Merge pull request #466 from sartography/feature/modify-spreadsheet-624
Feature/modify spreadsheet #624
This commit is contained in:
Dan Funk
GitHub
commit
78c9dc1b7b
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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.scripts.script import Script
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from io import BytesIO
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from openpyxl import load_workbook
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from openpyxl.writer.excel import save_virtual_workbook
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class ModifySpreadsheet(Script):
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@staticmethod
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def get_parameters(args, kwargs):
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parameters = {}
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if len(args) == 3 or ('irb_doc_code' in kwargs and 'cell' in kwargs and 'text' in kwargs):
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if 'irb_doc_code' in kwargs and 'line' in kwargs and 'text' in kwargs:
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parameters['irb_doc_code'] = (kwargs['irb_doc_code'])
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parameters['cell'] = (kwargs['cell'])
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parameters['text'] = (kwargs['text'])
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else:
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parameters['irb_doc_code'] = (args[0])
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parameters['cell'] = (args[1])
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parameters['text'] = (args[2])
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return parameters
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def get_description(self):
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return """Script to modify an existing spreadsheet.
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It inserts text into a spreadsheet in the cell indicated.
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Requires 'irb_doc_code', 'cell', and 'text' parameters.
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Example: modify_spreadsheet('Finance_BCA', 'C4', 'This is my inserted text')
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Example: modify_spreadsheet(irb_doc_code='Finance_BCA', cell='C4', text='This is my inserted text')
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"""
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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parameters = self.get_parameters(args, kwargs)
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if len(parameters) == 3:
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return True
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else:
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raise ApiError(code='missing_parameters',
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message='The modify_spreadsheet script requires 3 parameters: irb_doc_code, cell, and text')
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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parameters = self.get_parameters(args, kwargs)
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if len(parameters) == 3:
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spreadsheet = session.query(FileModel). \
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filter(FileModel.workflow_id == workflow_id). \
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filter(FileModel.irb_doc_code == parameters['irb_doc_code']).\
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first()
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if spreadsheet:
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spreadsheet_data = session.query(FileDataModel).\
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filter(FileDataModel.file_model_id==spreadsheet.id).\
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first()
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workbook = load_workbook(BytesIO(spreadsheet_data.data))
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sheet = workbook.active
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sheet[parameters['cell']] = parameters['text']
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data_string = save_virtual_workbook(workbook)
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spreadsheet_data.data = data_string
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session.commit()
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else:
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raise ApiError(code='missing_spreadsheet',
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message=f"The spreadshhet you want to modify does not exist. Workflow ID is {workflow_id}, and IRB Doc Code is {parameters['irb_doc_code']}")
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else:
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raise ApiError(code='missing_parameters',
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message='The modify_spreadsheet script requires 3 parameters: irb_doc_code, cell, and text')
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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_1wrf54p" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="4.2.0">
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<bpmn:process id="Process_ModifySpreadsheet" name="Modify Spreadsheet" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>Flow_03wyga3</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="Flow_03wyga3" sourceRef="StartEvent_1" targetRef="Activity_FileUpload" />
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<bpmn:sequenceFlow id="Flow_0msewj5" sourceRef="Activity_FileUpload" targetRef="Activity_GetModifyData" />
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<bpmn:sequenceFlow id="Flow_0fpc32g" sourceRef="Activity_GetModifyData" targetRef="Activity_ModifySpreadsheet" />
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<bpmn:sequenceFlow id="Flow_10ulj3l" sourceRef="Activity_ModifySpreadsheet" targetRef="Event_1d07dls" />
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<bpmn:endEvent id="Event_1d07dls">
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<bpmn:incoming>Flow_10ulj3l</bpmn:incoming>
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</bpmn:endEvent>
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<bpmn:userTask id="Activity_FileUpload" name="Upload Spreadsheet" camunda:formKey="FileUpload">
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<bpmn:extensionElements>
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<camunda:formData>
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<camunda:formField id="Finance_BCA" label="'File Upload'" type="file">
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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_03wyga3</bpmn:incoming>
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<bpmn:outgoing>Flow_0msewj5</bpmn:outgoing>
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</bpmn:userTask>
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<bpmn:scriptTask id="Activity_ModifySpreadsheet" name="Modify Spreadsheet">
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<bpmn:incoming>Flow_0fpc32g</bpmn:incoming>
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<bpmn:outgoing>Flow_10ulj3l</bpmn:outgoing>
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<bpmn:script>modify_spreadsheet('Finance_BCA', cell_indicator, input_text)</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:userTask id="Activity_GetModifyData" name="Get Modify Data" camunda:formKey="ModifyData">
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<bpmn:documentation>## File Upload
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{{ Finance_BCA }}</bpmn:documentation>
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<bpmn:extensionElements>
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<camunda:formData>
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<camunda:formField id="cell_indicator" label="Cell Indicator" type="string">
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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:formField id="input_text" label="Input Text" type="string">
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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_0msewj5</bpmn:incoming>
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<bpmn:outgoing>Flow_0fpc32g</bpmn:outgoing>
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</bpmn:userTask>
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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_ModifySpreadsheet">
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<bpmndi:BPMNEdge id="Flow_10ulj3l_di" bpmnElement="Flow_10ulj3l">
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<di:waypoint x="691" y="117" />
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<di:waypoint x="912" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_0fpc32g_di" bpmnElement="Flow_0fpc32g">
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<di:waypoint x="530" y="117" />
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<di:waypoint x="591" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_0msewj5_di" bpmnElement="Flow_0msewj5">
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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:BPMNEdge id="Flow_03wyga3_di" bpmnElement="Flow_03wyga3">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="270" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
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<dc:Bounds x="179" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Event_1d07dls_di" bpmnElement="Event_1d07dls">
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<dc:Bounds x="912" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_0jut75d_di" bpmnElement="Activity_FileUpload">
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<dc:Bounds x="270" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_0uk32ds_di" bpmnElement="Activity_ModifySpreadsheet">
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<dc:Bounds x="591" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_0hn4ju2_di" bpmnElement="Activity_GetModifyData">
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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:BPMNPlane>
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</bpmndi:BPMNDiagram>
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</bpmn:definitions>
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from tests.base_test import BaseTest
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from crc import app, session
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from crc.models.file import FileModel, FileDataModel
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from crc.services.user_file_service import UserFileService
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from io import BytesIO
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from openpyxl import load_workbook
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import os
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class TestModifySpreadsheet(BaseTest):
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def upload_spreadsheet(self, workflow, task, irb_doc_code):
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filepath = os.path.join(app.root_path, '..', 'tests', 'data',
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'modify_spreadsheet', 'test_spreadsheet.xlsx')
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with open(filepath, 'br') as f_open:
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ss_data = f_open.read()
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file_model = UserFileService.add_workflow_file(workflow_id=workflow.id,
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task_spec_name=task.name,
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name="test_spreadsheet.xlsx", content_type="text",
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binary_data=ss_data, irb_doc_code=irb_doc_code)
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workflow_api = self.complete_form(workflow, task, {irb_doc_code: {'id': file_model.id}})
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return workflow_api
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@staticmethod
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def get_sheet(workflow_id, irb_doc_code):
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spreadsheet = session.query(FileModel). \
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filter(FileModel.workflow_id == workflow_id). \
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filter(FileModel.irb_doc_code == irb_doc_code). \
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first()
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spreadsheet_data = session.query(FileDataModel). \
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filter(FileDataModel.file_model_id == spreadsheet.id). \
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first()
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workbook = load_workbook(BytesIO(spreadsheet_data.data))
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sheet = workbook.active
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return sheet
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def test_modify_spreadsheet(self):
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irb_doc_code = 'Finance_BCA'
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cell_indicator = 'C4'
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input_text = 'This is my input text.'
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workflow = self.create_workflow('modify_spreadsheet')
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workflow_api = self.get_workflow_api(workflow)
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task = workflow_api.next_task
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workflow_api = self.upload_spreadsheet(workflow, task, irb_doc_code)
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sheet = self.get_sheet(workflow.id, irb_doc_code)
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self.assertEqual(None, sheet[cell_indicator].value)
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task = workflow_api.next_task
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self.complete_form(workflow, task, {'cell_indicator': cell_indicator,
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'input_text': input_text})
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sheet = self.get_sheet(workflow.id, irb_doc_code)
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self.assertEqual(input_text, sheet[cell_indicator].value)
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def test_missing_spreadsheet(self):
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"""The modify_spreadsheet has Finance_BCA hard-coded as the spreadsheet to modify.
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In this test we upload a spreadsheet with a different doc code,
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and assert that we raise an error when the Finance_BCA spreadsheet does not exist"""
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irb_doc_code = 'Finance_GPRF'
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cell_indicator = 'C4'
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input_text = 'This is my input text.'
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workflow = self.create_workflow('modify_spreadsheet')
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workflow_api = self.get_workflow_api(workflow)
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task = workflow_api.next_task
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workflow_api = self.upload_spreadsheet(workflow, task, irb_doc_code)
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task = workflow_api.next_task
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with self.assertRaises(AssertionError):
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self.complete_form(workflow, task, {'cell_indicator': cell_indicator,
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'input_text': input_text})
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