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cr-connect-workflow
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Merge remote-tracking branch 'origin/dev' into feature/python_eval

This commit is contained in:
Dan Funk 2020-08-27 14:33:16 -04:00
parent b39fd73bc0 1d636ea5ae
commit 1052dff549
6 changed files with 191 additions and 0 deletions
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70
crc/scripts/study_sponsors.py Normal file
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@ -0,0 +1,70 @@
import json
from crc.api.common import ApiError
from crc.scripts.script import Script
from crc.services.protocol_builder import ProtocolBuilderService
class StudySponsors(Script):
"""Please see the detailed description that is provided below. """
pb = ProtocolBuilderService()
# This is used for test/workflow validation, as well as documentation.
example_data = [
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2453,
"SP_NAME": "Abbott Ltd",
"SP_TYPE": "Private",
"SP_TYPE_GROUP_NAME": None,
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2387,
"SP_NAME": "Abbott-Price",
"SP_TYPE": "Incoming Sub Award",
"SP_TYPE_GROUP_NAME": "Government",
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 1996,
"SP_NAME": "Abernathy-Heidenreich",
"SP_TYPE": "Foundation/Not for Profit",
"SP_TYPE_GROUP_NAME": "Other External Funding",
"SS_STUDY": 2
}
]
def example_to_string(self, key):
return json.dumps(self.example_data['StudyInfo'][key], indent=2, separators=(',', ': '))
def get_description(self):
return ""
# return """
# Returns a list of sponsors related to a study in the following format:
# {{example}}
#z """.format(example=json.dumps(self.example_data, index=2, separators=(',', ': ')))
def check_args(self, args):
if len(args) > 0:
raise ApiError(code="invalid_argument",
message="The Sponsor script does not take any arguments. "
"It returns the list of sponsors for the current study only. ")
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
"""For validation only, pretend no results come back from pb"""
self.check_args(args)
return self.example_data
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
self.check_args(args)
retval = ProtocolBuilderService.get_sponsors(study_id)
# Check on returning box, as in return Box(retval) - may not work with list.
return retval

5
crc/services/protocol_builder.py
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@ -13,6 +13,7 @@ class ProtocolBuilderService(object):
INVESTIGATOR_URL = app.config['PB_INVESTIGATORS_URL']
REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
SPONSORS_URL = app.config['PB_STUDY_DETAILS_URL']
@staticmethod
def is_enabled():
@ -54,6 +55,10 @@ class ProtocolBuilderService(object):
def get_study_details(study_id) -> {}:
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.STUDY_DETAILS_URL)
@staticmethod
def get_sponsors(study_id) -> {}:
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.SPONSORS_URL)
@staticmethod
def __enabled_or_raise():
if not ProtocolBuilderService.is_enabled():

26
tests/data/pb_responses/sponsors.json Normal file
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@ -0,0 +1,26 @@
[
{
"COMMONRULEAGENCY": null,
"SPONSOR_ID": 2453,
"SP_NAME": "Abbott Ltd",
"SP_TYPE": "Private",
"SP_TYPE_GROUP_NAME": null,
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": null,
"SPONSOR_ID": 2387,
"SP_NAME": "Abbott-Price",
"SP_TYPE": "Incoming Sub Award",
"SP_TYPE_GROUP_NAME": "Government",
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": null,
"SPONSOR_ID": 1996,
"SP_NAME": "Abernathy-Heidenreich",
"SP_TYPE": "Foundation/Not for Profit",
"SP_TYPE_GROUP_NAME": "Other External Funding",
"SS_STUDY": 2
}
]

39
tests/data/study_sponsors/study_sponsors.bpmn Normal file
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<?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_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Process_0exnnpv" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="SequenceFlow_1nfe5m9" sourceRef="StartEvent_1" targetRef="Task_Script_Load_Study_Sponsors" />
<bpmn:scriptTask id="Task_Script_Load_Study_Sponsors" name="Load Study Sponsors">
<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
<bpmn:script>sponsors = study_sponsors()</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Sponsors" targetRef="EndEvent_171dj09" />
<bpmn:endEvent id="EndEvent_171dj09">
<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
</bpmn:endEvent>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0exnnpv">
<bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
<di:waypoint x="370" y="117" />
<di:waypoint x="452" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_1nfe5m9_di" bpmnElement="SequenceFlow_1nfe5m9">
<di:waypoint x="215" y="117" />
<di:waypoint x="270" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_1mp6xid_di" bpmnElement="Task_Script_Load_Study_Sponsors">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_171dj09_di" bpmnElement="EndEvent_171dj09">
<dc:Bounds x="452" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

39
tests/study/test_study_sponsors_script.py Normal file
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@ -0,0 +1,39 @@
from unittest.mock import patch
from tests.base_test import BaseTest
from crc import session, app
from crc.models.study import StudyModel
from crc.scripts.study_sponsors import StudySponsors
from crc.services.study_service import StudyService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
class TestSudySponsorsScript(BaseTest):
test_uid = "dhf8r"
test_study_id = 1
def test_study_sponsors_script_validation(self):
self.load_test_spec("study_sponsors")
WorkflowService.test_spec("study_sponsors") # This would raise errors if it didn't validate
@patch('crc.services.protocol_builder.requests.get')
def test_study_sponsors_script(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
app.config['PB_ENABLED'] = True
self.load_example_data()
self.create_reference_document()
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("study_sponsors")
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
WorkflowService.test_spec("study_sponsors")
processor = WorkflowProcessor(workflow_model)
processor.do_engine_steps()
self.assertTrue(processor.bpmn_workflow.is_completed())
data = processor.next_task().data
self.assertIn('sponsors', data)
self.assertEquals(3, len(data['sponsors']))

12
tests/test_protocol_builder.py
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@ -48,3 +48,15 @@ class TestProtocolBuilder(BaseTest):
self.assertIsNotNone(response)
self.assertEqual(64, len(response))
self.assertEqual(1234, response['IND_1'])
@patch('crc.services.protocol_builder.requests.get')
def test_get_study_sponsors(self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
response = ProtocolBuilderService.get_sponsors(self.test_study_id)
self.assertIsNotNone(response)
self.assertEqual(3, len(response))
self.assertEqual(2, response[0]["SS_STUDY"])
self.assertEqual(2453, response[0]["SPONSOR_ID"])
self.assertEqual("Abbott Ltd", response[0]["SP_NAME"])