sartography/cr-connect-workflow
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fix uhh some import statements?

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This commit is contained in:
alicia pritchett 2022-02-07 12:44:39 -05:00
parent ad095aaaf5
commit 732a8106da
1 changed files with 30 additions and 27 deletions
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57
crc/api/workflow.py
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@ -2,7 +2,7 @@ import uuid
from flask import g
from crc import session, WorkflowSpecService
from crc import session
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.api_models import WorkflowApiSchema
from crc.models.study import StudyModel, WorkflowMetadata, StudyStatus
@ -18,6 +18,9 @@ from crc.services.task_logging_service import TaskLoggingService
from crc.services.user_service import UserService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
from crc.services.workflow_spec_service import WorkflowSpecService
workflow_spec_service = WorkflowSpecService()
def all_specifications(libraries=False,standalone=False):
@ -25,13 +28,13 @@ def all_specifications(libraries=False,standalone=False):
raise ApiError('inconceivable!', 'You should specify libraries or standalone, but not both')
if libraries:
return WorkflowSpecService.get_libraries()
return workflow_spec_service.get_libraries()
if standalone:
return WorkflowSpecService.get_standalones()
return workflow_spec_service.get_standalones()
# return standard workflows (not library, not standalone)
categories = WorkflowSpecService.get_categories()
categories = workflow_spec_service.get_categories()
workflows = []
for cat in categories:
workflows.extend(cat.workflows)
@ -47,14 +50,14 @@ def add_workflow_specification(body):
if body['library'] is True or body['standalone'] is True:
body['category_id'] = None
new_spec = WorkflowSpecService.add_spec(body)
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.')
spec = WorkflowSpecService.get_spec(spec_id)
spec = workflow_spec_service.get_spec(spec_id)
if spec is None:
raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
@ -67,8 +70,8 @@ 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.')
spec = WorkflowSpecService.get_spec(spec_id)
library = WorkflowSpecService.get_library(library_id);
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:
@ -79,27 +82,27 @@ def validate_spec_and_library(spec_id,library_id):
def add_workflow_spec_library(spec_id, library_id):
validate_spec_and_library(spec_id, library_id)
libraries: WorkflowSpecService.get_libraries()
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 "' + library_id + '" is already attached.')
spec = WorkflowSpecService.get_spec(spec_id)
library = WorkflowSpecService.get_spec(library_id)
spec = workflow_spec_service.get_spec(spec_id)
library = workflow_spec_service.get_spec(library_id)
spec.libraries.push(library)
WorkflowSpecService.update_spec(spec_id)
workflow_spec_service.update_spec(spec_id)
return spec
def drop_workflow_spec_library(spec_id, library_id):
validate_spec_and_library(spec_id, library_id)
spec = WorkflowSpecService.get_spec(spec_id)
spec = workflow_spec_service.get_spec(spec_id)
# heres a piece of code that certainly wont work
library = WorkflowSpecService.get_spec(library_id)
library = workflow_spec_service.get_spec(library_id)
if library in spec.libraries:
spec.libraries.pop(library)
WorkflowSpecService.update_spec(spec_id)
workflow_spec_service.update_spec(spec_id)
return spec
@ -118,7 +121,7 @@ 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.')
spec = WorkflowSpecService.get_spec(spec_id)
spec = workflow_spec_service.get_spec(spec_id)
if spec is None:
raise ApiError('unknown_study', 'The spec "' + spec_id + '" is not recognized.')
@ -131,7 +134,7 @@ def update_workflow_specification(spec_id, body):
if body['library'] is True or body['standalone'] is True:
body['category_id'] = None
spec = WorkflowSpecService.update_spec(spec_id, body)
spec = workflow_spec_service.update_spec(spec_id, body)
return spec
@ -139,7 +142,7 @@ def delete_workflow_specification(spec_id):
if spec_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
spec = WorkflowSpecService.get_spec(spec_id)
spec = workflow_spec_service.get_spec(spec_id)
if spec is None:
raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
@ -155,7 +158,7 @@ def delete_workflow_specification(spec_id):
WorkflowService.delete_workflow_spec_task_events(spec_id)
# .delete() doesn't work when we need a cascade. Must grab the record, and explicitly delete
WorkflowSpecService.delete_spec(spec_id)
workflow_spec_service.delete_spec(spec_id)
# Reorder the remaining specs
WorkflowService.cleanup_workflow_spec_display_order(spec.category_id)
@ -165,9 +168,9 @@ def reorder_workflow_specification(spec_id, direction):
if direction not in ('up', 'down'):
raise ApiError(code='bad_direction',
message='The direction must be `up` or `down`.')
spec = WorkflowSpecService.get_spec(spec_id)
spec = workflow_spec_service.get_spec(spec_id)
if spec:
ordered_specs = WorkflowSpecService.reorder_spec(spec, direction)
ordered_specs = workflow_spec_service.reorder_spec(spec, 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.')
@ -322,22 +325,22 @@ def __update_task(processor, task, data, user):
def list_workflow_spec_categories():
return WorkflowSpecService.get_workflow_categories()
return workflow_spec_service.get_workflow_categories()
def get_workflow_spec_category(cat_id):
return WorkflowSpecService.get_workflow_category(cat_id)
return workflow_spec_service.get_workflow_category(cat_id)
def add_workflow_spec_category(body):
return WorkflowSpecService.add_category(body)
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.')
category = WorkflowSpecService.update_category(cat_id, body)
category = workflow_spec_service.update_category(cat_id, body)
if category is None:
raise ApiError('unknown_category', 'The category "' + cat_id + '" is not recognized.')
@ -358,9 +361,9 @@ def reorder_workflow_spec_category(cat_id, direction):
raise ApiError(code='bad_direction',
message='The direction must be `up` or `down`.')
WorkflowService.cleanup_workflow_spec_category_display_order()
category = WorkflowSpecService.get_category(cat_id)
category = workflow_spec_service.get_category(cat_id)
if category:
ordered_categories = WorkflowSpecService.reorder_workflow_spec_category(category, direction)
ordered_categories = workflow_spec_service.reorder_workflow_spec_category(category, direction)
return ordered_categories
else:
raise ApiError(code='bad_category_id',