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https://github.com/sartography/cr-connect-workflow.git
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4ec6e403f5
2. Reference Files and Spec Files are written to disk, they do not exist in the database at all.
268 lines
14 KiB
Python
268 lines
14 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 crc.services.user_file_service import UserFileService
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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.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(id=None, 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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# 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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UserFileService.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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UserFileService.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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UserFileService.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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UserFileService.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("ApiError: 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'])
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