From 699d0ab7971f3ddfe5181fcbf75a7da19acda687 Mon Sep 17 00:00:00 2001 From: alicia pritchett Date: Fri, 4 Feb 2022 15:31:36 -0500 Subject: [PATCH] updated method calls in workflow.py except for reordering --- crc/api/workflow.py | 105 ++++++++------------------ crc/services/workflow_spec_service.py | 8 +- 2 files changed, 35 insertions(+), 78 deletions(-) diff --git a/crc/api/workflow.py b/crc/api/workflow.py index 3e4f7cdb..54684228 100644 --- a/crc/api/workflow.py +++ b/crc/api/workflow.py @@ -10,6 +10,7 @@ from crc.models.study import StudyModel, WorkflowMetadata, StudyStatus from crc.models.task_event import TaskEventModel, TaskEvent, TaskEventSchema from crc.models.task_log import TaskLogModelSchema, TaskLogQuery, TaskLogQuerySchema from crc.models.workflow import WorkflowModel +from crc.services import workflow_spec_service from crc.services.error_service import ValidationErrorService from crc.services.lookup_service import LookupService from crc.services.spec_file_service import SpecFileService @@ -42,36 +43,30 @@ def all_specifications(libraries=False,standalone=False): def add_workflow_specification(body): - # TODO: change the category identifier to display_name - category_id = body['category_id'] - # TODO: modify this method to call out to filesystem - WorkflowService.cleanup_workflow_spec_display_order(category_id) + category_id = body['display_name'] + # TODO: fix reordering + # WorkflowService.cleanup_workflow_spec_display_order(category_id) # TODO: why is the display_order coming from the body? alicia does not know - count = session.query(WorkflowSpecModel).filter_by(category_id=category_id).count() - body['display_order'] = count + # count = session.query(WorkflowSpecModel).filter_by(category_id=category_id).count() + #body['display_order'] = count # Libraries and standalone workflows don't get a category_id if body['library'] is True or body['standalone'] is True: body['category_id'] = None - # TODO: modify this to workflow_spec_service.add_spec(body); - new_spec: WorkflowSpecModel = WorkflowSpecModelSchema().load(body, session=session) - session.add(new_spec) - session.commit() - return WorkflowSpecModelSchema().dump(new_spec) + + new_spec = workflow_spec_service.add_spec(body) + return new_spec def get_workflow_specification(spec_id): if spec_id is None: raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.') - - # TODO: modify this to workflow_spec_service.get_spec(spec_id); - spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first() + spec = workflow_spec_service.get_spec(spec_id) if spec is None: raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.') - # TODO: return a spec - return WorkflowSpecModelSchema().dump(spec) + return spec def validate_spec_and_library(spec_id,library_id): if spec_id is None: @@ -79,9 +74,8 @@ def validate_spec_and_library(spec_id,library_id): if library_id is None: raise ApiError('unknown_spec', 'Please provide a valid Library Specification ID.') - # TODO: modify this to workflow_spec_service.get_spec(spec_id); - spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first() - library: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=library_id).first() + spec = workflow_spec_service.get_spec(spec_id) + library = workflow_spec_service.get_library(library_id); if spec is None: raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.') if library is None: @@ -90,30 +84,22 @@ def validate_spec_and_library(spec_id,library_id): raise ApiError('unknown_spec', 'Linked workflow spec is not a library.') -def add_workflow_spec_library(spec_id,library_id): +def add_workflow_spec_library(spec_id, library_id): validate_spec_and_library(spec_id, library_id) - # TODO: modify to get_libraries() - libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all() + libraries: workflow_spec_service.get_libraries() libraryids = [x.library_spec_id for x in libraries] if library_id in libraryids: raise ApiError('unknown_spec', 'The Library Specification "' + spec_id + '" is already attached.') - # TODO: modify this to add_library(newlib) - newlib = WorkflowLibraryModel() - newlib.workflow_spec_id = spec_id - newlib.library_spec_id = library_id - session.add(newlib) - session.commit() - libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all() - return WorkflowLibraryModelSchema(many=True).dump(libraries) + # TODO: this used to return all libraries. maybe we still want that here + newlib = workflow_spec_service.add_library(spec_id, library_id) + return newlib def drop_workflow_spec_library(spec_id,library_id): - # TODO: modify this to delete_library(newlib) validate_spec_and_library(spec_id, library_id) - session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id,library_spec_id=library_id).delete() - session.commit() - libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all() - return WorkflowLibraryModelSchema(many=True).dump(libraries) + workflow_spec_service.delete_library(library_id) + # TODO: this used to return all libraries. maybe we still want that here + return workflow_spec_service.get_libraries() def validate_workflow_specification(spec_id, study_id=None, test_until=None): @@ -131,9 +117,7 @@ def validate_workflow_specification(spec_id, study_id=None, test_until=None): def update_workflow_specification(spec_id, body): if spec_id is None: raise ApiError('unknown_spec', 'Please provide a valid Workflow Spec ID.') - - # TODO: replace this with a call to get_workflow_spec(spec_id); - spec = session.query(WorkflowSpecModel).filter_by(id=spec_id).first() + spec = workflow_spec_service.get_spec(spec_id) if spec is None: raise ApiError('unknown_study', 'The spec "' + spec_id + '" is not recognized.') @@ -146,20 +130,15 @@ def update_workflow_specification(spec_id, body): if body['library'] is True or body['standalone'] is True: body['category_id'] = None - # TODO: modify this to workflow_spec_service.update_spec(spec_id, body); - schema = WorkflowSpecModelSchema() - spec = schema.load(body, session=session, instance=spec, partial=True) - session.add(spec) - session.commit() - return schema.dump(spec) + spec = workflow_spec_service.update_spec(spec_id, body) + return spec def delete_workflow_specification(spec_id): if spec_id is None: raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.') - # TODO: replace this with a call to get_workflow_spec(spec_id); - spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first() + spec = workflow_spec_service.get_spec(spec_id) # TODO: replace this with category display name category_id = spec.category_id @@ -353,35 +332,22 @@ def __update_task(processor, task, data, user): def list_workflow_spec_categories(): - # TODO: modify this to get_workflow_categories() - schema = WorkflowSpecCategoryModelSchema(many=True) - return schema.dump(session.query(WorkflowSpecCategoryModel).order_by(WorkflowSpecCategoryModel.display_order).all()) + return workflow_spec_service.get_workflow_categories() def get_workflow_spec_category(cat_id): - # TODO: modify this to get_workflow_category(category) - schema = WorkflowSpecCategoryModelSchema() - return schema.dump(session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first()) + return workflow_spec_service.get_workflow_category(cat_id) def add_workflow_spec_category(body): - # TODO: modify this to add_workflow_category(body) - WorkflowService.cleanup_workflow_spec_category_display_order() - count = session.query(WorkflowSpecCategoryModel).count() - body['display_order'] = count - schema = WorkflowSpecCategoryModelSchema() - new_cat: WorkflowSpecCategoryModel = schema.load(body, session=session) - session.add(new_cat) - session.commit() - return schema.dump(new_cat) + return workflow_spec_service.add_category(body) def update_workflow_spec_category(cat_id, body): if cat_id is None: raise ApiError('unknown_category', 'Please provide a valid Workflow Spec Category ID.') - # TODO: modify this to update_workflow_category(cat_id, body) - category = session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first() + category = workflow_spec_service.update_category(cat_id, body) if category is None: raise ApiError('unknown_category', 'The category "' + cat_id + '" is not recognized.') @@ -390,20 +356,11 @@ def update_workflow_spec_category(cat_id, body): # There is a separate endpoint for that body['display_order'] = category.display_order - schema = WorkflowSpecCategoryModelSchema() - category = schema.load(body, session=session, instance=category, partial=True) - session.add(category) - session.commit() - return schema.dump(category) + return category def delete_workflow_spec_category(cat_id): - # TODO: modify this to delete_workflow_category(category) - session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).delete() - session.commit() - # Reorder the remaining categories - WorkflowService.cleanup_workflow_spec_category_display_order() - + workflow_spec_service.delete_category(cat_id) def reorder_workflow_spec_category(cat_id, direction): # TODO: fix reordering here too diff --git a/crc/services/workflow_spec_service.py b/crc/services/workflow_spec_service.py index 64719508..c090d800 100644 --- a/crc/services/workflow_spec_service.py +++ b/crc/services/workflow_spec_service.py @@ -186,16 +186,16 @@ class WorkflowSpecService(FileSystemService): return process_elements[0].attrib['id'] # TODO Methods i would add... - # delete_workflow_spec(spec_id) - # get_workflow_spec(spec_id) + # delete_spec(spec_id) + # get_spec(spec_id) # update_spec(spec_id, body) # add_spec(body) # Other methods i would add, maybe not here.. # add_library(body) # get_libraries() - # get_library(library) - # delete_library(library) + # get_library(spec_id, library_id) + # delete_library(library_id) # get_workflow_categories() # get_workflow_category(category, body)