
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return specs
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@staticmethod
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@staticmethod
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def get_primary_workflow(workflow_spec_id):
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def get_primary_workflow(workflow_spec_id):
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# Returns the FileModel of the primary workflow for a workflow_spec
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# Returns the FileModel of the primary workflow for a workflow_spec
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@ -0,0 +1,35 @@
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"""empty message
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Revision ID: a931e2b7b070
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Revises: 47b10b171d7c
|
||||||
|
Create Date: 2021-07-12 08:46:08.814577
|
||||||
|
|
||||||
|
"""
|
||||||
|
from alembic import op
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||||||
|
import sqlalchemy as sa
|
||||||
|
|
||||||
|
|
||||||
|
# revision identifiers, used by Alembic.
|
||||||
|
revision = 'a931e2b7b070'
|
||||||
|
down_revision = 'bbf064082623'
|
||||||
|
branch_labels = None
|
||||||
|
depends_on = None
|
||||||
|
|
||||||
|
|
||||||
|
def upgrade():
|
||||||
|
# ### commands auto generated by Alembic - please adjust! ###
|
||||||
|
op.create_table('workflow_library',
|
||||||
|
sa.Column('id', sa.Integer(), nullable=False),
|
||||||
|
sa.Column('workflow_spec_id', sa.String(), nullable=True),
|
||||||
|
sa.Column('library_spec_id', sa.String(), nullable=True),
|
||||||
|
sa.ForeignKeyConstraint(['library_spec_id'], ['workflow_spec.id'], ),
|
||||||
|
sa.ForeignKeyConstraint(['workflow_spec_id'], ['workflow_spec.id'], ),
|
||||||
|
sa.PrimaryKeyConstraint('id')
|
||||||
|
)
|
||||||
|
# ### end Alembic commands ###
|
||||||
|
|
||||||
|
|
||||||
|
def downgrade():
|
||||||
|
# ### commands auto generated by Alembic - please adjust! ###
|
||||||
|
op.drop_table('workflow_library')
|
||||||
|
# ### end Alembic commands ###
|
|
@ -0,0 +1,28 @@
|
||||||
|
"""empty message
|
||||||
|
|
||||||
|
Revision ID: b0f38c78db40
|
||||||
|
Revises: a931e2b7b070
|
||||||
|
Create Date: 2021-07-14 09:30:42.562825
|
||||||
|
|
||||||
|
"""
|
||||||
|
from alembic import op
|
||||||
|
import sqlalchemy as sa
|
||||||
|
|
||||||
|
|
||||||
|
# revision identifiers, used by Alembic.
|
||||||
|
revision = 'b0f38c78db40'
|
||||||
|
down_revision = 'a931e2b7b070'
|
||||||
|
branch_labels = None
|
||||||
|
depends_on = None
|
||||||
|
|
||||||
|
|
||||||
|
def upgrade():
|
||||||
|
# ### commands auto generated by Alembic - please adjust! ###
|
||||||
|
op.add_column('workflow_spec', sa.Column('library', sa.Boolean(), nullable=True))
|
||||||
|
# ### end Alembic commands ###
|
||||||
|
|
||||||
|
|
||||||
|
def downgrade():
|
||||||
|
# ### commands auto generated by Alembic - please adjust! ###
|
||||||
|
op.drop_column('workflow_spec', 'library')
|
||||||
|
# ### end Alembic commands ###
|
Loading…
Reference in New Issue