Add SFTP uploader #607
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| # Copyright (c) University College London Hospitals NHS Foundation Trust | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
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| """Uploader subclass for SFTP.""" | ||
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| import os | ||
| from collections.abc import Generator | ||
| from contextlib import contextmanager | ||
| from typing import BinaryIO, Optional | ||
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| import paramiko | ||
| from loguru import logger | ||
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| from core.exports import ParquetExport | ||
| from core.uploader._orthanc import StudyTags, get_study_zip_archive | ||
| from core.uploader.base import Uploader | ||
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| class SFTPUploader(Uploader): | ||
| """Upload strategy for an SFTP server.""" | ||
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| def __init__(self, project_slug: str, keyvault_alias: Optional[str]) -> None: | ||
| """Create instance of parent class""" | ||
| super().__init__(project_slug, keyvault_alias) | ||
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| def _set_config(self) -> None: | ||
| """Set the configuration for the SFTP uploader.""" | ||
| # Use the Azure KV alias as prefix if it exists, otherwise use the project name | ||
| az_prefix = self.keyvault_alias | ||
| az_prefix = az_prefix if az_prefix else self.project_slug | ||
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| # Get SFTP connection details from keyvault | ||
| self.host = self.keyvault.fetch_secret(f"{az_prefix}--sftp--host") | ||
| self.username = self.keyvault.fetch_secret(f"{az_prefix}--sftp--username") | ||
| self.password = self.keyvault.fetch_secret(f"{az_prefix}--sftp--password") | ||
| self.port = int(self.keyvault.fetch_secret(f"{az_prefix}--sftp--port")) | ||
| self.known_hosts_path = self.keyvault.fetch_secret(f"{az_prefix}--sftp--known-hosts-path") | ||
|
Member
Author
There was a problem hiding this comment. Might make more sense to pass in the host key itself, instead of a |
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| def _upload_dicom_image(self, study_id: str, study_tags: StudyTags) -> None: | ||
| """ | ||
| Upload DICOM image via SFTP. | ||
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| :param study_id: Orthanc Study ID | ||
| :param study_tags: Study tags containing metadata | ||
| """ | ||
| # Get DICOM zip archive from Orthanc | ||
| zip_content = get_study_zip_archive(study_id) | ||
| self.send_via_sftp( | ||
| zip_content, | ||
| study_tags.pseudo_anon_image_id, | ||
| remote_directory=self.project_slug, | ||
| ) | ||
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| def send_via_sftp( | ||
| self, zip_content: BinaryIO, pseudo_anon_image_id: str, remote_directory: str | ||
| ) -> None: | ||
| """Send the zip content to the SFTP server.""" | ||
| filename = f"{pseudo_anon_image_id}.zip" | ||
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| with self._connect_client() as sftp_client: | ||
| _sftp_create_remote_directory(sftp_client, remote_directory) | ||
| sftp_client.chdir(remote_directory) | ||
| sftp_client.putfo(zip_content, filename) | ||
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| def upload_parquet_files(self, parquet_export: ParquetExport, remote_directory: str) -> None: | ||
| """ | ||
| Upload parquet to SFTP under <project name>/<extract datetime>/parquet. | ||
| :param parquet_export: instance of the ParquetExport class | ||
| The final directory structure will look like this: | ||
| <project-slug> | ||
| ├── <extract_datetime_slug> | ||
| │ └── parquet | ||
| │ ├── omop | ||
| │ │ └── public | ||
| │ │ └── PROCEDURE_OCCURRENCE.parquet | ||
| │ └── radiology | ||
| │ └── IMAGE_LINKER.parquet | ||
| ├── <pseudonymised_ID_DICOM_dataset_1>.zip | ||
| └── <pseudonymised_ID_DICOM_dataset_2>.zip | ||
| ... | ||
| """ | ||
| logger.info("Starting SFTP upload of files for '{}'", parquet_export.project_slug) | ||
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| source_root_dir = parquet_export.current_extract_base | ||
| source_files = [f for f in source_root_dir.rglob("*.parquet") if f.is_file()] | ||
| if not source_files: | ||
| msg = f"No files found in {source_root_dir}" | ||
| raise FileNotFoundError(msg) | ||
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| parquet_dir = f"{parquet_export.project_slug}/{parquet_export.extract_time_slug}/parquet" | ||
| upload_dir = f"{remote_directory}/{parquet_dir}" | ||
| with self._connect_client() as sftp_client: | ||
| _sftp_create_remote_directory(sftp_client, upload_dir) | ||
| for source_path in source_files: | ||
| sftp_client.chdir(None) # reset | ||
| sftp_client.chdir(upload_dir) | ||
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| source_rel_path = source_path.relative_to(source_root_dir) | ||
| source_rel_dir = source_rel_path.parent | ||
| source_filename_only = source_rel_path.relative_to(source_rel_dir) | ||
| _sftp_create_remote_directory(sftp_client, str(source_rel_dir)) | ||
| sftp_client.chdir(str(source_rel_dir)) | ||
| sftp_client.put(source_path, str(source_filename_only)) | ||
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| logger.info("Finished SFTP upload of files for '{}'", parquet_export.project_slug) | ||
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| @contextmanager | ||
| def _connect_client(self) -> Generator[paramiko.SFTPClient, None, None]: | ||
| """Connect to the SFTP client as a context manager""" | ||
| ssh_client = paramiko.SSHClient() | ||
| ssh_client.set_missing_host_key_policy(paramiko.RejectPolicy()) | ||
| ssh_client.load_host_keys(self.known_hosts_path) | ||
| ssh_client.connect( | ||
| self.host, port=self.port, username=self.username, password=self.password | ||
| ) | ||
| sftp_client = ssh_client.open_sftp() | ||
| try: | ||
| yield sftp_client | ||
| finally: | ||
| sftp_client.close() | ||
| ssh_client.close() | ||
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| def _sftp_create_remote_directory(sftp_client: paramiko.SFTPClient, directory: str) -> None: | ||
| """ | ||
| Create remote directory and its parents if it doesn't exist. | ||
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| :param sftp_client: SFTP client instance | ||
| :param directory: Directory path to create | ||
| """ | ||
| try: | ||
| sftp_client.stat(directory) | ||
| except OSError: | ||
| parent_dir = os.path.dirname(directory) # noqa: PTH120 | ||
| _sftp_create_remote_directory(sftp_client, str(parent_dir)) | ||
| sftp_client.mkdir(directory) | ||
| logger.debug(f"Created remote directory: {directory}") | ||
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Probably makes more sense to pass in a private SSH key here for authentication, instead of password.