cr-connect-workflow/tests/test_api.py

import json
from datetime import datetime, tzinfo, timezone

from crc import session
from crc.models.file import FileModel
from crc.models.study import StudyModel, StudyModelSchema, ProtocolBuilderStatus
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
    WorkflowApiSchema
from tests.base_test import BaseTest


class TestStudy(BaseTest):

    def test_study_basics(self):
        self.load_example_data()
        study = session.query(StudyModel).first()
        self.assertIsNotNone(study)

    def test_add_study(self):
        self.load_example_data()
        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",
        }
        rv = self.app.post('/v1.0/study',
                           content_type="application/json",
                           data=json.dumps(StudyModelSchema().dump(study)))
        self.assert_success(rv)
        db_study = session.query(StudyModel).filter_by(id=12345).first()
        self.assertIsNotNone(db_study)
        self.assertEqual(study["title"], db_study.title)
        self.assertAlmostEqual(study["last_updated"], db_study.last_updated)
        self.assertEqual(study["protocol_builder_status"], db_study.protocol_builder_status)
        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)

    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.complete
        rv = self.app.put('/v1.0/study/%i' % study.id,
                           content_type="application/json",
                           data=json.dumps(StudyModelSchema().dump(study)))
        self.assert_success(rv)
        db_study = session.query(StudyModel).filter_by(id=study.id).first()
        self.assertIsNotNone(db_study)
        self.assertEqual(study.title, db_study.title)
        self.assertEqual(study.protocol_builder_status, db_study.protocol_builder_status)

    def test_study_api_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,
                          content_type="application/json")
        self.assert_success(rv)
        json_data = json.loads(rv.get_data(as_text=True))
        study2 = StudyModelSchema().load(json_data, session=session)
        self.assertEqual(study, study2)
        self.assertEqual(study.id, study2.id)
        self.assertEqual(study.title, study2.title)
        self.assertEqual(study.last_updated, study2.last_updated)
        self.assertEqual(study.protocol_builder_status, study2.protocol_builder_status)
        self.assertEqual(study.primary_investigator_id, study2.primary_investigator_id)
        self.assertEqual(study.sponsor, study2.sponsor)
        self.assertEqual(study.ind_number, study2.ind_number)

    def test_list_workflow_specifications(self):
        self.load_example_data()
        spec = session.query(WorkflowSpecModel).first()
        rv = self.app.get('/v1.0/workflow-specification',
                          follow_redirects=True,
                          content_type="application/json")
        self.assert_success(rv)
        json_data = json.loads(rv.get_data(as_text=True))
        specs = WorkflowSpecModelSchema(many=True).load(json_data, session=session)
        spec2 = specs[0]
        self.assertEqual(spec.id, spec2.id)
        self.assertEqual(spec.display_name, spec2.display_name)
        self.assertEqual(spec.description, spec2.description)

    def test_add_new_workflow_specification(self):
        self.load_example_data();
        num_before = session.query(WorkflowSpecModel).count()
        spec = WorkflowSpecModel(id='make_cookies', display_name='Cooooookies',
                                 description='Om nom nom delicious cookies')
        rv = self.app.post('/v1.0/workflow-specification', content_type="application/json",
                           data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
        self.assert_success(rv)
        db_spec = session.query(WorkflowSpecModel).filter_by(id='make_cookies').first()
        self.assertEqual(spec.display_name, db_spec.display_name)
        num_after = session.query(WorkflowSpecModel).count()
        self.assertEqual(num_after, num_before + 1)

    def test_get_workflow_specification(self):
        self.load_example_data()
        db_spec = session.query(WorkflowSpecModel).first()
        rv = self.app.get('/v1.0/workflow-specification/%s' % db_spec.id)
        self.assert_success(rv)
        json_data = json.loads(rv.get_data(as_text=True))
        api_spec = WorkflowSpecModelSchema().load(json_data, session=session)
        self.assertEqual(db_spec, api_spec)


    # def test_modify_workflow_specification(self):
    #     """ You can't change a unique id. """
    #     self.load_example_data()
    #     old_id = 'random_fact'
    #     spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=old_id).first()
    #     """:type: WorkflowSpecModel"""
    #
    #     spec.id = 'odd_datum'
    #     num_before = session.query(WorkflowSpecModel).count()
    #
    #     rv = self.app.post('/v1.0/workflow-specification?spec_id=%s' % old_id, content_type="application/json",
    #                        data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
    #     self.assert_success(rv)
    #     db_spec = session.query(WorkflowSpecModel).filter_by(id=spec.id).first()
    #     self.assertEqual(spec.display_name, db_spec.display_name)
    #
    #     num_old_after = session.query(WorkflowSpecModel).filter_by(id=old_id).count()
    #     self.assertEqual(num_old_after, 0)
    #
    #     num_after = session.query(WorkflowSpecModel).count()
    #     self.assertEqual(num_after, num_before)

    def test_delete_workflow_specification(self):
        self.load_example_data()
        spec_id = 'random_fact'

        num_specs_before = session.query(WorkflowSpecModel).filter_by(id=spec_id).count()
        self.assertEqual(num_specs_before, 1)

        num_files_before = session.query(FileModel).filter_by(workflow_spec_id=spec_id).count()
        num_workflows_before = session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id).count()
        self.assertGreater(num_files_before + num_workflows_before, 0)

        rv = self.app.delete('/v1.0/workflow-specification/' + spec_id)
        self.assert_success(rv)

        num_specs_after = session.query(WorkflowSpecModel).filter_by(id=spec_id).count()
        self.assertEqual(0, num_specs_after)

        # Make sure that all items in the database with the workflow spec ID are deleted as well.
        num_files_after = session.query(FileModel).filter_by(workflow_spec_id=spec_id).count()
        num_workflows_after = session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id).count()
        self.assertEqual(num_files_after + num_workflows_after, 0)

    def test_add_workflow_to_study(self):
        self.load_example_data()
        study = session.query(StudyModel).first()
        self.assertEqual(0, session.query(WorkflowModel).count())
        spec = session.query(WorkflowSpecModel).first()
        rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
                           data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
        self.assert_success(rv)
        self.assertEqual(1, session.query(WorkflowModel).count())
        workflow_model = session.query(WorkflowModel).first()
        self.assertEqual(study.id, workflow_model.study_id)
        self.assertEqual(WorkflowStatus.user_input_required, workflow_model.status)
        self.assertIsNotNone(workflow_model.bpmn_workflow_json)
        self.assertEqual(spec.id, workflow_model.workflow_spec_id)

        json_data = json.loads(rv.get_data(as_text=True))
        workflow2 = WorkflowApiSchema().load(json_data)
        self.assertEqual(workflow_model.id, workflow2.id)

    def test_delete_workflow(self):
        self.load_example_data()
        study = session.query(StudyModel).first()
        spec = session.query(WorkflowSpecModel).first()
        rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
                           data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
        self.assertEqual(1, session.query(WorkflowModel).count())
        json_data = json.loads(rv.get_data(as_text=True))
        workflow = WorkflowApiSchema().load(json_data)
        rv = self.app.delete('/v1.0/workflow/%i' % workflow.id)
        self.assert_success(rv)
        self.assertEqual(0, session.query(WorkflowModel).count())