FileModel => DocumentModel
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parent
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@ -1,7 +1,7 @@
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from crc import session
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from crc import session
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from crc.api.common import ApiError
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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.data_store import DataStoreModel
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from crc.models.file import FileModel
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from crc.models.file import DocumentModel
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from crc.models.task_event import TaskEventModel
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from crc.models.task_event import TaskEventModel
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from crc.scripts.script import Script
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from crc.scripts.script import Script
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from crc.services.document_service import DocumentService
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from crc.services.document_service import DocumentService
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@ -38,14 +38,14 @@ class DeleteTaskData(Script):
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TaskEventModel.study_id == study_id).filter(TaskEventModel.task_name == task_spec_name).filter_by(
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TaskEventModel.study_id == study_id).filter(TaskEventModel.task_name == task_spec_name).filter_by(
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action=WorkflowService.TASK_ACTION_COMPLETE).delete()
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action=WorkflowService.TASK_ACTION_COMPLETE).delete()
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files_to_delete = session.query(FileModel). \
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files_to_delete = session.query(DocumentModel). \
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filter(FileModel.workflow_id == workflow_id). \
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filter(DocumentModel.workflow_id == workflow_id). \
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filter(FileModel.task_spec == task_spec_name).all()
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filter(DocumentModel.task_spec == task_spec_name).all()
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# delete files
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# delete files
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for file in files_to_delete:
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for file in files_to_delete:
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UserFileService().delete_file(file.id)
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UserFileService().delete_file(file.id)
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# delete the data store
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# delete the data store
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session.query(DataStoreModel). \
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# session.query(DataStoreModel). \
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filter(DataStoreModel.file_id == file.id).delete()
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# filter(DataStoreModel.file_id == file.id).delete()
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@ -1,7 +1,7 @@
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from crc import session
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from crc import session
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from crc.api.common import ApiError
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from crc.api.common import ApiError
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from crc.api.file import to_file_api
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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.models.file import DocumentModel, FileSchema
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from crc.scripts.script import Script
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from crc.scripts.script import Script
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from crc.services.study_service import StudyService
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from crc.services.study_service import StudyService
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@ -36,7 +36,7 @@ class GetZippedFiles(Script):
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zip_filename = 'attachments.zip'
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zip_filename = 'attachments.zip'
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file_ids = kwargs['file_ids']
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file_ids = kwargs['file_ids']
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files = session.query(FileModel).filter(FileModel.id.in_(file_ids)).all()
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files = session.query(DocumentModel).filter(DocumentModel.id.in_(file_ids)).all()
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if files:
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if files:
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# Create a temporary zipfile with the requested files
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# Create a temporary zipfile with the requested files
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with tempfile.NamedTemporaryFile() as temp_file:
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with tempfile.NamedTemporaryFile() as temp_file:
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@ -44,8 +44,8 @@ class GetZippedFiles(Script):
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for file in files:
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for file in files:
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zip_key_words = doc_info[file.irb_doc_code]['zip_key_words']
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zip_key_words = doc_info[file.irb_doc_code]['zip_key_words']
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file_name = f'{study_id} {zip_key_words} {file.name}'
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file_name = f'{study_id} {zip_key_words} {file.name}'
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file_data = session.query(FileDataModel).filter(FileDataModel.file_model_id == file.id).first()
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# file_data = session.query(FileDataModel).filter(FileDataModel.file_model_id == file.id).first()
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zfw.writestr(file_name, file_data.data)
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zfw.writestr(file_name, file.data)
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with open(temp_file.name, mode='rb') as handle:
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with open(temp_file.name, mode='rb') as handle:
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if 'doc_code' in kwargs:
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if 'doc_code' in kwargs:
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@ -1,6 +1,6 @@
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from crc import session
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from crc import session
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from crc.api.common import ApiError
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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.models.file import DocumentModel
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from crc.scripts.script import Script
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from crc.scripts.script import Script
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from io import BytesIO
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from io import BytesIO
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@ -44,19 +44,16 @@ class ModifySpreadsheet(Script):
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parameters = self.get_parameters(args, kwargs)
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parameters = self.get_parameters(args, kwargs)
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if len(parameters) == 3:
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if len(parameters) == 3:
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spreadsheet = session.query(FileModel). \
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spreadsheet = session.query(DocumentModel). \
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filter(FileModel.workflow_id == workflow_id). \
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filter(DocumentModel.workflow_id == workflow_id). \
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filter(FileModel.irb_doc_code == parameters['irb_doc_code']).\
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filter(DocumentModel.irb_doc_code == parameters['irb_doc_code']).\
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first()
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first()
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if spreadsheet:
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if spreadsheet:
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spreadsheet_data = session.query(FileDataModel).\
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workbook = load_workbook(BytesIO(spreadsheet.data))
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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 = workbook.active
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sheet[parameters['cell']] = parameters['text']
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sheet[parameters['cell']] = parameters['text']
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data_string = save_virtual_workbook(workbook)
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data_string = save_virtual_workbook(workbook)
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spreadsheet_data.data = data_string
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spreadsheet.data = data_string
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session.commit()
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session.commit()
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else:
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else:
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raise ApiError(code='missing_spreadsheet',
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raise ApiError(code='missing_spreadsheet',
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