sartography/cr-connect-workflow
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Merge pull request #576 from sartography/dev

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dev to main
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Dan Funk 2022-12-02 11:00:24 -05:00 committed by GitHub
commit 51ae2c7f94
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6 changed files with 24 additions and 7 deletions
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8
crc/models/api_models.py
View File

@ -188,6 +188,7 @@ class NavigationItemSchema(ma.Schema):
item.children = children
return item
class DocumentDirectorySchema(ma.Schema):
level = marshmallow.fields.String()
file = marshmallow.fields.Nested(FileSchema)
@ -212,7 +213,7 @@ class DocumentDirectory(object):
class WorkflowApi(object):
def __init__(self, id, status, next_task, navigation,
workflow_spec_id,
last_updated, is_review, title, study_id, state, is_admin_workflow=False):
last_updated, is_review, title, study_id, state, user_id, is_admin_workflow=False):
self.id = id
self.status = status
self.next_task = next_task # The next task that requires user input.
@ -223,6 +224,7 @@ class WorkflowApi(object):
self.is_review = is_review
self.study_id = study_id or ''
self.state = state
self.user_id = user_id
self.is_admin_workflow = is_admin_workflow
@ -231,7 +233,7 @@ class WorkflowApiSchema(ma.Schema):
model = WorkflowApi
fields = ["id", "status", "next_task", "navigation",
"workflow_spec_id", "total_tasks", "completed_tasks",
"last_updated", "is_review", "title", "study_id", "state", "is_admin_workflow"]
"last_updated", "is_review", "title", "study_id", "state", "user_id", "is_admin_workflow"]
unknown = INCLUDE
status = EnumField(WorkflowStatus)
@ -243,7 +245,7 @@ class WorkflowApiSchema(ma.Schema):
def make_workflow(self, data, **kwargs):
keys = ['id', 'status', 'next_task', 'navigation',
'workflow_spec_id',
"last_updated", "is_review", "title", "study_id", "state", "is_admin_workflow"]
"last_updated", "is_review", "title", "study_id", "state", "user_id", "is_admin_workflow"]
filtered_fields = {key: data[key] for key in keys}
filtered_fields['next_task'] = TaskSchema().make_task(data['next_task'])
return WorkflowApi(**filtered_fields)

11
crc/services/workflow_service.py
View File

@ -684,6 +684,12 @@ class WorkflowService(object):
WorkflowService.update_navigation(navigation, processor)
return navigation
@staticmethod
def get_workflow_user_id(workflow_id):
user_id = db.session.query(WorkflowModel.user_id).\
filter(WorkflowModel.id == workflow_id).scalar()
return user_id
@staticmethod
def processor_to_workflow_api(processor: WorkflowProcessor, next_task=None):
"""Returns an API model representing the state of the current workflow, if requested, and
@ -693,8 +699,10 @@ class WorkflowService(object):
spec_service = WorkflowSpecService()
spec = spec_service.get_spec(processor.workflow_spec_id)
is_admin_workflow = WorkflowService.is_admin_workflow(processor.workflow_spec_id)
workflow_id = processor.get_workflow_id()
user_id = WorkflowService.get_workflow_user_id(workflow_id)
workflow_api = WorkflowApi(
id=processor.get_workflow_id(),
id=workflow_id,
status=processor.get_status(),
next_task=None,
navigation=WorkflowService.get_navigation(processor),
@ -704,6 +712,7 @@ class WorkflowService(object):
title=spec.display_name,
study_id=processor.workflow_model.study_id or None,
state=processor.workflow_model.state,
user_id=user_id,
is_admin_workflow=is_admin_workflow
)
if not next_task: # The Next Task can be requested to be a certain task, useful for parallel tasks.

2
deploy/requirements.txt
View File

@ -38,7 +38,7 @@ jinja2==2.11.3
jsonschema==3.2.0
ldap3==2.8.1
lxml==4.9.1
mako==1.1.3
mako==1.2.2
markdown==3.3.3
markupsafe==1.1.1
marshmallow==3.9.1

2
tests/base_test.py
View File

@ -306,6 +306,7 @@ class BaseTest(unittest.TestCase):
content_type="application/json")
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
json_data['user_id'] = user.uid
workflow_api = WorkflowApiSchema().load(json_data)
return workflow_api
@ -361,6 +362,7 @@ class BaseTest(unittest.TestCase):
json_data = json.loads(rv.get_data(as_text=True))
# Assure task events are updated on the model
json_data['user_id'] = user_uid
workflow = WorkflowApiSchema().load(json_data)
# Assure a record exists in the Task Events

4
tests/test_multi_instance_tasks_api.py
View File

@ -41,6 +41,7 @@ class TestMultiinstanceTasksApi(BaseTest):
@patch('crc.services.protocol_builder.requests.get')
def test_parallel_multi_instance(self, mock_get):
user = self.create_user()
# Assure we get nine investigators back from the API Call, as set in the investigators.json file.
app.config['PB_ENABLED'] = True
@ -63,10 +64,11 @@ class TestMultiinstanceTasksApi(BaseTest):
for i in random.sample(range(5), 5):
task_id = ready_items[i].task_id
rv = self.app.put('/v1.0/workflow/%i/task/%s/set_token' % (workflow.id, task_id),
headers=self.logged_in_headers(),
headers=self.logged_in_headers(user),
content_type="application/json")
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
json_data['user_id'] = user.uid
workflow_api = WorkflowApiSchema().load(json_data)
data = workflow_api.next_task.data
data['investigator']['email'] = "dhf8r@virginia.edu"

4
tests/test_tasks_api.py
View File

@ -330,6 +330,7 @@ class TestTasksApi(BaseTest):
self.assertEqual(WorkflowStatus.complete, workflow_api.status)
def test_update_task_resets_token(self):
user = self.create_user()
workflow = self.create_workflow('exclusive_gateway')
# Start the workflow.
@ -350,10 +351,11 @@ class TestTasksApi(BaseTest):
# Make the old task the current task.
rv = self.app.put('/v1.0/workflow/%i/task/%s/set_token' % (workflow.id, first_task.id),
headers=self.logged_in_headers(),
headers=self.logged_in_headers(user),
content_type="application/json")
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
json_data['user_id'] = user.uid
workflow_api = WorkflowApiSchema().load(json_data)
# Assure the Next Task is the one we just reset the token to be on.