Upload DICOM images with FTPS

orthanc/orthanc-anon/plugin/pixl.py

@@ -31,6 +31,7 @@
 
 import requests
 import yaml
+from core import upload
 from decouple import config
 from pydicom import dcmread
 
@@ -156,6 +157,34 @@ def SendViaStow(resourceId):
         orthanc.LogError("Failed to send via STOW")
 
 
+def SendViaFTPS(resourceId):
+    """
+    Makes a POST API call to upload the resource to a dicom-web server
+    using orthanc credentials as authorisation
+    """
+    ORTHANC_USERNAME = config("ORTHANC_USERNAME")
+    ORTHANC_PASSWORD = config("ORTHANC_PASSWORD")
+
+    orthanc_url = "http://localhost:8042"
+
+    # Query orthanc-anon for the study
+    query = f"{orthanc_url}/studies/{resourceId}/archive"
+    try:
+        response_study = requests.get(
+            query, verify=False, auth=(ORTHANC_USERNAME, ORTHANC_PASSWORD)
+        )
+        if response_study.status_code != 200:
+            raise RuntimeError(f"Could not download archive of resource '{resourceId}'")
+    except requests.exceptions.RequestException:
+        orthanc.LogError(f"Failed to query'{resourceId}'")
+
+    # get the zip content
+    zip_content = response_study.content
+    logging.info("Downloaded data: %s", zip_content)
+
+    upload.upload_content(zip_content, resourceId)
+
+
 def ShouldAutoRoute():
     """
     Checks whether ORTHANC_AUTOROUTE_ANON_TO_AZURE environment variable is

pixl_core/src/core/_database.py

@@ -0,0 +1,80 @@
+#  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.
+
+"""Interaction with the PIXL database."""
+from typing import TYPE_CHECKING
+
+from decouple import config
+from sqlalchemy import URL, create_engine
+from sqlalchemy.orm import sessionmaker
+
+from core.database import Extract, Image
+
+if TYPE_CHECKING:
+    from datetime import datetime
+
+url = URL.create(
+    drivername="postgresql+psycopg2",
+    username=config("PIXL_DB_USER", default="None"),
+    password=config("PIXL_DB_PASSWORD", default="None"),
+    host=config("PIXL_DB_HOST", default="None"),
+    port=config("PIXL_DB_PORT", default=1),
+    database=config("PIXL_DB_NAME", default="None"),
+)
+
+engine = create_engine(url)
+
+
+def get_project_slug_from_db(hashed_value: str) -> Image:
+    PixlSession = sessionmaker(engine)
+    with PixlSession() as pixl_session, pixl_session.begin():
+        existing_image = (
+            pixl_session.query(Image)
+            .filter(
+                Image.hashed_identifier == hashed_value,
+            )
+            .one()
+        )
+
+        existing_extract = (
+            pixl_session.query(Extract)
+            .filter(
+                Extract.extract_id == existing_image.extract_id,
+            )
+            .one()
+        )
+
+        return existing_extract.slug
+
+
+def update_exported_at_and_save(hashed_value: str, date_time: datetime) -> Image:
+    PixlSession = sessionmaker(engine)
+    with PixlSession() as pixl_session, pixl_session.begin():
+        existing_image = (
+            pixl_session.query(Image)
+            .filter(
+                Image.hashed_identifier == hashed_value,
+            )
+            .one()
+        )
+        existing_image.exported_at = date_time
+        pixl_session.add(existing_image)
+
+        updated_image = (
+            pixl_session.query(Image)
+            .filter(Image.hashed_identifier == hashed_value, Image.exported_at == date_time)
+            .one_or_none()
+        )
+
+        return updated_image

pixl_core/src/core/upload.py

@@ -3,35 +3,47 @@
 import ftplib
 import logging
 import os
+from datetime import datetime
 from ftplib import FTP_TLS
 from pathlib import Path
 
+from core._database import get_project_slug_from_db, update_exported_at_and_save
+
 logger = logging.getLogger(__name__)
 
 # Make a DSHUploader class that takes a project slug and study pseudonymised id?
 
 
 def upload_file(local_file_path: Path) -> str:
+    """Upload local file to hardcoded directory in ftp server."""
+    output_filename = local_file_path.name
+    # Store the file using a binary handler
+    with local_file_path.open("rb") as file_content:
+        upload_content(file_content, output_filename)
+
+
+def upload_content(content: bytes, pseudo_anon_id: str) -> str:
     """Upload local file to hardcoded directory in ftp server."""
     ftp = _connect_to_ftp()
 
     # Create the remote directory if it doesn't exist
     # TODO: rename destination to {project-slug}/{study-pseduonymised-id}.zip
+    remote_directory = get_project_slug_from_db(pseudo_anon_id)
 
-    remote_directory = "new-extract"
     _create_and_set_as_cwd(ftp, remote_directory)
+    output_filename = pseudo_anon_id + ".zip"
 
-    output_filename = local_file_path.name
     # Store the file using a binary handler
-    with local_file_path.open("rb") as local_file:
-        command = f"STOR {output_filename}"
-        logger.info("Running %s", command)
-        ftp.storbinary(command, local_file)
+    command = f"STOR {output_filename}"
+    logger.info("Running %s", command)
+    ftp.storbinary(command, content)
 
     # Close the FTP connection
     ftp.quit()
     logger.info("Done!")
 
+    update_exported_at_and_save(datetime.now)
+
     return f"{remote_directory} / {output_filename}"