Zarr Metadata Streaming Integration

package.json

@@ -111,7 +111,9 @@
     "tailwindcss-animate": "^1.0.7",
     "use-debounce": "^10.0.2",
     "uuid": "^11.0.3",
+    "vite-plugin-node-polyfills": "^0.24.0",
     "wordcloud": "^1.2.2",
+    "zarrita": "^0.5.2",
     "zod": "^3.25.49",
     "zustand": "^5.0.6"
   },

python/mdvtools/metadata/__init__.py

@@ -0,0 +1,10 @@
+"""
+Metadata extraction and processing module for MDV.
+
+This module provides functionality for fetching and processing metadata
+from various dataset formats including Zarr stores and SpatialData datasets.
+"""
+
+from .routes import register_metadata_routes
+
+__all__ = ['register_metadata_routes']

python/mdvtools/metadata/routes.py

@@ -0,0 +1,111 @@
+"""
+Flask routes for metadata extraction functionality.
+
+This module contains all the route handlers for fetching metadata from
+various dataset formats including Zarr stores and SpatialData datasets.
+"""
+
+import os
+import asyncio
+from flask import request, jsonify
+from mdvtools.zarr_utils import get_zarr_extractor
+from mdvtools.logging_config import get_logger
+
+logger = get_logger(__name__)
+
+def register_metadata_routes(project_bp, project):
+    """
+    Register metadata-related routes with the project blueprint.
+
+    Args:
+        project_bp: The Flask blueprint to register routes with
+        project: The MDVProject instance
+    """
+
+    @project_bp.route("/get_metadata", methods=["GET"])
+    def get_metadata():
+        """
+        Fetch metadata from a dataset URL (supports Zarr and SpatialData formats).
+
+        Query Parameters:
+            url: The URL of the dataset to fetch metadata from
+
+        Returns:
+            JSON response with metadata structure or error message
+        """
+        logger.info("=== METADATA REQUEST ===")
+        logger.info(f"Request method: {request.method}")
+        logger.info(f"Request path: {request.path}")
+        logger.info(f"Request args: {request.args}")
+        logger.info(f"Project: {project.id}")
+
+        dataset_url = None
+        try:
+            dataset_url = request.args.get('url')
+            logger.info(f"Extracted dataset_url: {dataset_url}")
+
+            if not dataset_url:
+                logger.info("ERROR: Missing 'url' parameter")
+                return jsonify({
+                    "error": "Missing 'url' parameter",
+                    "message": "Please provide a 'url' query parameter with the dataset URL"
+                }), 400
+
+            # Validate URL format
+            if not dataset_url.startswith(('http://', 'https://')):
+                logger.info(f"ERROR: Invalid URL format: {dataset_url}")
+                return jsonify({
+                    "error": "Invalid URL format", 
+                    "message": "URL must start with http:// or https://"
+                }), 400
+
+            # Convert localhost to host.docker.internal if running in Docker
+            if 'localhost' in dataset_url and os.path.exists('/.dockerenv'):
+                dataset_url = dataset_url.replace('localhost', 'host.docker.internal')
+                logger.info(f"Running in Docker, converted URL to: {dataset_url}")
+
+            logger.info(f"URL validation passed, fetching metadata for: {dataset_url}")
+
+            # Extract metadata using zarr utilities (supports both Zarr and SpatialData)
+            logger.info("Getting metadata extractor...")
+            extractor = get_zarr_extractor()
+            logger.info(f"Metadata extractor: {extractor}")
+
+            logger.info("Calling fetch_zarr_metadata...")
+            print("Creating new event loop for async metadata call...")
+            # Run the async function in the current event loop
+            loop = asyncio.new_event_loop()
+            asyncio.set_event_loop(loop)
+            try:
+                print("Running fetch_zarr_metadata in event loop...")
+                metadata = loop.run_until_complete(extractor.fetch_zarr_metadata(dataset_url))
+                print(f"Event loop completed, metadata type: {type(metadata)}")
+            except Exception as loop_e:
+                print(f"Exception in event loop: {loop_e}")
+                raise loop_e
+            finally:
+                print("Closing event loop...")
+                loop.close()
+                print("Event loop closed")
+            logger.info(f"Metadata extraction successful, keys: {list(metadata.keys()) if isinstance(metadata, dict) else type(metadata)}")
+            print(f"Metadata extraction successful, keys: {list(metadata.keys()) if isinstance(metadata, dict) else type(metadata)}")
+
+            response_data = {
+                "success": True,
+                "metadata": metadata,
+                "url": dataset_url
+            }
+            logger.info("Returning successful response")
+            return jsonify(response_data)
+
+        except Exception as e:
+            logger.info(f"EXCEPTION in get_metadata: {str(e)}")
+            logger.info(f"Exception type: {type(e)}")
+            import traceback
+            logger.info(f"Full traceback: {traceback.format_exc()}")
+
+            return jsonify({
+                "error": "Metadata extraction failed",
+                "message": str(e),
+                "url": dataset_url
+            }), 500

python/mdvtools/server.py

@@ -28,10 +28,12 @@
 from datetime import datetime
 from typing import Optional
 import threading
+import asyncio
 import scanpy as sc
 from mdvtools.conversions import convert_scanpy_to_mdv
 from mdvtools.server_extension import MDVServerOptions
 from mdvtools.logging_config import get_logger
+from mdvtools.metadata import register_metadata_routes
 
 
 logger = get_logger(__name__)
@@ -101,6 +103,9 @@ def create_app(
     for extension in options.extensions:
         extension.register_routes(project, project_bp)
 
+    # Register metadata routes
+    register_metadata_routes(project_bp, project)
+
 
     @project_bp.route("/")
     def project_index():
@@ -154,6 +159,7 @@ def get_json_file(file: str):
                     return f"Problem parsing state file: {e}", 500
         return send_file(path)
 
+
     # gets the raw byte data and packages it in the correct response
     @project_bp.route("/get_data", methods=["POST"])
     def get_data():