Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev
This commit is contained in:
Dan
commit
2caf548719
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@ -163,7 +163,7 @@ def get_task_events(action = None, workflow = None, study = None):
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study = session.query(StudyModel).filter(StudyModel.id == event.study_id).first()
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workflow = session.query(WorkflowModel).filter(WorkflowModel.id == event.workflow_id).first()
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workflow_meta = WorkflowMetadata.from_workflow(workflow)
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if study.status in [StudyStatus.open_for_enrollment, StudyStatus.in_progress]:
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if study and study.status in [StudyStatus.open_for_enrollment, StudyStatus.in_progress]:
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task_events.append(TaskEvent(event, study, workflow_meta))
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return TaskEventSchema(many=True).dump(task_events)
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@ -18,7 +18,7 @@ class StudyInfo(Script):
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"""Please see the detailed description that is provided below. """
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pb = ProtocolBuilderService()
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type_options = ['info', 'investigators', 'roles', 'details', 'documents', 'protocol', 'sponsors']
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type_options = ['info', 'investigators', 'roles', 'details', 'documents', 'sponsors']
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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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@ -110,9 +110,6 @@ class StudyInfo(Script):
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},
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"details":
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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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@ -392,8 +389,6 @@ Returns information specific to the protocol.
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retval = self.pb.get_sponsors(study_id)
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if cmd == 'documents':
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retval = StudyService().get_documents_status(study_id)
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if cmd == 'protocol':
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retval = StudyService().get_protocol(study_id)
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return self.box_it(retval, prefix)
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@ -6,11 +6,13 @@ from typing import List
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import flask
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import requests
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from SpiffWorkflow import WorkflowException
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from SpiffWorkflow.bpmn.PythonScriptEngine import Box
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from SpiffWorkflow.exceptions import WorkflowTaskExecException
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from ldap3.core.exceptions import LDAPSocketOpenError
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from crc import db, session, app
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from crc.api.common import ApiError
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from crc.models.data_store import DataStoreModel
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from crc.models.email import EmailModel
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from crc.models.file import FileDataModel, FileModel, FileModelSchema, File, LookupFileModel, LookupDataModel
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from crc.models.ldap import LdapSchema
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@ -297,21 +299,27 @@ class StudyService(object):
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if hasattr(flask.g,'user'):
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token = flask.g.user.encode_auth_token()
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for file in doc_files:
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doc['files'].append({'file_id': file.id,
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file_data = {'file_id': file.id,
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'name': file.name,
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'url': app.config['APPLICATION_ROOT']+
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'file/' + str(file.id) +
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'/download?auth_token='+
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urllib.parse.quote_plus(token),
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'workflow_id': file.workflow_id})
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'workflow_id': file.workflow_id
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}
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data = db.session.query(DataStoreModel).filter(DataStoreModel.file_id==file.id).all()
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data_store_data = {}
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for d in data:
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data_store_data[d.key] = d.value
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file_data["data_store"] = data_store_data
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doc['files'].append(Box(file_data))
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# update the document status to match the status of the workflow it is in.
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if 'status' not in doc or doc['status'] is None:
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workflow: WorkflowModel = session.query(WorkflowModel).filter_by(id=file.workflow_id).first()
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doc['status'] = workflow.status.value
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documents[code] = doc
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return documents
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return Box(documents)
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@staticmethod
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def get_investigators(study_id, all=False):
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@ -355,16 +363,6 @@ class StudyService(object):
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app.logger.info("Failed to connect to LDAP Server.")
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return {}
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@staticmethod
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def get_protocol(study_id):
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"""Returns the study protocol, if it has been uploaded."""
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file = db.session.query(FileModel) \
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.filter_by(study_id=study_id) \
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.filter_by(form_field_key='Study_Protocol_Document') \
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.first()
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return FileModelSchema().dump(file)
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@staticmethod
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def synch_with_protocol_builder_if_enabled(user):
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"""Assures that the studies we have locally for the given user are
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@ -1,12 +1,12 @@
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{
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"DSMB": null,
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"DSMB_FREQUENCY": null,
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"GCRC_NUMBER": null,
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"IBC_NUMBER": null,
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"IDE": null,
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"IND_1": 1234,
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"IND_2": null,
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"IND_3": null,
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"DSMB": 1,
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"DSMB_FREQUENCY": 2,
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"GCRC_NUMBER": "9",
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"IBC_NUMBER": "7",
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"IDE": "12345",
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"IND_1": "1234",
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"IND_2": "2345",
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"IND_3": "3456",
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"IRBREVIEWERADMIN": null,
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"IS_ADULT_PARTICIPANT": null,
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"IS_APPROVED_DEVICE": null,
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@ -61,6 +61,6 @@
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"NON_UVA_LOCATION": null,
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"OTHER_VULNERABLE_DESC": null,
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"PRC_NUMBER": null,
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"SPONSORS_PROTOCOL_REVISION_DATE": null,
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"SPONSORS_PROTOCOL_REVISION_DATE": "2021-04-20",
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"UPLOAD_COMPLETE": null
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}
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@ -0,0 +1,78 @@
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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_07672t3" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
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<bpmn:process id="Process_StudyInfo" name="Study Info" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_0wpuk5u</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="SequenceFlow_0wpuk5u" sourceRef="StartEvent_1" targetRef="Task_WhichInfo" />
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<bpmn:userTask id="Task_WhichInfo" name="Which Info" camunda:formKey="WhichForm">
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<bpmn:extensionElements>
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<camunda:formData>
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<camunda:formField id="which" label="Which" type="enum">
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<camunda:value id="info" name="Info" />
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<camunda:value id="investigators" name="Investigators" />
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<camunda:value id="roles" name="Roles" />
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<camunda:value id="details" name="Details" />
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<camunda:value id="documents" name="Documents" />
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<camunda:value id="sponsors" name="Sponsors" />
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</camunda:formField>
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</camunda:formData>
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</bpmn:extensionElements>
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<bpmn:incoming>SequenceFlow_0wpuk5u</bpmn:incoming>
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<bpmn:outgoing>SequenceFlow_0vpsh2s</bpmn:outgoing>
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</bpmn:userTask>
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<bpmn:sequenceFlow id="SequenceFlow_0vpsh2s" sourceRef="Task_WhichInfo" targetRef="Task_GetInfo" />
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<bpmn:scriptTask id="Task_GetInfo" name="Get Info">
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<bpmn:incoming>SequenceFlow_0vpsh2s</bpmn:incoming>
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<bpmn:outgoing>SequenceFlow_0y0c2i4</bpmn:outgoing>
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<bpmn:script>info = study_info(which)</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:sequenceFlow id="SequenceFlow_0y0c2i4" sourceRef="Task_GetInfo" targetRef="Task_PrintInfo" />
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<bpmn:manualTask id="Task_PrintInfo" name="Print Info">
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<bpmn:documentation># Info
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<div><span>info is {{info}}</span></div>
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</bpmn:documentation>
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<bpmn:incoming>SequenceFlow_0y0c2i4</bpmn:incoming>
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<bpmn:outgoing>SequenceFlow_1s1u06z</bpmn:outgoing>
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</bpmn:manualTask>
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<bpmn:endEvent id="EndEvent_0681rbo">
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<bpmn:incoming>SequenceFlow_1s1u06z</bpmn:incoming>
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</bpmn:endEvent>
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<bpmn:sequenceFlow id="SequenceFlow_1s1u06z" sourceRef="Task_PrintInfo" targetRef="EndEvent_0681rbo" />
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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_StudyInfo">
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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:BPMNEdge id="SequenceFlow_0wpuk5u_di" bpmnElement="SequenceFlow_0wpuk5u">
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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="UserTask_1id33on_di" bpmnElement="Task_WhichInfo">
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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:BPMNEdge id="SequenceFlow_0vpsh2s_di" bpmnElement="SequenceFlow_0vpsh2s">
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<di:waypoint x="370" y="117" />
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<di:waypoint x="430" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="ScriptTask_0vpqnbr_di" bpmnElement="Task_GetInfo">
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<dc:Bounds x="430" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNEdge id="SequenceFlow_0y0c2i4_di" bpmnElement="SequenceFlow_0y0c2i4">
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<di:waypoint x="530" y="117" />
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<di:waypoint x="590" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="ManualTask_09vvuig_di" bpmnElement="Task_PrintInfo">
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<dc:Bounds x="590" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="EndEvent_0681rbo_di" bpmnElement="EndEvent_0681rbo">
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<dc:Bounds x="752" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNEdge id="SequenceFlow_1s1u06z_di" bpmnElement="SequenceFlow_1s1u06z">
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<di:waypoint x="690" y="117" />
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<di:waypoint x="752" y="117" />
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</bpmndi:BPMNEdge>
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</bpmndi:BPMNPlane>
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</bpmndi:BPMNDiagram>
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</bpmn:definitions>
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@ -14,6 +14,7 @@ from crc.scripts.study_info import StudyInfo
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from crc.services.file_service import FileService
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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.scripts.file_data_set import FileDataSet
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class TestStudyDetailsDocumentsScript(BaseTest):
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@ -93,3 +94,23 @@ class TestStudyDetailsDocumentsScript(BaseTest):
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docs = StudyInfo().do_task_validate_only(task, study.id, workflow_model.id, "documents")
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self.assertTrue(isinstance(docs, Box))
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@patch('crc.services.protocol_builder.requests.get')
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def test_study_info_returns_document_data_store_values_with_documents(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('required_docs.json')
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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("two_forms")
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workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
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irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
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file = FileService.add_workflow_file(workflow_id=workflow_model.id,
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name="anything.png", content_type="text",
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binary_data=b'1234', irb_doc_code=irb_code)
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processor = WorkflowProcessor(workflow_model)
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task = processor.next_task()
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FileDataSet().do_task(task, study.id, workflow_model.id, key="ginger", value="doodle", file_id=file.id)
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docs = StudyInfo().do_task(task, study.id, workflow_model.id, "documents")
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self.assertTrue(isinstance(docs, Box))
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self.assertEquals(1, len(docs.UVACompl_PRCAppr.files))
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self.assertEquals("doodle", docs.UVACompl_PRCAppr.files[0].data_store.ginger)
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@ -47,7 +47,7 @@ class TestProtocolBuilder(BaseTest):
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response = ProtocolBuilderService.get_study_details(self.test_study_id)
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self.assertIsNotNone(response)
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self.assertEqual(64, len(response))
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self.assertEqual(1234, response['IND_1'])
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self.assertEqual('1234', response['IND_1'])
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@patch('crc.services.protocol_builder.requests.get')
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def test_get_study_sponsors(self, mock_get):
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|
|
|
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|
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@ -0,0 +1,79 @@
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from tests.base_test import BaseTest
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from crc.scripts.study_info import StudyInfo
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from crc import app
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from unittest.mock import patch
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from crc.services.protocol_builder import ProtocolBuilderService
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|
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class TestStudyInfoScript(BaseTest):
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|
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test_uid = "dhf8r"
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test_study_id = 1
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def do_work(self, info_type):
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app.config['PB_ENABLED'] = True
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self.load_example_data()
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workflow = self.create_workflow('study_info_script')
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workflow_api = self.get_workflow_api(workflow)
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# grab study_info directly from script
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study_info = StudyInfo().do_task(workflow_api.study_id, workflow.study.id, workflow.id, info_type)
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# grab study info through a workflow
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first_task = workflow_api.next_task
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self.complete_form(workflow, first_task, {'which': info_type})
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workflow_api = self.get_workflow_api(workflow)
|
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second_task = workflow_api.next_task
|
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|
||||
return study_info, second_task
|
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|
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def test_info_script_info(self):
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study_info, second_task = self.do_work(info_type='info')
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|
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self.assertEqual(study_info['title'], second_task.data['info']['title'])
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self.assertEqual(study_info['primary_investigator_id'], second_task.data['info']['primary_investigator_id'])
|
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self.assertIn(study_info['title'], second_task.documentation)
|
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|
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@patch('crc.services.protocol_builder.requests.get')
|
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def test_info_script_investigators(self, mock_get):
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app.config['PB_ENABLED'] = True
|
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mock_get.return_value.ok = True
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mock_get.return_value.text = self.protocol_builder_response('investigators.json')
|
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response = ProtocolBuilderService.get_investigators(self.test_study_id)
|
||||
study_info, second_task = self.do_work(info_type='investigators')
|
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for i in range(len(response)):
|
||||
r = response[i]
|
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s = second_task.data['info'][response[i]['INVESTIGATORTYPE']]
|
||||
self.assertEqual(r['INVESTIGATORTYPEFULL'], s['label'])
|
||||
|
||||
# def test_info_script_roles(self):
|
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# study_info, second_task = self.do_work(info_type='roles')
|
||||
# self.assertEqual(study_info, second_task.data['info'])
|
||||
|
||||
@patch('crc.services.protocol_builder.requests.get')
|
||||
def test_info_script_details(self, mock_get):
|
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app.config['PB_ENABLED'] = True
|
||||
mock_get.return_value.ok = True
|
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mock_get.return_value.text = self.protocol_builder_response('study_details.json')
|
||||
response = ProtocolBuilderService.get_study_details(self.test_study_id)
|
||||
study_info, second_task = self.do_work(info_type='details')
|
||||
self.assertEqual(response['IBC_NUMBER'], second_task.data['info']['IBC_NUMBER'])
|
||||
self.assertEqual(response['IDE'], second_task.data['info']['IDE'])
|
||||
self.assertEqual(response['IND_1'], second_task.data['info']['IND_1'])
|
||||
self.assertEqual(response['IND_2'], second_task.data['info']['IND_2'])
|
||||
self.assertEqual(response['IND_3'], second_task.data['info']['IND_3'])
|
||||
|
||||
# def test_info_script_documents(self):
|
||||
# study_info, second_task = self.do_work(info_type='documents')
|
||||
# self.assertEqual(study_info, second_task.data['info'])
|
||||
|
||||
@patch('crc.services.protocol_builder.requests.get')
|
||||
def test_info_script_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)
|
||||
study_info, second_task = self.do_work(info_type='sponsors')
|
||||
for i in range(len(response)):
|
||||
self.assertEqual(response[i]['SPONSOR_ID'], second_task.data['info'][i]['SPONSOR_ID'])
|
||||
self.assertEqual(response[i]['SP_NAME'], second_task.data['info'][i]['SP_NAME'])
|
||||
self.assertEqual(response[i]['SS_STUDY'], second_task.data['info'][i]['SS_STUDY'])
|
||||
|
|
@ -0,0 +1,27 @@
|
|||
from tests.base_test import BaseTest
|
||||
|
||||
from crc import session
|
||||
from crc.models.user import UserModel
|
||||
from crc.services.user_service import UserService
|
||||
from crc.services.workflow_service import WorkflowService
|
||||
|
||||
from example_data import ExampleDataLoader
|
||||
|
||||
import json
|
||||
|
||||
|
||||
class TestWorkflowApi(BaseTest):
|
||||
|
||||
def test_get_task_events(self):
|
||||
|
||||
self.load_example_data()
|
||||
spec = ExampleDataLoader().create_spec('hello_world', 'Hello World', category_id=0, standalone=True, from_tests=True)
|
||||
user = session.query(UserModel).first()
|
||||
self.assertIsNotNone(user)
|
||||
WorkflowService.get_workflow_from_spec(spec.id, user)
|
||||
|
||||
rv = self.app.get(f'/v1.0/task_events',
|
||||
follow_redirects=True,
|
||||
content_type="application/json",
|
||||
headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
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Reference in New Issue