Some minor cleanup on the study status and automatic events. I wanted to avoid having one database model automatically generating other database models as a side effect. The study service now has full responsiblity to recording study events.
To help in running tests, adding __init__.py methods to all the test directories.
This commit is contained in:
Dan Funk
parent
4f05d99cf0
commit
85ad477b2b
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@ -23,14 +23,12 @@ def add_study(body):
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primary_investigator_id=body['primary_investigator_id'],
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last_updated=datetime.now(),
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status=StudyStatus.in_progress)
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study_model.update_event(
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status=StudyStatus.in_progress,
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event_type=StudyEventType.automatic,
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user_uid=g.user.uid
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)
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session.add(study_model)
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StudyService.add_study_update_event(study_model,
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status=StudyStatus.in_progress,
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event_type=StudyEventType.user,
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user_uid=g.user.uid)
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errors = StudyService._add_all_workflow_specs_to_study(study_model)
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session.commit()
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study = StudyService().get_study(study_model.id)
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@ -40,6 +38,7 @@ def add_study(body):
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def update_study(study_id, body):
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"""Pretty limited, but allows manual modifications to the study status """
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if study_id is None:
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raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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@ -48,7 +47,20 @@ def update_study(study_id, body):
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raise ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
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study: Study = StudyForUpdateSchema().load(body)
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study.update_model(study_model)
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status = StudyStatus(study.status)
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study_model.last_updated = datetime.now()
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if study_model.status != status:
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study_model.status = status
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StudyService.add_study_update_event(study_model, status, StudyEventType.user,
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user_uid=UserService.current_user().uid if UserService.has_user() else None,
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comment='' if not hasattr(study, 'comment') else study.comment,
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)
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if status == StudyStatus.open_for_enrollment:
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study_model.enrollment_date = study.enrollment_date
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session.add(study_model)
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session.commit()
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# Need to reload the full study to return it to the frontend
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@ -61,36 +61,6 @@ class StudyModel(db.Model):
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self.irb_status = IrbStatus.incomplete_in_protocol_builder
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self.status = StudyStatus.in_progress
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self.update_event(
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status=StudyStatus.in_progress,
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event_type=StudyEventType.automatic,
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user_uid=self.user_uid
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)
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if pbs.HSRNUMBER:
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self.irb_status = IrbStatus.hsr_assigned
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self.status = StudyStatus.open_for_enrollment
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self.update_event(
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status=StudyStatus.open_for_enrollment,
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event_type=StudyEventType.automatic,
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user_uid=self.user_uid
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)
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if self.on_hold:
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self.status = StudyStatus.hold
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self.update_event(
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status=StudyStatus.hold,
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event_type=StudyEventType.automatic,
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user_uid=self.user_uid
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)
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def update_event(self, status, event_type, user_uid, comment=''):
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study_event = StudyEvent(study=self,
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status=status,
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event_type=event_type,
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user_uid=user_uid,
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comment=comment)
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db.session.add(study_event)
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db.session.commit()
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class StudyEvent(db.Model):
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@ -202,24 +172,6 @@ class Study(object):
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instance = cls(**args)
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return instance
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def update_model(self, study_model: StudyModel):
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"""As the case for update was very reduced, it's mostly and specifically
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updating only the study status and generating a history record
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"""
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status = StudyStatus(self.status)
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study_model.last_updated = datetime.datetime.now()
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study_model.status = status
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if status == StudyStatus.open_for_enrollment:
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study_model.enrollment_date = self.enrollment_date
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study_model.update_event(
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status=status,
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comment='' if not hasattr(self, 'comment') else self.comment,
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event_type=StudyEventType.user,
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user_uid=UserService.current_user().uid if UserService.has_user() else None
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)
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def model_args(self):
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"""Arguments that can be passed into the Study Model to update it."""
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self_dict = self.__dict__.copy()
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@ -12,7 +12,8 @@ from crc.api.common import ApiError
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from crc.models.file import FileModel, FileModelSchema, File
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from crc.models.ldap import LdapSchema
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from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
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from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowMetadata, StudyEventType
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from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowMetadata, StudyEventType, StudyEvent, \
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IrbStatus
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from crc.models.task_event import TaskEventModel, TaskEvent
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from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
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WorkflowStatus
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@ -253,30 +254,54 @@ class StudyService(object):
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db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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# Update all studies from the protocol builder, create new studies as needed.
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# Futher assures that every active study (that does exist in the protocol builder)
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# Further assures that every active study (that does exist in the protocol builder)
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# has a reference to every available workflow (though some may not have started yet)
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for pb_study in pb_studies:
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new_status = None
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db_study = next((s for s in db_studies if s.id == pb_study.STUDYID), None)
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if not db_study:
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db_study = StudyModel(id=pb_study.STUDYID)
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db_study.status = None # Force a new sa
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new_status = StudyStatus.in_progress
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session.add(db_study)
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db_studies.append(db_study)
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if pb_study.HSRNUMBER:
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db_study.irb_status = IrbStatus.hsr_assigned
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if db_study.status != StudyStatus.open_for_enrollment:
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new_status = StudyStatus.open_for_enrollment
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db_study.update_from_protocol_builder(pb_study)
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StudyService._add_all_workflow_specs_to_study(db_study)
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# If there is a new automatic status change and there isn't a manual change in place, record it.
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if new_status and db_study.status != StudyStatus.hold:
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db_study.status = new_status
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StudyService.add_study_update_event(db_study,
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status=new_status,
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event_type=StudyEventType.automatic)
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# Mark studies as inactive that are no longer in Protocol Builder
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for study in db_studies:
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pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
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if not pb_study:
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if not pb_study and study.status != StudyStatus.abandoned:
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study.status = StudyStatus.abandoned
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study.update_event(
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StudyService.add_study_update_event(study,
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status=StudyStatus.abandoned,
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event_type=StudyEventType.automatic,
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user_uid=study.user_uid
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)
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event_type=StudyEventType.automatic)
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db.session.commit()
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@staticmethod
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def add_study_update_event(study, status, event_type, user_uid=None, comment=''):
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study_event = StudyEvent(study=study,
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status=status,
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event_type=event_type,
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user_uid=user_uid,
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comment=comment)
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db.session.add(study_event)
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db.session.commit()
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@staticmethod
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def __update_status_of_workflow_meta(workflow_metas, status):
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# Update the status on each workflow
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@ -135,7 +135,7 @@ class TestStudyApi(BaseTest):
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study_event = session.query(StudyEvent).first()
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self.assertIsNotNone(study_event)
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self.assertEqual(study_event.status, StudyStatus.in_progress)
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self.assertEqual(study_event.event_type, StudyEventType.automatic)
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self.assertEqual(study_event.event_type, StudyEventType.user)
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self.assertFalse(study_event.comment)
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self.assertEqual(study_event.user_uid, self.test_uid)
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@ -145,7 +145,7 @@ class TestStudyApi(BaseTest):
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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_schema = StudySchema().dump(study)
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study_schema['status'] = StudyStatus.in_progress.value
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study_schema['status'] = StudyStatus.hold.value
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study_schema['comment'] = update_comment
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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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@ -159,7 +159,7 @@ class TestStudyApi(BaseTest):
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# Making sure events history is being properly recorded
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study_event = session.query(StudyEvent).first()
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self.assertIsNotNone(study_event)
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self.assertEqual(study_event.status, StudyStatus.in_progress)
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self.assertEqual(study_event.status, StudyStatus.hold)
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self.assertEqual(study_event.event_type, StudyEventType.user)
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self.assertEqual(study_event.comment, update_comment)
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self.assertEqual(study_event.user_uid, self.test_uid)
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@ -221,7 +221,7 @@ class TestStudyApi(BaseTest):
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# Automatic events check
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in_progress_events = session.query(StudyEvent).filter_by(status=StudyStatus.in_progress)
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self.assertEqual(in_progress_events.count(), 3) # 3 studies were started
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self.assertEqual(in_progress_events.count(), 1) # 1 study is in progress
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abandoned_events = session.query(StudyEvent).filter_by(status=StudyStatus.abandoned)
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self.assertEqual(abandoned_events.count(), 1) # 1 study has been abandoned
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