cr-connect-workflow/tests/study/test_study_service.py

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.protocol_builder import ProtocolBuilderStatus
from crc.models.study import StudyModel, StudyStatus
from crc.models.user import UserModel
from crc.models.workflow import WorkflowModel, WorkflowStatus, \
    WorkflowSpecCategoryModel
from crc.services.file_service import FileService
from crc.services.study_service import StudyService
from crc.services.workflow_processor import WorkflowProcessor
from example_data import ExampleDataLoader


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):

        # clear it all out.
        from example_data import ExampleDataLoader
        ExampleDataLoader.clean_db()

        # Assure some basic models are in place, This is a damn mess.  Our database models need an overhaul to make
        # this easier - better relationship modeling is now critical.
        cat = WorkflowSpecCategoryModel(name="approvals", display_name="Approvals", display_order=0)
        db.session.add(cat)
        db.session.commit()
        self.load_test_spec("top_level_workflow", master_spec=True, category_id=cat.id)
        user = db.session.query(UserModel).filter(UserModel.uid == "dhf8r").first()
        if not user:
            user = UserModel(uid="dhf8r", email_address="whatever@stuff.com", display_name="Stayathome Smellalots")
            db.session.add(user)
            db.session.commit()
        else:
            for study in db.session.query(StudyModel).all():
                StudyService().delete_study(study.id)

        study = StudyModel(title="My title", status=StudyStatus.in_progress, user_uid=user.uid)
        db.session.add(study)

        self.load_test_spec("random_fact", category_id=cat.id)

        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()
        # Assure there is a master specification, one standard spec, and lookup tables.
        ExampleDataLoader().load_reference_documents()
        return user

    @patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs')  # mock_docs
    def test_total_tasks_updated(self, mock_docs):
        """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)

        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.
        studies = StudyService.get_studies_for_user(user)
        self.assertTrue(len(studies) == 1)
        self.assertTrue(len(studies[0].categories) == 1)
        self.assertTrue(len(studies[0].categories[0].workflows) == 1)

        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.
        studies = StudyService.get_studies_for_user(user)
        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)
        self.assertIsNotNone(workflow.spec_version)

        # 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)
        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_required_docs')  # mock_docs
    def test_get_required_docs(self, mock_docs):
        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)

        user = self.create_user_with_study_and_workflow()
        studies = StudyService.get_studies_for_user(user)
        study = studies[0]


        study_service = StudyService()
        documents = study_service.get_documents_status(study_id=study.id)  # 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("CRC", 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):

        # 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.
        FileService.add_workflow_file(workflow_id=workflow.id,
                                      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]['file_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.
        FileService.add_workflow_file(workflow_id=workflow1.id,
                                      name="anything.png", content_type="text",
                                      binary_data=b'1234', irb_doc_code="UVACompl_PRCAppr" )
        FileService.add_workflow_file(workflow_id=workflow1.id,
                                      name="anything.png", content_type="text",
                                      binary_data=b'1234', irb_doc_code="AD_Consent_Model")
        FileService.add_workflow_file(workflow_id=workflow2.id,
                                      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.load_example_data()

        # 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("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.load_example_data()

        # 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'])