188 lines
9.2 KiB
Python
188 lines
9.2 KiB
Python
import json
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from datetime import datetime, tzinfo, timezone
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from crc import session
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from crc.models.file import FileModel
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from crc.models.study import StudyModel, StudyModelSchema, ProtocolBuilderStatus
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from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
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WorkflowModelSchema, TaskSchema
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from tests.base_test import BaseTest
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class TestStudy(BaseTest):
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def test_study_basics(self):
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self.load_example_data()
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study = session.query(StudyModel).first()
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self.assertIsNotNone(study)
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def test_add_study(self):
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self.load_example_data()
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study = {
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"id": 12345,
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"title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents for Interstellar Spacecraft",
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"last_updated": datetime.now(tz=timezone.utc),
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"protocol_builder_status": ProtocolBuilderStatus.in_process,
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"primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
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"sponsor": "Sirius Cybernetics Corporation",
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"ind_number": "567890",
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}
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rv = self.app.post('/v1.0/study',
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content_type="application/json",
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data=json.dumps(StudyModelSchema().dump(study)))
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self.assert_success(rv)
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db_study = session.query(StudyModel).filter_by(id=12345).first()
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self.assertIsNotNone(db_study)
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self.assertEqual(study["title"], db_study.title)
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self.assertAlmostEqual(study["last_updated"], db_study.last_updated)
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self.assertEqual(study["protocol_builder_status"], db_study.protocol_builder_status)
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self.assertEqual(study["primary_investigator_id"], db_study.primary_investigator_id)
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self.assertEqual(study["sponsor"], db_study.sponsor)
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self.assertEqual(study["ind_number"], db_study.ind_number)
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def test_update_study(self):
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self.load_example_data()
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study: StudyModel = session.query(StudyModel).first()
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study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility"
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study.protocol_builder_status = ProtocolBuilderStatus.complete
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rv = self.app.put('/v1.0/study/%i' % study.id,
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content_type="application/json",
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data=json.dumps(StudyModelSchema().dump(study)))
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self.assert_success(rv)
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db_study = session.query(StudyModel).filter_by(id=study.id).first()
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self.assertIsNotNone(db_study)
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self.assertEqual(study.title, db_study.title)
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self.assertEqual(study.protocol_builder_status, db_study.protocol_builder_status)
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def test_study_api_get_single_study(self):
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self.load_example_data()
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study = session.query(StudyModel).first()
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rv = self.app.get('/v1.0/study/%i' % study.id,
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follow_redirects=True,
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content_type="application/json")
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self.assert_success(rv)
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json_data = json.loads(rv.get_data(as_text=True))
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study2 = StudyModelSchema().load(json_data, session=session)
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self.assertEqual(study, study2)
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self.assertEqual(study.id, study2.id)
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self.assertEqual(study.title, study2.title)
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self.assertEqual(study.last_updated, study2.last_updated)
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self.assertEqual(study.protocol_builder_status, study2.protocol_builder_status)
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self.assertEqual(study.primary_investigator_id, study2.primary_investigator_id)
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self.assertEqual(study.sponsor, study2.sponsor)
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self.assertEqual(study.ind_number, study2.ind_number)
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def test_list_workflow_specifications(self):
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self.load_example_data()
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spec = session.query(WorkflowSpecModel).first()
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rv = self.app.get('/v1.0/workflow-specification',
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follow_redirects=True,
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content_type="application/json")
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self.assert_success(rv)
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json_data = json.loads(rv.get_data(as_text=True))
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specs = WorkflowSpecModelSchema(many=True).load(json_data, session=session)
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spec2 = specs[0]
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self.assertEqual(spec.id, spec2.id)
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self.assertEqual(spec.display_name, spec2.display_name)
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self.assertEqual(spec.description, spec2.description)
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def test_add_new_workflow_specification(self):
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self.load_example_data();
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num_before = session.query(WorkflowSpecModel).count()
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spec = WorkflowSpecModel(id='make_cookies', display_name='Cooooookies',
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description='Om nom nom delicious cookies')
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rv = self.app.post('/v1.0/workflow-specification', content_type="application/json",
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data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
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self.assert_success(rv)
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db_spec = session.query(WorkflowSpecModel).filter_by(id='make_cookies').first()
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self.assertEqual(spec.display_name, db_spec.display_name)
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num_after = session.query(WorkflowSpecModel).count()
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self.assertEqual(num_after, num_before + 1)
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def test_get_workflow_specification(self):
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self.load_example_data()
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db_spec = session.query(WorkflowSpecModel).first()
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rv = self.app.get('/v1.0/workflow-specification/%s' % db_spec.id)
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self.assert_success(rv)
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json_data = json.loads(rv.get_data(as_text=True))
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api_spec = WorkflowSpecModelSchema().load(json_data, session=session)
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self.assertEqual(db_spec, api_spec)
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# def test_modify_workflow_specification(self):
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# """ You can't change a unique id. """
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# self.load_example_data()
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# old_id = 'random_fact'
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# spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=old_id).first()
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# """:type: WorkflowSpecModel"""
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#
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# spec.id = 'odd_datum'
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# num_before = session.query(WorkflowSpecModel).count()
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#
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# rv = self.app.post('/v1.0/workflow-specification?spec_id=%s' % old_id, content_type="application/json",
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# data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
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# self.assert_success(rv)
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# db_spec = session.query(WorkflowSpecModel).filter_by(id=spec.id).first()
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# self.assertEqual(spec.display_name, db_spec.display_name)
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#
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# num_old_after = session.query(WorkflowSpecModel).filter_by(id=old_id).count()
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# self.assertEqual(num_old_after, 0)
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#
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# num_after = session.query(WorkflowSpecModel).count()
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# self.assertEqual(num_after, num_before)
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def test_delete_workflow_specification(self):
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self.load_example_data()
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spec_id = 'random_fact'
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num_specs_before = session.query(WorkflowSpecModel).filter_by(id=spec_id).count()
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self.assertEqual(num_specs_before, 1)
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num_files_before = session.query(FileModel).filter_by(workflow_spec_id=spec_id).count()
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num_workflows_before = session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id).count()
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self.assertGreater(num_files_before + num_workflows_before, 0)
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rv = self.app.delete('/v1.0/workflow-specification/' + spec_id)
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self.assert_success(rv)
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num_specs_after = session.query(WorkflowSpecModel).filter_by(id=spec_id).count()
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self.assertEqual(0, num_specs_after)
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# Make sure that all items in the database with the workflow spec ID are deleted as well.
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num_files_after = session.query(FileModel).filter_by(workflow_spec_id=spec_id).count()
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num_workflows_after = session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id).count()
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self.assertEqual(num_files_after + num_workflows_after, 0)
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def test_add_workflow_to_study(self):
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self.load_example_data()
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study = session.query(StudyModel).first()
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self.assertEqual(0, session.query(WorkflowModel).count())
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spec = session.query(WorkflowSpecModel).first()
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rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
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data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
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self.assert_success(rv)
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self.assertEqual(1, session.query(WorkflowModel).count())
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workflow = session.query(WorkflowModel).first()
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self.assertEqual(study.id, workflow.study_id)
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self.assertEqual(WorkflowStatus.user_input_required, workflow.status)
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self.assertIsNotNone(workflow.bpmn_workflow_json)
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self.assertEqual(spec.id, workflow.workflow_spec_id)
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json_data = json.loads(rv.get_data(as_text=True))
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workflow2 = WorkflowModelSchema().load(json_data, session=session)
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self.assertEqual(workflow.id, workflow2.id)
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def test_delete_workflow(self):
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self.load_example_data()
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study = session.query(StudyModel).first()
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spec = session.query(WorkflowSpecModel).first()
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rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
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data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
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self.assertEqual(1, session.query(WorkflowModel).count())
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json_data = json.loads(rv.get_data(as_text=True))
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workflow = WorkflowModelSchema().load(json_data, session=session)
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rv = self.app.delete('/v1.0/workflow/%i' % workflow.id)
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self.assert_success(rv)
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self.assertEqual(0, session.query(WorkflowModel).count())
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