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cr-connect-workflow
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Fixes for backend code after removing `name` column from `workflow_spec` and `workflow_spec_category` tables

This commit is contained in:
mike cullerton 2021-10-05 14:17:41 -04:00
parent fb660182aa
commit 572ca1db6b
6 changed files with 27 additions and 32 deletions
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2
crc/api/workflow_sync.py
View File

@ -153,7 +153,7 @@ def create_or_update_local_spec(remote,workflow_spec_id):
# Set the category # Set the category
if specdict['category'] is not None: if specdict['category'] is not None:
local_category = session.query(WorkflowSpecCategoryModel).\ local_category = session.query(WorkflowSpecCategoryModel).\
filter(WorkflowSpecCategoryModel.name == specdict['category']['name']).first() filter(WorkflowSpecCategoryModel.id == specdict['category']['id']).first()
local_category = WorkflowSpecCategoryModelSchema().load(specdict['category'], session=session, local_category = WorkflowSpecCategoryModelSchema().load(specdict['category'], session=session,
instance=local_category) instance=local_category)
session.add(local_category) session.add(local_category)

11
crc/models/study.py
View File

@ -104,12 +104,11 @@ class StudyEvent(db.Model):
class WorkflowMetadata(object): class WorkflowMetadata(object):
def __init__(self, id, name = None, display_name = None, description = None, spec_version = None, def __init__(self, id, display_name = None, description = None, spec_version = None,
category_id = None, category_display_name = None, state: WorkflowState = None, category_id = None, category_display_name = None, state: WorkflowState = None,
status: WorkflowStatus = None, total_tasks = None, completed_tasks = None, status: WorkflowStatus = None, total_tasks = None, completed_tasks = None,
is_review=None,display_order = None, state_message = None): is_review=None,display_order = None, state_message = None):
self.id = id self.id = id
self.name = name
self.display_name = display_name self.display_name = display_name
self.description = description self.description = description
self.spec_version = spec_version self.spec_version = spec_version
@ -128,8 +127,7 @@ class WorkflowMetadata(object):
def from_workflow(cls, workflow: WorkflowModel): def from_workflow(cls, workflow: WorkflowModel):
is_review = FileService.is_workflow_review(workflow.workflow_spec_id) is_review = FileService.is_workflow_review(workflow.workflow_spec_id)
instance = cls( instance = cls(
id=workflow.id, id=workflow.workflow_spec_id,
name=workflow.workflow_spec.name,
display_name=workflow.workflow_spec.display_name, display_name=workflow.workflow_spec.display_name,
description=workflow.workflow_spec.description, description=workflow.workflow_spec.description,
spec_version=workflow.spec_version(), spec_version=workflow.spec_version(),
@ -150,7 +148,7 @@ class WorkflowMetadataSchema(ma.Schema):
status = EnumField(WorkflowStatus) status = EnumField(WorkflowStatus)
class Meta: class Meta:
model = WorkflowMetadata model = WorkflowMetadata
additional = ["id", "name", "display_name", "description", additional = ["id", "display_name", "description",
"total_tasks", "completed_tasks", "display_order", "total_tasks", "completed_tasks", "display_order",
"category_id", "is_review", "category_display_name", "state_message"] "category_id", "is_review", "category_display_name", "state_message"]
unknown = INCLUDE unknown = INCLUDE
@ -159,7 +157,6 @@ class WorkflowMetadataSchema(ma.Schema):
class Category(object): class Category(object):
def __init__(self, model: WorkflowSpecCategoryModel): def __init__(self, model: WorkflowSpecCategoryModel):
self.id = model.id self.id = model.id
self.name = model.name
self.display_name = model.display_name self.display_name = model.display_name
self.display_order = model.display_order self.display_order = model.display_order
self.admin = model.admin self.admin = model.admin
@ -169,7 +166,7 @@ class CategorySchema(ma.Schema):
workflows = fields.List(fields.Nested(WorkflowMetadataSchema), dump_only=True) workflows = fields.List(fields.Nested(WorkflowMetadataSchema), dump_only=True)
class Meta: class Meta:
model = Category model = Category
additional = ["id", "name", "display_name", "display_order", "admin"] additional = ["id", "display_name", "display_order", "admin"]
unknown = INCLUDE unknown = INCLUDE

2
crc/models/workflow.py
View File

@ -60,11 +60,9 @@ class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
category = marshmallow.fields.Nested(WorkflowSpecCategoryModelSchema, dump_only=True) category = marshmallow.fields.Nested(WorkflowSpecCategoryModelSchema, dump_only=True)
libraries = marshmallow.fields.Function(lambda obj: [{'id':x.library.id, libraries = marshmallow.fields.Function(lambda obj: [{'id':x.library.id,
'name':x.library.name,
'display_name':x.library.display_name} for x in 'display_name':x.library.display_name} for x in
obj.libraries] ) obj.libraries] )
parents = marshmallow.fields.Function(lambda obj: [{'id':x.parent.id, parents = marshmallow.fields.Function(lambda obj: [{'id':x.parent.id,
'name':x.parent.name,
'display_name':x.parent.display_name} for x in 'display_name':x.parent.display_name} for x in
obj.parents] ) obj.parents] )

14
crc/scripts/reset_workflow.py
View File

@ -13,13 +13,13 @@ class ResetWorkflow(Script):
I.e., a new PI""" I.e., a new PI"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs): def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
return hasattr(kwargs, 'workflow_name') return hasattr(kwargs, 'reset_id')
def do_task(self, task, study_id, workflow_id, *args, **kwargs): def do_task(self, task, study_id, workflow_id, *args, **kwargs):
if 'workflow_name' in kwargs.keys(): if 'reset_id' in kwargs.keys():
workflow_name = kwargs['workflow_name'] reset_id = kwargs['reset_id']
workflow_spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(name=workflow_name).first() workflow_spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=reset_id).first()
if workflow_spec: if workflow_spec:
workflow_model: WorkflowModel = session.query(WorkflowModel).filter_by( workflow_model: WorkflowModel = session.query(WorkflowModel).filter_by(
workflow_spec_id=workflow_spec.id, workflow_spec_id=workflow_spec.id,
@ -35,7 +35,7 @@ class ResetWorkflow(Script):
else: else:
raise ApiError(code='missing_workflow_spec', raise ApiError(code='missing_workflow_spec',
message=f'No WorkflowSpecModel returned. \ message=f'No WorkflowSpecModel returned. \
name: {workflow_name}') id: {workflow_id}')
else: else:
raise ApiError(code='missing_workflow_name', raise ApiError(code='missing_workflow_id',
message='Reset workflow requires a workflow name') message='Reset workflow requires a workflow id')

22
crc/services/study_service.py
View File

@ -433,26 +433,26 @@ class StudyService(object):
for wfm in workflow_metas: for wfm in workflow_metas:
wfm.state_message = '' wfm.state_message = ''
# do we have a status for you # do we have a status for you
if wfm.name not in status.keys(): if wfm.id not in status.keys():
warnings.append(ApiError("missing_status", "No status specified for workflow %s" % wfm.name)) warnings.append(ApiError("missing_status", "No status specified for workflow %s" % wfm.id))
continue continue
if not isinstance(status[wfm.name], dict): if not isinstance(status[wfm.id], dict):
warnings.append(ApiError(code='invalid_status', warnings.append(ApiError(code='invalid_status',
message=f'Status must be a dictionary with "status" and "message" keys. Name is {wfm.name}. Status is {status[wfm.name]}')) message=f'Status must be a dictionary with "status" and "message" keys. Name is {wfm.id}. Status is {status[wfm.id]}'))
continue continue
if 'status' not in status[wfm.name].keys(): if 'status' not in status[wfm.id].keys():
warnings.append(ApiError("missing_status", warnings.append(ApiError("missing_status",
"Workflow '%s' does not have a status setting" % wfm.name)) "Workflow '%s' does not have a status setting" % wfm.id))
continue continue
if not WorkflowState.has_value(status[wfm.name]['status']): if not WorkflowState.has_value(status[wfm.id]['status']):
warnings.append(ApiError("invalid_state", warnings.append(ApiError("invalid_state",
"Workflow '%s' can not be set to '%s', should be one of %s" % ( "Workflow '%s' can not be set to '%s', should be one of %s" % (
wfm.name, status[wfm.name]['status'], ",".join(WorkflowState.list()) wfm.id, status[wfm.id]['status'], ",".join(WorkflowState.list())
))) )))
continue continue
wfm.state = WorkflowState[status[wfm.name]['status']] wfm.state = WorkflowState[status[wfm.id]['status']]
if 'message' in status[wfm.name].keys(): if 'message' in status[wfm.id].keys():
wfm.state_message = status[wfm.name]['message'] wfm.state_message = status[wfm.id]['message']
return warnings return warnings
@staticmethod @staticmethod

8
crc/services/workflow_service.py
View File

@ -115,7 +115,7 @@ class WorkflowService(object):
except Exception as e: except Exception as e:
app.logger.error(f"Error running waiting task for workflow #%i (%s) for study #%i. %s" % app.logger.error(f"Error running waiting task for workflow #%i (%s) for study #%i. %s" %
(workflow_model.id, (workflow_model.id,
workflow_model.workflow_spec.name, workflow_model.workflow_spec.id,
workflow_model.study_id, workflow_model.study_id,
str(e))) str(e)))
@ -137,8 +137,8 @@ class WorkflowService(object):
study_model = session.query(StudyModel).filter(StudyModel.id == validate_study_id).first() study_model = session.query(StudyModel).filter(StudyModel.id == validate_study_id).first()
spec_model = session.query(WorkflowSpecModel).filter(WorkflowSpecModel.id == spec_id).first() spec_model = session.query(WorkflowSpecModel).filter(WorkflowSpecModel.id == spec_id).first()
status = StudyService._get_study_status(study_model) status = StudyService._get_study_status(study_model)
if spec_model.name in status and status[spec_model.name]['status'] == 'disabled': if spec_model.id in status and status[spec_model.id]['status'] == 'disabled':
raise ApiError(code='disabled_workflow', message=f"This workflow is disabled. {status[spec_model.name]['message']}") raise ApiError(code='disabled_workflow', message=f"This workflow is disabled. {status[spec_model.id]['message']}")
workflow_model = WorkflowService.make_test_workflow(spec_id, validate_study_id) workflow_model = WorkflowService.make_test_workflow(spec_id, validate_study_id)
try: try:
processor = WorkflowProcessor(workflow_model, validate_only=True) processor = WorkflowProcessor(workflow_model, validate_only=True)
@ -149,7 +149,7 @@ class WorkflowService(object):
exit_task = processor.bpmn_workflow.do_engine_steps(exit_at=test_until) exit_task = processor.bpmn_workflow.do_engine_steps(exit_at=test_until)
if (exit_task != None): if (exit_task != None):
raise ApiError.from_task("validation_break", raise ApiError.from_task("validation_break",
f"The validation has been exited early on task '{exit_task.task_spec.name}' and was parented by ", f"The validation has been exited early on task '{exit_task.task_spec.id}' and was parented by ",
exit_task.parent) exit_task.parent)
tasks = processor.bpmn_workflow.get_tasks(SpiffTask.READY) tasks = processor.bpmn_workflow.get_tasks(SpiffTask.READY)
for task in tasks: for task in tasks: