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Merge pull request #333 from sartography/check-study-script-273 

Check study script #273
This commit is contained in:
Dan Funk 2021-07-07 11:28:32 -04:00 committed by GitHub
parent db9b228735 8145ff9025
commit 2ed436327f
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7 changed files with 127 additions and 0 deletions
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1
config/default.py
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@ -63,6 +63,7 @@ PB_REQUIRED_DOCS_URL = environ.get('PB_REQUIRED_DOCS_URL', default=PB_BASE_URL +
PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL + "study?studyid=%i")
PB_SPONSORS_URL = environ.get('PB_SPONSORS_URL', default=PB_BASE_URL + "sponsors?studyid=%i")
PB_IRB_INFO_URL = environ.get('PB_IRB_INFO_URL', default=PB_BASE_URL + "current_irb_info/%i")
PB_CHECK_STUDY_URL = environ.get('PB_CHECK_STUDY_URL', default=PB_BASE_URL + "check_study/%i")
# Ldap Configuration
LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/') # No trailing slash or http://

30
crc/scripts/check_study.py Normal file
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@ -0,0 +1,30 @@
from crc.scripts.script import Script
from crc.api.common import ApiError
from crc.services.protocol_builder import ProtocolBuilderService
from crc.services.study_service import StudyService
class CheckStudy(Script):
pb = ProtocolBuilderService()
def get_description(self):
return """Returns the Check Study data for a Study"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
study = StudyService.get_study(study_id)
if study:
return {"DETAIL": "Passed validation.", "STATUS": "No Error"}
else:
raise ApiError.from_task(code='bad_study',
message=f'No study for study_id {study_id}',
task=task)
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
check_study = self.pb.check_study(study_id)
if check_study:
return check_study
else:
raise ApiError.from_task(code='missing_check_study',
message='There was a problem checking information for this study.',
task=task)

5
crc/services/protocol_builder.py
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@ -15,6 +15,7 @@ class ProtocolBuilderService(object):
STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
SPONSORS_URL = app.config['PB_SPONSORS_URL']
IRB_INFO_URL = app.config['PB_IRB_INFO_URL']
CHECK_STUDY_URL = app.config['PB_CHECK_STUDY_URL']
@staticmethod
def is_enabled():
@ -64,6 +65,10 @@ class ProtocolBuilderService(object):
def get_sponsors(study_id) -> {}:
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.SPONSORS_URL)
@staticmethod
def check_study(study_id) -> {}:
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.CHECK_STUDY_URL)
@staticmethod
def __enabled_or_raise():
if not ProtocolBuilderService.is_enabled():

53
tests/data/check_study_script/check_study_script.bpmn Normal file
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@ -0,0 +1,53 @@
<?xml version="1.0" encoding="UTF-8"?>
<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_3fd9241" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.0.0-dev">
<bpmn:process id="Process_9d7b2c2" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>Flow_17nzcku</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="Flow_17nzcku" sourceRef="StartEvent_1" targetRef="Activity_GetCheckStudy" />
<bpmn:scriptTask id="Activity_GetCheckStudy" name="Get Check Study">
<bpmn:incoming>Flow_17nzcku</bpmn:incoming>
<bpmn:outgoing>Flow_0oozrfg</bpmn:outgoing>
<bpmn:script>check_study = check_study()</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_0oozrfg" sourceRef="Activity_GetCheckStudy" targetRef="Activity_DisplayCheckStudy" />
<bpmn:manualTask id="Activity_DisplayCheckStudy" name="Display Check Study">
<bpmn:documentation># Check Study
&lt;div&gt;&lt;span&gt;{{check_study}}&lt;/span&gt;&lt;/div&gt;</bpmn:documentation>
<bpmn:incoming>Flow_0oozrfg</bpmn:incoming>
<bpmn:outgoing>Flow_10sc31i</bpmn:outgoing>
</bpmn:manualTask>
<bpmn:endEvent id="Event_0embsc7">
<bpmn:incoming>Flow_10sc31i</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="Flow_10sc31i" sourceRef="Activity_DisplayCheckStudy" targetRef="Event_0embsc7" />
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_9d7b2c2">
<bpmndi:BPMNEdge id="Flow_10sc31i_di" bpmnElement="Flow_10sc31i">
<di:waypoint x="530" y="177" />
<di:waypoint x="592" y="177" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0oozrfg_di" bpmnElement="Flow_0oozrfg">
<di:waypoint x="370" y="177" />
<di:waypoint x="430" y="177" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_17nzcku_di" bpmnElement="Flow_17nzcku">
<di:waypoint x="215" y="177" />
<di:waypoint x="270" y="177" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="159" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1f9d5ew_di" bpmnElement="Activity_GetCheckStudy">
<dc:Bounds x="270" y="137" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_01vscea_di" bpmnElement="Activity_DisplayCheckStudy">
<dc:Bounds x="430" y="137" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Event_0embsc7_di" bpmnElement="Event_0embsc7">
<dc:Bounds x="592" y="159" width="36" height="36" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

3
tests/data/pb_responses/check_study.json Normal file
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@ -0,0 +1,3 @@
[
{"DETAIL": "Passed validation.", "STATUS": "No Error"}
]

25
tests/scripts/test_check_study.py Normal file
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@ -0,0 +1,25 @@
from tests.base_test import BaseTest
from crc import app
from unittest.mock import patch
class TestCheckStudy(BaseTest):
def test_check_study_script_validation(self):
self.load_example_data()
spec_model = self.load_test_spec('check_study_script')
rv = self.app.get('/v1.0/workflow-specification/%s/validate' % spec_model.id, headers=self.logged_in_headers())
self.assertEqual([], rv.json)
@patch('crc.services.protocol_builder.requests.get')
def test_check_study(self, mock_get):
app.config['PB_ENABLED'] = True
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('check_study.json')
workflow = self.create_workflow('check_study_script')
workflow_api = self.get_workflow_api(workflow)
task = workflow_api.next_task
self.assertIn('DETAIL', task.documentation)
self.assertIn('STATUS', task.documentation)

10
tests/test_protocol_builder.py
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@ -72,3 +72,13 @@ class TestProtocolBuilder(BaseTest):
self.assertEqual('IRB Event 1', response[0]["IRBEVENT"])
self.assertEqual('IRB Event 2', response[1]["IRBEVENT"])
self.assertEqual('IRB Event 3', response[2]["IRBEVENT"])
@patch('crc.services.protocol_builder.requests.get')
def test_check_study(self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('check_study.json')
response = ProtocolBuilderService.check_study(self.test_study_id)
self.assertIsNotNone(response)
self.assertIn('DETAIL', response[0].keys())
self.assertIn('STATUS', response[0].keys())