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https://github.com/sartography/cr-connect-workflow.git
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Merge branch 'feature/spec_files_wthout_db' of github.com:sartography/cr-connect-workflow into feature/spec_files_wthout_db
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Dan
commit
1d7ecad51f
@ -9,7 +9,6 @@ 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_log import TaskLogModelSchema, TaskLogQuery, TaskLogQuerySchema
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from crc.models.workflow import WorkflowModel
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from crc.services import workflow_spec_service
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from crc.services.error_service import ValidationErrorService
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from crc.services.lookup_service import LookupService
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from crc.services.spec_file_service import SpecFileService
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@ -20,20 +19,20 @@ from crc.services.workflow_processor import WorkflowProcessor
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from crc.services.workflow_service import WorkflowService
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from crc.services.workflow_spec_service import WorkflowSpecService
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workflow_spec_service = WorkflowSpecService()
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spec_service = WorkflowSpecService()
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def all_specifications(libraries=False,standalone=False):
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if libraries and standalone:
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raise ApiError('inconceivable!', 'You should specify libraries or standalone, but not both')
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if libraries:
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return workflow_spec_service.get_libraries()
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return spec_service.get_libraries()
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if standalone:
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return workflow_spec_service.get_standalones()
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return spec_service.get_standalones()
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# return standard workflows (not library, not standalone)
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categories = workflow_spec_service.get_categories()
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categories = spec_service.get_categories()
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workflows = []
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for cat in categories:
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workflows.extend(cat.workflows)
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@ -49,14 +48,14 @@ def add_workflow_specification(body):
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if body['library'] is True or body['standalone'] is True:
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body['category_id'] = None
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new_spec = workflow_spec_service.add_spec(body)
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new_spec = spec_service.add_spec(body)
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return new_spec
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def get_workflow_specification(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 = workflow_spec_service.get_spec(spec_id)
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spec = spec_service.get_spec(spec_id)
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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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@ -69,8 +68,8 @@ def validate_spec_and_library(spec_id,library_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 = workflow_spec_service.get_spec(spec_id)
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library = workflow_spec_service.get_library(library_id);
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spec = spec_service.get_spec(spec_id)
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library = spec_service.get_library(library_id);
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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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@ -81,27 +80,27 @@ def validate_spec_and_library(spec_id,library_id):
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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: workflow_spec_service.get_libraries()
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libraries: spec_service.get_libraries()
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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 "' + library_id + '" is already attached.')
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spec = workflow_spec_service.get_spec(spec_id)
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library = workflow_spec_service.get_spec(library_id)
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spec = spec_service.get_spec(spec_id)
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library = spec_service.get_spec(library_id)
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spec.libraries.push(library)
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workflow_spec_service.update_spec(spec_id)
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spec_service.update_spec(spec_id)
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return spec
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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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spec = workflow_spec_service.get_spec(spec_id)
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spec = spec_service.get_spec(spec_id)
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# heres a piece of code that certainly wont work
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library = workflow_spec_service.get_spec(library_id)
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library = spec_service.get_spec(library_id)
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if library in spec.libraries:
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spec.libraries.pop(library)
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workflow_spec_service.update_spec(spec_id)
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spec_service.update_spec(spec_id)
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return spec
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@ -120,7 +119,7 @@ def validate_workflow_specification(spec_id, study_id=None, test_until=None):
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def update_workflow_specification(spec_id, body):
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if spec_id is None:
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raise ApiError('unknown_spec', 'Please provide a valid Workflow Spec ID.')
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spec = workflow_spec_service.get_spec(spec_id)
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spec = spec_service.get_spec(spec_id)
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if spec is None:
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raise ApiError('unknown_study', 'The spec "' + spec_id + '" is not recognized.')
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@ -133,7 +132,7 @@ def update_workflow_specification(spec_id, body):
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if body['library'] is True or body['standalone'] is True:
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body['category_id'] = None
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spec = workflow_spec_service.update_spec(spec_id, body)
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spec = spec_service.update_spec(spec_id, body)
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return spec
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@ -141,7 +140,7 @@ def delete_workflow_specification(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 = workflow_spec_service.get_spec(spec_id)
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spec = spec_service.get_spec(spec_id)
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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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@ -157,7 +156,7 @@ def delete_workflow_specification(spec_id):
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WorkflowService.delete_workflow_spec_task_events(spec_id)
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# .delete() doesn't work when we need a cascade. Must grab the record, and explicitly delete
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workflow_spec_service.delete_spec(spec_id)
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spec_service.delete_spec(spec_id)
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# Reorder the remaining specs
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WorkflowService.cleanup_workflow_spec_display_order(spec.category_id)
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@ -167,9 +166,9 @@ def reorder_workflow_specification(spec_id, direction):
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if direction not in ('up', 'down'):
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raise ApiError(code='bad_direction',
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message='The direction must be `up` or `down`.')
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spec = workflow_spec_service.get_spec(spec_id)
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spec = spec_service.get_spec(spec_id)
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if spec:
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ordered_specs = workflow_spec_service.reorder_spec(spec, direction)
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ordered_specs = spec_service.reorder_spec(spec, direction)
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else:
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raise ApiError(code='bad_spec_id',
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message=f'The spec_id {spec_id} did not return a specification. Please check that it is valid.')
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@ -323,22 +322,22 @@ def __update_task(processor, task, data, user):
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def list_workflow_spec_categories():
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return workflow_spec_service.get_workflow_categories()
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return spec_service.get_categories()
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def get_workflow_spec_category(cat_id):
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return workflow_spec_service.get_workflow_category(cat_id)
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return spec_service.get_category(cat_id)
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def add_workflow_spec_category(body):
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return workflow_spec_service.add_category(body)
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return spec_service.add_category(body)
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def update_workflow_spec_category(cat_id, body):
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if cat_id is None:
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raise ApiError('unknown_category', 'Please provide a valid Workflow Spec Category ID.')
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category = workflow_spec_service.update_category(cat_id, body)
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category = spec_service.update_category(cat_id, body)
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if category is None:
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raise ApiError('unknown_category', 'The category "' + cat_id + '" is not recognized.')
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@ -351,7 +350,7 @@ def update_workflow_spec_category(cat_id, body):
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def delete_workflow_spec_category(cat_id):
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workflow_spec_service.delete_category(cat_id)
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spec_service.delete_category(cat_id)
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def reorder_workflow_spec_category(cat_id, direction):
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@ -359,9 +358,9 @@ def reorder_workflow_spec_category(cat_id, direction):
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raise ApiError(code='bad_direction',
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message='The direction must be `up` or `down`.')
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WorkflowService.cleanup_workflow_spec_category_display_order()
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category = workflow_spec_service.get_category(cat_id)
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category = spec_service.get_category(cat_id)
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if category:
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ordered_categories = workflow_spec_service.reorder_workflow_spec_category(category, direction)
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ordered_categories = spec_service.reorder_workflow_spec_category(category, direction)
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return ordered_categories
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else:
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raise ApiError(code='bad_category_id',
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@ -78,9 +78,6 @@ class WorkflowSpecService(FileSystemService):
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spec_list.sort(key=lambda w: w.display_order)
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return spec_list
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def get_standalones(self) -> List[WorkflowSpecInfo]:
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pass
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def get_categories(self) -> List[WorkflowSpecCategory]:
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"""Returns the categories as a list in display order"""
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cat_list = list(self.categories.values())
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