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Merge pull request #483 from sartography/chore/study-status-changes-653
Chore/study status changes #653
This commit is contained in:
Dan Funk
GitHub
commit
eae0b5286e
@ -18,6 +18,7 @@ class StudyStatus(enum.Enum):
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hold = 'hold'
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open_for_enrollment = 'open_for_enrollment'
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abandoned = 'abandoned'
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cr_connect_complete = 'cr_connect_complete'
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class ProgressStatus(enum.Enum):
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37
crc/scripts/set_study_status.py
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37
crc/scripts/set_study_status.py
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@ -0,0 +1,37 @@
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from crc import session
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from crc.api.common import ApiError
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from crc.models.study import StudyModel, StudyStatus
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from crc.scripts.script import Script
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class SetStudyStatus(Script):
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@staticmethod
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def get_study_status_values():
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study_status_values = []
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for item in StudyStatus:
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study_status_values.append(item.value)
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return study_status_values
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def get_description(self):
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study_status_values = self.get_study_status_values()
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return f"Set the study status. Requires a study status. Study status must be in {study_status_values}."
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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study_status_values = self.get_study_status_values()
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if len(args) == 1:
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if args[0] in study_status_values:
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return True
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else:
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raise ApiError(code='bad_parameter',
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message=f"The set_study_status script requires 1 parameter, from 'in_progress', 'hold', 'open_for_enrollment', 'abandoned', or 'cr_connect_complete'. You sent: {args[0]}.")
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else:
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raise ApiError(code='bad_parameter_count',
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message=f'The set_study_status script requires 1 parameter, {len(args)} were given.')
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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study_status_values = self.get_study_status_values()
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if len(args) == 1:
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if args[0] in study_status_values:
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study = session.query(StudyModel).filter(StudyModel.id==study_id).first()
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study.status = StudyStatus(args[0]).value
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session.commit()
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42
migrations/versions/cf57eba23a16_new_study_status.py
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42
migrations/versions/cf57eba23a16_new_study_status.py
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@ -0,0 +1,42 @@
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"""new study status 'cr_connect_complete'
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Revision ID: cf57eba23a16
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Revises: 3c56c894ff5c
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Create Date: 2022-03-03 08:04:24.292180
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"""
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from alembic import op
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import sqlalchemy as sa
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from crc.models.study import StudyModel, StudyStatus
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# revision identifiers, used by Alembic.
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revision = 'cf57eba23a16'
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down_revision = '3c56c894ff5c'
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branch_labels = None
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depends_on = None
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def upgrade():
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# add cr_connect_complete to studystatus
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op.execute('ALTER TYPE studystatus RENAME TO studystatus_old;')
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op.execute("CREATE TYPE studystatus AS ENUM('in_progress', 'hold', 'open_for_enrollment', 'abandoned', 'cr_connect_complete')")
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op.execute("ALTER TABLE study ALTER COLUMN status TYPE studystatus USING status::text::studystatus;")
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op.execute('DROP TYPE studystatus_old;')
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def downgrade():
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# Removing cr_connect_complete, so change those to in_progress first
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bind = op.get_bind()
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session = sa.orm.Session(bind=bind)
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session.flush()
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studies = session.query(StudyModel).filter(StudyModel.status=='cr_connect_complete').all()
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for study in studies:
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study.status = StudyStatus('in_progress')
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session.commit()
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# delete cr_connect_complete from studystatus
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op.execute('ALTER TYPE studystatus RENAME TO studystatus_old;')
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op.execute("CREATE TYPE studystatus AS ENUM('in_progress', 'hold', 'open_for_enrollment', 'abandoned')")
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op.execute("ALTER TABLE study ALTER COLUMN status TYPE studystatus USING status::text::studystatus;")
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op.execute('DROP TYPE studystatus_old;')
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51
tests/data/set_study_status/set_study_status.bpmn
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51
tests/data/set_study_status/set_study_status.bpmn
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@ -0,0 +1,51 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_7fa2a49" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="4.2.0">
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<bpmn:process id="Process_SetStudyStatus" name="Set Study Status" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>Flow_1id1rb8</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="Flow_1id1rb8" sourceRef="StartEvent_1" targetRef="Activity_Pause" />
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<bpmn:endEvent id="Event_0ky05kq">
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<bpmn:incoming>Flow_0kxs039</bpmn:incoming>
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</bpmn:endEvent>
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<bpmn:sequenceFlow id="Flow_0kxs039" sourceRef="Activity_SetStudyStatus" targetRef="Event_0ky05kq" />
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<bpmn:scriptTask id="Activity_SetStudyStatus" name="Set Study Status">
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<bpmn:incoming>Flow_1wyotj4</bpmn:incoming>
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<bpmn:outgoing>Flow_0kxs039</bpmn:outgoing>
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<bpmn:script>set_study_status('cr_connect_complete')</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:sequenceFlow id="Flow_1wyotj4" sourceRef="Activity_Pause" targetRef="Activity_SetStudyStatus" />
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<bpmn:manualTask id="Activity_Pause" name="Pause">
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<bpmn:incoming>Flow_1id1rb8</bpmn:incoming>
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<bpmn:outgoing>Flow_1wyotj4</bpmn:outgoing>
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</bpmn:manualTask>
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</bpmn:process>
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<bpmndi:BPMNDiagram id="BPMNDiagram_1">
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<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_SetStudyStatus">
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<bpmndi:BPMNEdge id="Flow_1id1rb8_di" bpmnElement="Flow_1id1rb8">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="280" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_0kxs039_di" bpmnElement="Flow_0kxs039">
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<di:waypoint x="570" y="117" />
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<di:waypoint x="642" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_1wyotj4_di" bpmnElement="Flow_1wyotj4">
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<di:waypoint x="380" y="117" />
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<di:waypoint x="470" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
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<dc:Bounds x="179" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Event_0ky05kq_di" bpmnElement="Event_0ky05kq">
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<dc:Bounds x="642" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_1mxl8q8_di" bpmnElement="Activity_SetStudyStatus">
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<dc:Bounds x="470" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_1ds8uv8_di" bpmnElement="Activity_Pause">
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<dc:Bounds x="280" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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</bpmndi:BPMNPlane>
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</bpmndi:BPMNDiagram>
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</bpmn:definitions>
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22
tests/scripts/test_set_study_status.py
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22
tests/scripts/test_set_study_status.py
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@ -0,0 +1,22 @@
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from tests.base_test import BaseTest
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from crc import session
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from crc.models.study import StudyModel
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class TestSetStudyStatus(BaseTest):
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def test_set_study_status(self):
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workflow = self.create_workflow('set_study_status')
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workflow_api = self.get_workflow_api(workflow)
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task = workflow_api.next_task
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# assert we start with in_progress
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status = session.query(StudyModel.status).filter(StudyModel.id==workflow.study_id).scalar()
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self.assertEqual('in_progress', status.value)
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# the workflow sets the status to cr_connect_complete
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self.complete_form(workflow, task, {})
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status = session.query(StudyModel.status).filter(StudyModel.id==workflow.study_id).scalar()
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self.assertEqual('cr_connect_complete', status.value)
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