Adding a study sponsors script to return details about study sponsors
This commit is contained in:
Dan Funk
parent
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import json
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from crc.api.common import ApiError
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from crc.scripts.script import Script
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from crc.services.protocol_builder import ProtocolBuilderService
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class StudySponsors(Script):
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"""Please see the detailed description that is provided below. """
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pb = ProtocolBuilderService()
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# This is used for test/workflow validation, as well as documentation.
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example_data = [
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{
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"COMMONRULEAGENCY": None,
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"SPONSOR_ID": 2453,
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"SP_NAME": "Abbott Ltd",
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"SP_TYPE": "Private",
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"SP_TYPE_GROUP_NAME": None,
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"SS_STUDY": 2
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},
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{
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"COMMONRULEAGENCY": None,
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"SPONSOR_ID": 2387,
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"SP_NAME": "Abbott-Price",
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"SP_TYPE": "Incoming Sub Award",
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"SP_TYPE_GROUP_NAME": "Government",
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"SS_STUDY": 2
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},
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{
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"COMMONRULEAGENCY": None,
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"SPONSOR_ID": 1996,
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"SP_NAME": "Abernathy-Heidenreich",
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"SP_TYPE": "Foundation/Not for Profit",
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"SP_TYPE_GROUP_NAME": "Other External Funding",
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"SS_STUDY": 2
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}
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]
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def example_to_string(self, key):
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return json.dumps(self.example_data['StudyInfo'][key], indent=2, separators=(',', ': '))
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def get_description(self):
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return ""
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# return """
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# Returns a list of sponsors related to a study in the following format:
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# {{example}}
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#z """.format(example=json.dumps(self.example_data, index=2, separators=(',', ': ')))
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def check_args(self, args):
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if len(args) > 0:
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raise ApiError(code="invalid_argument",
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message="The Sponsor script does not take any arguments. "
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"It returns the list of sponsors for the current study only. ")
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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"""For validation only, pretend no results come back from pb"""
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self.check_args(args)
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return self.example_data
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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self.check_args(args)
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retval = ProtocolBuilderService.get_sponsors(study_id)
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# Check on returning box, as in return Box(retval) - may not work with list.
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return retval
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@ -13,6 +13,7 @@ class ProtocolBuilderService(object):
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INVESTIGATOR_URL = app.config['PB_INVESTIGATORS_URL']
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INVESTIGATOR_URL = app.config['PB_INVESTIGATORS_URL']
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REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
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REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
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STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
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STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
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SPONSORS_URL = app.config['PB_STUDY_DETAILS_URL']
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@staticmethod
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@staticmethod
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def is_enabled():
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def is_enabled():
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@ -54,6 +55,10 @@ class ProtocolBuilderService(object):
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def get_study_details(study_id) -> {}:
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def get_study_details(study_id) -> {}:
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return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.STUDY_DETAILS_URL)
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return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.STUDY_DETAILS_URL)
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@staticmethod
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def get_sponsors(study_id) -> {}:
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return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.SPONSORS_URL)
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@staticmethod
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@staticmethod
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def __enabled_or_raise():
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def __enabled_or_raise():
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if not ProtocolBuilderService.is_enabled():
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if not ProtocolBuilderService.is_enabled():
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[
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{
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"COMMONRULEAGENCY": null,
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"SPONSOR_ID": 2453,
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"SP_NAME": "Abbott Ltd",
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"SP_TYPE": "Private",
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"SP_TYPE_GROUP_NAME": null,
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"SS_STUDY": 2
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},
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{
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"COMMONRULEAGENCY": null,
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"SPONSOR_ID": 2387,
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"SP_NAME": "Abbott-Price",
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"SP_TYPE": "Incoming Sub Award",
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"SP_TYPE_GROUP_NAME": "Government",
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"SS_STUDY": 2
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},
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{
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"COMMONRULEAGENCY": null,
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"SPONSOR_ID": 1996,
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"SP_NAME": "Abernathy-Heidenreich",
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"SP_TYPE": "Foundation/Not for Profit",
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"SP_TYPE_GROUP_NAME": "Other External Funding",
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"SS_STUDY": 2
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}
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]
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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_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
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<bpmn:process id="Process_0exnnpv" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="SequenceFlow_1nfe5m9" sourceRef="StartEvent_1" targetRef="Task_Script_Load_Study_Sponsors" />
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<bpmn:scriptTask id="Task_Script_Load_Study_Sponsors" name="Load Study Sponsors">
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<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
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<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
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<bpmn:script>sponsors = study_sponsors()</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Sponsors" targetRef="EndEvent_171dj09" />
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<bpmn:endEvent id="EndEvent_171dj09">
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<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
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</bpmn:endEvent>
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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_0exnnpv">
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<bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
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<di:waypoint x="370" y="117" />
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<di:waypoint x="452" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="SequenceFlow_1nfe5m9_di" bpmnElement="SequenceFlow_1nfe5m9">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="270" 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="ScriptTask_1mp6xid_di" bpmnElement="Task_Script_Load_Study_Sponsors">
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<dc:Bounds x="270" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="EndEvent_171dj09_di" bpmnElement="EndEvent_171dj09">
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<dc:Bounds x="452" y="99" width="36" height="36" />
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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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<?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_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
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<bpmn:process id="Process_0exnnpv" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="SequenceFlow_1nfe5m9" sourceRef="StartEvent_1" targetRef="Task_Script_Load_Study_Sponsors" />
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<bpmn:scriptTask id="Task_Script_Load_Study_Sponsors" name="Load Study Sponsors">
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<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
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<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
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<bpmn:script>sponsors = study_sponsors()</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Sponsors" targetRef="EndEvent_171dj09" />
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<bpmn:endEvent id="EndEvent_171dj09">
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<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
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</bpmn:endEvent>
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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_0exnnpv">
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<bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
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<di:waypoint x="370" y="117" />
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<di:waypoint x="452" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="SequenceFlow_1nfe5m9_di" bpmnElement="SequenceFlow_1nfe5m9">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="270" 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="ScriptTask_1mp6xid_di" bpmnElement="Task_Script_Load_Study_Sponsors">
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<dc:Bounds x="270" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="EndEvent_171dj09_di" bpmnElement="EndEvent_171dj09">
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<dc:Bounds x="452" y="99" width="36" height="36" />
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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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from unittest.mock import patch
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from tests.base_test import BaseTest
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from crc import session, app
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from crc.models.study import StudyModel
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from crc.scripts.study_sponsors import StudySponsors
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from crc.services.study_service import StudyService
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from crc.services.workflow_processor import WorkflowProcessor
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from crc.services.workflow_service import WorkflowService
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class TestSudySponsorsScript(BaseTest):
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test_uid = "dhf8r"
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test_study_id = 1
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def test_study_sponsors_script_validation(self):
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self.load_test_spec("study_sponsors")
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WorkflowService.test_spec("study_sponsors") # This would raise errors if it didn't validate
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@patch('crc.services.protocol_builder.requests.get')
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def test_study_sponsors_script(self, mock_get):
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mock_get.return_value.ok = True
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mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
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app.config['PB_ENABLED'] = True
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self.load_example_data()
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self.create_reference_document()
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study = session.query(StudyModel).first()
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workflow_spec_model = self.load_test_spec("study_sponsors")
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workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
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WorkflowService.test_spec("study_sponsors")
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processor = WorkflowProcessor(workflow_model)
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processor.do_engine_steps()
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self.assertTrue(processor.bpmn_workflow.is_completed())
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data = processor.next_task().data
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self.assertIn('sponsors', data)
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self.assertEquals(3, len(data['sponsors']))
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