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cr-connect-workflow
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new methods

This commit is contained in:
alicia pritchett 2022-02-04 14:45:52 -05:00
parent 6765afbd02
commit 2fb6746f6b
2 changed files with 48 additions and 0 deletions
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30
crc/api/workflow.py
View File

@ -42,13 +42,18 @@ def all_specifications(libraries=False,standalone=False):
def add_workflow_specification(body): def add_workflow_specification(body):
# TODO: change the category identifier to display_name
category_id = body['category_id'] category_id = body['category_id']
# TODO: modify this method to call out to filesystem
WorkflowService.cleanup_workflow_spec_display_order(category_id) 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() count = session.query(WorkflowSpecModel).filter_by(category_id=category_id).count()
body['display_order'] = count body['display_order'] = count
# Libraries and standalone workflows don't get a category_id # Libraries and standalone workflows don't get a category_id
if body['library'] is True or body['standalone'] is True: if body['library'] is True or body['standalone'] is True:
body['category_id'] = None body['category_id'] = None
# TODO: modify this to workflow_spec_service.add_spec(body);
new_spec: WorkflowSpecModel = WorkflowSpecModelSchema().load(body, session=session) new_spec: WorkflowSpecModel = WorkflowSpecModelSchema().load(body, session=session)
session.add(new_spec) session.add(new_spec)
session.commit() session.commit()
@ -59,11 +64,13 @@ def get_workflow_specification(spec_id):
if spec_id is None: if spec_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.') 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: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
if spec is None: if spec is None:
raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.') raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
# TODO: return a spec
return WorkflowSpecModelSchema().dump(spec) return WorkflowSpecModelSchema().dump(spec)
def validate_spec_and_library(spec_id,library_id): def validate_spec_and_library(spec_id,library_id):
@ -71,6 +78,8 @@ def validate_spec_and_library(spec_id,library_id):
raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.') raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
if library_id is None: if library_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Library Specification ID.') 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() spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
library: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=library_id).first() library: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=library_id).first()
if spec is None: if spec is None:
@ -83,10 +92,13 @@ def validate_spec_and_library(spec_id,library_id):
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) 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: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
libraryids = [x.library_spec_id for x in libraries] libraryids = [x.library_spec_id for x in libraries]
if library_id in libraryids: if library_id in libraryids:
raise ApiError('unknown_spec', 'The Library Specification "' + spec_id + '" is already attached.') raise ApiError('unknown_spec', 'The Library Specification "' + spec_id + '" is already attached.')
# TODO: modify this to add_library(newlib)
newlib = WorkflowLibraryModel() newlib = WorkflowLibraryModel()
newlib.workflow_spec_id = spec_id newlib.workflow_spec_id = spec_id
newlib.library_spec_id = library_id newlib.library_spec_id = library_id
@ -96,6 +108,7 @@ def add_workflow_spec_library(spec_id,library_id):
return WorkflowLibraryModelSchema(many=True).dump(libraries) return WorkflowLibraryModelSchema(many=True).dump(libraries)
def drop_workflow_spec_library(spec_id,library_id): def drop_workflow_spec_library(spec_id,library_id):
# TODO: modify this to delete_library(newlib)
validate_spec_and_library(spec_id, library_id) 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.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id,library_spec_id=library_id).delete()
session.commit() session.commit()
@ -118,6 +131,8 @@ def validate_workflow_specification(spec_id, study_id=None, test_until=None):
def update_workflow_specification(spec_id, body): def update_workflow_specification(spec_id, body):
if spec_id is None: if spec_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Workflow Spec ID.') 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 = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
if spec is None: if spec is None:
@ -131,6 +146,7 @@ def update_workflow_specification(spec_id, body):
if body['library'] is True or body['standalone'] is True: if body['library'] is True or body['standalone'] is True:
body['category_id'] = None body['category_id'] = None
# TODO: modify this to workflow_spec_service.update_spec(spec_id, body);
schema = WorkflowSpecModelSchema() schema = WorkflowSpecModelSchema()
spec = schema.load(body, session=session, instance=spec, partial=True) spec = schema.load(body, session=session, instance=spec, partial=True)
session.add(spec) session.add(spec)
@ -142,12 +158,15 @@ def delete_workflow_specification(spec_id):
if spec_id is None: if spec_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.') 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: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
# TODO: replace this with category display name
category_id = spec.category_id category_id = spec.category_id
if spec is None: if spec is None:
raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.') raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
# TODO : think about this
# Delete all workflow models related to this specification # Delete all workflow models related to this specification
WorkflowService.delete_workflow_spec_workflow_models(spec_id) WorkflowService.delete_workflow_spec_workflow_models(spec_id)
@ -158,11 +177,13 @@ def delete_workflow_specification(spec_id):
WorkflowService.delete_workflow_spec_task_events(spec_id) WorkflowService.delete_workflow_spec_task_events(spec_id)
# TODO: replace this with a call to delete_workflow_spec(spec_id);
# .delete() doesn't work when we need a cascade. Must grab the record, and explicitly delete # .delete() doesn't work when we need a cascade. Must grab the record, and explicitly delete
workflow_spec = session.query(WorkflowSpecModel).filter_by(id=spec_id).first() workflow_spec = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
session.delete(workflow_spec) session.delete(workflow_spec)
session.commit() session.commit()
# TODO: fix reordering
# Reorder the remaining specs # Reorder the remaining specs
WorkflowService.cleanup_workflow_spec_display_order(category_id) WorkflowService.cleanup_workflow_spec_display_order(category_id)
@ -171,6 +192,8 @@ def reorder_workflow_specification(spec_id, direction):
if direction not in ('up', 'down'): if direction not in ('up', 'down'):
raise ApiError(code='bad_direction', raise ApiError(code='bad_direction',
message='The direction must be `up` or `down`.') message='The direction must be `up` or `down`.')
# TODO: modify this to workflow_spec_service.get_workflow_spec(spec_id)
# TODO: fix reordering
spec = session.query(WorkflowSpecModel).filter(WorkflowSpecModel.id == spec_id).first() spec = session.query(WorkflowSpecModel).filter(WorkflowSpecModel.id == spec_id).first()
if spec: if spec:
WorkflowService.cleanup_workflow_spec_display_order(spec.category_id) WorkflowService.cleanup_workflow_spec_display_order(spec.category_id)
@ -330,16 +353,19 @@ def __update_task(processor, task, data, user):
def list_workflow_spec_categories(): def list_workflow_spec_categories():
# TODO: modify this to get_workflow_categories()
schema = WorkflowSpecCategoryModelSchema(many=True) schema = WorkflowSpecCategoryModelSchema(many=True)
return schema.dump(session.query(WorkflowSpecCategoryModel).order_by(WorkflowSpecCategoryModel.display_order).all()) return schema.dump(session.query(WorkflowSpecCategoryModel).order_by(WorkflowSpecCategoryModel.display_order).all())
def get_workflow_spec_category(cat_id): def get_workflow_spec_category(cat_id):
# TODO: modify this to get_workflow_category(category)
schema = WorkflowSpecCategoryModelSchema() schema = WorkflowSpecCategoryModelSchema()
return schema.dump(session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first()) return schema.dump(session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first())
def add_workflow_spec_category(body): def add_workflow_spec_category(body):
# TODO: modify this to add_workflow_category(body)
WorkflowService.cleanup_workflow_spec_category_display_order() WorkflowService.cleanup_workflow_spec_category_display_order()
count = session.query(WorkflowSpecCategoryModel).count() count = session.query(WorkflowSpecCategoryModel).count()
body['display_order'] = count body['display_order'] = count
@ -354,6 +380,7 @@ def update_workflow_spec_category(cat_id, body):
if cat_id is None: if cat_id is None:
raise ApiError('unknown_category', 'Please provide a valid Workflow Spec Category ID.') 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 = session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first()
if category is None: if category is None:
@ -371,6 +398,7 @@ def update_workflow_spec_category(cat_id, body):
def delete_workflow_spec_category(cat_id): 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.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).delete()
session.commit() session.commit()
# Reorder the remaining categories # Reorder the remaining categories
@ -378,10 +406,12 @@ def delete_workflow_spec_category(cat_id):
def reorder_workflow_spec_category(cat_id, direction): def reorder_workflow_spec_category(cat_id, direction):
# TODO: fix reordering here too
if direction not in ('up', 'down'): if direction not in ('up', 'down'):
raise ApiError(code='bad_direction', raise ApiError(code='bad_direction',
message='The direction must be `up` or `down`.') message='The direction must be `up` or `down`.')
WorkflowService.cleanup_workflow_spec_category_display_order() WorkflowService.cleanup_workflow_spec_category_display_order()
# TODO: modify this to get_workflow_category(category)
category = session.query(WorkflowSpecCategoryModel).\ category = session.query(WorkflowSpecCategoryModel).\
filter(WorkflowSpecCategoryModel.id == cat_id).first() filter(WorkflowSpecCategoryModel.id == cat_id).first()
if category: if category:

18
crc/services/workflow_spec_service.py
View File

@ -152,3 +152,21 @@ class WorkflowSpecService(FileSystemService):
return process_elements[0].attrib['id'] return process_elements[0].attrib['id']
# TODO Methods i would add...
# delete_workflow_spec(spec_id)
# get_workflow_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_workflow_categories()
# get_workflow_category(category, body)
# add_workflow_category(body)
# update_workflow_category(category, body)
# delete_workflow_category(category)