Adds documents_status StudyInfo script. Adds Documents & Approvals workflow spec.
This commit is contained in:
Aaron Louie
parent
2e601719ad
commit
d91f690388
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@ -48,7 +48,7 @@ For example:
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def get_documents(self, study_id, pb_docs):
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"""Takes data from the protocol builder, and merges it with data from the IRB Pro Categories spreadsheet to return
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pertinant details about the required documents."""
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pertinent details about the required documents."""
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doc_dictionary = FileService.get_file_reference_dictionary()
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required_docs = {}
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@ -3,6 +3,7 @@ from ldap3.core.exceptions import LDAPSocketOpenError
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from crc import session, app
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from crc.api.common import ApiError
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from crc.models.study import StudyModel, StudySchema
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from crc.models.workflow import WorkflowStatus
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from crc.scripts.script import Script
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from crc.services.ldap_service import LdapService
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from crc.services.protocol_builder import ProtocolBuilderService
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@ -14,7 +15,7 @@ class StudyInfo(Script):
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"""Just your basic class that can pull in data from a few api endpoints and do a basic task."""
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pb = ProtocolBuilderService()
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type_options = ['info', 'investigators', 'details', 'approvals']
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type_options = ['info', 'investigators', 'details', 'approvals', 'documents_status']
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def get_description(self):
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return """StudyInfo [TYPE], where TYPE is one of 'info', 'investigators', or 'details'
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@ -47,7 +48,27 @@ class StudyInfo(Script):
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"NETBADGEID": "dhf8r"
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},
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"details":
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{}
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{},
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"approvals": {
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"id": 321,
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"display_name": "IRB API Details",
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"name": "irb_api_details",
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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_status": [
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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': False,
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'code': 'AD_CoCApp'
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}
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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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@ -71,6 +92,9 @@ class StudyInfo(Script):
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self.add_data_to_task(task, {cmd: self.pb.get_study_details(study_id)})
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if cmd == 'approvals':
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self.add_data_to_task(task, {cmd: StudyService().get_approvals(study_id)})
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if cmd == 'documents_status':
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self.add_data_to_task(task, {cmd: StudyService().get_documents_status(study_id)})
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task.data["study"] = study_info
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@ -4,11 +4,14 @@ from SpiffWorkflow import WorkflowException
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from crc import db, session
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from crc.api.common import ApiError
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from crc.models.file import FileModel
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from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
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from crc.models.stats import WorkflowStatsModel, TaskEventModel
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from crc.models.study import StudyModel, Study, Category, WorkflowMetadata
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from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
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WorkflowStatus
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from crc.scripts.documents import Documents
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from crc.services.file_service import FileService
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from crc.services.protocol_builder import ProtocolBuilderService
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from crc.services.workflow_processor import WorkflowProcessor
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@ -64,13 +67,13 @@ class StudyService(object):
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@staticmethod
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def get_approvals(study_id):
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"""Returns a list of category objects, in the correct order."""
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"""Returns a list of approval workflows."""
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cat = session.query(WorkflowSpecCategoryModel).filter_by(name="approvals").first()
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specs = session.query(WorkflowSpecModel).filter_by(category_id=cat.id).all()
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spec_ids = [spec.id for spec in specs]
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workflows = session.query(WorkflowModel)\
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.filter(WorkflowModel.study_id == study_id)\
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.filter(WorkflowModel.workflow_spec_id.in_(spec_ids))\
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workflows = session.query(WorkflowModel) \
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.filter(WorkflowModel.study_id == study_id) \
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.filter(WorkflowModel.workflow_spec_id.in_(spec_ids)) \
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.all()
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approvals = []
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@ -80,11 +83,44 @@ class StudyService(object):
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'id': workflow.id,
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'display_name': workflow.workflow_spec.display_name,
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'name': workflow.workflow_spec.display_name,
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'status': workflow.status,
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'status': workflow.status.value,
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'workflow_spec_id': workflow.workflow_spec_id,
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})
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return approvals
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@staticmethod
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def get_documents_status(study_id):
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"""Returns a list of required documents and related workflow status."""
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doc_service = Documents()
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# Get PB required docs
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pb_docs = ProtocolBuilderService.get_required_docs(study_id)
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# Get required docs for study
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study_docs = doc_service.get_documents(study_id=study_id, pb_docs=pb_docs)
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# Container for results
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documents = []
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# For each required doc, get file(s)
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for code, doc in study_docs.items():
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doc['study_id'] = study_id
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doc['code'] = code
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doc_files = FileService.get_files(study_id=study_id, irb_doc_code=code)
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# For each file, get associated workflow status
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for file in doc_files:
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doc['file_id'] = file.id
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doc['workflow_id'] = file.workflow_id
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if 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.append(doc)
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return documents
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@staticmethod
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def synch_all_studies_with_protocol_builder(user):
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"""Assures that the studies we have locally for the given user are
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@ -135,10 +171,10 @@ class StudyService(object):
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@staticmethod
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def __get_workflow_metas(study_id):
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# Add in the Workflows for each category
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workflow_models = db.session.query(WorkflowModel).\
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join(WorkflowSpecModel).\
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filter(WorkflowSpecModel.is_master_spec == False).\
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filter(WorkflowModel.study_id == study_id).\
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workflow_models = db.session.query(WorkflowModel). \
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join(WorkflowSpecModel). \
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filter(WorkflowSpecModel.is_master_spec == False). \
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filter(WorkflowModel.study_id == study_id). \
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all()
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workflow_metas = []
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for workflow in workflow_models:
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@ -0,0 +1,85 @@
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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" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_00j2iu5" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
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<bpmn:process id="Process_1gmf4la" isExecutable="true">
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<bpmn:documentation />
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>Flow_1k3su2q</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:endEvent id="EndEvent_1qvyxg7">
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<bpmn:incoming>Flow_0m7unlb</bpmn:incoming>
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</bpmn:endEvent>
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<bpmn:sequenceFlow id="Flow_0m7unlb" sourceRef="Activity_DisplayDocsAndApprovals" targetRef="EndEvent_1qvyxg7" />
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<bpmn:manualTask id="Activity_DisplayDocsAndApprovals" name="Display Documents and Approvals">
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<bpmn:documentation>## Approvals
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| Name | Status | Help |
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|:-------------- |:-------- |:------ |
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{% for approval in StudyInfo.approvals -%}
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| [{{approval.display_name}}](/workflow/{{approval.id}}) | {{approval.status}} | [Context here](/help/{{approval.workflow_spec_id}}) |
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{% endfor -%}
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## Documents
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| Code | Status | Help |
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|:-------------- |:-------- |:------ |
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{% for doc in study.documents_status -%}
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| [{{doc.code}}](/study/{{doc.study_id}}/workflow/{{doc.workflow_id}}) | {{doc.status}} | [Context here](/help/{{doc.workflow_spec_id}}) |
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{% endfor -%}
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</bpmn:documentation>
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<bpmn:extensionElements>
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<camunda:properties>
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<camunda:property name="display_name" value="Documents and Approvals" />
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</camunda:properties>
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</bpmn:extensionElements>
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<bpmn:incoming>Flow_142jtxs</bpmn:incoming>
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<bpmn:outgoing>Flow_0m7unlb</bpmn:outgoing>
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</bpmn:manualTask>
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<bpmn:scriptTask id="Activity_0a14x7j" name="Load Approvals">
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<bpmn:incoming>Flow_0c7ryff</bpmn:incoming>
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<bpmn:outgoing>Flow_142jtxs</bpmn:outgoing>
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<bpmn:script>StudyInfo approvals</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:scriptTask id="Activity_1aju60t" name="Load Documents">
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<bpmn:incoming>Flow_1k3su2q</bpmn:incoming>
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<bpmn:outgoing>Flow_0c7ryff</bpmn:outgoing>
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<bpmn:script>StudyInfo documents_status</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:sequenceFlow id="Flow_142jtxs" sourceRef="Activity_0a14x7j" targetRef="Activity_DisplayDocsAndApprovals" />
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<bpmn:sequenceFlow id="Flow_0c7ryff" sourceRef="Activity_1aju60t" targetRef="Activity_0a14x7j" />
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<bpmn:sequenceFlow id="Flow_1k3su2q" sourceRef="StartEvent_1" targetRef="Activity_1aju60t" />
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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_1gmf4la">
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<bpmndi:BPMNEdge id="Flow_0m7unlb_di" bpmnElement="Flow_0m7unlb">
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<di:waypoint x="710" y="117" />
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<di:waypoint x="782" 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="192" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="EndEvent_1qvyxg7_di" bpmnElement="EndEvent_1qvyxg7">
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<dc:Bounds x="782" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_19nawos_di" bpmnElement="Activity_DisplayDocsAndApprovals">
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<dc:Bounds x="610" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_1bxk8h3_di" bpmnElement="Activity_0a14x7j">
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<dc:Bounds x="440" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_07ytvmv_di" bpmnElement="Activity_1aju60t">
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<dc:Bounds x="290" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNEdge id="Flow_142jtxs_di" bpmnElement="Flow_142jtxs">
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<di:waypoint x="540" y="117" />
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<di:waypoint x="610" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_0c7ryff_di" bpmnElement="Flow_0c7ryff">
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<di:waypoint x="390" y="117" />
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<di:waypoint x="440" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_1k3su2q_di" bpmnElement="Flow_1k3su2q">
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<di:waypoint x="228" y="117" />
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<di:waypoint x="290" 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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@ -79,6 +79,12 @@ class ExampleDataLoader:
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description="TBD",
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category_id=0,
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display_order=1)
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self.create_spec(id="documents_approvals",
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name="documents_approvals",
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display_name="Documents & Approvals",
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description="TBD",
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category_id=0,
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display_order=2)
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# Core Info
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self.create_spec(id="core_info",
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