mirror of
https://github.com/sartography/cr-connect-workflow.git
synced 2025-02-23 13:18:35 +00:00
3442655bd1
1. Avoid ever re-generating the list of scripts that can be used in a script task. Terribly expensive as we call eval constantly, and it never ever changes once the app starts. (see script.py changes, and comments) 2. Cache the DocumentStatus list in the flask session, so we calculate it at most once per API Call. It's at least .25 seconds per call. (see study_sevice) 3. We called UserFileService.get_files_for_study (which runs a db query EVERY time) for every possible document type. Now we run the query once (study service line 321) 4. When returning a workflow, we looped through every single task in that workflow's navigation, and called the expensive spiff_task_to_api_task just to figure out it's proper display name. We run a much faster and more efficient method to calculate the display name naow (see workflow_service on lie 680, and 799) 5. A hellton of @timeit and sincetime() calls, that I want to leave in, to help debug any slowness on production.
260 lines
13 KiB
Python
260 lines
13 KiB
Python
import json
|
|
from datetime import datetime
|
|
from unittest.mock import patch
|
|
|
|
from tests.base_test import BaseTest
|
|
|
|
from crc import db, app
|
|
from crc.models.study import StudyModel, StudyStatus, StudyAssociatedSchema
|
|
from crc.models.user import UserModel
|
|
from crc.models.workflow import WorkflowModel, WorkflowStatus, WorkflowSpecCategory
|
|
from crc.services.ldap_service import LdapService
|
|
from crc.services.study_service import StudyService
|
|
from crc.services.workflow_processor import WorkflowProcessor
|
|
from crc.services.user_file_service import UserFileService
|
|
from crc.services.user_service import UserService
|
|
from crc.services.workflow_spec_service import WorkflowSpecService
|
|
|
|
|
|
class TestStudyService(BaseTest):
|
|
"""Largely tested via the test_study_api, and time is tight, but adding new tests here."""
|
|
|
|
def create_user_with_study_and_workflow(self):
|
|
self.load_test_spec("top_level_workflow", master_spec=True)
|
|
cat = WorkflowSpecCategory(id="approvals", display_name="Approvals", display_order=0, admin=False)
|
|
self.workflow_spec_service.add_category(cat)
|
|
self.load_test_spec("random_fact", category_id=cat.id)
|
|
user = self.create_user()
|
|
study = StudyModel(title="My title", status=StudyStatus.in_progress, user_uid=user.uid)
|
|
db.session.add(study)
|
|
db.session.commit()
|
|
self.assertIsNotNone(study.id)
|
|
workflow = WorkflowModel(workflow_spec_id="random_fact", study_id=study.id,
|
|
status=WorkflowStatus.not_started, last_updated=datetime.utcnow())
|
|
db.session.add(workflow)
|
|
db.session.commit()
|
|
return user
|
|
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
|
|
def test_total_tasks_updated(self, mock_docs, mock_details):
|
|
"""Assure that as a users progress is available when getting a list of studies for that user."""
|
|
app.config['PB_ENABLED'] = True
|
|
docs_response = self.protocol_builder_response('required_docs.json')
|
|
mock_docs.return_value = json.loads(docs_response)
|
|
details_response = self.protocol_builder_response('study_details.json')
|
|
mock_details.return_value = json.loads(details_response)
|
|
|
|
user = self.create_user_with_study_and_workflow()
|
|
|
|
# The load example data script should set us up a user and at least one study, one category, and one workflow.
|
|
spec_service = WorkflowSpecService()
|
|
categories = spec_service.get_categories()
|
|
studies = StudyService().get_studies_for_user(user, categories)
|
|
self.assertTrue(len(studies) == 1)
|
|
self.assertTrue(len(studies[0].categories) == 1)
|
|
self.assertEqual(1, len(studies[0].categories[0].workflows))
|
|
|
|
workflow = next(iter(studies[0].categories[0].workflows)) # Workflows is a set.
|
|
|
|
# workflow should not be started, and it should have 0 completed tasks, and 0 total tasks.
|
|
self.assertEqual(WorkflowStatus.not_started, workflow.status)
|
|
self.assertEqual(0, workflow.total_tasks)
|
|
self.assertEqual(0, workflow.completed_tasks)
|
|
|
|
# Initialize the Workflow with the workflow processor.
|
|
workflow_model = db.session.query(WorkflowModel).filter(WorkflowModel.id == workflow.id).first()
|
|
processor = WorkflowProcessor(workflow_model)
|
|
processor.do_engine_steps()
|
|
|
|
# Assure the workflow is now started, and knows the total and completed tasks.
|
|
spec_service = WorkflowSpecService()
|
|
categories = spec_service.get_categories()
|
|
studies = StudyService().get_studies_for_user(user, categories)
|
|
workflow = next(iter(studies[0].categories[0].workflows)) # Workflows is a set.
|
|
# self.assertEqual(WorkflowStatus.user_input_required, workflow.status)
|
|
self.assertTrue(workflow.total_tasks > 0)
|
|
self.assertEqual(0, workflow.completed_tasks)
|
|
|
|
# Complete a task
|
|
task = processor.next_task()
|
|
processor.complete_task(task)
|
|
processor.save()
|
|
|
|
# Assure the workflow has moved on to the next task.
|
|
studies = StudyService().get_studies_for_user(user, spec_service.get_categories())
|
|
workflow = next(iter(studies[0].categories[0].workflows)) # Workflows is a set.
|
|
self.assertEqual(1, workflow.completed_tasks)
|
|
|
|
# Get approvals
|
|
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
|
|
def test_get_required_docs(self, mock_docs, mock_details):
|
|
self.create_reference_document()
|
|
app.config['PB_ENABLED'] = True
|
|
# mock out the protocol builder
|
|
docs_response = self.protocol_builder_response('required_docs.json')
|
|
mock_docs.return_value = json.loads(docs_response)
|
|
details_response = self.protocol_builder_response('study_details.json')
|
|
mock_details.return_value = json.loads(details_response)
|
|
|
|
user = self.create_user_with_study_and_workflow()
|
|
spec_service = WorkflowSpecService()
|
|
categories = spec_service.get_categories()
|
|
studies = StudyService().get_studies_for_user(user, categories)
|
|
study = studies[0]
|
|
|
|
|
|
study_service = StudyService()
|
|
documents = study_service.get_documents_status(study_id=study.id, force=True) # Mocked out, any random study id works.
|
|
self.assertIsNotNone(documents)
|
|
self.assertTrue("UVACompl_PRCAppr" in documents.keys())
|
|
self.assertEqual("UVACompl_PRCAppr", documents["UVACompl_PRCAppr"]['code'])
|
|
self.assertEqual("UVA Compliance / PRC Approval", documents["UVACompl_PRCAppr"]['display_name'])
|
|
self.assertEqual("Cancer Center's PRC Approval Form", documents["UVACompl_PRCAppr"]['description'])
|
|
self.assertEqual("UVA Compliance", documents["UVACompl_PRCAppr"]['category1'])
|
|
self.assertEqual("PRC Approval", documents["UVACompl_PRCAppr"]['category2'])
|
|
self.assertEqual("", documents["UVACompl_PRCAppr"]['category3'])
|
|
self.assertEqual("Study Team", documents["UVACompl_PRCAppr"]['who_uploads?'])
|
|
self.assertEqual(0, documents["UVACompl_PRCAppr"]['count'])
|
|
self.assertEqual(True, documents["UVACompl_PRCAppr"]['required'])
|
|
self.assertEqual(6, documents["UVACompl_PRCAppr"]['id'])
|
|
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
|
|
def test_get_documents_has_file_details(self, mock_docs):
|
|
self.create_reference_document()
|
|
# mock out the protocol builder
|
|
docs_response = self.protocol_builder_response('required_docs.json')
|
|
mock_docs.return_value = json.loads(docs_response)
|
|
|
|
user = self.create_user_with_study_and_workflow()
|
|
|
|
# Add a document to the study with the correct code.
|
|
workflow = self.create_workflow('docx')
|
|
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
|
|
UserFileService.add_workflow_file(workflow_id=workflow.id,
|
|
task_spec_name='t1',
|
|
name="anything.png", content_type="text",
|
|
binary_data=b'1234', irb_doc_code=irb_code)
|
|
|
|
docs = StudyService().get_documents_status(workflow.study_id)
|
|
self.assertIsNotNone(docs)
|
|
self.assertEqual("not_started", docs["UVACompl_PRCAppr"]['status'])
|
|
self.assertEqual(1, docs["UVACompl_PRCAppr"]['count'])
|
|
self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0])
|
|
self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0]['id'])
|
|
self.assertEqual(workflow.id, docs["UVACompl_PRCAppr"]['files'][0]['workflow_id'])
|
|
|
|
def test_get_all_studies(self):
|
|
user = self.create_user_with_study_and_workflow()
|
|
study = db.session.query(StudyModel).filter_by(user_uid=user.uid).first()
|
|
self.assertIsNotNone(study)
|
|
|
|
# Add a document to the study with the correct code.
|
|
workflow1 = self.create_workflow('docx', study=study)
|
|
workflow2 = self.create_workflow('empty_workflow', study=study)
|
|
|
|
# Add files to both workflows.
|
|
UserFileService.add_workflow_file(workflow_id=workflow1.id,
|
|
task_spec_name="t1",
|
|
name="anything.png", content_type="text",
|
|
binary_data=b'1234', irb_doc_code="UVACompl_PRCAppr" )
|
|
UserFileService.add_workflow_file(workflow_id=workflow1.id,
|
|
task_spec_name="t1",
|
|
name="anything.png", content_type="text",
|
|
binary_data=b'1234', irb_doc_code="AD_Consent_Model")
|
|
UserFileService.add_workflow_file(workflow_id=workflow2.id,
|
|
task_spec_name="t1",
|
|
name="anything.png", content_type="text",
|
|
binary_data=b'1234', irb_doc_code="UVACompl_PRCAppr" )
|
|
|
|
studies = StudyService().get_all_studies_with_files()
|
|
self.assertEqual(1, len(studies))
|
|
self.assertEqual(3, len(studies[0].files))
|
|
|
|
|
|
|
|
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_docs
|
|
def test_get_personnel_roles(self, mock_docs):
|
|
self.create_reference_document()
|
|
|
|
# mock out the protocol builder
|
|
docs_response = self.protocol_builder_response('investigators.json')
|
|
mock_docs.return_value = json.loads(docs_response)
|
|
|
|
workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
|
|
investigators = StudyService().get_investigators(workflow.study_id, all=True)
|
|
|
|
self.assertEqual(10, len(investigators))
|
|
|
|
# dhf8r is in the ldap mock data.
|
|
self.assertEqual("dhf8r", investigators['PI']['user_id'])
|
|
self.assertEqual("Dan Funk", investigators['PI']['display_name']) # Data from ldap
|
|
self.assertEqual("Primary Investigator", investigators['PI']['label']) # Data from xls file.
|
|
self.assertEqual("Always", investigators['PI']['display']) # Data from xls file.
|
|
|
|
# asd3v is not in ldap, so an error should be returned.
|
|
self.assertEqual("asd3v", investigators['DC']['user_id'])
|
|
self.assertEqual("ApiError: Unable to locate a user with id asd3v in LDAP. ", investigators['DC']['error']) # Data from ldap
|
|
|
|
# No value is provided for Department Chair
|
|
self.assertIsNone(investigators['DEPT_CH']['user_id'])
|
|
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_docs
|
|
def test_get_study_personnel(self, mock_docs):
|
|
self.create_reference_document()
|
|
|
|
# mock out the protocol builder
|
|
docs_response = self.protocol_builder_response('investigators.json')
|
|
mock_docs.return_value = json.loads(docs_response)
|
|
|
|
workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
|
|
investigators = StudyService().get_investigators(workflow.study_id, all=False)
|
|
|
|
self.assertEqual(5, len(investigators))
|
|
|
|
# dhf8r is in the ldap mock data.
|
|
self.assertEqual("dhf8r", investigators['PI']['user_id'])
|
|
self.assertEqual("Dan Funk", investigators['PI']['display_name']) # Data from ldap
|
|
self.assertEqual("Primary Investigator", investigators['PI']['label']) # Data from xls file.
|
|
self.assertEqual("Always", investigators['PI']['display']) # Data from xls file.
|
|
|
|
# Both Alex and Aaron are SI, and both should be returned.
|
|
self.assertEqual("ajl2j", investigators['SI']['user_id'])
|
|
self.assertEqual("cah3us", investigators['SI_2']['user_id'])
|
|
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
|
|
def test_get_user_studies(self, mock_details):
|
|
details_response = self.protocol_builder_response('study_details.json')
|
|
mock_details.return_value = json.loads(details_response)
|
|
|
|
user = self.create_user_with_study_and_workflow()
|
|
spec_service = WorkflowSpecService()
|
|
categories = spec_service.get_categories()
|
|
studies = StudyService().get_studies_for_user(user, categories)
|
|
# study_details has a valid REVIEW_TYPE, so we should get 1 study back
|
|
self.assertEqual(1, len(studies))
|
|
|
|
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
|
|
def test_get_user_studies_bad_review_type(self, mock_details):
|
|
details_response = self.protocol_builder_response('study_details_bad_review_type.json')
|
|
mock_details.return_value = json.loads(details_response)
|
|
|
|
spec_service = WorkflowSpecService()
|
|
categories = spec_service.get_categories()
|
|
user = self.create_user_with_study_and_workflow()
|
|
studies = StudyService().get_studies_for_user(user, categories)
|
|
# study_details has an invalid REVIEW_TYPE, so we should get 0 studies back
|
|
self.assertEqual(0, len(studies))
|
|
|
|
def test_study_associates(self):
|
|
user = self.create_user_with_study_and_workflow()
|
|
study = db.session.query(StudyModel).first()
|
|
associates = StudyService.get_study_associates(study.id)
|
|
self.assertEquals(1, len(associates))
|
|
assoc_json = StudyAssociatedSchema(many=True).dump(associates)
|
|
print(assoc_json)
|
|
self.assertEquals("Dan", assoc_json[0]['ldap_info']['given_name'])
|