Merge remote-tracking branch 'origin/chore/update_specs' into feature/previous_task
# Conflicts: # Pipfile.lock Assuring that all documents from the xls spreadsheet are loaded when doing validations.
This commit is contained in:
Dan Funk
commit
07e58e923d
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@ -61,32 +61,13 @@ class StudyInfo(Script):
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"status": WorkflowStatus.not_started.value,
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"workflow_spec_id": "irb_api_details",
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},
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"documents": {
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"AD_CoCApp":
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{
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'category1': 'Ancillary Document',
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'category2': 'CoC Application',
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'category3': '',
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'Who Uploads?': 'CRC',
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'Id': '12',
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'Name': 'Certificate of Confidentiality Application',
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'count': 0,
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'required': True,
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'code': 'AD_CoCApp',
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'display_name': 'Certificate of Confidentiality Application',
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'file_id': 123,
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'task_id': 'abcdef14236890',
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'workflow_id': 456,
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'workflow_spec_id': 'irb_api_details',
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'status': 'complete',
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}
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},
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'protocol': {
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id: 0,
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}
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}
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}
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self.add_data_to_task(task=task, data=data["study"])
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self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
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def do_task(self, task, study_id, *args, **kwargs):
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self.check_args(args)
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@ -104,7 +104,7 @@ class StudyService(object):
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@staticmethod
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def get_documents_status(study_id):
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"""Returns a list of documents related to the study, if they are required, and any file information
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"""Returns a list of documents related to the study, and any file information
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that is available.."""
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# Get PB required docs
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@ -70,6 +70,9 @@
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<camunda:property id="placeholder" value="Limit Length: 11" />
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<camunda:property id="hide_expression" value="model.CTG_NA && model.CTG_NA.enumNoRegister" />
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</camunda:properties>
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<camunda:validation>
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<camunda:constraint name="max_length" config="11" />
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</camunda:validation>
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</camunda:formField>
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<camunda:formField id="CTG_StudyType" label="ClinicalTrials.gov Study Type" type="enum">
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<camunda:properties>
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@ -307,6 +310,18 @@
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<bpmndi:BPMNShape id="StartEvent_1mhzkcr_di" bpmnElement="StartEvent_1mhzkcr">
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<dc:Bounds x="-218" y="307" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_1y1qon7_di" bpmnElement="UserTask_1y1qon7">
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<dc:Bounds x="620" y="340" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_01zzzg9_di" bpmnElement="UserTask_01zzzg9">
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<dc:Bounds x="620" y="460" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_0gtuk1e_di" bpmnElement="UserTask_EnterMultiSiteInfo">
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<dc:Bounds x="620" y="210" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_0ebxkp7_di" bpmnElement="UserTask_0ebxkp7">
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<dc:Bounds x="620" y="90" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_0vthni9_di" bpmnElement="Activity_10nxpt2">
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<dc:Bounds x="-120" y="285" width="100" height="80" />
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</bpmndi:BPMNShape>
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@ -319,18 +334,6 @@
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<bpmndi:BPMNShape id="Activity_0x7b58m_di" bpmnElement="Activity_PBMultiSiteCheckQ28">
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<dc:Bounds x="350" y="285" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_01zzzg9_di" bpmnElement="UserTask_01zzzg9">
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<dc:Bounds x="620" y="460" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_1y1qon7_di" bpmnElement="UserTask_1y1qon7">
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<dc:Bounds x="620" y="340" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_0gtuk1e_di" bpmnElement="UserTask_EnterMultiSiteInfo">
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<dc:Bounds x="620" y="210" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_0ebxkp7_di" bpmnElement="UserTask_0ebxkp7">
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<dc:Bounds x="620" y="90" 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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@ -50,7 +50,7 @@
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<bpmn:sequenceFlow id="SequenceFlow_157c6e9" sourceRef="ExclusiveGateway_0m1n8mu" targetRef="Task_0xn3d6z" />
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<bpmn:sequenceFlow id="SequenceFlow_1oh6eq7" sourceRef="ExclusiveGateway_0m1n8mu" targetRef="Task_0dj66yz" />
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<bpmn:userTask id="Task_0dj66yz" name="Enter Contract Funded" camunda:formKey="FormKey_ContractFunded">
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<bpmn:documentation>#### Process:
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<bpmn:documentation>#### Process:
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The study team uploads the executed copy of the contract(s) after they receive it from the Office of Grants and Contracts, after the following process components are completed outside of the Clinical Research Connect:
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@ -119,14 +119,14 @@ If you have any questions about the process, contact contract negotiator or Offi
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<di:waypoint x="682" y="337" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="SequenceFlow_0afrh4e_di" bpmnElement="SequenceFlow_0afrh4e">
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<di:waypoint x="460" y="160" />
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<di:waypoint x="570" y="160" />
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<di:waypoint x="460" y="190" />
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<di:waypoint x="570" y="190" />
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<di:waypoint x="570" y="312" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="SequenceFlow_0bvhrqu_di" bpmnElement="SequenceFlow_0bvhrqu">
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<di:waypoint x="250" y="312" />
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<di:waypoint x="250" y="160" />
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<di:waypoint x="360" y="160" />
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<di:waypoint x="250" y="190" />
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<di:waypoint x="360" y="190" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="SequenceFlow_1uxqr6o_di" bpmnElement="SequenceFlow_1uxqr6o">
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<di:waypoint x="158" y="337" />
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@ -144,14 +144,14 @@ If you have any questions about the process, contact contract negotiator or Offi
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<bpmndi:BPMNShape id="ParallelGateway_0f68xmc_di" bpmnElement="ExclusiveGateway_0tqopul">
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<dc:Bounds x="545" y="312" width="50" height="50" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_1fv8l08_di" bpmnElement="Task_0xn3d6z">
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<dc:Bounds x="360" y="430" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_0tz5ojx_di" bpmnElement="Task_0dj66yz">
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<dc:Bounds x="360" y="297" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_1fv8l08_di" bpmnElement="Task_0xn3d6z">
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<dc:Bounds x="360" y="430" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="UserTask_03iirsg_di" bpmnElement="UserTask_03iirsg">
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<dc:Bounds x="360" y="120" width="100" height="80" />
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<dc:Bounds x="360" y="150" 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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@ -17,6 +17,8 @@
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<camunda:formField id="HoldNotes" label="Why was this study moved to Hold Status?" type="textarea">
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<camunda:properties>
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<camunda:property id="rows" value="5" />
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<camunda:property id="group" value="Reason for Hold Notes" />
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<camunda:property id="repeat" value="Reason for Hold Notes" />
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</camunda:properties>
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</camunda:formField>
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</camunda:formData>
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@ -11,7 +11,7 @@
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</inputExpression>
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</input>
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<output id="output_1" label="Investigator's Brochure(s) Uploaded?" name="isInvestigatorsBrochure" typeRef="boolean" />
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<output id="OutputClause_1f3mlfn" label="Investigator's Broshure Form Banner" name="ElementDoc_InvestigatorsBrochure" typeRef="string" />
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<output id="OutputClause_1f3mlfn" label="Investigator's Brochure Form Banner" name="ElementDoc_InvestigatorsBrochure" typeRef="string" />
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<rule id="DecisionRule_0zvgaym">
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<inputEntry id="UnaryTests_0mwq0my">
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<text>0</text>
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@ -7,7 +7,7 @@
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<decisionTable id="decisionTable_1">
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<input id="input_1" label="Pharmacy Manual Upload Count">
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<inputExpression id="inputExpression_1" typeRef="integer">
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<text>StudyInfo.documents.DrugDevDoc_PharmManual.count</text>
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<text>StudyInfo.documents["DrugDevDoc_PharmManual"]["count"]</text>
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</inputExpression>
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</input>
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<output id="output_1" label="Pharmacy Manual(s) Uploaded?" name="isPharmacyManual" typeRef="boolean" />
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@ -6,8 +6,8 @@
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</extensionElements>
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<decisionTable id="DecisionTable_1mjqwlv">
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<input id="InputClause_18pwfqu" label="Required Doc Keys">
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<inputExpression id="LiteralExpression_1y84stb" typeRef="boolean" expressionLanguage="feel">
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<text>StudyInfo.documents.Study_DataSecurityPlan.required</text>
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<inputExpression id="LiteralExpression_1y84stb" typeRef="boolean" expressionLanguage="python">
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<text>StudyInfo.documents['Study_DataSecurityPlan']['required']</text>
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</inputExpression>
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</input>
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<output id="OutputClause_05y0j7c" label="data_security_plan" name="data_security_plan" typeRef="string" />
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@ -7,7 +7,7 @@
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<decisionTable id="decisionTable_1">
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<input id="InputClause_1ki80j6" label="required doc ids">
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<inputExpression id="LiteralExpression_10mfcy7" typeRef="boolean" expressionLanguage="Python">
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<text>StudyInfo.documents.UVACompl_PRCAppr.required</text>
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<text>StudyInfo.documents['UVACompl_PRCAppr']['required']</text>
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</inputExpression>
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</input>
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<output id="output_1" label="enter_core_info" name="enter_core_info" typeRef="string" />
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@ -1,5 +1,5 @@
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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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1kudwnk" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
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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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1kudwnk" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
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<bpmn:process id="Process_0jhpidf" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_1ees8ka</bpmn:outgoing>
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@ -26,7 +26,12 @@
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<bpmn:outgoing>Flow_0pwtiqm</bpmn:outgoing>
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</bpmn:parallelGateway>
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<bpmn:sequenceFlow id="Flow_0pwtiqm" sourceRef="Gateway_12tpgcy" targetRef="Activity_0f295la" />
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<bpmn:parallelGateway id="Gateway_1nta7st">
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<bpmn:parallelGateway id="Gateway_1nta7st" name="Some Name">
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<bpmn:extensionElements>
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<camunda:properties>
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<camunda:property name="display_name" value="Some Name" />
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</camunda:properties>
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</bpmn:extensionElements>
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<bpmn:incoming>SequenceFlow_17ct47v</bpmn:incoming>
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<bpmn:outgoing>Flow_1m8285h</bpmn:outgoing>
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<bpmn:outgoing>Flow_18pl92p</bpmn:outgoing>
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@ -211,6 +216,9 @@
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Gateway_1m22g4p_di" bpmnElement="Gateway_1nta7st">
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<dc:Bounds x="468" y="414" width="50" height="50" />
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<bpmndi:BPMNLabel>
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<dc:Bounds x="462" y="471" width="62" height="14" />
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</bpmndi:BPMNLabel>
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_16cm213_di" bpmnElement="Activity_16cm213">
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<dc:Bounds x="550" y="650" width="100" height="80" />
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|
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Binary file not shown.
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@ -221,6 +221,7 @@ class ExampleDataLoader:
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is_status = filename.lower() == 'status.bpmn'
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is_primary = filename.lower() == id + '.bpmn'
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file = None
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try:
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file = open(file_path, 'rb')
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data = file.read()
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|
|
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@ -0,0 +1,60 @@
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"""empty message
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Revision ID: 89073ca446a3
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Revises: 1685be1cc232
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Create Date: 2020-05-05 11:09:00.307363
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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 sqlalchemy.dialects import postgresql
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# revision identifiers, used by Alembic.
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revision = '89073ca446a3'
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down_revision = '1685be1cc232'
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branch_labels = None
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depends_on = None
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def upgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.drop_table('workflow_stats')
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op.add_column('task_event', sa.Column('action', sa.String(), nullable=True))
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op.add_column('task_event', sa.Column('mi_count', sa.Integer(), nullable=True))
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op.add_column('task_event', sa.Column('mi_index', sa.Integer(), nullable=True))
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op.add_column('task_event', sa.Column('mi_type', sa.String(), nullable=True))
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op.add_column('task_event', sa.Column('process_name', sa.String(), nullable=True))
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op.add_column('task_event', sa.Column('task_name', sa.String(), nullable=True))
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op.add_column('task_event', sa.Column('task_title', sa.String(), nullable=True))
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op.add_column('task_event', sa.Column('task_type', sa.String(), nullable=True))
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op.add_column('workflow', sa.Column('last_updated', sa.DateTime(), nullable=True))
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# ### end Alembic commands ###
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def downgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.drop_column('workflow', 'last_updated')
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op.drop_column('task_event', 'task_type')
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op.drop_column('task_event', 'task_title')
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op.drop_column('task_event', 'task_name')
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op.drop_column('task_event', 'process_name')
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op.drop_column('task_event', 'mi_type')
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op.drop_column('task_event', 'mi_index')
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op.drop_column('task_event', 'mi_count')
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op.drop_column('task_event', 'action')
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op.create_table('workflow_stats',
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sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False),
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sa.Column('study_id', sa.INTEGER(), autoincrement=False, nullable=False),
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sa.Column('workflow_id', sa.INTEGER(), autoincrement=False, nullable=False),
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sa.Column('workflow_spec_id', sa.VARCHAR(), autoincrement=False, nullable=True),
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sa.Column('spec_version', sa.VARCHAR(), autoincrement=False, nullable=True),
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sa.Column('num_tasks_total', sa.INTEGER(), autoincrement=False, nullable=True),
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sa.Column('num_tasks_complete', sa.INTEGER(), autoincrement=False, nullable=True),
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sa.Column('num_tasks_incomplete', sa.INTEGER(), autoincrement=False, nullable=True),
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sa.Column('last_updated', postgresql.TIMESTAMP(), autoincrement=False, nullable=True),
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sa.ForeignKeyConstraint(['study_id'], ['study.id'], name='workflow_stats_study_id_fkey'),
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sa.ForeignKeyConstraint(['workflow_id'], ['workflow.id'], name='workflow_stats_workflow_id_fkey'),
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sa.ForeignKeyConstraint(['workflow_spec_id'], ['workflow_spec.id'], name='workflow_stats_workflow_spec_id_fkey'),
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sa.PrimaryKeyConstraint('id', name='workflow_stats_pkey')
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)
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# ### end Alembic commands ###
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@ -392,9 +392,9 @@ class TestWorkflowProcessor(BaseTest):
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self.assertTrue("enter_core_info" in data)
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self.assertEqual("required", data["enter_core_info"])
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# It should mark the Data Security Plan as required, because InfoSec Approval (24) is included in required docs.
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# self.assertTrue("data_security_plan" in data)
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# self.assertEqual("required", data["data_security_plan"])
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# It should mark Personnel as required, because StudyInfo.investigators is not empty.
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self.assertTrue("personnel" in data)
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self.assertEqual("required", data["personnel"])
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# It should mark the sponsor funding source as disabled since the funding required (12) is not included in the required docs.
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self.assertTrue("sponsor_funding_source" in data)
|
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|
|
|
|||
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Reference in New Issue