Zarr Metadata Streaming Integration #262
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Introduces a new ZarrMetadataDialog for exploring locally hosted Xenium Zarr dataset metadata, including dialog components, utility functions for metadata extraction, and integration into the menu bar with a new 'Add Remote Datasource' button. This enables users to fetch and inspect remote Zarr datasets directly from the UI.
- zarr<3.0: core array and metadata parsing - fsspec^2025.7.0: flexible filesystem + HTTP access - requests^2.32.5: robust HTTP client for dataset fetching
The dialog now fetches metadata directly from the backend API, removing mock responses. Includes updated placeholders for local datasets and streamlined error messages for MVP testing.
Adds ZarrMetadataExtractor and supporting utilities to parse and normalize Zarr dataset structure.
- Exposes new GET /zarr/metadata?url=... route - Integrates with ZarrMetadataExtractor to fetch and normalize dataset metadata - Returns structured JSON with dataset groups, arrays, and attributes - Provides error handling for invalid URLs, missing files, or format issues
- added automatic dataset format detection in ZarrMetadataExtractor (zarr_utils.py) - implemented specialized processors for SpatialData (images, points, shapes, AnnData tables) - responses now include a datasetFormat field (spatialdata or zarr) - enhanced dialog to display SpatialData-specific details (image scales, table components, etc.)
- created python/mdvtools/metadata/ package - extracted /get_metadata endpoint logic (lines 160–246 from server.py) into metadata/routes.py - updated server.py to import and register routes via register_metadata_routes(project_bp, project) - removed original endpoint code from server.py - cleaned up unused imports (now scoped to the metadata module)
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This draft introduces the first working version of Zarr metadata streaming integration into MDV, enabling the backend to fetch and the frontend to display metadata from both standard Zarr stores and SpatialData datasets hosted at HTTP/HTTPS URLs.
Key Features
zarr<3.0,fsspec^2025.7.0, andrequests^2.32.5zarr_utils.py):ZarrMetadataExtractorwith:datasetFormat) in responses/project/<id>/get_metadataZarrMetadataDialog.tsx):Next Steps
Extract metadata integration logic (modules, endpoints, etc.) into a dedicated submodule under
mdvtoolsto reduce complexity inserver.pyand project scriptsProceed with hydration architecture as outlined in the proposal document (https://cmdoxford.atlassian.net/wiki/x/AYAgvg)