133 lines
5.8 KiB
Python
133 lines
5.8 KiB
Python
import io
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import connexion
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from flask import send_file
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from crc import session
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from crc.api.common import ApiErrorSchema, ApiError
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from crc.models.file import FileModelSchema, FileModel, FileDataModel
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from crc.models.workflow import WorkflowSpecModel
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from crc.services.file_service import FileService
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def get_files(workflow_spec_id=None, study_id=None, workflow_id=None, task_id=None, form_field_key=None):
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if all(v is None for v in [workflow_spec_id, study_id, workflow_id, task_id, form_field_key]):
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return ApiErrorSchema().dump(ApiError('missing_parameter',
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'Please specify at least one of workflow_spec_id, study_id, '
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'workflow_id, and task_id for this file in the HTTP parameters')), 400
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results = FileService.get_files(workflow_spec_id, study_id, workflow_id, task_id, form_field_key)
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return FileModelSchema(many=True).dump(results)
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def get_reference_files():
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results = FileService.get_files(is_reference=True)
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return FileModelSchema(many=True).dump(results)
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def add_file(workflow_spec_id=None, study_id=None, workflow_id=None, task_id=None, form_field_key=None):
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all_none = all(v is None for v in [workflow_spec_id, study_id, workflow_id, task_id, form_field_key])
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missing_some = (workflow_spec_id is None) and (None in [study_id, workflow_id, task_id, form_field_key])
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if all_none or missing_some:
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return ApiErrorSchema().dump(ApiError('missing_parameter',
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'Please specify either a workflow_spec_id or all 3 of study_id, '
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'workflow_id, task_id and field_id for this file in the HTTP parameters')), 404
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if 'file' not in connexion.request.files:
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return ApiErrorSchema().dump(ApiError('invalid_file',
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'Expected a file named "file" in the multipart form request')), 404
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file = connexion.request.files['file']
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if workflow_spec_id:
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workflow_spec = session.query(WorkflowSpecModel).filter_by(id=workflow_spec_id).first()
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file_model = FileService.add_workflow_spec_file(workflow_spec, file.filename, file.content_type, file.stream.read())
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else:
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file_model = FileService.add_form_field_file(study_id, workflow_id, task_id, form_field_key, file.filename, file.content_type, file.stream.read())
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return FileModelSchema().dump(file_model)
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def get_reference_file(name):
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file_data = FileService.get_reference_file_data(name)
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return send_file(
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io.BytesIO(file_data.data),
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attachment_filename=file_data.file_model.name,
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mimetype=file_data.file_model.content_type,
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cache_timeout=-1 # Don't cache these files on the browser.
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)
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def set_reference_file(name):
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"""Uses the file service to manage reference-files. They will be used in script tasks to compute values."""
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if 'file' not in connexion.request.files:
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raise ApiError('invalid_file',
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'Expected a file named "file" in the multipart form request', status_code=400)
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file = connexion.request.files['file']
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name_extension = FileService.get_extension(name)
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file_extension = FileService.get_extension(file.filename)
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if name_extension != file_extension:
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raise ApiError('invalid_file_type',
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"The file you uploaded has an extension '%s', but it should have an extension of '%s' " %
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(file_extension, name_extension))
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file_models = FileService.get_files(name=name, is_reference=True)
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if len(file_models) == 0:
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file_model = FileService.add_reference_file(name, file.content_type, file.stream.read())
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else:
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file_model = file_models[0]
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FileService.update_file(file_models[0], file.stream.read(), file.content_type)
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return FileModelSchema().dump(file_model)
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def update_file_data(file_id):
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file_model = session.query(FileModel).filter_by(id=file_id).with_for_update().first()
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file = connexion.request.files['file']
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if file_model is None:
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return ApiErrorSchema().dump(ApiError('no_such_file', 'The file id you provided does not exist')), 404
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file_model = FileService.update_file(file_model, file.stream.read(), file.content_type)
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return FileModelSchema().dump(file_model)
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def get_file_data(file_id):
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file_data = FileService.get_file_data(file_id)
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if file_data is None:
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return ApiErrorSchema().dump(ApiError('no_such_file', 'The file id you provided does not exist')), 404
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return send_file(
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io.BytesIO(file_data.data),
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attachment_filename=file_data.file_model.name,
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mimetype=file_data.file_model.content_type,
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cache_timeout=-1 # Don't cache these files on the browser.
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)
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def get_file_info(file_id):
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file_model = session.query(FileModel).filter_by(id=file_id).with_for_update().first()
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if file_model is None:
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return ApiErrorSchema().dump(ApiError('no_such_file', 'The file id you provided does not exist')), 404
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return FileModelSchema().dump(file_model)
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def update_file_info(file_id, body):
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if file_id is None:
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error = ApiError('unknown_file', 'Please provide a valid File ID.')
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return ApiErrorSchema.dump(error), 404
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file_model = session.query(FileModel).filter_by(id=file_id).first()
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if file_model is None:
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error = ApiError('unknown_file_model', 'The file_model "' + file_id + '" is not recognized.')
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return ApiErrorSchema.dump(error), 404
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file_model = FileModelSchema().load(body, session=session)
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session.add(file_model)
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session.commit()
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return FileModelSchema().dump(file_model)
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def delete_file(file_id):
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session.query(FileDataModel).filter_by(file_model_id=file_id).delete()
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session.query(FileModel).filter_by(id=file_id).delete()
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session.commit()
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