sartography/cr-connect-workflow
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heres the categories

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This commit is contained in:
alicia pritchett 2022-02-07 15:45:09 -05:00
parent a4fb00b0ed
commit aa9807a543
1 changed files with 20 additions and 15 deletions
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35
crc/api/workflow.py
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@ -8,7 +8,7 @@ from crc.models.api_models import WorkflowApiSchema
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.models.workflow import WorkflowModel, WorkflowSpecInfoSchema, WorkflowSpecCategorySchema
from crc.services.error_service import ValidationErrorService
from crc.services.lookup_service import LookupService
from crc.services.spec_file_service import SpecFileService
@ -26,17 +26,19 @@ def all_specifications(libraries=False,standalone=False):
raise ApiError('inconceivable!', 'You should specify libraries or standalone, but not both')
if libraries:
return spec_service.get_libraries()
workflows = spec_service.get_libraries()
return WorkflowSpecInfoSchema(many=True).dump(workflows)
if standalone:
return spec_service.get_standalones()
workflows = spec_service.get_standalones()
return WorkflowSpecInfoSchema(many=True).dump(workflows)
# return standard workflows (not library, not standalone)
categories = spec_service.get_categories()
workflows = []
for cat in categories:
workflows.extend(cat.workflows)
return workflows
return WorkflowSpecInfoSchema(many=True).dump(workflows)
def add_workflow_specification(body):
@ -49,7 +51,7 @@ def add_workflow_specification(body):
body['category_id'] = None
new_spec = spec_service.add_spec(body)
return new_spec
return WorkflowSpecInfoSchema().dump(new_spec)
def get_workflow_specification(spec_id):
@ -60,7 +62,7 @@ def get_workflow_specification(spec_id):
if spec is None:
raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
return spec
return WorkflowSpecInfoSchema().dump(spec)
def validate_spec_and_library(spec_id,library_id):
if spec_id is None:
@ -89,7 +91,7 @@ def add_workflow_spec_library(spec_id, library_id):
library = spec_service.get_spec(library_id)
spec.libraries.push(library)
spec_service.update_spec(spec_id)
return spec
return WorkflowSpecInfoSchema().dump(spec)
def drop_workflow_spec_library(spec_id, library_id):
@ -101,7 +103,7 @@ def drop_workflow_spec_library(spec_id, library_id):
if library in spec.libraries:
spec.libraries.pop(library)
spec_service.update_spec(spec_id)
return spec
return WorkflowSpecInfoSchema().dump(spec)
def validate_workflow_specification(spec_id, study_id=None, test_until=None):
@ -133,7 +135,7 @@ def update_workflow_specification(spec_id, body):
body['category_id'] = None
spec = spec_service.update_spec(spec_id, body)
return spec
return WorkflowSpecInfoSchema().dump(spec)
def delete_workflow_specification(spec_id):
@ -172,7 +174,7 @@ def reorder_workflow_specification(spec_id, direction):
else:
raise ApiError(code='bad_spec_id',
message=f'The spec_id {spec_id} did not return a specification. Please check that it is valid.')
return ordered_specs
return WorkflowSpecInfoSchema(many=True).dump(ordered_specs)
def get_workflow_from_spec(spec_id):
@ -322,16 +324,19 @@ def __update_task(processor, task, data, user):
def list_workflow_spec_categories():
return spec_service.get_categories()
categories = spec_service.get_categories()
return WorkflowSpecCategorySchema(many=True).dump(categories)
def get_workflow_spec_category(cat_id):
return spec_service.get_category(cat_id)
category = spec_service.get_category(cat_id)
return WorkflowSpecCategorySchema().dump(category)
def add_workflow_spec_category(body):
return spec_service.add_category(body)
category = spec_service.add_category(body)
return WorkflowSpecCategorySchema().dump(category)
def update_workflow_spec_category(cat_id, body):
if cat_id is None:
@ -346,7 +351,7 @@ def update_workflow_spec_category(cat_id, body):
# There is a separate endpoint for that
body['display_order'] = category.display_order
return category
return WorkflowSpecCategorySchema().dump(category)
def delete_workflow_spec_category(cat_id):