mirror of
https://github.com/sartography/cr-connect-workflow.git
synced 2025-02-23 05:08:32 +00:00
4a916c1ee3
Created a Study object (seperate from the StudyModel) that can cronstructed on request, and contains a different data structure than we store in the DB. This allows us to return underlying Categories and Workflows in a clean way. Added a new status to workflows called "not_started", meaning we have not yet instantiated a processor or created a BPMN, they have no version yet and no stored data, just the possiblity of being started. The Top Level Workflow or "Master" workflow is now a part of the sample data, and loaded at all times. Removed the ability to "add a workflow to a study" and "remove a workflow from a study", a study contains all possible workflows by definition. Example data no longer creates users or studies, it just creates the specs.
248 lines
12 KiB
Python
248 lines
12 KiB
Python
import json
|
|
from datetime import datetime, timezone
|
|
from unittest.mock import patch
|
|
|
|
from crc import session
|
|
from crc.models.api_models import WorkflowApiSchema
|
|
from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudyDetailsSchema, \
|
|
ProtocolBuilderStudySchema
|
|
from crc.models.study import StudyModel, StudySchema
|
|
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
|
|
WorkflowSpecCategoryModel
|
|
from tests.base_test import BaseTest
|
|
|
|
|
|
class TestStudyApi(BaseTest):
|
|
|
|
TEST_STUDY = {
|
|
"id": 12345,
|
|
"title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents "
|
|
"for Interstellar Spacecraft",
|
|
"last_updated": datetime.now(tz=timezone.utc),
|
|
"protocol_builder_status": ProtocolBuilderStatus.IN_PROCESS,
|
|
"primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
|
|
"sponsor": "Sirius Cybernetics Corporation",
|
|
"ind_number": "567890",
|
|
"user_uid": "dhf8r",
|
|
}
|
|
|
|
def add_test_study(self):
|
|
rv = self.app.post('/v1.0/study',
|
|
content_type="application/json",
|
|
headers=self.logged_in_headers(),
|
|
data=json.dumps(StudySchema().dump(self.TEST_STUDY)))
|
|
self.assert_success(rv)
|
|
return json.loads(rv.get_data(as_text=True))
|
|
|
|
def test_study_basics(self):
|
|
self.load_example_data()
|
|
study = session.query(StudyModel).first()
|
|
self.assertIsNotNone(study)
|
|
|
|
def test_get_study(self):
|
|
"""Generic test, but pretty detailed, in that the study should return a categorized list of workflows
|
|
This starts with out loading the example data, to show that all the bases are covered from ground 0."""
|
|
new_study = self.add_test_study()
|
|
new_study = session.query(StudyModel).filter_by(id=new_study["id"]).first()
|
|
# Add a category
|
|
new_category = WorkflowSpecCategoryModel(id=21, name="test_cat", display_name="Test Category", display_order=0)
|
|
session.add(new_category)
|
|
session.commit()
|
|
# Create a workflow specification
|
|
self.create_workflow("random_fact", study=new_study, category_id=new_category.id)
|
|
# Assure there is a master specification, and it has the lookup files it needs.
|
|
spec = self.load_test_spec("top_level_workflow", master_spec=True)
|
|
self.create_reference_document()
|
|
|
|
api_response = self.app.get('/v1.0/study/%i' % new_study.id,
|
|
headers=self.logged_in_headers(), content_type="application/json")
|
|
self.assert_success(api_response)
|
|
study = StudySchema().loads(api_response.get_data(as_text=True))
|
|
|
|
self.assertEqual(study.title, self.TEST_STUDY['title'])
|
|
self.assertEqual(study.primary_investigator_id, self.TEST_STUDY['primary_investigator_id'])
|
|
self.assertEqual(study.sponsor, self.TEST_STUDY['sponsor'])
|
|
self.assertEqual(study.ind_number, self.TEST_STUDY['ind_number'])
|
|
self.assertEqual(study.user_uid, self.TEST_STUDY['user_uid'])
|
|
|
|
# Categories are read only, so switching to sub-scripting here.
|
|
category = [c for c in study.categories if c['name'] == "test_cat"][0]
|
|
self.assertEqual("test_cat", category['name'])
|
|
self.assertEqual("Test Category", category['display_name'])
|
|
self.assertEqual(1, len(category["workflows"]))
|
|
workflow = category["workflows"][0]
|
|
self.assertEqual("random_fact", workflow["name"])
|
|
self.assertEqual("optional", workflow["state"])
|
|
self.assertEqual("not_started", workflow["status"])
|
|
self.assertEqual(0, workflow["total_tasks"])
|
|
self.assertEqual(0, workflow["completed_tasks"])
|
|
|
|
def test_add_study(self):
|
|
self.load_example_data()
|
|
study = self.add_test_study()
|
|
db_study = session.query(StudyModel).filter_by(id=12345).first()
|
|
self.assertIsNotNone(db_study)
|
|
self.assertEqual(study["title"], db_study.title)
|
|
self.assertEqual(study["primary_investigator_id"], db_study.primary_investigator_id)
|
|
self.assertEqual(study["sponsor"], db_study.sponsor)
|
|
self.assertEqual(study["ind_number"], db_study.ind_number)
|
|
self.assertEqual(study["user_uid"], db_study.user_uid)
|
|
|
|
workflow_spec_count =session.query(WorkflowSpecModel).filter(WorkflowSpecModel.is_master_spec == False).count()
|
|
workflow_count = session.query(WorkflowModel).filter(WorkflowModel.study_id == 12345).count()
|
|
error_count = len(study["errors"])
|
|
self.assertEquals(workflow_spec_count, workflow_count + error_count)
|
|
|
|
def test_update_study(self):
|
|
self.load_example_data()
|
|
study: StudyModel = session.query(StudyModel).first()
|
|
study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility"
|
|
study.protocol_builder_status = ProtocolBuilderStatus.REVIEW_COMPLETE
|
|
rv = self.app.put('/v1.0/study/%i' % study.id,
|
|
content_type="application/json",
|
|
headers=self.logged_in_headers(),
|
|
data=json.dumps(StudySchema().dump(study)))
|
|
self.assert_success(rv)
|
|
json_data = json.loads(rv.get_data(as_text=True))
|
|
self.assertEqual(study.title, json_data['title'])
|
|
self.assertEqual(study.protocol_builder_status.name, json_data['protocol_builder_status'])
|
|
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies') # mock_studies
|
|
def test_get_all_studies(self, mock_studies, mock_details):
|
|
self.load_example_data()
|
|
s = StudyModel(
|
|
id=54321, # This matches one of the ids from the study_details_json data.
|
|
title='The impact of pandemics on dog owner sanity after 12 days',
|
|
user_uid='dhf8r',
|
|
)
|
|
session.add(s)
|
|
session.commit()
|
|
|
|
num_db_studies_before = session.query(StudyModel).count()
|
|
|
|
# Mock Protocol Builder responses
|
|
studies_response = self.protocol_builder_response('user_studies.json')
|
|
mock_studies.return_value = ProtocolBuilderStudySchema(many=True).loads(studies_response)
|
|
details_response = self.protocol_builder_response('study_details.json')
|
|
mock_details.return_value = ProtocolBuilderStudyDetailsSchema().loads(details_response)
|
|
|
|
# Make the api call to get all studies
|
|
api_response = self.app.get('/v1.0/study', headers=self.logged_in_headers(), content_type="application/json")
|
|
self.assert_success(api_response)
|
|
json_data = json.loads(api_response.get_data(as_text=True))
|
|
|
|
num_inactive = 0
|
|
num_active = 0
|
|
|
|
for study in json_data:
|
|
if study['inactive']:
|
|
num_inactive += 1
|
|
else:
|
|
num_active += 1
|
|
|
|
db_studies_after = session.query(StudyModel).all()
|
|
num_db_studies_after = len(db_studies_after)
|
|
self.assertGreater(num_db_studies_after, num_db_studies_before)
|
|
self.assertGreater(num_inactive, 0)
|
|
self.assertGreater(num_active, 0)
|
|
self.assertEqual(len(json_data), num_db_studies_after)
|
|
self.assertEqual(num_active + num_inactive, num_db_studies_after)
|
|
|
|
# Assure that the existing study is properly updated.
|
|
test_study = session.query(StudyModel).filter_by(id=54321).first()
|
|
self.assertFalse(test_study.inactive)
|
|
|
|
def test_get_single_study(self):
|
|
self.load_example_data()
|
|
study = session.query(StudyModel).first()
|
|
rv = self.app.get('/v1.0/study/%i' % study.id,
|
|
follow_redirects=True,
|
|
headers=self.logged_in_headers(),
|
|
content_type="application/json")
|
|
self.assert_success(rv)
|
|
json_data = json.loads(rv.get_data(as_text=True))
|
|
self.assertEqual(study.id, json_data['id'])
|
|
self.assertEqual(study.title, json_data['title'])
|
|
self.assertEqual(study.protocol_builder_status.name, json_data['protocol_builder_status'])
|
|
self.assertEqual(study.primary_investigator_id, json_data['primary_investigator_id'])
|
|
self.assertEqual(study.sponsor, json_data['sponsor'])
|
|
self.assertEqual(study.ind_number, json_data['ind_number'])
|
|
|
|
def test_delete_study(self):
|
|
self.load_example_data()
|
|
study = session.query(StudyModel).first()
|
|
rv = self.app.delete('/v1.0/study/%i' % study.id, headers=self.logged_in_headers())
|
|
self.assert_success(rv)
|
|
|
|
# """
|
|
# Workflow Specs that have been made available (or not) to a particular study via the status.bpmn should be flagged
|
|
# as available (or not) when the list of a study's workflows is retrieved.
|
|
# """
|
|
# @patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies')
|
|
# @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators')
|
|
# @patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs')
|
|
# @patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details')
|
|
# def test_workflow_spec_status(self,
|
|
# mock_details,
|
|
# mock_required_docs,
|
|
# mock_investigators,
|
|
# mock_studies):
|
|
#
|
|
# # Mock Protocol Builder response
|
|
# studies_response = self.protocol_builder_response('user_studies.json')
|
|
# mock_studies.return_value = ProtocolBuilderStudySchema(many=True).loads(studies_response)
|
|
#
|
|
# investigators_response = self.protocol_builder_response('investigators.json')
|
|
# mock_investigators.return_value = ProtocolBuilderInvestigatorSchema(many=True).loads(investigators_response)
|
|
#
|
|
# required_docs_response = self.protocol_builder_response('required_docs.json')
|
|
# mock_required_docs.return_value = ProtocolBuilderRequiredDocumentSchema(many=True).loads(required_docs_response)
|
|
#
|
|
# details_response = self.protocol_builder_response('study_details.json')
|
|
# mock_details.return_value = ProtocolBuilderStudyDetailsSchema().loads(details_response)
|
|
#
|
|
# self.load_example_data()
|
|
# study = session.query(StudyModel).first()
|
|
# study_id = study.id
|
|
#
|
|
# # Add status workflow
|
|
# self.load_test_spec('top_level_workflow')
|
|
#
|
|
# # Assure the top_level_workflow is added to the study
|
|
# top_level_spec = session.query(WorkflowSpecModel).filter_by(is_master_spec=True).first()
|
|
# self.assertIsNotNone(top_level_spec)
|
|
#
|
|
#
|
|
#
|
|
# for is_active in [False, True]:
|
|
# # Set all workflow specs to inactive|active
|
|
# update_status_response = self.app.put('/v1.0/workflow/%i/task/%s/data' % (status_workflow.id, status_task_id),
|
|
# headers=self.logged_in_headers(),
|
|
# content_type="application/json",
|
|
# data=json.dumps({'some_input': is_active}))
|
|
# self.assert_success(update_status_response)
|
|
# json_workflow_api = json.loads(update_status_response.get_data(as_text=True))
|
|
# updated_workflow_api: WorkflowApi = WorkflowApiSchema().load(json_workflow_api)
|
|
# self.assertIsNotNone(updated_workflow_api)
|
|
# self.assertEqual(updated_workflow_api.status, WorkflowStatus.complete)
|
|
# self.assertIsNotNone(updated_workflow_api.last_task)
|
|
# self.assertIsNotNone(updated_workflow_api.last_task['data'])
|
|
# self.assertIsNotNone(updated_workflow_api.last_task['data']['some_input'])
|
|
# self.assertEqual(updated_workflow_api.last_task['data']['some_input'], is_active)
|
|
#
|
|
# # List workflows for study
|
|
# response_after = self.app.get('/v1.0/study/%i/workflows' % study.id,
|
|
# content_type="application/json",
|
|
# headers=self.logged_in_headers())
|
|
# self.assert_success(response_after)
|
|
#
|
|
# json_data_after = json.loads(response_after.get_data(as_text=True))
|
|
# workflows_after = WorkflowApiSchema(many=True).load(json_data_after)
|
|
# self.assertEqual(len(specs), len(workflows_after))
|
|
#
|
|
# # All workflows should be inactive|active
|
|
# for workflow in workflows_after:
|
|
# self.assertEqual(workflow.is_active, is_active)
|
|
|