feat: upload drs object endpoint

cloud_storage_handler/api/elixircloud/csh/controllers.py

@@ -1,15 +1,127 @@
 """ELIXIR's Cloud Storage Handler controllers."""
 
+import hashlib
 import logging
+import os
+import tempfile
+import uuid
 from http import HTTPStatus
 
-from flask import jsonify
+from flask import current_app, jsonify, request
+from minio import S3Error
 
 logger = logging.getLogger(__name__)
 
+TUS_UPLOAD_DIR = tempfile.gettempdir()
+
 
 def home():
     """Endpoint to return a welcome message."""
     return jsonify(
         {"message": "Welcome to the Cloud Storage Handler server!"}
     ), HTTPStatus.OK
+
+
+def compute_file_hash(file_path):
+    """Compute SHA-256 hash of the file."""
+    hash_sha256 = hashlib.sha256()
+    with open(file_path, "rb") as f:
+        for chunk in iter(lambda: f.read(4096), b""):
+            hash_sha256.update(chunk)
+    return hash_sha256.hexdigest()
+
+
+def initiate_upload():
+    """Initiate TUS upload, creates object and returns object_id."""
+    object_id = str(uuid.uuid4())
+    object_path = os.path.join(TUS_UPLOAD_DIR, f"{object_id}.temp")
+    os.makedirs(TUS_UPLOAD_DIR, exist_ok=True)
+
+    open(object_path, "wb").close()
+
+    return jsonify({"object_id": object_id}), HTTPStatus.CREATED
+
+
+def upload_chunk(object_id):
+    """Upload a object chunk based on object_id and content-range."""
+    if request.method == "OPTIONS":
+        response = jsonify({"status": "CORS preflight check"})
+        response.headers.add("Access-Control-Allow-Origin", "*")
+        response.headers.add(
+            "Access-Control-Allow-Methods", "GET, POST, PATCH, PUT, DELETE, OPTIONS"
+        )
+        response.headers.add(
+            "Access-Control-Allow-Headers", "Content-Type,Authorization"
+        )
+
+    object_path = os.path.join(TUS_UPLOAD_DIR, f"{object_id}.temp")
+    if not os.path.exists(object_path):
+        return jsonify({"error": "object not found"}), HTTPStatus.NOT_FOUND
+
+    try:
+        content_range = request.headers.get("Content-Range")
+        start_byte = int(content_range.split(" ")[1].split("-")[0])
+
+        with open(object_path, "r+b") as f:
+            f.seek(start_byte)
+            f.write(request.data)
+
+        return jsonify(
+            {"message": "Chunk uploaded successfully"}
+        ), HTTPStatus.NO_CONTENT
+    except Exception as e:
+        return jsonify({"error": str(e)}), HTTPStatus.INTERNAL_SERVER_ERROR
+
+
+def complete_upload(object_id):
+    """Complete upload by transferring the object to MinIO after TUS upload."""
+    minio_config = current_app.config.foca.custom.minio
+    bucket_name = minio_config.bucket_name
+    minio_client = current_app.config.foca.custom.minio.client.client
+    object_path = os.path.join(TUS_UPLOAD_DIR, f"{object_id}.temp")
+
+    if not os.path.exists(object_path):
+        return jsonify({"error": "object not found"}), HTTPStatus.NOT_FOUND
+
+    try:
+        # Compute the file's hash
+        file_hash = compute_file_hash(object_path)
+
+        # Check if an object with the same hash exists in MinIO
+        found_duplicate = False
+        for obj in minio_client.list_objects(bucket_name):
+            obj_info = minio_client.stat_object(bucket_name, obj.object_name)
+            if (
+                "file-hash" in obj_info.metadata
+                and obj_info.metadata["file-hash"] == file_hash
+            ):
+                found_duplicate = True
+                break
+
+        if found_duplicate:
+            os.remove(object_path)
+            return jsonify(
+                {"message": "Duplicate object detected. Upload skipped."}
+            ), HTTPStatus.CONFLICT
+
+        minio_client.fput_object(
+            bucket_name=bucket_name,
+            object_name=object_id,
+            file_path=object_path,
+            content_type="application/octet-stream",
+        )
+
+        os.remove(object_path)
+
+        return jsonify(
+            {"message": "Upload complete and object stored in MinIO"}
+        ), HTTPStatus.OK
+
+    except S3Error as e:
+        return jsonify(
+            {"error": f"Failed to upload to MinIO: {str(e)}"}
+        ), HTTPStatus.INTERNAL_SERVER_ERROR
+    except Exception as e:
+        return jsonify(
+            {"error": f"An unexpected error occurred: {str(e)}"}
+        ), HTTPStatus.INTERNAL_SERVER_ERROR

cloud_storage_handler/api/specs/specs.yaml

@@ -35,4 +35,72 @@ paths:
           description: The request is malformed.
         '500':
           description: An unexpected error occurred.
+  /upload/initiate:
+    post:
+      summary: Initiate TUS upload session
+      operationId: initiate_upload
+      tags:
+        - Upload
+      responses:
+        "201":
+          description: TUS upload session initiated
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  object_id:
+                    type: string
+                    description: Unique identifier for the upload session
+  /upload/{object_id}/chunk:
+    patch:
+      summary: Upload a file chunk
+      operationId: upload_chunk
+      tags:
+        - Upload
+      parameters:
+        - in: path
+          name: object_id
+          required: true
+          schema:
+            type: string
+          description: Unique identifier for the upload session
+      requestBody:
+        required: true
+        content:
+          application/octet-stream:
+            schema:
+              type: string
+              format: binary
+      responses:
+        "204":
+          description: Chunk uploaded successfully
+        "404":
+          description: File not found
+  /upload/complete/{object_id}:
+    post:
+      summary: Complete upload and store in MinIO
+      operationId: complete_upload
+      tags:
+        - Upload
+      parameters:
+        - in: path
+          name: object_id
+          required: true
+          schema:
+            type: string
+          description: Unique identifier for the upload session
+      responses:
+        "200":
+          description: Upload complete and file stored in MinIO
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  message:
+                    type: string
+                    description: Confirmation message
+        "404":
+          description: File not found
 ...

deployment/config.yaml

@@ -21,6 +21,8 @@ security:
       - userinfo
       - public_key
     validation_checks: all
+  cors:
+    enabled: True
 
 api:
   specs: