Merge pull request #374 from sartography/zip-documents-379
Zip documents #379
This commit is contained in:
Dan Funk
GitHub
commit
9605bd3c1b
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@ -1,6 +1,7 @@
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from crc import session
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from crc.api.common import ApiError
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from crc.models.file import FileModel, FileDataModel
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from crc.api.file import to_file_api
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from crc.models.file import FileModel, FileDataModel, FileSchema
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from crc.scripts.script import Script
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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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@ -46,10 +47,10 @@ class GetZippedFiles(Script):
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zfw.writestr(file_name, file_data.data)
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with open(temp_file.name, mode='rb') as handle:
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file_model = FileService().add_workflow_file(workflow_id, None, task.name, zip_filename,
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file_model = FileService().add_workflow_file(workflow_id, None, task.get_name(), zip_filename,
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'application/zip', handle.read())
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return file_model
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# return file_model
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return FileSchema().dump(to_file_api(file_model))
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else:
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raise ApiError(code='missing_file_ids',
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message='You must include a list of file_ids.')
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@ -0,0 +1,83 @@
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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_d37e36c" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="4.2.0">
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<bpmn:process id="Process_SayHello" name="Say Hello" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>Flow_1o4d6ut</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="Flow_1o4d6ut" sourceRef="StartEvent_1" targetRef="Activity_GetFileIDs" />
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<bpmn:userTask id="Activity_GetFileIDs" name="Get File IDs" camunda:formKey="GetName">
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<bpmn:extensionElements>
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<camunda:formData>
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<camunda:formField id="file_id" label="File ID" type="long">
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<camunda:properties>
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<camunda:property id="repeat" value="file_ids" />
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</camunda:properties>
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<camunda:validation>
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<camunda:constraint name="required" config="True" />
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</camunda:validation>
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</camunda:formField>
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</camunda:formData>
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</bpmn:extensionElements>
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<bpmn:incoming>Flow_1o4d6ut</bpmn:incoming>
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<bpmn:outgoing>Flow_1ga7oo5</bpmn:outgoing>
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</bpmn:userTask>
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<bpmn:sequenceFlow id="Flow_1ga7oo5" sourceRef="Activity_GetFileIDs" targetRef="Activity_GetZip" />
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<bpmn:scriptTask id="Activity_GetZip" name="Get Zip">
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<bpmn:incoming>Flow_1ga7oo5</bpmn:incoming>
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<bpmn:outgoing>Flow_1uyi5u2</bpmn:outgoing>
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<bpmn:script>to_zip = []
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for file_id in file_ids:
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to_zip.append(file_id['file_id'])
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zip_file = get_zipped_files(file_ids=to_zip)</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:sequenceFlow id="Flow_1uyi5u2" sourceRef="Activity_GetZip" targetRef="Activity_DisplayZip" />
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<bpmn:manualTask id="Activity_DisplayZip" name="Display Zipped Files">
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<bpmn:documentation># To Zip
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{{ to_zip }}
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# Zip
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{{ zip_file }}</bpmn:documentation>
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<bpmn:incoming>Flow_1uyi5u2</bpmn:incoming>
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<bpmn:outgoing>Flow_0l42ysq</bpmn:outgoing>
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</bpmn:manualTask>
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<bpmn:endEvent id="Event_1sfhw21">
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<bpmn:incoming>Flow_0l42ysq</bpmn:incoming>
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</bpmn:endEvent>
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<bpmn:sequenceFlow id="Flow_0l42ysq" sourceRef="Activity_DisplayZip" targetRef="Event_1sfhw21" />
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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_SayHello">
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<bpmndi:BPMNEdge id="Flow_0l42ysq_di" bpmnElement="Flow_0l42ysq">
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<di:waypoint x="662" y="117" />
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<di:waypoint x="712" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_1uyi5u2_di" bpmnElement="Flow_1uyi5u2">
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<di:waypoint x="500" y="117" />
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<di:waypoint x="562" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_1ga7oo5_di" bpmnElement="Flow_1ga7oo5">
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<di:waypoint x="340" y="117" />
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<di:waypoint x="400" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_1o4d6ut_di" bpmnElement="Flow_1o4d6ut">
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<di:waypoint x="188" y="117" />
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<di:waypoint x="240" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="Activity_1jh8vhm_di" bpmnElement="Activity_DisplayZip">
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<dc:Bounds x="562" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_0ftuz3s_di" bpmnElement="Activity_GetFileIDs">
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<dc:Bounds x="240" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
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<dc:Bounds x="152" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_1qhfe35_di" bpmnElement="Activity_GetZip">
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<dc:Bounds x="400" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Event_1sfhw21_di" bpmnElement="Event_1sfhw21">
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<dc:Bounds x="712" 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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@ -1,10 +1,7 @@
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from tests.base_test import BaseTest
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from crc import session
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from crc.models.file import FileModel, FileDataModel
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from crc.models.workflow import WorkflowModel
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from crc.models.study import StudyModel
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from crc.scripts.get_zipped_files import GetZippedFiles
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from crc.models.file import FileDataModel
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from crc.services.file_service import FileService
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import io
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@ -16,40 +13,38 @@ class TestGetZippedFiles(BaseTest):
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def test_get_zipped_files(self):
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self.load_example_data()
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study = session.query(StudyModel).order_by(StudyModel.id.desc()).first()
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workflow = session.query(WorkflowModel).first()
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workflow = self.create_workflow('get_zip_file')
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study_id = workflow.study_id
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workflow_api = self.get_workflow_api(workflow)
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task = workflow_api.next_task
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# Add files to use in the test
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FileService.add_workflow_file(workflow_id=workflow.id,
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model_1 = FileService.add_workflow_file(workflow_id=workflow.id,
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name="document_1.png", content_type="text",
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task_spec_name=task.name,
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binary_data=b'1234', irb_doc_code='Study_Protocol_Document')
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FileService.add_workflow_file(workflow_id=workflow.id,
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model_2 = FileService.add_workflow_file(workflow_id=workflow.id,
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name="document_2.txt", content_type="text",
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task_spec_name=task.name,
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binary_data=b'1234', irb_doc_code='Study_App_Doc')
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FileService.add_workflow_file(workflow_id=workflow.id,
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model_3 = FileService.add_workflow_file(workflow_id=workflow.id,
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name="document_3.pdf", content_type="text",
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task_spec_name=task.name,
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binary_data=b'1234', irb_doc_code='Admin_AdvChklst')
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binary_data=b'1234', irb_doc_code='AD_Consent_Model')
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# Gather the file_ids
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file_ids = []
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files = session.query(FileModel).filter(FileModel.irb_doc_code != '').all()
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for file in files:
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file_ids.append(file.id)
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file_ids = [{'file_id': model_1.id}, {'file_id': model_2.id}, {'file_id': model_3.id}]
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workflow_api = self.complete_form(workflow, task, {'file_ids': file_ids})
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next_task = workflow_api.next_task
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file_model_id = next_task.data['zip_file']['id']
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# Send files to the zipper, receive file_model in return
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file_model = GetZippedFiles().do_task(task, study.id, workflow.id, file_ids=file_ids, filename='another_attachment.zip')
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file_data = session.query(FileDataModel).filter(FileDataModel.file_model_id == file_model.id).first()
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file_data = session.query(FileDataModel).filter(FileDataModel.file_model_id == file_model_id).first()
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# Test what we get back in the file_model
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# Test what we get back in the zipped file
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with zipfile.ZipFile(io.BytesIO(file_data.data), 'r') as zf:
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self.assertIsInstance(zf, zipfile.ZipFile)
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for name in zf.namelist():
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info = zf.getinfo(name)
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self.assertIn(os.path.basename(info.filename), ['1 Protocol document_1.png', '1 Application document_2.txt', '1 document_3.pdf'])
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self.assertIn(os.path.basename(info.filename), [f'{study_id} Protocol document_1.png', f'{study_id} Application document_2.txt', f'{study_id} Model document_3.pdf'])
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file = zf.read(name)
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self.assertEqual(b'1234', file)
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