From 897a77664c4d29437eb8df1462f423a22ec0b41d Mon Sep 17 00:00:00 2001 From: Pratiksha Sankhe Date: Mon, 28 Oct 2024 23:53:34 +0530 Subject: [PATCH] added upload endpoint Signed-off-by: Pratiksha Sankhe --- .../api/elixircloud/csh/controllers.py | 126 +++++++++++++++++- cloud_storage_handler/api/specs/specs.yaml | 68 ++++++++++ deployment/config.yaml | 2 + poetry.lock | 119 ++++++++--------- pyproject.toml | 1 + 5 files changed, 251 insertions(+), 65 deletions(-) diff --git a/cloud_storage_handler/api/elixircloud/csh/controllers.py b/cloud_storage_handler/api/elixircloud/csh/controllers.py index fb23a34..301999f 100644 --- a/cloud_storage_handler/api/elixircloud/csh/controllers.py +++ b/cloud_storage_handler/api/elixircloud/csh/controllers.py @@ -1,9 +1,13 @@ """ELIXIR's Cloud Storage Handler controllers.""" +import hashlib import logging +import os +import uuid from http import HTTPStatus -from flask import jsonify +from flask import Flask, current_app, jsonify, request +from minio import S3Error logger = logging.getLogger(__name__) @@ -13,3 +17,123 @@ def home(): return jsonify( {"message": "Welcome to the Cloud Storage Handler server!"} ), HTTPStatus.OK + + +app = Flask(__name__) + +app.config["TUS_UPLOAD_DIR"] = "/tmp/tus_uploads" +app.config["TUS_CHUNK_SIZE"] = 8 * 1024 + + +def get_chunks(object, chunk_size): + """Generator to yield chunks from object.""" + while True: + chunk = object.read(chunk_size) + if not chunk: + break + yield chunk + + +def compute_file_hash(file_path): + """Compute MD5 hash of the file.""" + hash_md5 = hashlib.md5() + with open(file_path, "rb") as f: + for chunk in iter(lambda: f.read(4096), b""): + hash_md5.update(chunk) + return hash_md5.hexdigest() + + +def initiate_upload(): + """Initiate TUS upload, creates object and returns object_id.""" + object_id = str(uuid.uuid4()) + object_path = os.path.join(app.config["TUS_UPLOAD_DIR"], f"{object_id}.temp") + os.makedirs(app.config["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(app.config["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(app.config["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 diff --git a/cloud_storage_handler/api/specs/specs.yaml b/cloud_storage_handler/api/specs/specs.yaml index 2c61d7f..bc4c121 100644 --- a/cloud_storage_handler/api/specs/specs.yaml +++ b/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 ... diff --git a/deployment/config.yaml b/deployment/config.yaml index 0fec9c0..31e387c 100644 --- a/deployment/config.yaml +++ b/deployment/config.yaml @@ -21,6 +21,8 @@ security: - userinfo - public_key validation_checks: all + cors: + enabled: True api: specs: diff --git a/poetry.lock b/poetry.lock index 562b3fa..c844900 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1772,70 +1772,61 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"] [[package]] name = "pymongo" -version = "4.10.1" +version = "4.8.0" description = "Python driver for MongoDB " optional = false python-versions = ">=3.8" 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