Merge branch 'feature/spec_files_wthout_db' of github.com:sartography/cr-connect-workflow into feature/spec_files_wthout_db
This commit is contained in:
Dan
commit
1abb2490e5
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@ -10,6 +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_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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@ -42,36 +43,30 @@ def all_specifications(libraries=False,standalone=False):
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def add_workflow_specification(body):
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# TODO: change the category identifier to display_name
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category_id = body['category_id']
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# TODO: modify this method to call out to filesystem
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WorkflowService.cleanup_workflow_spec_display_order(category_id)
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category_id = body['display_name']
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# TODO: fix reordering
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# WorkflowService.cleanup_workflow_spec_display_order(category_id)
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# TODO: why is the display_order coming from the body? alicia does not know
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count = session.query(WorkflowSpecModel).filter_by(category_id=category_id).count()
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body['display_order'] = count
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# count = session.query(WorkflowSpecModel).filter_by(category_id=category_id).count()
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#body['display_order'] = count
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# Libraries and standalone workflows don't get a category_id
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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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# TODO: modify this to workflow_spec_service.add_spec(body);
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new_spec: WorkflowSpecModel = WorkflowSpecModelSchema().load(body, session=session)
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session.add(new_spec)
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session.commit()
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return WorkflowSpecModelSchema().dump(new_spec)
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new_spec = workflow_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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# TODO: modify this to workflow_spec_service.get_spec(spec_id);
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spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
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spec = workflow_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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# TODO: return a spec
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return WorkflowSpecModelSchema().dump(spec)
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return spec
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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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@ -79,9 +74,8 @@ 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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# TODO: modify this to workflow_spec_service.get_spec(spec_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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spec = workflow_spec_service.get_spec(spec_id)
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library = workflow_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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@ -90,30 +84,22 @@ def validate_spec_and_library(spec_id,library_id):
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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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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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# TODO: modify to get_libraries()
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libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
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libraries: workflow_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 "' + spec_id + '" is already attached.')
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# TODO: modify this to add_library(newlib)
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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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# TODO: this used to return all libraries. maybe we still want that here
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newlib = workflow_spec_service.add_library(spec_id, library_id)
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return newlib
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def drop_workflow_spec_library(spec_id,library_id):
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# TODO: modify this to delete_library(newlib)
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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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workflow_spec_service.delete_library(library_id)
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# TODO: this used to return all libraries. maybe we still want that here
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return workflow_spec_service.get_libraries()
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def validate_workflow_specification(spec_id, study_id=None, test_until=None):
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@ -131,9 +117,7 @@ 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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# TODO: replace this with a call to get_workflow_spec(spec_id);
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spec = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
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spec = workflow_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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@ -146,20 +130,15 @@ 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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# TODO: modify this to workflow_spec_service.update_spec(spec_id, body);
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schema = WorkflowSpecModelSchema()
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spec = schema.load(body, session=session, instance=spec, partial=True)
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session.add(spec)
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session.commit()
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return schema.dump(spec)
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spec = workflow_spec_service.update_spec(spec_id, body)
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return spec
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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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# TODO: replace this with a call to get_workflow_spec(spec_id);
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spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
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spec = workflow_spec_service.get_spec(spec_id)
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# TODO: replace this with category display name
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category_id = spec.category_id
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@ -353,35 +332,22 @@ def __update_task(processor, task, data, user):
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def list_workflow_spec_categories():
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# TODO: modify this to get_workflow_categories()
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schema = WorkflowSpecCategoryModelSchema(many=True)
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return schema.dump(session.query(WorkflowSpecCategoryModel).order_by(WorkflowSpecCategoryModel.display_order).all())
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return workflow_spec_service.get_workflow_categories()
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def get_workflow_spec_category(cat_id):
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# TODO: modify this to get_workflow_category(category)
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schema = WorkflowSpecCategoryModelSchema()
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return schema.dump(session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first())
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return workflow_spec_service.get_workflow_category(cat_id)
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def add_workflow_spec_category(body):
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# TODO: modify this to add_workflow_category(body)
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WorkflowService.cleanup_workflow_spec_category_display_order()
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count = session.query(WorkflowSpecCategoryModel).count()
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body['display_order'] = count
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schema = WorkflowSpecCategoryModelSchema()
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new_cat: WorkflowSpecCategoryModel = schema.load(body, session=session)
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session.add(new_cat)
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session.commit()
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return schema.dump(new_cat)
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return workflow_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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# TODO: modify this to update_workflow_category(cat_id, body)
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category = session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first()
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category = workflow_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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@ -390,20 +356,11 @@ def update_workflow_spec_category(cat_id, body):
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# There is a separate endpoint for that
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body['display_order'] = category.display_order
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schema = WorkflowSpecCategoryModelSchema()
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category = schema.load(body, session=session, instance=category, partial=True)
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session.add(category)
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session.commit()
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return schema.dump(category)
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return category
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def delete_workflow_spec_category(cat_id):
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# TODO: modify this to delete_workflow_category(category)
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session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).delete()
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session.commit()
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# Reorder the remaining categories
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WorkflowService.cleanup_workflow_spec_category_display_order()
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workflow_spec_service.delete_category(cat_id)
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def reorder_workflow_spec_category(cat_id, direction):
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# TODO: fix reordering here too
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@ -211,4 +211,21 @@ class WorkflowSpecService(FileSystemService):
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return process_elements[0].attrib['id']
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# TODO Methods i would add...
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# delete_spec(spec_id)
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# get_spec(spec_id)
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# update_spec(spec_id, body)
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# add_spec(body)
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# Other methods i would add, maybe not here..
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# add_library(body)
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# get_libraries()
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# get_library(spec_id, library_id)
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# delete_library(library_id)
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# get_workflow_categories()
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# get_workflow_category(category, body)
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# add_workflow_category(body)
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# update_workflow_category(category, body)
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# delete_workflow_category(category)
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