268 lines
13 KiB
Python
268 lines
13 KiB
Python
import json
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from datetime import datetime
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from unittest.mock import patch
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from tests.base_test import BaseTest
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from crc import db, app
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from crc.models.study import StudyModel, StudyStatus, StudyAssociatedSchema
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from crc.models.user import UserModel
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from crc.models.workflow import WorkflowModel, WorkflowStatus, \
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WorkflowSpecCategoryModel
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from crc.services.file_service import FileService
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from crc.services.ldap_service import LdapService
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from crc.services.study_service import StudyService
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from crc.services.workflow_processor import WorkflowProcessor
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class TestStudyService(BaseTest):
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"""Largely tested via the test_study_api, and time is tight, but adding new tests here."""
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def create_user_with_study_and_workflow(self):
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# clear it all out.
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from example_data import ExampleDataLoader
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ExampleDataLoader.clean_db()
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# Assure some basic models are in place, This is a damn mess. Our database models need an overhaul to make
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# this easier - better relationship modeling is now critical.
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cat = WorkflowSpecCategoryModel(name="approvals", display_name="Approvals", display_order=0)
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db.session.add(cat)
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db.session.commit()
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self.load_test_spec("top_level_workflow", master_spec=True, category_id=cat.id)
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user = db.session.query(UserModel).filter(UserModel.uid == "dhf8r").first()
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if not user:
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ldap = LdapService.user_info('dhf8r')
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user = UserModel(uid="dhf8r", ldap_info=ldap)
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db.session.add(user)
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db.session.commit()
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else:
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for study in db.session.query(StudyModel).all():
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StudyService().delete_study(study.id)
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study = StudyModel(title="My title", status=StudyStatus.in_progress, user_uid=user.uid)
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db.session.add(study)
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self.load_test_spec("random_fact", category_id=cat.id)
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self.assertIsNotNone(study.id)
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workflow = WorkflowModel(workflow_spec_id="random_fact", study_id=study.id,
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status=WorkflowStatus.not_started, last_updated=datetime.utcnow())
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db.session.add(workflow)
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db.session.commit()
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# Assure there is a master specification, one standard spec, and lookup tables.
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ExampleDataLoader().load_reference_documents()
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return user
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
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def test_total_tasks_updated(self, mock_docs, mock_details):
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"""Assure that as a users progress is available when getting a list of studies for that user."""
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app.config['PB_ENABLED'] = True
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docs_response = self.protocol_builder_response('required_docs.json')
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mock_docs.return_value = json.loads(docs_response)
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details_response = self.protocol_builder_response('study_details.json')
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mock_details.return_value = json.loads(details_response)
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user = self.create_user_with_study_and_workflow()
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# The load example data script should set us up a user and at least one study, one category, and one workflow.
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studies = StudyService().get_studies_for_user(user)
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self.assertTrue(len(studies) == 1)
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self.assertTrue(len(studies[0].categories) == 1)
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self.assertTrue(len(studies[0].categories[0].workflows) == 1)
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workflow = next(iter(studies[0].categories[0].workflows)) # Workflows is a set.
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# workflow should not be started, and it should have 0 completed tasks, and 0 total tasks.
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self.assertEqual(WorkflowStatus.not_started, workflow.status)
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self.assertEqual(0, workflow.total_tasks)
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self.assertEqual(0, workflow.completed_tasks)
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# Initialize the Workflow with the workflow processor.
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workflow_model = db.session.query(WorkflowModel).filter(WorkflowModel.id == workflow.id).first()
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processor = WorkflowProcessor(workflow_model)
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processor.do_engine_steps()
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# Assure the workflow is now started, and knows the total and completed tasks.
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studies = StudyService().get_studies_for_user(user)
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workflow = next(iter(studies[0].categories[0].workflows)) # Workflows is a set.
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# self.assertEqual(WorkflowStatus.user_input_required, workflow.status)
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self.assertTrue(workflow.total_tasks > 0)
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self.assertEqual(0, workflow.completed_tasks)
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self.assertIsNotNone(workflow.spec_version)
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# Complete a task
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task = processor.next_task()
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processor.complete_task(task)
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processor.save()
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# Assure the workflow has moved on to the next task.
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studies = StudyService().get_studies_for_user(user)
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workflow = next(iter(studies[0].categories[0].workflows)) # Workflows is a set.
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self.assertEqual(1, workflow.completed_tasks)
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# Get approvals
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
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def test_get_required_docs(self, mock_docs, mock_details):
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app.config['PB_ENABLED'] = True
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# mock out the protocol builder
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docs_response = self.protocol_builder_response('required_docs.json')
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mock_docs.return_value = json.loads(docs_response)
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details_response = self.protocol_builder_response('study_details.json')
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mock_details.return_value = json.loads(details_response)
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user = self.create_user_with_study_and_workflow()
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studies = StudyService().get_studies_for_user(user)
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study = studies[0]
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study_service = StudyService()
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documents = study_service.get_documents_status(study_id=study.id) # Mocked out, any random study id works.
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self.assertIsNotNone(documents)
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self.assertTrue("UVACompl_PRCAppr" in documents.keys())
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self.assertEqual("UVACompl_PRCAppr", documents["UVACompl_PRCAppr"]['code'])
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self.assertEqual("UVA Compliance / PRC Approval", documents["UVACompl_PRCAppr"]['display_name'])
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self.assertEqual("Cancer Center's PRC Approval Form", documents["UVACompl_PRCAppr"]['description'])
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self.assertEqual("UVA Compliance", documents["UVACompl_PRCAppr"]['category1'])
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self.assertEqual("PRC Approval", documents["UVACompl_PRCAppr"]['category2'])
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self.assertEqual("", documents["UVACompl_PRCAppr"]['category3'])
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self.assertEqual("Study Team", documents["UVACompl_PRCAppr"]['who_uploads?'])
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self.assertEqual(0, documents["UVACompl_PRCAppr"]['count'])
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self.assertEqual(True, documents["UVACompl_PRCAppr"]['required'])
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self.assertEqual(6, documents["UVACompl_PRCAppr"]['id'])
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
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def test_get_documents_has_file_details(self, mock_docs):
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# mock out the protocol builder
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docs_response = self.protocol_builder_response('required_docs.json')
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mock_docs.return_value = json.loads(docs_response)
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user = self.create_user_with_study_and_workflow()
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# Add a document to the study with the correct code.
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workflow = self.create_workflow('docx')
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irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
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FileService.add_workflow_file(workflow_id=workflow.id,
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task_spec_name='t1',
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name="anything.png", content_type="text",
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binary_data=b'1234', irb_doc_code=irb_code)
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docs = StudyService().get_documents_status(workflow.study_id)
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self.assertIsNotNone(docs)
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self.assertEqual("not_started", docs["UVACompl_PRCAppr"]['status'])
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self.assertEqual(1, docs["UVACompl_PRCAppr"]['count'])
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self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0])
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self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0]['id'])
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self.assertEqual(workflow.id, docs["UVACompl_PRCAppr"]['files'][0]['workflow_id'])
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def test_get_all_studies(self):
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user = self.create_user_with_study_and_workflow()
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study = db.session.query(StudyModel).filter_by(user_uid=user.uid).first()
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self.assertIsNotNone(study)
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# Add a document to the study with the correct code.
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workflow1 = self.create_workflow('docx', study=study)
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workflow2 = self.create_workflow('empty_workflow', study=study)
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# Add files to both workflows.
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FileService.add_workflow_file(workflow_id=workflow1.id,
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task_spec_name="t1",
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name="anything.png", content_type="text",
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binary_data=b'1234', irb_doc_code="UVACompl_PRCAppr" )
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FileService.add_workflow_file(workflow_id=workflow1.id,
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task_spec_name="t1",
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name="anything.png", content_type="text",
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binary_data=b'1234', irb_doc_code="AD_Consent_Model")
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FileService.add_workflow_file(workflow_id=workflow2.id,
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task_spec_name="t1",
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name="anything.png", content_type="text",
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binary_data=b'1234', irb_doc_code="UVACompl_PRCAppr" )
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studies = StudyService().get_all_studies_with_files()
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self.assertEqual(1, len(studies))
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self.assertEqual(3, len(studies[0].files))
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_docs
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def test_get_personnel_roles(self, mock_docs):
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self.load_example_data()
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# mock out the protocol builder
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docs_response = self.protocol_builder_response('investigators.json')
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mock_docs.return_value = json.loads(docs_response)
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workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
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investigators = StudyService().get_investigators(workflow.study_id, all=True)
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self.assertEqual(10, len(investigators))
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# dhf8r is in the ldap mock data.
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self.assertEqual("dhf8r", investigators['PI']['user_id'])
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self.assertEqual("Dan Funk", investigators['PI']['display_name']) # Data from ldap
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self.assertEqual("Primary Investigator", investigators['PI']['label']) # Data from xls file.
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self.assertEqual("Always", investigators['PI']['display']) # Data from xls file.
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# asd3v is not in ldap, so an error should be returned.
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self.assertEqual("asd3v", investigators['DC']['user_id'])
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self.assertEqual("Unable to locate a user with id asd3v in LDAP", investigators['DC']['error']) # Data from ldap
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# No value is provided for Department Chair
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self.assertIsNone(investigators['DEPT_CH']['user_id'])
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_docs
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def test_get_study_personnel(self, mock_docs):
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self.load_example_data()
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# mock out the protocol builder
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docs_response = self.protocol_builder_response('investigators.json')
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mock_docs.return_value = json.loads(docs_response)
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workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
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investigators = StudyService().get_investigators(workflow.study_id, all=False)
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self.assertEqual(5, len(investigators))
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# dhf8r is in the ldap mock data.
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self.assertEqual("dhf8r", investigators['PI']['user_id'])
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self.assertEqual("Dan Funk", investigators['PI']['display_name']) # Data from ldap
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self.assertEqual("Primary Investigator", investigators['PI']['label']) # Data from xls file.
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self.assertEqual("Always", investigators['PI']['display']) # Data from xls file.
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# Both Alex and Aaron are SI, and both should be returned.
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self.assertEqual("ajl2j", investigators['SI']['user_id'])
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self.assertEqual("cah3us", investigators['SI_2']['user_id'])
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
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def test_get_user_studies(self, mock_details):
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details_response = self.protocol_builder_response('study_details.json')
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mock_details.return_value = json.loads(details_response)
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user = self.create_user_with_study_and_workflow()
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studies = StudyService().get_studies_for_user(user)
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# study_details has a valid REVIEW_TYPE, so we should get 1 study back
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self.assertEqual(1, len(studies))
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
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def test_get_user_studies_bad_review_type(self, mock_details):
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details_response = self.protocol_builder_response('study_details_bad_review_type.json')
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mock_details.return_value = json.loads(details_response)
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user = self.create_user_with_study_and_workflow()
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studies = StudyService().get_studies_for_user(user)
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# study_details has an invalid REVIEW_TYPE, so we should get 0 studies back
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self.assertEqual(0, len(studies))
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def test_study_associates(self):
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user = self.create_user_with_study_and_workflow()
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study = db.session.query(StudyModel).first()
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associates = StudyService.get_study_associates(study.id)
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self.assertEquals(1, len(associates))
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assoc_json = StudyAssociatedSchema(many=True).dump(associates)
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print(assoc_json)
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self.assertEquals("Dan", assoc_json[0]['ldap_info']['given_name']) |