diff --git a/.cursor/settings.json b/.cursor/settings.json new file mode 100644 index 0000000..7ff7a3d --- /dev/null +++ b/.cursor/settings.json @@ -0,0 +1,15 @@ +{ + // Note: Python environments are version-specific. Choose one: + // For spatialdata 0.5.0: python/v0.5.0/.venv/bin/python3 + // For spatialdata 0.6.1: python/v0.6.1/.venv/bin/python3 + "python.defaultInterpreterPath": "${workspaceFolder}/python/v0.6.1/.venv/bin/python3", + "python.terminal.activateEnvironment": true, + "[python]": { + "editor.defaultFormatter": "ms-python.black-formatter", + "editor.formatOnSave": true + }, + "python.analysis.extraPaths": [ + "${workspaceFolder}/python" + ] +} + diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..5200901 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,92 @@ +name: Test + +on: + push: + branches: + - main + pull_request: + branches: + - main + +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Setup pnpm + uses: pnpm/action-setup@v4 + with: + version: 10 + run_install: false + + - uses: actions/setup-node@v4 + with: + node-version: '22' + cache: 'pnpm' + + - uses: astral-sh/setup-uv@v4 + with: + version: "latest" + + - name: Install dependencies + run: pnpm install --frozen-lockfile + + - name: Build packages + run: pnpm build + + - name: Cache uv environments + uses: actions/cache@v4 + with: + path: ~/.cache/uv + # could be overkill always running all versions in CI, may review in future. + key: ${{ runner.os }}-uv-${{ hashFiles('python/v0.5.0/pyproject.toml', 'python/v0.6.1/pyproject.toml', 'python/v0.7.0/pyproject.toml') }} + + # Note: Version-specific environments are set up automatically by the fixture generation script + # No need to manually sync here unless you want to pre-warm the cache + + - name: Generate test fixtures (Python spatialdata 0.5.0, 0.6.1, and 0.7.0) + run: pnpm test:fixtures:generate + + - name: Run unit tests + run: pnpm test:unit + + - name: Run integration tests with local server + shell: bash + run: | + # Verify fixtures exist before starting server + if [ ! -d "test-fixtures/v0.5.0/blobs.zarr" ]; then + echo "Error: Fixtures not found at test-fixtures/v0.5.0/blobs.zarr" + echo "Listing test-fixtures directory:" + ls -la test-fixtures/ || echo "test-fixtures directory does not exist" + exit 1 + fi + + # Start test server in background + pnpm test:server & + SERVER_PID=$! + + # Wait for server to be ready (up to ~30s) + # Check both root and a fixture path to ensure server is fully ready + for i in {1..30}; do + if curl -sSf http://localhost:8080/ >/dev/null && \ + curl -sSf http://localhost:8080/v0.5.0/blobs.zarr/zmetadata >/dev/null; then + echo "Test server is up and serving fixtures" + break + fi + echo "Waiting for test server on http://localhost:8080/ ..." + sleep 1 + done + + # Small additional delay to ensure server is fully ready + sleep 2 + + # Run integration tests (will hit http://localhost:8080/…) + pnpm test:integration + + # Clean up server + kill "$SERVER_PID" || true \ No newline at end of file diff --git a/.gitignore b/.gitignore index 9d64d2a..2540208 100644 --- a/.gitignore +++ b/.gitignore @@ -9,13 +9,23 @@ build/ # Testing coverage/ +test-fixtures/ +validation-results/ + +# Python virtual environments (version-specific, completely separate) +python/v0.5.0/.venv/ +python/v0.6.1/.venv/ +python/v0.5.0/uv.lock +python/v0.6.1/uv.lock # Environment .env .env.local # IDE -.vscode/ +# Note: .vscode/settings.json and .cursor/settings.json are committed for Python interpreter setup +.vscode/launch.json +.vscode/tasks.json .idea/ *.swp *.swo diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..7ff7a3d --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,15 @@ +{ + // Note: Python environments are version-specific. Choose one: + // For spatialdata 0.5.0: python/v0.5.0/.venv/bin/python3 + // For spatialdata 0.6.1: python/v0.6.1/.venv/bin/python3 + "python.defaultInterpreterPath": "${workspaceFolder}/python/v0.6.1/.venv/bin/python3", + "python.terminal.activateEnvironment": true, + "[python]": { + "editor.defaultFormatter": "ms-python.black-formatter", + "editor.formatOnSave": true + }, + "python.analysis.extraPaths": [ + "${workspaceFolder}/python" + ] +} + diff --git a/README.md b/README.md index 0709b58..1593525 100644 --- a/README.md +++ b/README.md @@ -18,6 +18,8 @@ This monorepo contains: - Node.js >= 20 - pnpm >= 10 +- Python >= 3.12 (for generating test fixtures) +- [uv](https://github.com/astral-sh/uv) (Python package manager) ### Installation @@ -48,6 +50,231 @@ pnpm format pnpm docs:dev ``` +## Testing + +### Prerequisites for Testing + +To run the full test suite, you'll need: + +- Python >= 3.12 +- [uv](https://github.com/astral-sh/uv) - Python package manager + +#### Setting Up the Python Environment (not required for JS stuff, mostly generating test fixtures) + +The Python environment is managed by `uv` and defined in `python/pyproject.toml`. To set it up: + +**Installing uv:** +```bash +# Install uv (Unix/macOS) +curl -LsSf https://astral.sh/uv/install.sh | sh + +# Or using pip/pipx +pip install uv +# or +pipx install uv +``` + + +**Setting up the environments:** + +The project uses completely separate Python environments for each spatialdata version. Each version has its own directory with its own `pyproject.toml` and virtual environment: + +```bash +# Set up environment for spatialdata 0.5.0 +uv sync --directory python/v0.5.0 + +# Set up environment for spatialdata 0.6.1 +uv sync --directory python/v0.6.1 + +# Set up environment for spatialdata 0.7.0 +uv sync --directory python/v0.7.0 + +# Or set up all at once (the fixture generation script will do this automatically) +``` + +Each environment: +- Is completely independent with its own virtual environment at `python/v{version}/.venv/` +- Has its own `pyproject.toml` that pins a specific spatialdata version +- Is isolated from other versions (no shared base environment) + +**Note:** The fixture generation script automatically sets up these environments when needed. You only need to manually sync if you want to activate an environment directly or use it in your editor. + +**Version Mapping:** +- **spatialdata 0.5.0** uses **OME-NGFF 0.4** format (multiscales at top level) in **zarr v2** stores (consolidated `zmetadata`) +- **spatialdata 0.6.0+** uses **OME-NGFF 0.5** format (multiscales nested under `ome` key) in **zarr v3** stores (consolidated `zarr.json`) + +#### Editor Setup + +The project includes editor configuration files (`.vscode/settings.json` and `.cursor/settings.json`) that configure the Python interpreter to use one of the version-specific environments (defaults to v0.6.1). + +**VS Code / Cursor:** +- The Python interpreter is automatically configured when you open the workspace +- To switch versions: `Cmd/Ctrl+Shift+P` → "Python: Select Interpreter" → Choose: + - `./python/v0.5.0/.venv/bin/python3` for spatialdata 0.5.0 + - `./python/v0.6.1/.venv/bin/python3` for spatialdata 0.6.1 + - `./python/v0.7.0/.venv/bin/python3` for spatialdata 0.7.0 + +**Other editors:** +- Choose the appropriate virtual environment: + - `python/v0.5.0/.venv/bin/python3` for spatialdata 0.5.0 + - `python/v0.6.1/.venv/bin/python3` for spatialdata 0.6.1 + - `python/v0.7.0/.venv/bin/python3` for spatialdata 0.7.0 + + +### Running Tests + +```bash +# Run all tests (unit + integration) +pnpm test:all + +# Run only unit tests (fast, no fixtures needed) +pnpm test:unit + +# Run only integration tests (requires fixtures) +pnpm test:integration + +# Run tests from individual packages +pnpm test +``` + +### Generating Test Fixtures + +Test fixtures are generated on-demand using the Python `spatialdata` library. Each version uses a separate Python environment with the specific spatialdata version pinned to ensure accurate fixture generation. + +Fixtures are stored in `test-fixtures/` (excluded from git). + +```bash +# Generate fixtures for all spatialdata versions (0.5.0, 0.6.1, and 0.7.0) +# This will automatically set up the version-specific environments if needed +pnpm test:fixtures:generate + +# Generate fixtures for a specific version +pnpm test:fixtures:generate:0.5.0 +pnpm test:fixtures:generate:0.6.1 +pnpm test:fixtures:generate:0.7.0 +``` + +**How it works:** +- The script uses separate environments: `python/v0.5.0/`, `python/v0.6.1/`, and `python/v0.7.0/` +- Each environment has its own `pyproject.toml` with the spatialdata version pinned +- The script automatically runs `uv sync` for each environment before generating fixtures +- This ensures fixtures are generated with the exact spatialdata version being tested + +**Note:** Integration tests will automatically generate fixtures if they're missing, but you can pre-generate them for faster test runs. + +### Test Servers + +#### Test Fixture Server + +The test fixture server serves generated fixtures over HTTP for testing with `FetchStore`: + +```bash +# Start the test fixture server (runs on http://localhost:8080) +pnpm test:server +``` + +Once running, fixtures are accessible at: +- `http://localhost:8080/test-fixtures/v0.5.0/blobs.zarr` +- `http://localhost:8080/test-fixtures/v0.6.1/blobs.zarr` +- `http://localhost:8080/test-fixtures/v0.7.0/blobs.zarr` + +The server provides directory listings and serves all zarr metadata files with appropriate CORS headers. + +#### CORS Proxy Server + +The CORS proxy server allows accessing spatialdata stores that don't have CORS headers enabled. This is useful for local development when testing against remote stores. + +**Standalone Usage:** + +```bash +# Start the CORS proxy server (runs on http://localhost:8081) +pnpm test:proxy +``` + +**Usage:** + +Proxy a remote URL using query parameter: +``` +http://localhost:8081/?url=https://example.com/data.zarr/.zattrs +``` + +**Example:** + +If you have a spatialdata store at `https://example.com/mydata.zarr` that doesn't have CORS headers, you can access it through the proxy: + +```typescript +import { readZarr } from '@spatialdata/core'; + +// Instead of: +// const sdata = await readZarr('https://example.com/mydata.zarr'); + +// Use the proxy (query parameter form): +const sdata = await readZarr('http://localhost:8081/?url=https://example.com/mydata.zarr'); +``` + +**Automatic Proxy Management:** + +The validation script (`pnpm validate:datasets:js`) automatically manages its own proxy server. The proxy is started at the beginning of validation and stopped when complete, so you don't need to run it separately. + +**⚠️ Warning:** The CORS proxy is for local development only. It has no security restrictions and should never be exposed to the internet. + +### Dataset Validation + +The project includes a script to validate dataset compatibility with the JavaScript implementation using publicly available spatialdata datasets. + +#### Validating with JavaScript + +Test datasets with the JavaScript implementation in Node.js (outside browser): + +```bash +# First, build the packages +pnpm build + +# Validate all datasets with JS implementation +pnpm validate:datasets:js + +# Validate a specific dataset +pnpm validate:datasets:js -- --dataset "Xenium" + +# Output to a file +pnpm validate:datasets:js -- --output-file validation-results-js.md +``` + +**Note:** The validation script automatically starts its own CORS proxy server, uses it for all requests, and shuts it down when validation completes. You don't need to run `pnpm test:proxy` separately. + +#### Understanding the Results + +The validation script generates a table showing which datasets work with the JavaScript implementation: + +- ✅ Success: Dataset loaded successfully +- ❌ Failed: Dataset could not be loaded +- ⏭️ Not tested: Dataset was skipped + +The detailed results include: +- Element types present (images, labels, points, shapes, tables) +- Coordinate systems +- Error messages for failures + +This is useful for: +- Testing compatibility of the JavaScript implementation with real-world datasets +- Identifying issues with specific datasets +- Tracking which datasets are known to work or fail + +#### Output Formats + +The validation script supports multiple output formats: + +```bash +# Markdown (default) - Human-readable report +pnpm validate:datasets:js -- --output-format markdown --output-file results.md + +# JSON - Machine-readable results +pnpm validate:datasets:js -- --output-format json --output-file results.json + +# CSV - Spreadsheet-friendly format +pnpm validate:datasets:js -- --output-format csv --output-file results.csv +``` + ## 📝 License diff --git a/package.json b/package.json index 5f49638..6edf619 100644 --- a/package.json +++ b/package.json @@ -11,6 +11,16 @@ "scripts": { "build": "pnpm -r --filter='!docs' run build", "test": "pnpm -r --filter='!docs' run test", + "test:unit": "vitest run --exclude tests/integration/**", + "test:integration": "vitest run tests/integration", + "test:all": "pnpm test:unit && pnpm test:integration", + "test:fixtures:generate": "uv run python/scripts/generate_fixtures.py", + "test:fixtures:generate:0.5.0": "uv run python/scripts/generate_fixtures.py --version 0.5.0", + "test:fixtures:generate:0.6.1": "uv run python/scripts/generate_fixtures.py --version 0.6.1", + "test:fixtures:generate:0.7.0": "uv run python/scripts/generate_fixtures.py --version 0.7.0", + "test:server": "node scripts/test-server.js", + "test:proxy": "node scripts/cors-proxy.js", + "validate:datasets:js": "node scripts/validate-datasets-js.js", "lint": "biome check .", "format": "biome format --write .", "format:check": "biome format .", diff --git a/packages/core/src/index.test.ts b/packages/core/src/index.test.ts deleted file mode 100644 index 26e88ec..0000000 --- a/packages/core/src/index.test.ts +++ /dev/null @@ -1,49 +0,0 @@ -import { describe, expect, it } from 'vitest'; -import { coordinateTransformationSchema, spatialDataSchema } from './schemas/index.js'; - -describe('SpatialData Core', () => { - describe('schemas', () => { - it('should validate coordinate transformation', () => { - // coordinateTransformationSchema expects an array of transformations - const validTransforms = [ - { - type: 'affine', - affine: [ - [1, 0, 0], - [0, 1, 0], - ], - }, - ]; - - expect(() => coordinateTransformationSchema.parse(validTransforms)).not.toThrow(); - }); - - it('should validate spatial data metadata', () => { - // coordinateSystems values are arrays of transformations - const validMetadata = { - version: '0.1.0', - coordinateSystems: { - global: [ - { - type: 'affine', - affine: [ - [1, 0, 0], - [0, 1, 0], - ], - }, - ], - }, - }; - - expect(() => spatialDataSchema.parse(validMetadata)).not.toThrow(); - }); - - it('should reject invalid spatial data metadata', () => { - const invalidMetadata = { - version: 123, // should be string - }; - - expect(() => spatialDataSchema.parse(invalidMetadata)).toThrow(); - }); - }); -}); diff --git a/packages/core/src/models/VTableSource.ts b/packages/core/src/models/VTableSource.ts index 8066d9e..5cc56f4 100644 --- a/packages/core/src/models/VTableSource.ts +++ b/packages/core/src/models/VTableSource.ts @@ -15,12 +15,41 @@ async function getParquetModule() { // Dynamic import for code-splitting. parquet-wasm is a WebAssembly module // that needs to be initialized before use in browser environments. // In Node.js, the module loads WASM synchronously so no init is needed. - // (^^^ but why would it be invoked in node.js in the current version?) - const module = await import('parquet-wasm'); - if (typeof module.default === 'function') { - await module.default(); + // + // TODO: Replace with a more civilised parquet module that's built in a way we can actually consume. + // - probably ultimately may be using geoarrow-wasm / investigate deck.gl arrow layer + // think about how that fits our 'core' (no deck deps) vs 'vis' structure etc. + + // Try local import first (works in Node.js, tests, and production builds) + try { + const module = await import('parquet-wasm'); + if (typeof module.default === 'function') { + await module.default(); + } + return { readParquet: module.readParquet, readSchema: module.readSchema }; + } catch (error) { + // Local import failed, try CDN fallback (needed in vite dev server) + // Reference: https://observablehq.com/@kylebarron/geoparquet-on-the-web + console.warn( + '[VTableSource] Local parquet-wasm import failed, falling back to CDN version. ' + + 'This is a temporary workaround pending a better parquet module solution.', + error + ); + + try { + // @ts-ignore - CDN import not recognized by TypeScript + const cdnModule = await import('https://cdn.vitessce.io/parquet-wasm@2c23652/esm/parquet_wasm.js'); + await cdnModule.default(); + return { readParquet: cdnModule.readParquet, readSchema: cdnModule.readSchema }; + } catch (cdnError) { + // Both imports failed, throw an error + const localErrorMsg = error instanceof Error ? error.message : String(error); + const cdnErrorMsg = cdnError instanceof Error ? cdnError.message : String(cdnError); + throw new Error( + `Failed to load parquet-wasm from both local package and CDN. Local error: ${localErrorMsg}. CDN error: ${cdnErrorMsg}` + ); + } } - return { readParquet: module.readParquet, readSchema: module.readSchema }; } /** diff --git a/packages/core/src/models/index.ts b/packages/core/src/models/index.ts index dad2edd..98440d3 100644 --- a/packages/core/src/models/index.ts +++ b/packages/core/src/models/index.ts @@ -54,14 +54,14 @@ abstract class AbstractElement { this.key = key; this.url = `${sdata.url}/${name}/${key}`; - const { parsed } = sdata; - if (!parsed) { - throw new Error("Parsed store contents not available"); + const { tree } = sdata.rootStore; + if (!tree) { + throw new Error("Tree store contents not available"); } - if (!(name in parsed)) { + if (!(name in tree)) { throw new Error(`Unknown element type: ${name}`); } - const p1 = parsed[name] as ZarrTree; + const p1 = tree[name] as ZarrTree; if (!(key in p1)) { throw new Error(`Unknown element key: ${key}`); } @@ -205,11 +205,9 @@ export class TableElement extends AbstractElement<'tables'> { // parse attrs through schema const result = tableAttrsSchema.safeParse(this.rawAttrs); if (!result.success) { - console.warn(`Schema validation failed for ${params.name}/${params.key}:`, result.error.issues); - this.attrs = this.rawAttrs as TableAttrs; - } else { - this.attrs = result.data; - } + throw result.error; + } + this.attrs = result.data; } /** @@ -237,12 +235,9 @@ abstract class RasterElement extends AbstractSpat // Parse attrs through schema const result = rasterAttrsSchema.safeParse(this.rawAttrs); if (!result.success) { - console.warn(`Schema validation failed for ${params.name}/${params.key}:`, result.error.issues); - // Fall back to raw attrs cast - allows working with non-conformant data - this.attrs = this.rawAttrs as RasterAttrs; - } else { - this.attrs = result.data; + throw result.error; } + this.attrs = result.data; } /** @@ -338,15 +333,13 @@ export class ShapesElement extends AbstractSpatialElement<'shapes', ShapesAttrs> // Parse attrs through schema const result = shapesAttrsSchema.safeParse(this.rawAttrs); if (!result.success) { - console.warn(`Schema validation failed for shapes/${params.key}:`, result.error.issues); - this.attrs = this.rawAttrs as ShapesAttrs; - } else { - this.attrs = result.data; - } + throw result.error; + } + this.attrs = result.data; // Initialize the Vitessce-derived shapes source for loading geometry this.vShapes = new SpatialDataShapesSource({ - store: params.sdata.rootStore, + store: params.sdata.rootStore.zarritaStore, fileType: '.zarr' }); } @@ -396,13 +389,11 @@ export class PointsElement extends AbstractSpatialElement<'points', PointsAttrs> // Parse attrs through schema const result = pointsAttrsSchema.safeParse(this.rawAttrs); if (!result.success) { - console.warn(`Schema validation failed for points/${params.key}:`, result.error.issues); - this.attrs = this.rawAttrs as PointsAttrs; - } else { - this.attrs = result.data; + throw result.error; } + this.attrs = result.data; this.vPoints = new SpatialDataPointsSource({ - store: params.sdata.rootStore, + store: params.sdata.rootStore.zarritaStore, fileType: '.zarr' }); } @@ -486,22 +477,29 @@ export function loadElements( sdata: SDataProps, name: T ): Record | undefined { - const { parsed } = sdata; - if (!parsed) { - throw new Error("Parsed store contents not available"); + const { tree } = sdata.rootStore; + if (!tree) { + throw new Error("Tree store contents not available"); } - if (!(name in parsed)) { + if (!(name in tree)) { return undefined; } - const keys = Object.keys(parsed[name] as object); + const keys = Object.keys(tree[name] as object); if (keys.length === 0) { return undefined; } const result: Record = {}; for (const key of keys) { - result[key] = createElement(name, sdata, key); + try { + result[key] = createElement(name, sdata, key); + } catch (error) { + // we might want to take this more seriously - but this should prevent any crash + // and not have any worse symptom than the element not being there as a result(?) + // might be slightly confusing to get {} rather than undefined in that case + console.error(error); + } } return result; } diff --git a/packages/core/src/schemas/index.ts b/packages/core/src/schemas/index.ts index c962b40..0a74ce4 100644 --- a/packages/core/src/schemas/index.ts +++ b/packages/core/src/schemas/index.ts @@ -202,7 +202,8 @@ const omeroSchema = z.object({ start: z.number(), }) .optional(), - label: z.string().optional(), + // note - I think the schema says string but I encountered number in the wild. + label: z.coerce.string().optional(), family: z.string().optional(), color: z.string().optional(), active: z.boolean().optional(), @@ -245,6 +246,11 @@ export type NgffImage = z.infer; * Schema for spatialdata_attrs metadata (common to spatial elements). * Contains version info and other spatialdata-specific metadata. * Note: Transformations are stored at the top level of attrs, not inside spatialdata_attrs. + * + * IMPORTANT: The semantic meaning of `version` varies by element type: + * - For raster elements (images/labels): `version` is the spatialdata library version (e.g., '0.5.0', '0.6.1', '0.7.0') + * and does NOT control OME-NGFF format detection (which is determined by structure). + * - For shapes/points: `version` is the spatialdata format version (e.g., '0.1', '0.2') and IS used for format detection. */ export const spatialDataAttrsSchema = z .object({ @@ -255,10 +261,10 @@ export const spatialDataAttrsSchema = z export type SpatialDataAttrs = z.infer; /** - * Schema for raster element attrs (images & labels) - * Combines OME-NGFF multiscales with spatialdata_attrs + * Schema for raster element attrs in spatialdata 0.5.0 format + * Uses OME-NGFF 0.4 format with multiscales at the top level */ -export const rasterAttrsSchema = z +const rasterAttrs_OME_04_Schema = z .object({ multiscales: z .array( @@ -282,7 +288,92 @@ export const rasterAttrsSchema = z }) .passthrough(); -export type RasterAttrs = z.infer; +/** + * Schema for raster element attrs in spatialdata 0.6.1+ format + * Uses OME-NGFF 0.5 format with multiscales nested under 'ome' key + */ +const rasterAttrs_OME_05_Schema = z + .object({ + ome: z + .object({ + multiscales: z + .array( + z.object({ + name: z.string().optional(), + datasets: z + .array( + z.object({ + path: z.string(), + coordinateTransformations: coordinateTransformationSchema.optional(), + }) + ) + .min(1), + axes: axesSchema, + coordinateTransformations: coordinateTransformationSchema.optional(), + }) + ) + .min(1), + omero: omeroSchema.optional(), + }) + .passthrough(), + spatialdata_attrs: spatialDataAttrsSchema.optional(), + }) + .passthrough(); + +/** + * Schema for raster element attrs (images & labels) + * Supports both spatialdata 0.5.0 (OME-NGFF 0.4, top-level multiscales) and + * spatialdata 0.6.0+ (OME-NGFF 0.5, nested under 'ome') formats. + * Uses zod transform to normalize both formats to a consistent internal representation. + * + * NOTE: Format detection is STRUCTURAL (presence of 'ome' key), NOT based on + * spatialdata_attrs.version. The version field is metadata only and does not control + * which schema is applied. + */ +export const rasterAttrsSchema = z + .union([rasterAttrs_OME_04_Schema, rasterAttrs_OME_05_Schema]) + .transform((data): RasterAttrs => { + // Format detection is structural: if 'ome' key exists, it's OME-NGFF 0.5 format + // This is independent of spatialdata_attrs.version (which is library version metadata) + if ('ome' in data && data.ome && typeof data.ome === 'object') { + const omeData = data.ome as { + multiscales: unknown; + omero?: unknown; + [key: string]: unknown; + }; + return { + multiscales: omeData.multiscales as RasterAttrs['multiscales'], + omero: omeData.omero as RasterAttrs['omero'], + spatialdata_attrs: 'spatialdata_attrs' in data ? data.spatialdata_attrs : undefined, + // Preserve any other top-level fields + ...Object.fromEntries( + Object.entries(data).filter(([key]) => key !== 'ome' && key !== 'spatialdata_attrs') + ), + } as RasterAttrs; + } + + // Otherwise, it's already in the v0.5.0 format (top-level multiscales), return as-is + return data as RasterAttrs; + }); + +/** + * Internal type for the normalized raster attrs structure + * This is what we use internally after transformation + */ +export type RasterAttrs = { + multiscales: Array<{ + name?: string; + datasets: Array<{ + path: string; + coordinateTransformations?: z.infer; + }>; + axes: z.infer; + coordinateTransformations?: z.infer; + }>; + omero?: z.infer; + spatialdata_attrs?: z.infer; + [key: string]: unknown; +}; /** * Schema for shapes element attrs. diff --git a/packages/core/src/store/index.ts b/packages/core/src/store/index.ts index a1a2b73..42eb0db 100644 --- a/packages/core/src/store/index.ts +++ b/packages/core/src/store/index.ts @@ -25,7 +25,7 @@ export type { SpatialElement, AnyElement } from '../models'; export class SpatialData { readonly url: StoreLocation; - rootStore: zarr.Listable; + rootStore: ConsolidatedStore; // metadata: Record; //todo: add this, with type (validated by zod) images?: Elements<'images'>; @@ -34,15 +34,9 @@ export class SpatialData { shapes?: Elements<'shapes'>; tables?: Elements<'tables'>; - /** - * Keeping this for experimenting with this structure vs AnnData.js for Tables etc. - */ - parsed?: ZarrTree; - constructor(url: StoreLocation, rootStore: ConsolidatedStore, selection?: ElementName[], onBadFiles?: BadFileHandler) { this.url = url; - this.rootStore = rootStore.zarritaStore; - this.parsed = rootStore.tree; + this.rootStore = rootStore; const _selection = selection || ElementNames; for (const elementType of _selection) { // Load all elements of this type @@ -86,33 +80,42 @@ export class SpatialData { * to get more detailed info. */ toString() { - const nonEmptyElements = ElementNames.filter((name) => this[name] !== undefined); - if (nonEmptyElements.length === 0) { - return `SpatialData object, with associated Zarr store: ${this.url}\n(No elements loaded)`; - } - const elements = nonEmptyElements.map((name, i) => { - const element = this[name]; - const isLast = i === nonEmptyElements.length - 1; - const prefix = isLast ? '└──' : '├──'; - const childPrefix = isLast ? ' ' : '│ '; - if (element) { - const keys = Object.keys(element); - const children = keys.map((key, j) => { - const childIsLast = j === keys.length - 1; - const childBranch = childIsLast ? '└──' : '├──'; - return `${childPrefix}${childBranch} ${key}`; - }).join('\n'); - return `${prefix} ${name}:\n${children}`; + try { + const nonEmptyElements = ElementNames.filter((name) => this[name] !== undefined); + if (nonEmptyElements.length === 0) { + return `SpatialData object, with associated Zarr store: ${this.url}\n(No elements loaded)`; } - return `${prefix} ${name}: (empty)`; - }).join('\n'); - const cs = `with coordinate systems: ${this.coordinateSystems.join(', ')}`; - return `SpatialData object, with associated Zarr store: ${this.url}\nElements:\n${elements}\n${cs}`; + const elements = nonEmptyElements.map((name, i) => { + const element = this[name]; + const isLast = i === nonEmptyElements.length - 1; + const prefix = isLast ? '└──' : '├──'; + const childPrefix = isLast ? ' ' : '│ '; + if (element) { + const keys = Object.keys(element); + const children = keys.map((key, j) => { + const childIsLast = j === keys.length - 1; + const childBranch = childIsLast ? '└──' : '├──'; + return `${childPrefix}${childBranch} ${key}`; + }).join('\n'); + return `${prefix} ${name}:\n${children}`; + } + return `${prefix} ${name}: (empty)`; + }).join('\n'); + const cs = `with coordinate systems: ${this.coordinateSystems.join(', ')}`; + return `SpatialData object, with associated Zarr store: ${this.url}\nElements:\n${elements}\n${cs}`; + } catch (error) { + // this can happen if `this.coordinateSystems` trips over some invalid `attrs` where we did a bad `as Whatever` after validation fails... + // without the catch we get a really nasty crash. + // nb - we now don't allow elements to exist if the schema doesn't validate, but wouldn't be too suprised if we end up back here at some point... + // will inevitably have some SNAFU somewhere. + // sorry future code user/maintainer if that is so. + return `Corrupt SpatialData.toString(): '${error}'` + } } toJSON() { - if (!this.parsed) return this; - return serializeZarrTree(this.parsed); + if (!this.rootStore.tree) return this; + return serializeZarrTree(this.rootStore.tree); } } @@ -120,9 +123,10 @@ export async function readZarr(storeUrl: StoreLocation, selection?: ElementName[ // todo: this should be able to handle a store directly, not just a url // then there are some downstream changes required for the models/loaders etc. // rather than `tryConsolidated` here, lets have some `zarrextra` function instead. - const result = await openExtraConsolidated(storeUrl); + const normalizedSource = storeUrl.replace(/\/+$/, ''); //it'll be normalized by zarrextra as well, but we need this version for SpatialData constructor + const result = await openExtraConsolidated(normalizedSource); if (result.ok) { - return new SpatialData(storeUrl, result.value, selection, onBadFiles); + return new SpatialData(normalizedSource, result.value, selection, onBadFiles); } throw new Error(`${result.error}`); } diff --git a/packages/core/src/types.ts b/packages/core/src/types.ts index 5615593..ec1bca4 100644 --- a/packages/core/src/types.ts +++ b/packages/core/src/types.ts @@ -14,7 +14,7 @@ import type * as ad from 'anndata.js'; import type * as zarr from 'zarrita'; -import type { ZarrTree } from '@spatialdata/zarrextra'; +import type { ConsolidatedStore } from '@spatialdata/zarrextra'; /** * Element name constants and types @@ -87,8 +87,7 @@ export { Ok, Err, isOk, isErr, unwrap, unwrapOr } from '@spatialdata/zarrextra'; */ export type SDataProps = { url: StoreLocation; - parsed?: ZarrTree; onBadFiles?: BadFileHandler; selection?: ElementName[]; - rootStore: zarr.Listable; + rootStore: ConsolidatedStore; } \ No newline at end of file diff --git a/packages/core/src/vite-env.d.ts b/packages/core/src/vite-env.d.ts new file mode 100644 index 0000000..ed77210 --- /dev/null +++ b/packages/core/src/vite-env.d.ts @@ -0,0 +1,2 @@ +/// + diff --git a/packages/core/tests/schemas.spec.ts b/packages/core/tests/schemas.spec.ts new file mode 100644 index 0000000..7fbdff3 --- /dev/null +++ b/packages/core/tests/schemas.spec.ts @@ -0,0 +1,354 @@ +import { describe, expect, it } from 'vitest'; +import { + rasterAttrsSchema, + coordinateTransformationSchema, + shapesAttrsSchema, + pointsAttrsSchema, + tableAttrsSchema, + spatialDataSchema, +} from '../src/schemas/index.js'; + +describe('Schema Transformations', () => { + describe('rasterAttrsSchema - version normalization', () => { + //TODO: invert this type... + it('should normalize OME-NGFF 0.5 format (nested under ome) to internal format', () => { + // Note: spatialdata_attrs.version is library version metadata (e.g., '0.6.1', '0.7.0') + // Format detection is STRUCTURAL (presence of 'ome' key), not based on version + const omeNgff05Format = { + ome: { + multiscales: [ + { + name: 'test', + datasets: [{ path: '0' }], + axes: [ + { name: 'y', type: 'space' }, + { name: 'x', type: 'space' }, + ], + }, + ], + }, + spatialdata_attrs: { + version: '0.6.1', // Library version metadata (doesn't control format detection) + }, + }; + + const result = rasterAttrsSchema.parse(omeNgff05Format); + + // Should have multiscales at top level after transformation + expect(result.multiscales).toBeDefined(); + expect(result.multiscales).toHaveLength(1); + expect(result.multiscales[0].name).toBe('test'); + // Should not have 'ome' key in result + expect('ome' in result).toBe(false); + }); + + it('should accept OME-NGFF 0.4 format (top-level multiscales) as-is', () => { + // Note: Format detection is STRUCTURAL (no 'ome' key = OME-NGFF 0.4) + // spatialdata_attrs.version is library version metadata, not format version + const omeNgff04Format = { + multiscales: [ + { + name: 'test', + datasets: [{ path: '0' }], + axes: [ + { name: 'y', type: 'space' }, + { name: 'x', type: 'space' }, + ], + }, + ], + spatialdata_attrs: { + version: '0.5.0', // Library version metadata (doesn't control format detection) + }, + }; + + const result = rasterAttrsSchema.parse(omeNgff04Format); + + // Should have multiscales at top level + expect(result.multiscales).toBeDefined(); + expect(result.multiscales).toHaveLength(1); + expect(result.multiscales[0].name).toBe('test'); + }); + + it('should preserve omero data from OME-NGFF 0.5 format', () => { + // Format is determined by structure (presence of 'ome' key), not spatialdata_attrs.version + const omeNgff05Format = { + ome: { + multiscales: [ + { + name: 'test', + datasets: [{ path: '0' }], + axes: [ + { name: 'y', type: 'space' }, + { name: 'x', type: 'space' }, + ], + }, + ], + omero: { + channels: [ + { + label: 'channel1', + color: 'FF0000', + }, + ], + }, + }, + spatialdata_attrs: { + version: '0.6.1', // Library version metadata + }, + }; + + const result = rasterAttrsSchema.parse(omeNgff05Format); + + expect(result.omero).toBeDefined(); + expect(result.omero?.channels).toHaveLength(1); + expect(result.omero?.channels[0].label).toBe('channel1'); + }); + }); + + describe('coordinateTransformationSchema', () => { + it('should validate scale transformation', () => { + const transform = [ + { + type: 'scale' as const, + scale: [1.0, 2.0, 3.0], + }, + ]; + + expect(() => coordinateTransformationSchema.parse(transform)).not.toThrow(); + const result = coordinateTransformationSchema.parse(transform); + expect(result[0].type).toBe('scale'); + }); + + it('should validate translation transformation', () => { + const transform = [ + { + type: 'translation', + translation: [10.0, 20.0], + }, + ]; + + expect(() => coordinateTransformationSchema.parse(transform)).not.toThrow(); + }); + + it('should validate affine transformation', () => { + const transform = [ + { + type: 'affine', + affine: [ + [1, 0, 0], + [0, 1, 0], + [0, 0, 1], + ], + }, + ]; + + expect(() => coordinateTransformationSchema.parse(transform)).not.toThrow(); + }); + + it('should validate identity transformation', () => { + const transform = [ + { + type: 'identity', + }, + ]; + + expect(() => coordinateTransformationSchema.parse(transform)).not.toThrow(); + }); + + it('should validate sequence transformation', () => { + const transform = [ + { + type: 'sequence', + transformations: [ + { type: 'scale', scale: [2.0, 2.0] }, + { type: 'translation', translation: [10.0, 10.0] }, + ], + }, + ]; + + expect(() => coordinateTransformationSchema.parse(transform)).not.toThrow(); + }); + + it('should validate transformations with coordinate system references', () => { + const transform = [ + { + type: 'scale', + scale: [1.0, 2.0], + input: { + name: 'input_cs', + axes: [ + { name: 'x', type: 'space' }, + { name: 'y', type: 'space' }, + ], + }, + output: { + name: 'output_cs', + }, + }, + ]; + + expect(() => coordinateTransformationSchema.parse(transform)).not.toThrow(); + const result = coordinateTransformationSchema.parse(transform); + expect(result[0].input?.name).toBe('input_cs'); + expect(result[0].output?.name).toBe('output_cs'); + }); + + it('should reject empty transformation array', () => { + const transform: unknown[] = []; + + expect(() => coordinateTransformationSchema.parse(transform)).toThrow(); + }); + + // Tests from packages/core/src/index.test.ts + it('should validate coordinate transformation (from index.test.ts)', () => { + // coordinateTransformationSchema expects an array of transformations + const validTransforms = [ + { + type: 'affine', + affine: [ + [1, 0, 0], + [0, 1, 0], + ], + }, + ]; + + expect(() => coordinateTransformationSchema.parse(validTransforms)).not.toThrow(); + }); + }); + + describe('shapesAttrsSchema', () => { + it('should validate shapes attrs with transformations', () => { + const attrs = { + 'encoding-type': 'ngff:shapes', + axes: ['x', 'y'], + coordinateTransformations: [ + { + type: 'scale', + scale: [1.0, 1.0], + }, + ], + spatialdata_attrs: { + version: '0.6.1', // Library version metadata (for raster elements) + }, + }; + + expect(() => shapesAttrsSchema.parse(attrs)).not.toThrow(); + }); + + it('should accept shapes attrs without transformations', () => { + const attrs = { + 'encoding-type': 'ngff:shapes', + axes: ['x', 'y'], + }; + + expect(() => shapesAttrsSchema.parse(attrs)).not.toThrow(); + }); + }); + + describe('pointsAttrsSchema', () => { + it('should validate points attrs with transformations', () => { + const attrs = { + 'encoding-type': 'ngff:points', + axes: ['x', 'y'], + coordinateTransformations: [ + { + type: 'translation' as const, + translation: [10.0, 20.0], + }, + ], + spatialdata_attrs: { + version: '0.6.1', // Library version metadata (for raster elements) + }, + }; + + expect(() => pointsAttrsSchema.parse(attrs)).not.toThrow(); + }); + }); + + describe('tableAttrsSchema', () => { + it('should validate table attrs', () => { + const attrs = { + instance_key: 'cell_id', + region: 'shapes', + region_key: 'region_id', + 'spatialdata-encoding-type': 'ngff:regions_table', + }; + + expect(() => tableAttrsSchema.parse(attrs)).not.toThrow(); + }); + + it('should accept array region', () => { + const attrs = { + instance_key: 'cell_id', + region: ['shapes1', 'shapes2'], + region_key: 'region_id', + 'spatialdata-encoding-type': 'ngff:regions_table', + }; + + expect(() => tableAttrsSchema.parse(attrs)).not.toThrow(); + }); + }); + + describe('spatialDataSchema', () => { + it('should validate spatial data root metadata', () => { + const metadata = { + version: '0.1.0', + coordinateSystems: { + global: [ + { + type: 'affine' as const, + affine: [ + [1, 0, 0], + [0, 1, 0], + ], + }, + ], + }, + }; + + expect(() => spatialDataSchema.parse(metadata)).not.toThrow(); + const result = spatialDataSchema.parse(metadata); + expect(result.version).toBe('0.1.0'); + expect(result.coordinateSystems.global).toBeDefined(); + }); + + it('should reject invalid version type', () => { + const metadata = { + version: 123, // should be string + coordinateSystems: {}, + }; + + expect(() => spatialDataSchema.parse(metadata)).toThrow(); + }); + + // Tests from packages/core/src/index.test.ts + it('should validate spatial data metadata (from index.test.ts)', () => { + // coordinateSystems values are arrays of transformations + const validMetadata = { + version: '0.1.0', + coordinateSystems: { + global: [ + { + type: 'affine', + affine: [ + [1, 0, 0], + [0, 1, 0], + ], + }, + ], + }, + }; + + expect(() => spatialDataSchema.parse(validMetadata)).not.toThrow(); + }); + + it('should reject invalid spatial data metadata (from index.test.ts)', () => { + const invalidMetadata = { + version: 123, // should be string + }; + + expect(() => spatialDataSchema.parse(invalidMetadata)).toThrow(); + }); + }); +}); + diff --git a/packages/core/vite.config.ts b/packages/core/vite.config.ts index c26260c..6c055f5 100644 --- a/packages/core/vite.config.ts +++ b/packages/core/vite.config.ts @@ -18,6 +18,7 @@ export default defineConfig({ test: { globals: true, environment: 'node', + include: ['tests/**/*.spec.ts'], coverage: { provider: 'v8', reporter: ['text', 'json', 'html'], diff --git a/packages/react/package.json b/packages/react/package.json index d31a635..0bcbf20 100644 --- a/packages/react/package.json +++ b/packages/react/package.json @@ -33,6 +33,7 @@ "@types/react": "catalog:", "@types/react-dom": "catalog:", "@vitejs/plugin-react": "catalog:", + "jsdom": "catalog:", "typescript": "catalog:", "vite": "catalog:", "vite-plugin-dts": "catalog:", diff --git a/packages/react/tests/index.spec.tsx b/packages/react/tests/index.spec.tsx new file mode 100644 index 0000000..f8b7718 --- /dev/null +++ b/packages/react/tests/index.spec.tsx @@ -0,0 +1,28 @@ +import { describe, expect, it } from 'vitest'; +import * as ReactExports from '../src/index.js'; + +describe('@spatialdata/react', () => { + it('should export useSpatialData hook', () => { + expect(ReactExports.useSpatialData).toBeDefined(); + expect(typeof ReactExports.useSpatialData).toBe('function'); + }); + + it('should export SpatialDataProvider component', () => { + expect(ReactExports.SpatialDataProvider).toBeDefined(); + expect(typeof ReactExports.SpatialDataProvider).toBe('function'); + }); + + it('should export useSpatialDataContext hook', () => { + expect(ReactExports.useSpatialDataContext).toBeDefined(); + expect(typeof ReactExports.useSpatialDataContext).toBe('function'); + }); + + it('should have all expected exports', () => { + const exports = Object.keys(ReactExports); + expect(exports.length).toBeGreaterThan(0); + expect(exports).toContain('useSpatialData'); + expect(exports).toContain('SpatialDataProvider'); + expect(exports).toContain('useSpatialDataContext'); + }); +}); + diff --git a/packages/react/vite.config.ts b/packages/react/vite.config.ts index 54da95d..d499c26 100644 --- a/packages/react/vite.config.ts +++ b/packages/react/vite.config.ts @@ -1,10 +1,19 @@ import { fileURLToPath } from 'node:url'; import { defineViteConfig } from '../../vite.config.base'; +import { mergeConfig } from 'vite'; const pkgRoot = fileURLToPath(new URL('.', import.meta.url)); -export default defineViteConfig({ +const baseConfig = defineViteConfig({ pkgRoot, libName: 'SpatialDataReact', external: ['@spatialdata/core'], }); + +export default mergeConfig(baseConfig, { + test: { + globals: true, + environment: 'jsdom', + include: ['tests/**/*.spec.ts*'], + }, +}); diff --git a/packages/vis/package.json b/packages/vis/package.json index f504ebb..d879488 100644 --- a/packages/vis/package.json +++ b/packages/vis/package.json @@ -35,7 +35,7 @@ "@spatialdata/react": "workspace:*", "@uidotdev/usehooks": "^2.4.1", "@uiw/react-json-view": "2.0.0-alpha.39", - "@vivjs-experimental/viv": "catalog:", + "@hms-dbmi/viv": "catalog:", "deck.gl": "catalog:", "geotiff": "2.1.4-beta.0", "zustand": "^5.0.8" @@ -45,6 +45,7 @@ "@types/react": "catalog:", "@types/react-dom": "catalog:", "@vitejs/plugin-react": "catalog:", + "jsdom": "catalog:", "typescript": "catalog:", "vite": "catalog:", "vite-plugin-dts": "catalog:", diff --git a/packages/vis/src/ImageView/avivatorish/state.tsx b/packages/vis/src/ImageView/avivatorish/state.tsx index 057a1ea..5fe08e7 100644 --- a/packages/vis/src/ImageView/avivatorish/state.tsx +++ b/packages/vis/src/ImageView/avivatorish/state.tsx @@ -1,5 +1,5 @@ import { type PropsWithChildren, createContext, useContext } from "react"; -import type { loadBioformatsZarr, loadOmeTiff, loadOmeZarr } from "@vivjs-experimental/viv"; +import type { loadOmeTiff, loadOmeZarr } from "@hms-dbmi/viv"; import { createStore } from "zustand"; import { useStoreWithEqualityFn } from "zustand/traditional"; import type { EqFn, Selector, ZustandStore } from "./zustandTypes"; @@ -8,11 +8,10 @@ import type { EqFn, Selector, ZustandStore } from "./zustandTypes"; // ... not to mention HTJ2K? export type OME_TIFF = Awaited>; export type OME_ZARR = Awaited>; -export type BIO_ZARR = Awaited>; -export type PixelSource = OME_TIFF | OME_ZARR | BIO_ZARR; +export type PixelSource = OME_TIFF | OME_ZARR; // --- copied straight from Avivator's code::: with notes / changes for MDV (and now SpatialData.js) --- -import { RENDERING_MODES } from "@vivjs-experimental/viv"; +import { RENDERING_MODES } from "@hms-dbmi/viv"; const capitalize = (string: string) => string.charAt(0).toUpperCase() + string.slice(1); @@ -338,7 +337,7 @@ type OME_METADATA = OME_ZARR['metadata'] & { PhysicalSizeXUnit?: string; } } -export type Metadata = OME_TIFF['metadata'] | OME_METADATA | BIO_ZARR['metadata']; +export type Metadata = OME_TIFF['metadata'] | OME_METADATA; //export type Metadata = TiffPreviewProps["metadata"]; export const useMetadata = (): Metadata | undefined | null => { try { diff --git a/packages/vis/src/ImageView/avivatorish/utils.ts b/packages/vis/src/ImageView/avivatorish/utils.ts index d5a4771..6c612f9 100644 --- a/packages/vis/src/ImageView/avivatorish/utils.ts +++ b/packages/vis/src/ImageView/avivatorish/utils.ts @@ -3,15 +3,12 @@ import { fromBlob, fromUrl } from "geotiff"; import { Matrix4 } from "@math.gl/core"; import { - loadOmeTiff, - loadBioformatsZarr, loadOmeZarr, - loadMultiTiff, getChannelStats, RENDERING_MODES, ColorPalette3DExtensions, AdditiveColormap3DExtensions, -} from "@vivjs-experimental/viv"; +} from "@hms-dbmi/viv"; import { GLOBAL_SLIDER_DIMENSION_FIELDS } from "./constants"; import type { OME_TIFF, PixelSource } from "./state"; diff --git a/packages/vis/src/ImageView/index.tsx b/packages/vis/src/ImageView/index.tsx index bec9b29..3f27433 100644 --- a/packages/vis/src/ImageView/index.tsx +++ b/packages/vis/src/ImageView/index.tsx @@ -11,7 +11,7 @@ import { useChannelsStoreApi, DEFAULT_CHANNEL_STATE, } from './avivatorish/state'; -import { DetailView, VivViewer, getDefaultInitialViewState } from '@vivjs-experimental/viv'; +import { DetailView, VivViewer, getDefaultInitialViewState } from '@hms-dbmi/viv'; import { useImage } from './avivatorish/hooks'; /** diff --git a/packages/vis/tests/index.spec.tsx b/packages/vis/tests/index.spec.tsx new file mode 100644 index 0000000..60cf7cb --- /dev/null +++ b/packages/vis/tests/index.spec.tsx @@ -0,0 +1,43 @@ +import { describe, expect, it } from 'vitest'; +import * as VisExports from '../src/index.js'; + +describe('@spatialdata/vis', () => { + it('should export SpatialCanvas component', () => { + // SpatialCanvas is exported as a named export, not default + expect(VisExports.SpatialCanvas).toBeDefined(); + expect(typeof VisExports.SpatialCanvas).toBe('function'); + }); + + it('should export named components', () => { + expect(VisExports.Sketch).toBeDefined(); + expect(VisExports.SpatialDataTree).toBeDefined(); + expect(VisExports.Transforms).toBeDefined(); + expect(VisExports.ImageView).toBeDefined(); + expect(VisExports.Shapes).toBeDefined(); + expect(VisExports.Table).toBeDefined(); + }); + + it('should export SpatialCanvas hooks and utilities', () => { + expect(VisExports.SpatialCanvasProvider).toBeDefined(); + expect(VisExports.useSpatialCanvasStore).toBeDefined(); + expect(VisExports.useSpatialCanvasActions).toBeDefined(); + expect(VisExports.useSpatialCanvasStoreApi).toBeDefined(); + expect(VisExports.createSpatialCanvasStore).toBeDefined(); + expect(VisExports.useSpatialViewState).toBeDefined(); + expect(VisExports.useViewStateUrl).toBeDefined(); + }); + + it('should have all expected exports', () => { + const exports = Object.keys(VisExports); + expect(exports.length).toBeGreaterThan(0); + // Check for key exports + expect(exports).toContain('Sketch'); + expect(exports).toContain('SpatialDataTree'); + expect(exports).toContain('Transforms'); + expect(exports).toContain('ImageView'); + expect(exports).toContain('Shapes'); + expect(exports).toContain('Table'); + expect(exports).toContain('SpatialCanvasProvider'); + }); +}); + diff --git a/packages/vis/vite.config.ts b/packages/vis/vite.config.ts index 8aa31a0..b9b812d 100644 --- a/packages/vis/vite.config.ts +++ b/packages/vis/vite.config.ts @@ -1,10 +1,19 @@ import { fileURLToPath } from 'node:url'; import { defineViteConfig } from '../../vite.config.base'; +import { mergeConfig } from 'vite'; const pkgRoot = fileURLToPath(new URL('.', import.meta.url)); -export default defineViteConfig({ +const baseConfig = defineViteConfig({ pkgRoot, libName: 'SpatialDataVis', external: ['@spatialdata/core', '@spatialdata/react'], }); + +export default mergeConfig(baseConfig, { + test: { + globals: true, + environment: 'jsdom', + include: ['tests/**/*.spec.ts*'], + }, +}); diff --git a/packages/zarrextra/package.json b/packages/zarrextra/package.json index 22715a5..faf7f93 100644 --- a/packages/zarrextra/package.json +++ b/packages/zarrextra/package.json @@ -22,7 +22,8 @@ "test:coverage": "vitest run --coverage" }, "dependencies": { - "zarrita": "catalog:" + "zarrita": "catalog:", + "zod": "catalog:" }, "devDependencies": { "@types/node": "^22.10.5", diff --git a/packages/zarrextra/src/index.ts b/packages/zarrextra/src/index.ts index 9f6fa69..ce8a82d 100644 --- a/packages/zarrextra/src/index.ts +++ b/packages/zarrextra/src/index.ts @@ -1,44 +1,99 @@ import * as zarr from 'zarrita'; -import type { ZarrTree, ConsolidatedStore, ZAttrsAny, IntermediateConsolidatedStore } from './types'; +import type { ZarrTree, ConsolidatedStore, ZAttrsAny, IntermediateConsolidatedStore, ZarrV2Metadata, ZarrV3Metadata, ZarrV3GroupNode, ZarrV3ArrayNode } from './types'; import { ATTRS_KEY, ZARRAY_KEY } from './types'; import { Err, Ok, type Result } from './result'; +import { validateAndConvertV2Zarray, validateV3Zarray } from './zarrSchema'; /** * As of this writing, this returns a nested object, leaf nodes have async functions that return the zarr array. * * This traverses arbitrary group depth etc - handy for a generic zarr thing, but for SpatialData we can have * something more explicitly targetting the expected structure. + * + * Works directly with the normalized v3 metadata structure, extracting paths from metadata rather than + * relying on store.contents(). */ -export async function parseStoreContents(store: IntermediateConsolidatedStore): Promise { - // this can await get metadata without too much issue given we know it's already there... +async function parseStoreContents(store: IntermediateConsolidatedStore): Promise { + // Access metadata from consolidated_metadata.metadata + const metadata = store.zmetadata.consolidated_metadata?.metadata; + + if (!metadata || typeof metadata !== 'object') { + return {}; + } + + // Extract all paths from metadata and determine their types + const pathInfo = new Map(); + + for (const [path, node] of Object.entries(metadata)) { + if (node && typeof node === 'object' && 'node_type' in node) { + const isArray = node.node_type === 'array'; + pathInfo.set(path, { isArray, path, node }); + } + } + + // Sort paths by depth (shorter paths first) to build tree top-down + const sortedPaths = Array.from(pathInfo.entries()).sort((a, b) => { + const depthA = a[0].split('/').filter(p => p).length; + const depthB = b[0].split('/').filter(p => p).length; + return depthA - depthB; + }); + + // Open root for resolving array paths later + // this is throwing when I try to open http://localhost:8081/?url=https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zarr + // it gets to `open_group_v2`, `throw new NodeNotFoundError("v2 group", ...)` + // actually, multiple errors are thrown internally as it tries both v2 & v3 open, and we end up with a somewhat arbitrary error + // nb, downloading that xenium_rep2_io & opening from local server is ok. const root = await zarr.open(store, { kind: 'group' }); - const contents = store.contents().map(v => { - const pathParts = v.path.split('/'); - // might do something with the top-level element name - ie, make a different kind of object for each - - const path = pathParts.slice(1); - return { path, kind: v.kind, v }; - }).sort((a, b) => a.path.length - b.path.length).slice(1); // skip the root group itself - - + const tree: ZarrTree = {}; - for (const item of contents) { + + for (const [fullPath, info] of sortedPaths) { + // Skip root path + if (!fullPath || fullPath === '/' || fullPath === '') continue; + + // Normalize path: ensure it starts with / and doesn't end with / + const normalizedPath = fullPath.startsWith('/') ? fullPath : `/${fullPath}`; + const pathParts = normalizedPath.split('/').filter(p => p); + + if (pathParts.length === 0) continue; + let currentNode = tree; - for (const [i, part] of item.path.entries()) { + + // Build tree structure + for (const [i, part] of pathParts.entries()) { if (!(part in currentNode)) { - const leaf = (i === (item.path.length - 1)) && item.kind === "array"; - // get zattrs... says it's `async` but I strongly don't want it to actually be fetching unncessarily. - // current implementation will use the existing zmetadata and will need to be adapted to zarr.json in v3 - const attrs = await getZattrs(item.v.path, store); - if (leaf) { - const zarray = await getZattrs(item.v.path, store, ".zarray"); - // I suppose this could cache itself as well, but I'm not sure this is really for actual use + const isLeaf = i === pathParts.length - 1; + const isArray = isLeaf && info.isArray; + + // Get attributes for this path (normalizedPath already has leading /) + const currentPath = `/${pathParts.slice(0, i + 1).join('/')}` as zarr.AbsolutePath; + const attrs = getZattrs(currentPath, store); + + if (isArray) { + // Leaf array node - extract array metadata from the node + const arrayNode = info.node as ZarrV3ArrayNode; + const zarray: ZAttrsAny = { + shape: arrayNode.shape, + data_type: arrayNode.data_type, + chunk_grid: arrayNode.chunk_grid, + chunk_key_encoding: arrayNode.chunk_key_encoding, + fill_value: arrayNode.fill_value, + codecs: arrayNode.codecs, + dimension_names: arrayNode.dimension_names, + zarr_format: arrayNode.zarr_format, + node_type: arrayNode.node_type, + storage_transformers: arrayNode.storage_transformers, + }; + + // Capture currentPath by value to avoid closure issues + const arrayPath = currentPath; currentNode[part] = { [ATTRS_KEY]: attrs, - [ZARRAY_KEY]: zarray ?? ({} as ZAttrsAny), - get: () => zarr.open(root.resolve(item.v.path), { kind: 'array' }) + [ZARRAY_KEY]: zarray, + get: () => zarr.open(root.resolve(arrayPath), { kind: 'array' }) }; } else { + // Group node currentNode[part] = { [ATTRS_KEY]: attrs }; } } @@ -46,68 +101,269 @@ export async function parseStoreContents(store: IntermediateConsolidatedStore): currentNode = currentNode[part] as ZarrTree; } } + return tree; } +class ZarrSchemaError extends Error {} +/** + * Parse zarr v3 consolidated metadata from zarr.json + * The actual zarr v3 structure has metadata nested under consolidated_metadata.metadata + * We normalize it to have a top-level metadata field for internal use. + * Validates all array nodes in the metadata. + */ +async function parseZarrJson(zarrJson: unknown): Promise> { + if (!zarrJson || typeof zarrJson !== 'object') { + return Err(new ZarrSchemaError(`Invalid zarr.json: expected an object but got ${typeof zarrJson}`)); + } + + const parsed = zarrJson as ZarrV3Metadata; + + // Validate the structure + if (!parsed.consolidated_metadata || typeof parsed.consolidated_metadata !== 'object') { + return Err(new ZarrSchemaError('Invalid zarr.json: consolidated_metadata field is missing or not an object')); + } + + if (!parsed.consolidated_metadata.metadata || typeof parsed.consolidated_metadata.metadata !== 'object') { + return Err(new ZarrSchemaError('Invalid zarr.json: consolidated_metadata.metadata field is missing or not an object')); + } + + // Validate all array nodes in the metadata + const metadata = parsed.consolidated_metadata.metadata; + for (const [path, node] of Object.entries(metadata)) { + if (node && typeof node === 'object' && 'node_type' in node && node.node_type === 'array') { + try { + // Validate the array node and replace it with the validated version + const validatedNode = validateV3Zarray(node, path); + metadata[path] = validatedNode; + } catch (error) { + const errorMessage = error instanceof Error ? error.message : String(error); + return Err(new ZarrSchemaError(`Failed to validate v3 zarray metadata at path '${path}': ${errorMessage}`)); + } + } + } + + return Ok(parsed); +} + + +/** + * Normalize zarr v2 flat metadata to v3 structure + * Converts flat structure like { "path/.zattrs": {...}, "path/.zarray": {...} } + * to v3 structure with consolidated_metadata.metadata containing nodes + */ +function normalizeV2ToV3Metadata(v2Metadata: ZarrV2Metadata): ZarrV3Metadata { + const metadata: Record = {}; + + if (!v2Metadata.metadata || typeof v2Metadata.metadata !== 'object') { + return { + attributes: {}, + zarr_format: 3, + consolidated_metadata: { + kind: 'inline', + must_understand: false, + metadata: {} + }, + node_type: 'group' + }; + } + + // Group paths by their base path (without .zattrs, .zarray, .zgroup suffix) + const pathGroups = new Map(); + + // Iterate through flat path keys in v2 metadata + for (const [flatPath, value] of Object.entries(v2Metadata.metadata)) { + // Match patterns like "path/.zattrs", "path/.zarray", "path/.zgroup" + const match = flatPath.match(/^(?:(.+?)\/)?(\.zattrs|\.zarray|\.zgroup)$/); + if (match) { + const path = match[1] ?? ''; + const metadataType = match[2]; + if (!pathGroups.has(path)) { + pathGroups.set(path, {}); + } + const group = pathGroups.get(path); + if (group) { + if (metadataType === '.zattrs') { + group.zattrs = value; + } else if (metadataType === '.zarray') { + group.zarray = value; + } else if (metadataType === '.zgroup') { + group.zgroup = value; + } + } + } + } + + // Convert grouped paths to v3 node structure + for (const [path, group] of pathGroups.entries()) { + if (group.zarray) { + // Array node - validate and convert v2 zarray metadata + try { + const arrayNode = validateAndConvertV2Zarray(group.zarray, path); + // Merge attributes from zattrs if present + if (group.zattrs && typeof group.zattrs === 'object') { + arrayNode.attributes = group.zattrs as Record; + } + metadata[path] = arrayNode; + } catch (error) { + const errorMessage = error instanceof Error ? error.message : String(error); + throw new Error(`Failed to normalize v2 zarray metadata at path '${path}': ${errorMessage}`); + } + } else { + // Group node + metadata[path] = { + attributes: (group.zattrs && typeof group.zattrs === 'object') + ? (group.zattrs as Record) + : {}, + zarr_format: 3, + consolidated_metadata: { + kind: 'inline', + must_understand: false, + metadata: {} + }, + node_type: 'group' + }; + } + } + + return { + attributes: {}, + zarr_format: 3, + consolidated_metadata: { + kind: 'inline', + must_understand: false, + metadata + }, + node_type: 'group' + }; +} // we might not always use the FetchStore, this is for convenience & could change /** - * There is a tendency for .zmetadata to be misnamed as zmetadata... + * Try to open consolidated metadata from a zarr store. + * Supports both zarr v2 (.zmetadata) and v3 (zarr.json) formats. + * There is a tendency for .zmetadata to be misnamed as zmetadata in v2. + * + * Since we work directly with metadata and don't use contents(), we don't need + * zarrita's withConsolidated() - we just fetch the metadata files and normalize them. */ -export async function tryConsolidated(store: zarr.FetchStore): Promise { - // in future, first we'll try zarr.json - // and I'm sure we can make this implementation less ugly, kinda trivial though so cba for now. +async function tryConsolidated(store: zarr.FetchStore): Promise { //!!! nb - we need to also handle local files, in which case we don't fetch(url), we need another method - this is important + + // Normalize base URL to avoid double slashes when constructing metadata paths + const urlString = typeof store.url === 'string' ? store.url : store.url.toString(); + const baseUrl = urlString; + + // First, try zarr.json (v3 format) + try { + const zarrJsonPath = `${baseUrl.replace(/\/+$/, '')}/zarr.json`; + const response = await fetch(zarrJsonPath); + if (!response.ok) throw new Error(`HTTP ${response.status}`); + const zarrJson = await response.json(); + const parseResult = await parseZarrJson(zarrJson); + + if (!parseResult.ok) { + // Fall through to try v2 formats + throw parseResult.error; + } + + const v3Metadata = parseResult.value; + + // Return store with metadata properties + return Object.assign(store, { + zmetadata: v3Metadata + }); + } catch (e) { + // Fall through to try v2 formats for HTTP error. If it was a ZarrSchemaError, re-throw + if (e instanceof ZarrSchemaError) { + throw e; + } + } + + // Try .zmetadata (v2 format) try { - const path = `${store.url}/.zmetadata`; - // is there a zod schema we could be using here? - const zmetadata = await (await fetch(path)).json(); - const zarrita = await zarr.withConsolidated(store); - return { ...zarrita, zmetadata } + const path = `${baseUrl.replace(/\/+$/, '')}/.zmetadata`; + const zmetadata = await (await fetch(path)).json() as ZarrV2Metadata; + // Normalize v2 flat metadata to v3 nested format for consistent internal use + const v3Metadata = normalizeV2ToV3Metadata(zmetadata); + // Return store with metadata properties + return Object.assign(store, { + zmetadata: v3Metadata + }); } catch { + // Try zmetadata (v2 variant, misnamed) try { - const path = `${store.url}/zmetadata`; - const zmetadata = await (await fetch(path)).json(); - const zarrita = await zarr.withConsolidated(store, { metadataKey: 'zmetadata' }); - return { ...zarrita, zmetadata } - } catch { - throw new Error(`Couldn't open consolidated metadata for '${store.url}' - n.b. zarr v3 / spatialdata >0.5 is not supported yet`); + const path = `${baseUrl.replace(/\/+$/, '')}/zmetadata`; + const zmetadata = await (await fetch(path)).json() as ZarrV2Metadata; + // Normalize v2 flat metadata to v3 nested format for consistent internal use + const v3Metadata = normalizeV2ToV3Metadata(zmetadata); + // Return store with metadata properties + return Object.assign(store, { + zmetadata: v3Metadata, + metadataFormat: 'v3' as const + }); + } catch (e) { + throw new Error( + `Couldn't open consolidated metadata for '${store.url}'. Tried: zarr.json (v3), .zmetadata (v2), and zmetadata (v2 variant). Ensure the store has valid consolidated metadata. ${e}` + ); } } - - // nb for now we explicitly only support consolidated store, so if it doesn't find either key this is an error - // --- also note, as of writing zarrita doesn't support consolidated metadata on v3 stores - // - meaning in that case we might not use its `withConsolidated` function at all (especially since it's IMO not as useful as it should be even for v2), - // so we should refactor our parsing to not use `ListableStore.contents()` and probably avoid the extra fetch. - // return zarr.withConsolidated(store).catch(() => zarr.withConsolidated(store, { metadataKey: 'zmetadata' })); } /** * Try to open a consolidated `zarr` store and return a `Result`, + * Supports both zarr v2 and v3 formats. */ export async function openExtraConsolidated(source: string): Promise> { // could `source` also be a File or something? try { - const store = new zarr.FetchStore(source); + // Normalize source to avoid trailing slashes causing double-slash paths + const normalizedSource = source.replace(/\/+$/, ''); + + // why does this later end up thinking it should be able to do use HTTPMethd.PUT? + // seems inappropriate for a read-only store. + const store = new zarr.FetchStore(normalizedSource); const zarritaStore = await tryConsolidated(store); - if (!('contents' in zarritaStore)) { - return Err(new Error(`No consolidated metadata in store '${source}'`)); + // Validate that we have metadata (we no longer check for contents() since we don't use it) + + // Validate that we have metadata + if (!zarritaStore.zmetadata || typeof zarritaStore.zmetadata !== 'object') { + return Err(new Error(`Invalid consolidated metadata format in store '${source}'. Expected an object but got ${typeof zarritaStore.zmetadata}.`)); } + const tree = await parseStoreContents(zarritaStore); return Ok({ zarritaStore, tree }); } catch (error) { - return Err(new Error(`${error}`)); + const errorMessage = error instanceof Error ? error.message : String(error); + return Err(new Error(`Failed to open consolidated zarr store '${source}': ${errorMessage}`)); } } /** * Get zarr attributes from a consolidated store's metadata + * In zarr v3, attributes are stored in the `attributes` field of each node */ -export async function getZattrs(path: zarr.AbsolutePath, store: IntermediateConsolidatedStore, k=".zattrs"): Promise | undefined> { - const attrPath = `${path}/${k}`.slice(1); - const attr = store.zmetadata.metadata[attrPath]; //may be undefined, that's fine. - if (!attr) return undefined; - return attr; +function getZattrs(path: zarr.AbsolutePath, store: IntermediateConsolidatedStore, k=".zattrs"): Record | undefined { + const pathStr = path.slice(1); // Remove leading '/' + const metadata = store.zmetadata.consolidated_metadata?.metadata; + if (!metadata || typeof metadata !== 'object') { + return undefined; + } + + const node = metadata[pathStr]; + if (!node || typeof node !== 'object' || !('node_type' in node)) { + return undefined; + } + + // For backward compatibility, if k is ".zattrs", return the attributes field + // Otherwise, this function might be called with ".zarray" but in v3 we don't need that + // since array metadata is in the node itself + if (k === '.zattrs') { + return node.attributes; + } + + // For other keys, return undefined (legacy support) + return undefined; } /** diff --git a/packages/zarrextra/src/types.ts b/packages/zarrextra/src/types.ts index b9c8c68..e640bfb 100644 --- a/packages/zarrextra/src/types.ts +++ b/packages/zarrextra/src/types.ts @@ -43,9 +43,96 @@ export interface ZarrTree { } /** - * A zarrita store with the raw metadata appended as `zmetadata` - mostly for internal use and subject to revision. + * Zarr v2 consolidated metadata structure (.zmetadata) + * Has a flat metadata object with path keys like "path/.zattrs" */ -export type IntermediateConsolidatedStore = zarr.Listable & { zmetadata: any }; +export type ZarrV2Metadata = { + metadata: Record; +}; + +/** + * Zarr v3 array node metadata + */ +export type ZarrV3ArrayNode = { + shape: number[]; + data_type: string; + chunk_grid: { + name: string; + configuration: { + chunk_shape: number[]; + }; + }; + chunk_key_encoding: { + name: string; + configuration: { + separator: string; + }; + }; + fill_value: number | string | boolean; + codecs: Array<{ + name: string; + configuration?: Record; + }>; + attributes: Record; + dimension_names: string[]; + zarr_format: number; + node_type: 'array'; + storage_transformers: unknown[]; +}; + +/** + * Zarr v3 group node metadata + */ +export type ZarrV3GroupNode = { + attributes: Record; + zarr_format: number; + consolidated_metadata: { + kind: string; + must_understand: boolean; + metadata: Record; + }; + node_type: 'group'; +}; + +/** + * Zarr v3 consolidated metadata structure (zarr.json) + * The actual structure has metadata nested under consolidated_metadata.metadata + * with path keys like "images/blobs_image", "labels/blobs_labels", etc. + * Each entry can be either a group node or an array node. + */ +export type ZarrV3Metadata = { + attributes: Record; + zarr_format: number; + consolidated_metadata: { + kind: string; + must_understand: boolean; + metadata: Record; + }; + node_type: 'group'; +}; + +/** + * Union type for consolidated metadata (v2 or v3) + */ +export type ConsolidatedMetadata = ZarrV2Metadata | ZarrV3Metadata; + +/** + * Discriminated union to identify metadata format + */ +export type MetadataFormat = + | { format: 'v2'; metadata: ZarrV2Metadata } + | { format: 'v3'; metadata: ZarrV3Metadata }; + +/** + * A zarrita store with metadata appended as `zmetadata` - mostly for internal use and subject to revision. + * For zarr v3, metadata is in the actual structure with consolidated_metadata.metadata. + * For zarr v2, we normalize it to match the v3 structure internally. + * Uses `Store` (FetchStore) which already implements `Readable` - we work directly with metadata + * and don't need `contents()` from `Listable`. + */ +export type IntermediateConsolidatedStore = Store & { + zmetadata: ZarrV3Metadata; +}; /** * This type is liable to change in future - for now, it has `zarritaStore` which is the `ListableStore` from `zarrita`, * and `tree: ZarrTree` which has the object hierarchy as described in the consolidated metadata as a mostly "Plain Old Javascript Object", diff --git a/packages/zarrextra/src/zarrSchema.ts b/packages/zarrextra/src/zarrSchema.ts new file mode 100644 index 0000000..5dfb006 --- /dev/null +++ b/packages/zarrextra/src/zarrSchema.ts @@ -0,0 +1,297 @@ +import { z } from 'zod'; +import type { ZarrV3ArrayNode } from './types'; + +//-------- LLM generated schemas for generic zarr metadata --------// +// low - mid confidence in validity, need more testing +// (since writing the above, has been subject to at least some more human scrutiny) + + +/** + * Zod schema for non-negative integer (for shape dimensions) + */ +const nonNegativeInteger = z.number().int().nonnegative(); + +/** + * Zod schema for positive integer (for chunk dimensions) + */ +const positiveInteger = z.number().int().positive(); + +/** + * Zod schema for v2 filter object + */ +const v2FilterSchema = z.object({ + id: z.string(), + configuration: z.record(z.string(), z.unknown()).optional() +}).catchall(z.unknown()); + +/** + * Zod schema for v2 compressor object + */ +const v2CompressorSchema = z.object({ + id: z.string(), + configuration: z.record(z.string(), z.unknown()).optional() +}).catchall(z.unknown()); + +/** + * Zod schema for v3 codec + */ +const v3CodecSchema = z.object({ + name: z.string(), + configuration: z.record(z.string(), z.unknown()).optional() +}); + +/** + * Zod schema for v3 chunk_grid configuration + * Note: chunk_shape can be empty for scalar arrays (0-dimensional) + */ +const v3ChunkGridConfigSchema = z.object({ + chunk_shape: z.array(positiveInteger) +}); + +/** + * Zod schema for v3 chunk_grid + */ +const v3ChunkGridSchema = z.object({ + name: z.string(), + configuration: v3ChunkGridConfigSchema +}); + +/** + * Zod schema for v3 chunk_key_encoding + */ +const v3ChunkKeyEncodingSchema = z.object({ + name: z.string(), + configuration: z.object({ + separator: z.union([z.literal("/"), z.literal(".")]).default("/") + }) +}); + +/** v3 datatypes - note + * the listing at https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html misses 'string' + * making this fail on the first real object I tried it on. + * We may just allow it to pass more things if errors keep appearing here. + */ +const v3dtypeSchema = z.union([ + z.literal("bool"), + z.literal("int8"), + z.literal("int16"), + z.literal("int32"), + z.literal("int64"), + z.literal("uint8"), + z.literal("uint16"), + z.literal("uint32"), + z.literal("uint64"), + z.literal("float16"), + z.literal("float32"), + z.literal("float64"), + z.literal("complex64"), + z.literal("complex128"), + // "string" not listed in https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html + // but appears in some table data, e.g. 'tables/table/obs/_index' in v0.7.0/blobs.zarr, proably also others. + z.literal("string"), + // Raw bits format: "r*" where * is a variable size (multiple of 8) + z.string().regex(/^r\d+$/).superRefine((val, ctx) => { + const size = Number.parseInt(val.slice(1), 10); + if (size <= 0 || size % 8 !== 0) { + ctx.addIssue({ + code: "custom", + message: `'${val}' Raw bits size must be a positive multiple of 8` + }); + } + }), +]); + +/** + * Base v2 zarray schema (before refines) + * Note: shape and chunks can be empty arrays for scalar arrays (0-dimensional). + * In zarr, a scalar is represented as shape=[] and chunks=[]. + * When not empty, chunks must contain positive integers. + */ +const v2ZarrayBaseSchema = z.object({ + shape: z.array(nonNegativeInteger), + chunks: z.array(positiveInteger), // Empty array allowed for scalars; when not empty, values must be positive + dtype: z.string().min(1), + filters: z.array(v2FilterSchema).optional().nullable(), + compressor: v2CompressorSchema.optional().nullable(), + fill_value: z.union([z.number(), z.string(), z.boolean(), z.null()]).optional(), + dimension_names: z.array(z.string()).optional().nullable(), + zarr_format: z.number().optional() +}); + +type V2ZarrayInput = z.infer; + +/** + * Zod schema for v2 zarray metadata + * Handles both regular arrays and scalar arrays (empty shape/chunks) + */ +export const v2ZarraySchema = v2ZarrayBaseSchema.refine( + (data: V2ZarrayInput) => data.chunks.length === data.shape.length, + { + message: 'chunks length must match shape length', + path: ['chunks'] + } +).refine( + (data: V2ZarrayInput) => !data.dimension_names || data.dimension_names.length === data.shape.length, + { + message: 'dimension_names length must match shape length', + path: ['dimension_names'] + } +); +const storageTransformerSchema = z.object({ + name: z.string(), + configuration: z.unknown().optional() +}) +/** + * Base v3 zarray schema (before refines) + * Note: shape and chunk_shape can be empty arrays for scalar arrays (0-dimensional). + * In zarr, a scalar is represented as shape=[] and chunk_shape=[]. + */ +const v3ZarrayBaseSchema = z.object({ + shape: z.array(nonNegativeInteger), // Empty array allowed for scalars + data_type: v3dtypeSchema, //z.string().min(1), + chunk_grid: v3ChunkGridSchema, + chunk_key_encoding: v3ChunkKeyEncodingSchema.optional(), + fill_value: z.union([z.number(), z.string(), z.boolean()]).optional(), + codecs: z.array(v3CodecSchema).optional().nullable(), + dimension_names: z.array(z.string()).optional().nullable(), + storage_transformers: z.array(storageTransformerSchema).optional().nullable(), + zarr_format: z.number().optional(), + node_type: z.literal('array').optional(), + attributes: z.record(z.string(), z.json()).optional() +}); + +type V3ZarrayInput = z.infer; + +/** + * Zod schema for v3 zarray metadata (for hybrid formats) + * Handles both regular arrays and scalar arrays (empty shape/chunk_shape) + */ +export const v3ZarraySchema = v3ZarrayBaseSchema.refine( + (data: V3ZarrayInput) => data.chunk_grid.configuration.chunk_shape.length === data.shape.length, + { + message: 'chunk_shape length must match shape length', + path: ['chunk_grid', 'configuration', 'chunk_shape'] + } +).refine( + (data: V3ZarrayInput) => !data.dimension_names || data.dimension_names.length === data.shape.length, + { + message: 'dimension_names length must match shape length', + path: ['dimension_names'] + } +); + +/** + * Validate and convert v2 zarray metadata to v3 format + * Handles both pure v2 format (with chunks, dtype) and hybrid formats + * @throws Error if required fields are missing or invalid + */ +export function validateAndConvertV2Zarray( + zarray: unknown, + path: string +): ZarrV3ArrayNode { + if (!zarray || typeof zarray !== 'object') { + throw new Error(`Invalid .zarray metadata at path '${path}': expected an object`); + } + const obj = zarray as Record; + + // Check if this already has v3 fields (hybrid/partially converted format) + const hasV3Fields = 'data_type' in obj && 'chunk_grid' in obj; + const hasV2Fields = 'shape' in obj && 'chunks' in obj && 'dtype' in obj; + + if (hasV3Fields && !hasV2Fields) { + // Already in v3 format - validate v3 fields + return validateV3Zarray(zarray, path); + } + + // Validate v2 format + const parseResult = v2ZarraySchema.safeParse(zarray); + if (!parseResult.success) { + const errors = parseResult.error.issues.map((e: z.ZodIssue) => { + const pathStr = e.path.length > 0 ? `'${e.path.join('.')}'` : ''; + return `${pathStr}${pathStr ? ': ' : ''}${e.message}`; + }).join('; '); + throw new Error(`Invalid .zarray metadata at path '${path}': ${errors}`); + } + + const v2 = parseResult.data; + + // Convert v2 compressor and filters to v3 codecs + const codecs: ZarrV3ArrayNode['codecs'] = []; + + // Add filters first (if present) + if (v2.filters) { + for (const filter of v2.filters) { + codecs.push({ + name: filter.id, + configuration: filter.configuration + }); + } + } + + // Add compressor (if present and not null) + if (v2.compressor) { + codecs.push({ + name: v2.compressor.id, + configuration: v2.compressor.configuration + }); + } + + // Build v3 array node + return { + shape: v2.shape, + data_type: v2.dtype, + chunk_grid: { + name: 'regular', + configuration: { chunk_shape: v2.chunks } + }, + chunk_key_encoding: { + name: 'default', + configuration: { separator: '/' } + }, + fill_value: v2.fill_value ?? 0, + codecs, + attributes: {}, + dimension_names: v2.dimension_names ?? [], + zarr_format: 3, + node_type: 'array', + storage_transformers: [] + }; +} + +/** + * Validate v3 zarray metadata (for hybrid formats that already have v3 fields) + * @throws Error if required fields are missing or invalid + */ +export function validateV3Zarray( + zarray: unknown, + path: string +): ZarrV3ArrayNode { + const parseResult = v3ZarraySchema.safeParse(zarray); + if (!parseResult.success) { + const errors = parseResult.error.issues.map((e: z.core.$ZodIssue) => { + const pathStr = e.path.length > 0 ? `'${e.path.join('.')}'` : ''; + return `${pathStr}${pathStr ? ': ' : ''}${e.message}`; + }).join('; '); + throw new Error(`Invalid .zarray metadata at path '${path}': ${errors}`); + } + + const v3 = parseResult.data; + + return { + shape: v3.shape, + data_type: v3.data_type, + chunk_grid: v3.chunk_grid, + chunk_key_encoding: v3.chunk_key_encoding ?? { + name: 'default', + configuration: { separator: '/' } + }, + fill_value: v3.fill_value ?? 0, + codecs: v3.codecs ?? [], + attributes: {}, + dimension_names: v3.dimension_names ?? [], + zarr_format: 3, + node_type: 'array', + storage_transformers: v3.storage_transformers ?? [] + }; +} + diff --git a/packages/zarrextra/tests/zarrSchema.spec.ts b/packages/zarrextra/tests/zarrSchema.spec.ts new file mode 100644 index 0000000..78cb4bc --- /dev/null +++ b/packages/zarrextra/tests/zarrSchema.spec.ts @@ -0,0 +1,274 @@ +import { describe, expect, it } from 'vitest'; +import { + validateAndConvertV2Zarray, + validateV3Zarray, + v2ZarraySchema, + v3ZarraySchema, +} from '../src/zarrSchema.js'; + +describe('zarrextra - Zarr Schema Validation', () => { + describe('v2ZarraySchema', () => { + + it('should validate v2 zarray with filters and compressor', () => { + const zarray = { + shape: [100], + chunks: [10], + dtype: 'float64', + filters: [ + { id: 'delta', configuration: { dtype: 'float64' } }, + ], + compressor: { id: 'blosc', configuration: { cname: 'lz4' } }, + }; + + expect(() => v2ZarraySchema.parse(zarray)).not.toThrow(); + const result = v2ZarraySchema.parse(zarray); + expect(result.filters).toHaveLength(1); + expect(result.compressor?.id).toBe('blosc'); + }); + + it('should reject v2 zarray with mismatched shape/chunks length', () => { + const invalidZarray = { + shape: [100, 200], + chunks: [10], // Wrong length + dtype: 'float64', + }; + + expect(() => v2ZarraySchema.parse(invalidZarray)).toThrow(); + }); + + it('should reject v2 zarray with negative shape dimensions', () => { + const invalidZarray = { + shape: [-1, 100], + chunks: [10, 20], + dtype: 'float64', + }; + + expect(() => v2ZarraySchema.parse(invalidZarray)).toThrow(); + }); + + it('should reject v2 zarray with non-positive chunks', () => { + const invalidZarray = { + shape: [100], + chunks: [0], // Must be positive + dtype: 'float64', + }; + + expect(() => v2ZarraySchema.parse(invalidZarray)).toThrow(); + }); + + it('should reject v2 zarray with missing required fields', () => { + const invalidZarray = { + shape: [100], + // Missing chunks and dtype + }; + + expect(() => v2ZarraySchema.parse(invalidZarray)).toThrow(); + }); + + it('should validate v2 zarray with dimension_names matching shape length', () => { + const zarray = { + shape: [100, 200], + chunks: [10, 20], + dtype: 'float64', + dimension_names: ['y', 'x'], + }; + + expect(() => v2ZarraySchema.parse(zarray)).not.toThrow(); + const result = v2ZarraySchema.parse(zarray); + expect(result.dimension_names).toEqual(['y', 'x']); + }); + + it('should reject v2 zarray with dimension_names length mismatch', () => { + const invalidZarray = { + shape: [100, 200], + chunks: [10, 20], + dtype: 'float64', + dimension_names: ['y'], // Wrong length + }; + + expect(() => v2ZarraySchema.parse(invalidZarray)).toThrow(); + }); + + it('should validate v2 zarray with null fill_value', () => { + const zarray = { + shape: [100], + chunks: [10], + dtype: 'float64', + fill_value: null, // Valid for v2 + }; + + expect(() => v2ZarraySchema.parse(zarray)).not.toThrow(); + const result = v2ZarraySchema.parse(zarray); + expect(result.fill_value).toBeNull(); + }); + }); + + describe('v3ZarraySchema', () => { + + it('should validate v3 zarray with codecs', () => { + const zarray = { + shape: [100], + data_type: 'float64', + chunk_grid: { + name: 'regular', + configuration: { chunk_shape: [10] }, + }, + codecs: [ + { name: 'blosc', configuration: { cname: 'lz4' } }, + ], + }; + + expect(() => v3ZarraySchema.parse(zarray)).not.toThrow(); + const result = v3ZarraySchema.parse(zarray); + expect(result.codecs).toHaveLength(1); + expect(result.codecs?.[0]?.name).toBe('blosc'); + }); + + it('should reject v3 zarray with mismatched shape/chunk_shape length', () => { + const invalidZarray = { + shape: [100, 200], + data_type: 'float64', + chunk_grid: { + name: 'regular', + configuration: { chunk_shape: [10] }, // Wrong length + }, + }; + + expect(() => v3ZarraySchema.parse(invalidZarray)).toThrow(); + }); + + it('should reject v3 zarray with missing required fields', () => { + const invalidZarray = { + shape: [100], + // Missing data_type and chunk_grid + }; + + expect(() => v3ZarraySchema.parse(invalidZarray)).toThrow(); + }); + }); + + describe('validateAndConvertV2Zarray', () => { + it('should convert valid v2 zarray to v3 format', () => { + const v2Zarray = { + shape: [100, 200], + chunks: [10, 20], + dtype: 'float64', + fill_value: 0, + zarr_format: 2, + }; + + const result = validateAndConvertV2Zarray(v2Zarray, 'test/path'); + + expect(result.shape).toEqual([100, 200]); + expect(result.data_type).toBe('float64'); + expect(result.chunk_grid.configuration.chunk_shape).toEqual([10, 20]); + expect(result.chunk_grid.name).toBe('regular'); + expect(result.chunk_key_encoding.name).toBe('default'); + expect(result.zarr_format).toBe(3); + expect(result.node_type).toBe('array'); + }); + + it('should convert v2 filters and compressor to v3 codecs', () => { + const v2Zarray = { + shape: [100], + chunks: [10], + dtype: 'float64', + filters: [ + { id: 'delta', configuration: { dtype: 'float64' } }, + ], + compressor: { id: 'blosc', configuration: { cname: 'lz4' } }, + }; + + const result = validateAndConvertV2Zarray(v2Zarray, 'test/path'); + + expect(result.codecs).toHaveLength(2); + expect(result.codecs[0]?.name).toBe('delta'); + expect(result.codecs[1]?.name).toBe('blosc'); + }); + + it('should handle v2 zarray with dimension_names', () => { + const v2Zarray = { + shape: [100, 200], + chunks: [10, 20], + dtype: 'float64', + dimension_names: ['y', 'x'], + }; + + const result = validateAndConvertV2Zarray(v2Zarray, 'test/path'); + + expect(result.dimension_names).toEqual(['y', 'x']); + }); + + it('should handle v2 zarray with null fill_value', () => { + const v2Zarray = { + shape: [100], + chunks: [10], + dtype: 'float64', + fill_value: null, // Valid for v2 + }; + + const result = validateAndConvertV2Zarray(v2Zarray, 'test/path'); + // Note: validateAndConvertV2Zarray converts null fill_value to 0 default + // This is expected behavior for the conversion function + expect(result.fill_value).toBe(0); + }); + + it('should handle v2 zarray that is already in v3 format (hybrid)', () => { + const hybridZarray = { + shape: [100], + data_type: 'float64', + chunk_grid: { + name: 'regular', + configuration: { chunk_shape: [10] }, + }, + // Missing v2 fields (chunks, dtype) + }; + + // Should use v3 validation path + const result = validateAndConvertV2Zarray(hybridZarray, 'test/path'); + expect(result.data_type).toBe('float64'); + expect(result.chunk_grid.configuration.chunk_shape).toEqual([10]); + }); + }); + + describe('validateV3Zarray', () => { + + it('should provide default chunk_key_encoding if missing', () => { + const v3Zarray = { + shape: [100], + data_type: 'float64', + chunk_grid: { + name: 'regular', + configuration: { chunk_shape: [10] }, + }, + // Missing chunk_key_encoding + }; + + const result = validateV3Zarray(v3Zarray, 'test/path'); + + expect(result.chunk_key_encoding.name).toBe('default'); + expect(result.chunk_key_encoding.configuration.separator).toBe('/'); + }); + + it('should preserve provided optional fields', () => { + const v3Zarray = { + shape: [100], + data_type: 'float64', + chunk_grid: { + name: 'regular', + configuration: { chunk_shape: [10] }, + }, + fill_value: 42, + codecs: [{ name: 'blosc' }], + dimension_names: ['x'], + }; + + const result = validateV3Zarray(v3Zarray, 'test/path'); + + expect(result.fill_value).toBe(42); + expect(result.codecs).toHaveLength(1); + expect(result.dimension_names).toEqual(['x']); + }); + }); +}); + diff --git a/packages/zarrextra/vite.config.ts b/packages/zarrextra/vite.config.ts index c2c9499..3a786f8 100644 --- a/packages/zarrextra/vite.config.ts +++ b/packages/zarrextra/vite.config.ts @@ -26,6 +26,7 @@ export default defineConfig({ test: { globals: true, environment: 'node', + include: ['tests/**/*.spec.ts'], coverage: { provider: 'v8', reporter: ['text', 'json', 'html'], diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index cc4cfc8..8558466 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -6,6 +6,9 @@ settings: catalogs: default: + '@hms-dbmi/viv': + specifier: ^0.19.0 + version: 0.19.0 '@luma.gl/core': specifier: ~9.1.9 version: 9.1.10 @@ -24,9 +27,6 @@ catalogs: '@vitejs/plugin-react': specifier: ^4.3.4 version: 4.7.0 - '@vivjs-experimental/viv': - specifier: ^1.0.1 - version: 1.0.1 anndata.js: specifier: ^0.0.2 version: 0.0.2 @@ -36,6 +36,9 @@ catalogs: deck.gl: specifier: ~9.1.11 version: 9.1.15 + jsdom: + specifier: ^27.4.0 + version: 27.4.0 parquet-wasm: specifier: ^0.6.1 version: 0.6.1 @@ -85,7 +88,7 @@ importers: version: 4.5.4(@types/node@22.18.8)(rollup@4.52.4)(typescript@5.9.3)(vite@7.2.7(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0)) vitest: specifier: 'catalog:' - version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0) + version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(jsdom@27.4.0)(terser@5.44.0) docs: dependencies: @@ -183,7 +186,7 @@ importers: version: 4.5.4(@types/node@22.18.8)(rollup@4.52.4)(typescript@5.9.3)(vite@7.2.7(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0)) vitest: specifier: 'catalog:' - version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0) + version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(jsdom@27.4.0)(terser@5.44.0) packages/react: dependencies: @@ -215,6 +218,9 @@ importers: '@vitejs/plugin-react': specifier: 'catalog:' version: 4.7.0(vite@7.2.7(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0)) + jsdom: + specifier: 'catalog:' + version: 27.4.0 typescript: specifier: 'catalog:' version: 5.9.3 @@ -226,10 +232,13 @@ importers: version: 4.5.4(@types/node@22.18.8)(rollup@4.52.4)(typescript@5.9.3)(vite@7.2.7(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0)) vitest: specifier: 'catalog:' - version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0) + version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(jsdom@27.4.0)(terser@5.44.0) packages/vis: dependencies: + '@hms-dbmi/viv': + specifier: 'catalog:' + version: 0.19.0(9a614091add8d9561d5b393ea4eef7a1) '@luma.gl/core': specifier: 'catalog:' version: 9.1.10 @@ -248,9 +257,6 @@ importers: '@uiw/react-json-view': specifier: 2.0.0-alpha.39 version: 2.0.0-alpha.39(@babel/runtime@7.28.4)(react-dom@19.2.0(react@19.2.0))(react@19.2.0) - '@vivjs-experimental/viv': - specifier: 'catalog:' - version: 1.0.1(9a614091add8d9561d5b393ea4eef7a1) anndata.js: specifier: 'catalog:' version: 0.0.2 @@ -285,6 +291,9 @@ importers: '@vitejs/plugin-react': specifier: 'catalog:' version: 4.7.0(vite@7.2.7(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0)) + jsdom: + specifier: 'catalog:' + version: 27.4.0 typescript: specifier: 'catalog:' version: 5.9.3 @@ -296,13 +305,16 @@ importers: version: 4.5.4(@types/node@22.18.8)(rollup@4.52.4)(typescript@5.9.3)(vite@7.2.7(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0)) vitest: specifier: 'catalog:' - version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0) + version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(jsdom@27.4.0)(terser@5.44.0) packages/zarrextra: dependencies: zarrita: specifier: 'catalog:' version: 0.5.4 + zod: + specifier: 'catalog:' + version: 4.1.13 devDependencies: '@types/node': specifier: ^22.10.5 @@ -318,10 +330,13 @@ importers: version: 4.5.4(@types/node@22.18.8)(rollup@4.52.4)(typescript@5.9.3)(vite@7.2.7(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0)) vitest: specifier: 'catalog:' - version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0) + version: 3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(jsdom@27.4.0)(terser@5.44.0) packages: + '@acemir/cssom@0.9.31': + resolution: {integrity: 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snapshots: - '@luma.gl/shadertools' - '@luma.gl/webgl' - '@vivjs-experimental/viv@1.0.1(9a614091add8d9561d5b393ea4eef7a1)': - dependencies: - '@vivjs-experimental/constants': 1.0.1 - '@vivjs-experimental/extensions': 1.0.1(@deck.gl/core@9.1.15) - '@vivjs-experimental/layers': 1.0.1(95853861a3a9bfb6cf4e0bb4f1c1545a) - '@vivjs-experimental/loaders': 1.0.1 - '@vivjs-experimental/types': 1.0.1 - '@vivjs-experimental/viewers': 1.0.1(9a614091add8d9561d5b393ea4eef7a1) - '@vivjs-experimental/views': 1.0.1(95853861a3a9bfb6cf4e0bb4f1c1545a) - transitivePeerDependencies: - - '@deck.gl/core' - - '@deck.gl/geo-layers' - - '@deck.gl/layers' - - '@deck.gl/react' - - '@luma.gl/constants' - - '@luma.gl/core' - - '@luma.gl/engine' - - '@luma.gl/shadertools' - - '@luma.gl/webgl' - - react - '@volar/language-core@2.4.23': dependencies: '@volar/source-map': 2.4.23 @@ -11421,6 +11572,8 @@ snapshots: address@1.2.2: {} + agent-base@7.1.4: {} + aggregate-error@3.1.0: dependencies: clean-stack: 2.2.0 @@ -11626,6 +11779,10 @@ snapshots: batch@0.6.1: {} + bidi-js@1.0.3: + dependencies: + require-from-string: 2.0.2 + big.js@5.2.2: {} bignumber.js@9.3.1: {} @@ -12101,6 +12258,11 @@ snapshots: mdn-data: 2.0.30 source-map-js: 1.2.1 + css-tree@3.1.0: + dependencies: + mdn-data: 2.12.2 + source-map-js: 1.2.1 + css-what@6.2.2: {} cssdb@8.4.2: {} @@ -12168,6 +12330,13 @@ snapshots: dependencies: css-tree: 2.2.1 + cssstyle@5.3.7: + dependencies: + '@asamuzakjp/css-color': 4.1.1 + '@csstools/css-syntax-patches-for-csstree': 1.0.26 + css-tree: 3.1.0 + lru-cache: 11.2.5 + csstype@3.2.3: {} d3-array@2.12.1: @@ -12361,6 +12530,11 @@ snapshots: d3-transition: 3.0.1(d3-selection@3.0.0) d3-zoom: 3.0.0 + data-urls@6.0.1: + dependencies: + whatwg-mimetype: 5.0.0 + whatwg-url: 15.1.0 + de-indent@1.0.2: {} debounce@1.2.1: {} @@ -12373,6 +12547,8 @@ snapshots: dependencies: ms: 2.1.3 + decimal.js@10.6.0: {} + deck.gl@9.1.15(@arcgis/core@4.34.5)(@luma.gl/shadertools@9.1.10(@luma.gl/core@9.1.10))(@luma.gl/webgl@9.1.10(@luma.gl/core@9.1.10))(react-dom@19.2.0(react@19.2.0))(react@19.2.0): dependencies: '@deck.gl/aggregation-layers': 9.1.15(@deck.gl/core@9.1.15)(@deck.gl/layers@9.1.15(@deck.gl/core@9.1.15)(@loaders.gl/core@4.3.4)(@luma.gl/core@9.1.10)(@luma.gl/engine@9.1.10(@luma.gl/core@9.1.10)(@luma.gl/shadertools@9.1.10(@luma.gl/core@9.1.10))))(@luma.gl/core@9.1.10)(@luma.gl/engine@9.1.10(@luma.gl/core@9.1.10)(@luma.gl/shadertools@9.1.10(@luma.gl/core@9.1.10))) @@ -12718,8 +12894,6 @@ snapshots: eventemitter3@4.0.7: {} - eventemitter3@5.0.1: {} - events@3.3.0: {} eventsource-parser@3.0.6: {} @@ -13159,6 +13333,12 @@ snapshots: readable-stream: 2.3.8 wbuf: 1.7.3 + html-encoding-sniffer@6.0.0: + dependencies: + '@exodus/bytes': 1.10.0 + transitivePeerDependencies: + - '@noble/hashes' + html-escaper@2.0.2: {} html-minifier-terser@6.1.0: @@ -13230,6 +13410,13 @@ snapshots: http-parser-js@0.5.10: {} + http-proxy-agent@7.0.2: + dependencies: + agent-base: 7.1.4 + debug: 4.4.3 + transitivePeerDependencies: + - supports-color + http-proxy-middleware@2.0.9(@types/express@4.17.23): dependencies: '@types/http-proxy': 1.17.16 @@ -13255,6 +13442,13 @@ snapshots: quick-lru: 5.1.1 resolve-alpn: 1.2.1 + https-proxy-agent@7.0.6: + dependencies: + agent-base: 7.1.4 + debug: 4.4.3 + transitivePeerDependencies: + - supports-color + human-signals@2.1.0: {} hyperdyperid@1.2.0: {} @@ -13402,6 +13596,8 @@ snapshots: dependencies: isobject: 3.0.1 + is-potential-custom-element-name@1.0.1: {} + is-regex@1.2.1: dependencies: call-bound: 1.0.4 @@ -13482,6 +13678,34 @@ snapshots: dependencies: argparse: 2.0.1 + jsdom@27.4.0: + dependencies: + '@acemir/cssom': 0.9.31 + '@asamuzakjp/dom-selector': 6.7.6 + '@exodus/bytes': 1.10.0 + cssstyle: 5.3.7 + data-urls: 6.0.1 + decimal.js: 10.6.0 + html-encoding-sniffer: 6.0.0 + http-proxy-agent: 7.0.2 + https-proxy-agent: 7.0.6 + is-potential-custom-element-name: 1.0.1 + parse5: 8.0.0 + saxes: 6.0.0 + symbol-tree: 3.2.4 + tough-cookie: 6.0.0 + w3c-xmlserializer: 5.0.0 + webidl-conversions: 8.0.1 + whatwg-mimetype: 4.0.0 + whatwg-url: 15.1.0 + ws: 8.18.3 + xml-name-validator: 5.0.0 + transitivePeerDependencies: + - '@noble/hashes' + - bufferutil + - supports-color + - utf-8-validate + jsep@0.3.5: {} jsesc@3.1.0: {} @@ -13608,6 +13832,8 @@ snapshots: lowercase-keys@3.0.0: {} + lru-cache@11.2.5: {} + lru-cache@5.1.1: dependencies: yallist: 3.1.1 @@ -13847,6 +14073,8 @@ snapshots: mdn-data@2.0.30: {} + mdn-data@2.12.2: {} + media-typer@0.3.0: {} memfs@4.49.0: @@ -14370,11 +14598,6 @@ snapshots: eventemitter3: 4.0.7 p-timeout: 3.2.0 - p-queue@7.4.1: - dependencies: - eventemitter3: 5.0.1 - p-timeout: 5.1.0 - p-retry@6.2.1: dependencies: '@types/retry': 0.12.2 @@ -14385,8 +14608,6 @@ snapshots: dependencies: p-finally: 1.0.0 - p-timeout@5.1.0: {} - package-json@8.1.1: dependencies: got: 12.6.1 @@ -14441,6 +14662,10 @@ snapshots: dependencies: entities: 6.0.1 + parse5@8.0.0: + dependencies: + entities: 6.0.1 + parseurl@1.3.3: {} pascal-case@3.1.2: @@ -15382,6 +15607,10 @@ snapshots: sax@1.4.3: {} + saxes@6.0.0: + dependencies: + xmlchars: 2.2.0 + scheduler@0.27.0: {} schema-dts@1.1.5: {} @@ -15741,6 +15970,8 @@ snapshots: react: 19.2.1 use-sync-external-store: 1.6.0(react@19.2.1) + symbol-tree@3.2.4: {} + tabbable@6.3.0: {} table-layout@4.1.1: @@ -15804,6 +16035,12 @@ snapshots: tinyspy@4.0.4: {} + tldts-core@7.0.19: {} + + tldts@7.0.19: + dependencies: + tldts-core: 7.0.19 + to-regex-range@5.0.1: dependencies: is-number: 7.0.0 @@ -15812,6 +16049,14 @@ snapshots: totalist@3.0.1: {} + tough-cookie@6.0.0: + dependencies: + tldts: 7.0.19 + + tr46@6.0.0: + dependencies: + punycode: 2.3.1 + tree-dump@1.1.0(tslib@2.8.1): dependencies: tslib: 2.8.1 @@ -16053,7 +16298,7 @@ snapshots: jiti: 1.21.7 terser: 5.44.0 - vitest@3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(terser@5.44.0): + vitest@3.2.4(@types/debug@4.1.12)(@types/node@22.18.8)(jiti@1.21.7)(jsdom@27.4.0)(terser@5.44.0): dependencies: '@types/chai': 5.2.2 '@vitest/expect': 3.2.4 @@ -16081,6 +16326,7 @@ snapshots: optionalDependencies: '@types/debug': 4.1.12 '@types/node': 22.18.8 + jsdom: 27.4.0 transitivePeerDependencies: - jiti - less @@ -16097,6 +16343,10 @@ snapshots: vscode-uri@3.1.0: {} + w3c-xmlserializer@5.0.0: + dependencies: + xml-name-validator: 5.0.0 + watchpack@2.4.4: dependencies: glob-to-regexp: 0.4.1 @@ -16110,6 +16360,8 @@ snapshots: web-worker@1.5.0: {} + webidl-conversions@8.0.1: {} + webpack-bundle-analyzer@4.10.2: dependencies: '@discoveryjs/json-ext': 0.5.7 @@ -16245,6 +16497,15 @@ snapshots: wgsl_reflect@1.2.3: {} + whatwg-mimetype@4.0.0: {} + + whatwg-mimetype@5.0.0: {} + + whatwg-url@15.1.0: + dependencies: + tr46: 6.0.0 + webidl-conversions: 8.0.1 + which@2.0.2: dependencies: isexe: 2.0.0 @@ -16295,8 +16556,12 @@ snapshots: dependencies: sax: 1.4.3 + xml-name-validator@5.0.0: {} + xml-utils@1.10.2: {} + xmlchars@2.2.0: {} + xmldoc@2.0.2: dependencies: sax: 1.4.3 @@ -16312,11 +16577,6 @@ snapshots: yocto-queue@1.2.1: {} - zarr@0.6.3: - dependencies: - numcodecs: 0.2.2 - p-queue: 7.4.1 - zarrita@0.5.1: dependencies: '@zarrita/storage': 0.1.3 diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml index 1506479..7fb9c1d 100644 --- a/pnpm-workspace.yaml +++ b/pnpm-workspace.yaml @@ -9,7 +9,7 @@ catalog: '@types/react': ^19.2.0 '@types/react-dom': ^19.2.0 '@vitejs/plugin-react': ^4.3.4 - '@vivjs-experimental/viv': ^1.0.1 + '@hms-dbmi/viv': ^0.19.0 anndata.js: ^0.0.2 apache-arrow: ^17.0.0 deck.gl: ~9.1.11 @@ -22,3 +22,4 @@ catalog: vitest: ^3.1.4 zarrita: ^0.5.4 zod: ^4.1.13 + jsdom: ^27.4.0 diff --git a/python/.python-version b/python/.python-version new file mode 100644 index 0000000..e0aad9e --- /dev/null +++ b/python/.python-version @@ -0,0 +1,2 @@ +3.12 + diff --git a/python/scripts/generate_fixtures.py b/python/scripts/generate_fixtures.py new file mode 100644 index 0000000..15a7083 --- /dev/null +++ b/python/scripts/generate_fixtures.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python3 +""" +Wrapper script to generate test fixtures for all spatialdata versions. + +This script coordinates running the version-specific fixture generation scripts +located in python/v0.5.0/, python/v0.6.1/, and python/v0.7.0/. +""" + +import argparse +import subprocess +import sys +from pathlib import Path + + +def main(): + parser = argparse.ArgumentParser( + description="Generate test fixtures for SpatialData.ts" + ) + parser.add_argument( + "--version", + type=str, + choices=["0.5.0", "0.6.1", "0.7.0"], + default=None, + help="SpatialData version to generate fixtures for (default: all)", + ) + parser.add_argument( + "--output-dir", + type=str, + default="test-fixtures", + help="Output directory for fixtures (default: test-fixtures)", + ) + + args = parser.parse_args() + + # Get project root + script_path = Path(__file__) + project_root = script_path.parent.parent.parent + output_dir = project_root / args.output_dir + + versions = [args.version] if args.version else ["0.5.0", "0.6.1", "0.7.0"] + + success = True + for version in versions: + env_dir = project_root / "python" / f"v{version}" + version_script = env_dir / "generate_fixtures.py" + + if not version_script.exists(): + print(f"Error: Script not found at {version_script}") + print(f" Make sure the environment directory exists: {env_dir}") + success = False + continue + + # Ensure the environment is set up + print(f"\n{'='*60}") + print(f"Setting up environment for spatialdata {version}...") + print(f"{'='*60}") + sync_result = subprocess.run( + ["uv", "sync", "--directory", str(env_dir)], + cwd=project_root, + capture_output=True, + text=True, + ) + + if sync_result.returncode != 0: + print(f"Error setting up environment for version {version}:") + print(sync_result.stderr) + success = False + continue + + # Run the version-specific script in its environment + print(f"\n{'='*60}") + print(f"Generating fixtures for spatialdata {version}...") + print(f"{'='*60}") + result = subprocess.run( + [ + "uv", "run", + "--directory", str(env_dir), + str(version_script), + "--output-dir", str(output_dir), + ], + cwd=project_root, + ) + + if result.returncode != 0: + print(f"Failed to generate fixtures for version {version}") + success = False + + if success: + print("\n" + "="*60) + print("✓ All fixtures generated successfully!") + print("="*60) + else: + print("\n" + "="*60) + print("✗ Some fixtures failed to generate") + print("="*60) + sys.exit(1) + + +if __name__ == "__main__": + main() diff --git a/python/scripts/validate_datasets.py b/python/scripts/validate_datasets.py new file mode 100755 index 0000000..36911c7 --- /dev/null +++ b/python/scripts/validate_datasets.py @@ -0,0 +1,492 @@ +#!/usr/bin/env python3 +""" +Validate spatialdata dataset compatibility across different versions. + +This script tests loading publicly available spatialdata datasets from +spatialdata.scverse.org against different versions of the spatialdata library +to establish a baseline of what works with each version. +""" + +import argparse +import json +import subprocess +import sys +from dataclasses import dataclass, asdict +from pathlib import Path +from typing import Optional +from datetime import datetime +from multiprocessing import Pool, cpu_count + + +@dataclass +class ValidationResult: + """Result of validating a dataset with a specific version.""" + dataset_name: str + dataset_url: str + spatialdata_version: str + success: bool + error_type: Optional[str] = None + error_message: Optional[str] = None + elements: Optional[dict] = None + coordinate_systems: Optional[list] = None + + def to_dict(self): + """Convert to dictionary for JSON serialization.""" + return asdict(self) + + +# Dataset definitions from https://spatialdata.scverse.org/en/stable/tutorials/notebooks/datasets/README.html +DATASETS = [ + { + "name": "Visium HD (Mouse intestin)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_hd_3.0.0_io.zarr/", + }, + { + "name": "Visium (Breast cancer)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zarr/", + }, + { + "name": "Xenium (Breast cancer - Rep1)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zarr/", + }, + { + "name": "Xenium (Breast cancer - Rep2)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zarr/", + }, + { + "name": "CyCIF (Lung adenocarcinoma)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr/", + }, + { + "name": "MERFISH (Mouse brain)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr/", + }, + { + "name": "MIBI-TOF (Colorectal carcinoma)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr/", + }, + { + "name": "Imaging Mass Cytometry (Multiple cancers)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr/", + }, + { + "name": "Molecular Cartography (Mouse Liver)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/mouse_liver.zarr", + }, + { + "name": "SpaceM (Hepa/NIH3T3 cells)", + "url": "https://s3.embl.de/spatialdata/spatialdata-sandbox/spacem_helanih3t3.zarr", + }, +] + + +def validate_with_version(dataset: dict, version: str, project_root: Path, verbose: bool = False) -> ValidationResult: + """ + Validate a dataset with a specific spatialdata version. + + This runs a subprocess with the version-specific environment to test loading the dataset. + """ + env_dir = project_root / "python" / f"v{version}" + + if verbose: + print(f" Loading spatialdata library (v{version})...", file=sys.stderr, flush=True) + + # Create a temporary Python script to run in the version-specific environment + test_script = f""" +import sys +import json +import spatialdata as sd + +def test_load(): + try: + print("Loading dataset...", file=sys.stderr, flush=True) + # Try to read the dataset + sdata = sd.read_zarr({json.dumps(dataset['url'])}) + + # Extract basic info + elements = {{}} + for element_type in ["images", "labels", "points", "shapes", "tables"]: + if hasattr(sdata, element_type): + attr = getattr(sdata, element_type) + if isinstance(attr, dict): + elements[element_type] = list(attr.keys()) + elif attr is not None: + elements[element_type] = True + + # Get coordinate systems + coordinate_systems = None + if hasattr(sdata, "coordinate_systems"): + cs = sdata.coordinate_systems + if isinstance(cs, dict): + coordinate_systems = list(cs.keys()) + elif isinstance(cs, list): + coordinate_systems = cs + elif cs is not None: + coordinate_systems = [str(cs)] + + result = {{ + "success": True, + "elements": elements, + "coordinate_systems": coordinate_systems, + }} + print(json.dumps(result)) + + except Exception as e: + error_type = type(e).__name__ + error_message = str(e) + result = {{ + "success": False, + "error_type": error_type, + "error_message": error_message, + }} + print(json.dumps(result)) + sys.exit(1) + +if __name__ == "__main__": + test_load() +""" + + # Run the test script in the version-specific environment + try: + result = subprocess.run( + ["uv", "run", "--directory", str(env_dir), "python", "-c", test_script], + capture_output=True, + text=True, + timeout=120, # 2 minute timeout per dataset + cwd=project_root, + ) + + # Parse the JSON output + try: + output = json.loads(result.stdout.strip().split('\n')[-1]) + return ValidationResult( + dataset_name=dataset["name"], + dataset_url=dataset["url"], + spatialdata_version=version, + success=output.get("success", False), + error_type=output.get("error_type"), + error_message=output.get("error_message"), + elements=output.get("elements"), + coordinate_systems=output.get("coordinate_systems"), + ) + except (json.JSONDecodeError, IndexError) as e: + # If we couldn't parse the output, something went wrong + return ValidationResult( + dataset_name=dataset["name"], + dataset_url=dataset["url"], + spatialdata_version=version, + success=False, + error_type="ParseError", + error_message=f"Could not parse output: {result.stdout}\nStderr: {result.stderr}", + ) + + except subprocess.TimeoutExpired: + return ValidationResult( + dataset_name=dataset["name"], + dataset_url=dataset["url"], + spatialdata_version=version, + success=False, + error_type="TimeoutError", + error_message="Dataset loading timed out after 120 seconds", + ) + except Exception as e: + return ValidationResult( + dataset_name=dataset["name"], + dataset_url=dataset["url"], + spatialdata_version=version, + success=False, + error_type=type(e).__name__, + error_message=str(e), + ) + + +def generate_markdown_table(results: list[ValidationResult]) -> str: + """Generate a markdown table from validation results.""" + + # Group results by dataset + datasets = {} + for result in results: + if result.dataset_name not in datasets: + datasets[result.dataset_name] = {} + datasets[result.dataset_name][result.spatialdata_version] = result + + # Generate table + lines = [] + lines.append("# SpatialData Dataset Compatibility Report") + lines.append(f"\nGenerated: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}\n") + lines.append("## Summary") + lines.append("") + lines.append("| Dataset | v0.5.0 | v0.6.1 | v0.7.0 | URL |") + lines.append("|---------|--------|--------|--------|-----|") + + for dataset_name in sorted(datasets.keys()): + versions = datasets[dataset_name] + v050 = versions.get("0.5.0") + v061 = versions.get("0.6.1") + v070 = versions.get("0.7.0") + + v050_status = "✅" if v050 and v050.success else "❌" if v050 else "⏭️" + v061_status = "✅" if v061 and v061.success else "❌" if v061 else "⏭️" + v070_status = "✅" if v070 and v070.success else "❌" if v070 else "⏭️" + + # Get URL from first available result + url = (v050 or v061 or v070).dataset_url if (v050 or v061 or v070) else "" + url_short = url.split("spatialdata-sandbox/")[-1] if "spatialdata-sandbox/" in url else url + + lines.append(f"| {dataset_name} | {v050_status} | {v061_status} | {v070_status} | `{url_short}` |") + + lines.append("") + lines.append("Legend: ✅ Success | ❌ Failed | ⏭️ Not tested") + lines.append("") + + # Add detailed error information + lines.append("## Detailed Results") + lines.append("") + + for dataset_name in sorted(datasets.keys()): + versions = datasets[dataset_name] + lines.append(f"### {dataset_name}") + lines.append("") + + for version in ["0.5.0", "0.6.1", "0.7.0"]: + result = versions.get(version) + if not result: + continue + + lines.append(f"#### spatialdata v{version}") + lines.append("") + + if result.success: + lines.append("**Status:** ✅ Success") + lines.append("") + + if result.elements: + lines.append("**Elements:**") + for element_type, items in result.elements.items(): + if isinstance(items, list): + lines.append(f"- {element_type}: {', '.join(items)}") + else: + lines.append(f"- {element_type}: present") + lines.append("") + + if result.coordinate_systems: + lines.append(f"**Coordinate Systems:** {', '.join(result.coordinate_systems)}") + lines.append("") + else: + lines.append("**Status:** ❌ Failed") + lines.append("") + lines.append(f"**Error Type:** `{result.error_type}`") + lines.append("") + lines.append("**Error Message:**") + lines.append("```") + lines.append(result.error_message or "No error message") + lines.append("```") + lines.append("") + + lines.append("---") + lines.append("") + + return "\n".join(lines) + + +def generate_csv_table(results: list[ValidationResult]) -> str: + """Generate a CSV table from validation results.""" + import csv + import io + + output = io.StringIO() + writer = csv.writer(output) + + # Write header + writer.writerow([ + "Dataset Name", + "Dataset URL", + "SpatialData Version", + "Success", + "Error Type", + "Error Message", + "Elements", + "Coordinate Systems", + ]) + + # Write rows + for result in results: + elements_str = json.dumps(result.elements) if result.elements else "" + cs_str = json.dumps(result.coordinate_systems) if result.coordinate_systems else "" + + writer.writerow([ + result.dataset_name, + result.dataset_url, + result.spatialdata_version, + result.success, + result.error_type or "", + result.error_message or "", + elements_str, + cs_str, + ]) + + return output.getvalue() + + +def validate_single(args_tuple): + """Helper function for multiprocessing pool.""" + dataset, version, project_root, verbose = args_tuple + return validate_with_version(dataset, version, project_root, verbose) + + +def main(): + parser = argparse.ArgumentParser( + description="Validate spatialdata dataset compatibility across versions" + ) + parser.add_argument( + "--version", + type=str, + choices=["0.5.0", "0.6.1", "0.7.0"], + default=None, + help="SpatialData version to test (default: all)", + ) + parser.add_argument( + "--dataset", + type=str, + default=None, + help="Specific dataset name to test (default: all)", + ) + parser.add_argument( + "--output-format", + type=str, + choices=["markdown", "csv", "json"], + default="markdown", + help="Output format (default: markdown)", + ) + parser.add_argument( + "--output-file", + type=str, + default=None, + help="Output file path (default: print to stdout)", + ) + parser.add_argument( + "--workers", + type=int, + default=min(4, cpu_count()), + help=f"Number of parallel workers (default: min(4, {cpu_count()}))", + ) + parser.add_argument( + "--no-parallel", + action="store_true", + help="Disable parallel processing (run sequentially)", + ) + parser.add_argument( + "--verbose", + action="store_true", + help="Show detailed progress information", + ) + + args = parser.parse_args() + + # Get project root + project_root = Path(__file__).parent.parent.parent + + # Filter datasets if specific one requested + datasets = DATASETS + if args.dataset: + datasets = [d for d in DATASETS if args.dataset.lower() in d["name"].lower()] + if not datasets: + print(f"Error: No dataset matching '{args.dataset}' found", file=sys.stderr) + print("\nAvailable datasets:", file=sys.stderr) + for d in DATASETS: + print(f" - {d['name']}", file=sys.stderr) + sys.exit(1) + + # Determine versions to test + versions = [args.version] if args.version else ["0.5.0", "0.6.1", "0.7.0"] + + # Ensure environments are set up + for version in versions: + env_dir = project_root / "python" / f"v{version}" + print(f"Setting up environment for spatialdata {version}...", file=sys.stderr) + result = subprocess.run( + ["uv", "sync", "--directory", str(env_dir)], + cwd=project_root, + capture_output=True, + ) + if result.returncode != 0: + print(f"Error setting up environment for version {version}", file=sys.stderr) + print(result.stderr.decode(), file=sys.stderr) + sys.exit(1) + + # Run validation + results = [] + total = len(datasets) * len(versions) + + print(f"\nValidating {len(datasets)} dataset(s) with {len(versions)} version(s)...", file=sys.stderr) + + if args.no_parallel: + print("Running sequentially (parallel processing disabled)", file=sys.stderr) + else: + print(f"Using {args.workers} parallel worker(s)", file=sys.stderr) + + print("Note: Most time is spent importing spatialdata, not downloading datasets", file=sys.stderr) + print("", file=sys.stderr) + + # Prepare arguments for validation + validation_tasks = [ + (dataset, version, project_root, args.verbose) + for dataset in datasets + for version in versions + ] + + if args.no_parallel: + # Sequential processing + for i, task in enumerate(validation_tasks): + dataset, version, project_root, verbose = task + print(f"[{i+1}/{total}] Testing {dataset['name']} with spatialdata v{version}...", file=sys.stderr, flush=True) + + result = validate_with_version(dataset, version, project_root, verbose) + results.append(result) + + status = "✅" if result.success else "❌" + print(f" {status} {dataset['name']} (v{version})", file=sys.stderr, flush=True) + if not result.success: + print(f" Error: {result.error_type}", file=sys.stderr, flush=True) + print("", file=sys.stderr, flush=True) + else: + # Parallel processing using process pool + print("Starting validation pool...", file=sys.stderr, flush=True) + print("", file=sys.stderr, flush=True) + + with Pool(processes=args.workers) as pool: + # Use imap to get results as they complete + for i, result in enumerate(pool.imap(validate_single, validation_tasks)): + results.append(result) + + status = "✅" if result.success else "❌" + print(f"[{i+1}/{total}] {status} {result.dataset_name} (v{result.spatialdata_version})", file=sys.stderr, flush=True) + if not result.success and args.verbose: + print(f" Error: {result.error_type}", file=sys.stderr, flush=True) + + print("", file=sys.stderr) + print("Validation complete!", file=sys.stderr) + print("", file=sys.stderr) + + # Generate output + if args.output_format == "markdown": + output = generate_markdown_table(results) + elif args.output_format == "csv": + output = generate_csv_table(results) + elif args.output_format == "json": + output = json.dumps([r.to_dict() for r in results], indent=2) + else: + output = "" + + # Write output + if args.output_file: + output_path = Path(args.output_file) + output_path.parent.mkdir(parents=True, exist_ok=True) + output_path.write_text(output) + print(f"Results written to: {output_path}", file=sys.stderr) + else: + print(output) + + +if __name__ == "__main__": + main() diff --git a/python/v0.5.0/generate_fixtures.py b/python/v0.5.0/generate_fixtures.py new file mode 100755 index 0000000..0346128 --- /dev/null +++ b/python/v0.5.0/generate_fixtures.py @@ -0,0 +1,176 @@ +#!/usr/bin/env python3 +""" +Generate test fixtures using spatialdata library (version 0.5.0). + +This script generates spatialdata zarr stores for testing with spatialdata 0.5.0. +It runs in the python/v0.5.0/ environment which has spatialdata==0.5.0 pinned. +""" + +import sys +from pathlib import Path + +# Add scripts directory to path if we need shared utilities +script_dir = Path(__file__).parent +sys.path.insert(0, str(script_dir.parent / "scripts")) + + + +def generate_fixtures(output_dir: Path): + """Generate test fixtures for spatialdata version 0.5.0.""" + from spatialdata.datasets import blobs + import spatialdata as sd + version = "0.5.0" + print(f"Generating fixtures for spatialdata version {version}...") + + # Verify we're using the correct version + actual_version = sd.__version__ + if actual_version != version: + print(f"⚠️ Warning: Expected version {version} but got {actual_version}") + print(" This may indicate the wrong environment is active.") + + # Create output directory + version_dir = output_dir / f"v{version}" + version_dir.mkdir(parents=True, exist_ok=True) + + # Generate a simple spatialdata object using blobs dataset + print("Creating spatialdata object with blobs dataset...") + sdata = blobs() + + # Workaround for spatialdata 0.5.0 bug: Remove points that have Identity transformations + # which can't be serialized to JSON. This is a known issue in 0.5.0. + if hasattr(sdata, "points") and sdata.points: + print("Removing points data (workaround for spatialdata 0.5.0 JSON serialization bug)...") + # Clear points - handle both dict and list cases + if isinstance(sdata.points, dict): + sdata.points.clear() + elif isinstance(sdata.points, list): + sdata.points.clear() + else: + # Try to delete the attribute + try: + delattr(sdata, "points") + except: # noqa: E722 + # If that fails, set to empty dict + sdata.points = {} + + # Save to zarr store + store_path = version_dir / "blobs.zarr" + + # Remove existing store if it exists (to allow regenerating fixtures) + import shutil + import os + if os.path.exists(store_path) or os.path.isdir(store_path): + print(f"Removing existing fixture at {store_path}...") + try: + if os.path.isdir(store_path): + shutil.rmtree(store_path) + elif os.path.isfile(store_path): + os.remove(store_path) + except Exception as e: + print(f"Warning: Could not remove existing fixture: {e}") + + # Double-check it's gone + if os.path.exists(store_path): + print(f"Warning: Store path still exists after removal attempt: {store_path}") + # Force remove + try: + shutil.rmtree(store_path, ignore_errors=True) + except: # noqa: E722 + pass + + print(f"Saving to {store_path}...") + + # Use spatialdata's write method + # Note: spatialdata 0.5.0 has a known issue with JSON serialization of Identity + # transformations when writing points. We'll catch this and clean up. + try: + # Try with overwrite first (for newer versions) + try: + sdata.write(store_path, overwrite=True) + except TypeError: + # If overwrite parameter doesn't exist, try without it + sdata.write(store_path) + except Exception as e: + # Clean up any partially written store + if os.path.exists(store_path): + try: + if os.path.isdir(store_path): + shutil.rmtree(store_path) + else: + os.remove(store_path) + except: # noqa: E722 + pass + + error_msg = str(e) + error_type = type(e).__name__ + + # Check for JSON serialization issues (known bug in spatialdata 0.5.0) + if "JSON" in error_msg or "serializable" in error_msg.lower() or "Identity" in error_msg: + print(f"\n⚠️ Error: {error_type}: {error_msg}") + print("\nThis appears to be a known issue with spatialdata 0.5.0 where") + print("Identity transformations cannot be serialized to JSON when writing points.") + raise RuntimeError( + f"Failed to generate fixtures due to spatialdata 0.5.0 bug: {error_msg}" + ) from e + else: + # Re-raise other errors + raise + + print(f"✓ Generated fixture at {store_path}") + + # Print some metadata about what was generated + print("\nGenerated elements:") + for element_type in ["images", "labels", "points", "shapes", "tables"]: + elements = getattr(sdata, element_type, None) + if elements: + # Handle both dict and list cases + if isinstance(elements, dict): + print(f" - {element_type}: {len(elements)} element(s)") + for name in elements.keys(): + print(f" * {name}") + elif isinstance(elements, list): + print(f" - {element_type}: {len(elements)} element(s)") + for i, elem in enumerate(elements): + print(f" * element_{i}") + else: + print(f" - {element_type}: present") + + if hasattr(sdata, "coordinate_systems"): + if isinstance(sdata.coordinate_systems, dict): + print(f"\nCoordinate systems: {list(sdata.coordinate_systems.keys())}") + elif isinstance(sdata.coordinate_systems, list): + print(f"\nCoordinate systems: {sdata.coordinate_systems}") + else: + print(f"\nCoordinate systems: {sdata.coordinate_systems}") + + print(f"\nUsing spatialdata version {actual_version}") + + return store_path + + +def main(): + import argparse + + parser = argparse.ArgumentParser( + description="Generate test fixtures for SpatialData.ts using spatialdata 0.5.0" + ) + parser.add_argument( + "--output-dir", + type=str, + default="test-fixtures", + help="Output directory for fixtures (default: test-fixtures)", + ) + + args = parser.parse_args() + + # Get project root (parent of python/ directory) + project_root = Path(__file__).parent.parent.parent + output_dir = project_root / args.output_dir + + generate_fixtures(output_dir) + print("\n✓ Fixtures generated successfully!") + + +if __name__ == "__main__": + main() + diff --git a/python/v0.5.0/pyproject.toml b/python/v0.5.0/pyproject.toml new file mode 100644 index 0000000..2bc1fc1 --- /dev/null +++ b/python/v0.5.0/pyproject.toml @@ -0,0 +1,9 @@ +[project] +name = "spatialdata-test-fixtures-v0.5.0" +version = "0.1.0" +description = "Test fixture generation for SpatialData.ts using spatialdata 0.5.0" +requires-python = ">=3.12" +dependencies = [ + "spatialdata==0.5.0", +] + diff --git a/python/v0.6.1/generate_fixtures.py b/python/v0.6.1/generate_fixtures.py new file mode 100755 index 0000000..051418e --- /dev/null +++ b/python/v0.6.1/generate_fixtures.py @@ -0,0 +1,125 @@ +#!/usr/bin/env python3 +""" +Generate test fixtures using spatialdata library (version 0.6.1). + +This script generates spatialdata zarr stores for testing with spatialdata 0.6.1. +It runs in the python/v0.6.1/ environment which has spatialdata==0.6.1 pinned. +""" + +import sys +from pathlib import Path + +# Add scripts directory to path if we need shared utilities +script_dir = Path(__file__).parent +sys.path.insert(0, str(script_dir.parent / "scripts")) + + +def generate_fixtures(output_dir: Path): + """Generate test fixtures for spatialdata version 0.6.1.""" + from spatialdata.datasets import blobs + import spatialdata as sd + version = "0.6.1" + print(f"Generating fixtures for spatialdata version {version}...") + + # Verify we're using the correct version + actual_version = sd.__version__ + if actual_version != version: + print(f"⚠️ Warning: Expected version {version} but got {actual_version}") + print(" This may indicate the wrong environment is active.") + + # Create output directory + version_dir = output_dir / f"v{version}" + version_dir.mkdir(parents=True, exist_ok=True) + + # Generate a simple spatialdata object using blobs dataset + print("Creating spatialdata object with blobs dataset...") + sdata = blobs() + + # Save to zarr store + store_path = version_dir / "blobs.zarr" + + # Remove existing store if it exists (to allow regenerating fixtures) + import shutil + if store_path.exists(): + print(f"Removing existing fixture at {store_path}...") + shutil.rmtree(store_path) + + print(f"Saving to {store_path}...") + + # Use spatialdata's write method + # The API may vary by version, so we try different methods + try: + # Try the standard write method with overwrite (most common) + sdata.write(store_path, overwrite=True) + except TypeError: + # If overwrite parameter doesn't exist, try without it + # (older versions might not support it) + sdata.write(store_path) + except ValueError as e: + # Handle "already exists" errors + if "already exists" in str(e).lower(): + # Shouldn't happen since we removed it, but handle anyway + shutil.rmtree(store_path) + sdata.write(store_path) + else: + # Re-raise other ValueError exceptions + raise + + print(f"✓ Generated fixture at {store_path}") + + # Print some metadata about what was generated + print("\nGenerated elements:") + for element_type in ["images", "labels", "points", "shapes", "tables"]: + elements = getattr(sdata, element_type, None) + if elements: + # Handle both dict and list cases + if isinstance(elements, dict): + print(f" - {element_type}: {len(elements)} element(s)") + for name in elements.keys(): + print(f" * {name}") + elif isinstance(elements, list): + print(f" - {element_type}: {len(elements)} element(s)") + for i, elem in enumerate(elements): + print(f" * element_{i}") + else: + print(f" - {element_type}: present") + + if hasattr(sdata, "coordinate_systems"): + if isinstance(sdata.coordinate_systems, dict): + print(f"\nCoordinate systems: {list(sdata.coordinate_systems.keys())}") + elif isinstance(sdata.coordinate_systems, list): + print(f"\nCoordinate systems: {sdata.coordinate_systems}") + else: + print(f"\nCoordinate systems: {sdata.coordinate_systems}") + + print(f"\nUsing spatialdata version {actual_version}") + + return store_path + + +def main(): + import argparse + + parser = argparse.ArgumentParser( + description="Generate test fixtures for SpatialData.ts using spatialdata 0.6.1" + ) + parser.add_argument( + "--output-dir", + type=str, + default="test-fixtures", + help="Output directory for fixtures (default: test-fixtures)", + ) + + args = parser.parse_args() + + # Get project root (parent of python/ directory) + project_root = Path(__file__).parent.parent.parent + output_dir = project_root / args.output_dir + + generate_fixtures(output_dir) + print("\n✓ Fixtures generated successfully!") + + +if __name__ == "__main__": + main() + diff --git a/python/v0.6.1/pyproject.toml b/python/v0.6.1/pyproject.toml new file mode 100644 index 0000000..661bc55 --- /dev/null +++ b/python/v0.6.1/pyproject.toml @@ -0,0 +1,9 @@ +[project] +name = "spatialdata-test-fixtures-v0.6.1" +version = "0.1.0" +description = "Test fixture generation for SpatialData.ts using spatialdata 0.6.1" +requires-python = ">=3.12" +dependencies = [ + "spatialdata==0.6.1", +] + diff --git a/python/v0.7.0/generate_fixtures.py b/python/v0.7.0/generate_fixtures.py new file mode 100755 index 0000000..bc21313 --- /dev/null +++ b/python/v0.7.0/generate_fixtures.py @@ -0,0 +1,125 @@ +#!/usr/bin/env python3 +""" +Generate test fixtures using spatialdata library (version 0.7.0). + +This script generates spatialdata zarr stores for testing with spatialdata 0.7.0. +It runs in the python/v0.7.0/ environment which has spatialdata==0.7.0 pinned. +""" + +import sys +from pathlib import Path + +# Add scripts directory to path if we need shared utilities +script_dir = Path(__file__).parent +sys.path.insert(0, str(script_dir.parent / "scripts")) + + +def generate_fixtures(output_dir: Path): + """Generate test fixtures for spatialdata version 0.7.0.""" + from spatialdata.datasets import blobs + import spatialdata as sd + version = "0.7.0" + print(f"Generating fixtures for spatialdata version {version}...") + + # Verify we're using the correct version + actual_version = sd.__version__ + if actual_version != version: + print(f"⚠️ Warning: Expected version {version} but got {actual_version}") + print(" This may indicate the wrong environment is active.") + + # Create output directory + version_dir = output_dir / f"v{version}" + version_dir.mkdir(parents=True, exist_ok=True) + + # Generate a simple spatialdata object using blobs dataset + print("Creating spatialdata object with blobs dataset...") + sdata = blobs() + + # Save to zarr store + store_path = version_dir / "blobs.zarr" + + # Remove existing store if it exists (to allow regenerating fixtures) + import shutil + if store_path.exists(): + print(f"Removing existing fixture at {store_path}...") + shutil.rmtree(store_path) + + print(f"Saving to {store_path}...") + + # Use spatialdata's write method + # The API may vary by version, so we try different methods + try: + # Try the standard write method with overwrite (most common) + sdata.write(store_path, overwrite=True) + except TypeError: + # If overwrite parameter doesn't exist, try without it + # (older versions might not support it) + sdata.write(store_path) + except ValueError as e: + # Handle "already exists" errors + if "already exists" in str(e).lower(): + # Shouldn't happen since we removed it, but handle anyway + shutil.rmtree(store_path) + sdata.write(store_path) + else: + # Re-raise other ValueError exceptions + raise + + print(f"✓ Generated fixture at {store_path}") + + # Print some metadata about what was generated + print("\nGenerated elements:") + for element_type in ["images", "labels", "points", "shapes", "tables"]: + elements = getattr(sdata, element_type, None) + if elements: + # Handle both dict and list cases + if isinstance(elements, dict): + print(f" - {element_type}: {len(elements)} element(s)") + for name in elements.keys(): + print(f" * {name}") + elif isinstance(elements, list): + print(f" - {element_type}: {len(elements)} element(s)") + for i, elem in enumerate(elements): + print(f" * element_{i}") + else: + print(f" - {element_type}: present") + + if hasattr(sdata, "coordinate_systems"): + if isinstance(sdata.coordinate_systems, dict): + print(f"\nCoordinate systems: {list(sdata.coordinate_systems.keys())}") + elif isinstance(sdata.coordinate_systems, list): + print(f"\nCoordinate systems: {sdata.coordinate_systems}") + else: + print(f"\nCoordinate systems: {sdata.coordinate_systems}") + + print(f"\nUsing spatialdata version {actual_version}") + + return store_path + + +def main(): + import argparse + + parser = argparse.ArgumentParser( + description="Generate test fixtures for SpatialData.ts using spatialdata 0.7.0" + ) + parser.add_argument( + "--output-dir", + type=str, + default="test-fixtures", + help="Output directory for fixtures (default: test-fixtures)", + ) + + args = parser.parse_args() + + # Get project root (parent of python/ directory) + project_root = Path(__file__).parent.parent.parent + output_dir = project_root / args.output_dir + + generate_fixtures(output_dir) + print("\n✓ Fixtures generated successfully!") + + +if __name__ == "__main__": + main() + diff --git a/python/v0.7.0/pyproject.toml b/python/v0.7.0/pyproject.toml new file mode 100644 index 0000000..c55a906 --- /dev/null +++ b/python/v0.7.0/pyproject.toml @@ -0,0 +1,9 @@ +[project] +name = "spatialdata-test-fixtures-v0.7.0" +version 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requests to any URL and adds CORS headers to responses. + * This allows accessing spatialdata stores that don't have CORS headers + * from browser-based applications. + * + * WARNING: This is for local development only. No security features are included. + */ + +import { createServer } from 'node:http'; +import { URL, fileURLToPath } from 'node:url'; +import { resolve } from 'node:path'; + +const PORT = process.env.PORT || 8081; + +/** + * Add CORS headers to a response + */ +export function addCorsHeaders(res) { + res.setHeader('Access-Control-Allow-Origin', '*'); + res.setHeader('Access-Control-Allow-Methods', 'GET, HEAD, OPTIONS, POST, PUT, DELETE'); + res.setHeader('Access-Control-Allow-Headers', '*'); + res.setHeader('Access-Control-Expose-Headers', '*'); + res.setHeader('Access-Control-Max-Age', '86400'); +} + +/** + * Handle OPTIONS preflight requests + */ +export function handleOptions(req, res) { + addCorsHeaders(res); + res.writeHead(200); + res.end(); +} + +/** + * Proxy a request to the target URL + */ +export async function proxyRequest(req, res, targetUrl) { + try { + const url = new URL(targetUrl); + + // Build fetch options + const fetchOptions = { + method: req.method, + headers: { ...req.headers }, + }; + + // Remove host header (will be set by fetch) + const { host, 'content-length': contentLength, ...safeHeaders } = fetchOptions.headers; + fetchOptions.headers = safeHeaders; + + // Forward request body for POST/PUT + let body = null; + if (req.method === 'POST' || req.method === 'PUT') { + const chunks = []; + for await (const chunk of req) { + chunks.push(chunk); + } + body = Buffer.concat(chunks); + if (body.length > 0) { + fetchOptions.body = body; + } + } + + // Make the request + const response = await fetch(targetUrl, fetchOptions); + + // Add CORS headers + addCorsHeaders(res); + + // Copy response headers (except CORS-related ones which we set) + const headersToSkip = new Set([ + 'access-control-allow-origin', + 'access-control-allow-methods', + 'access-control-allow-headers', + 'access-control-expose-headers', + 'access-control-max-age', + ]); + + response.headers.forEach((value, key) => { + if (!headersToSkip.has(key.toLowerCase())) { + res.setHeader(key, value); + } + }); + + // Set status code + res.writeHead(response.status, res.getHeaders()); + + // Stream response body + if (response.body) { + const reader = response.body.getReader(); + const pump = async () => { + try { + while (true) { + const { done, value } = await reader.read(); + if (done) { + res.end(); + break; + } + res.write(value); + } + } catch (error) { + console.error('Error streaming response:', error); + res.end(); + } + }; + pump(); + } else { + res.end(); + } + } catch (error) { + console.error('Error proxying request:', error); + addCorsHeaders(res); + res.writeHead(500, { 'Content-Type': 'text/plain' }); + res.end(`Proxy Error: ${error.message}`); + } +} + +/** + * Handle HTTP request + */ +export async function handleRequest(req, res) { + // Handle OPTIONS preflight + if (req.method === 'OPTIONS') { + handleOptions(req, res); + return; + } + + try { + // Extract target URL from query parameter or path + const url = new URL(req.url, `http://${req.headers.host}`); + let targetUrl = url.searchParams.get('url') || url.pathname.slice(1); + // Also support paths like /url=https://... by stripping the "url=" prefix + if (targetUrl.startsWith('url=')) { + targetUrl = targetUrl.slice(4); + } + + if (!targetUrl) { + addCorsHeaders(res); + res.writeHead(400, { 'Content-Type': 'text/plain' }); + res.end('Usage: /?url= or /'); + return; + } + + // Validate URL (lightweight check without rejecting valid-but-unexpected forms) + if (!/^https?:\/\//i.test(targetUrl)) { + // console.log(`'${targetUrl}' didn't validate, but yolo...`); + addCorsHeaders(res); + res.writeHead(400, { 'Content-Type': 'text/plain' }); + res.end('Invalid URL. Please provide a full URL starting with http:// or https:// (e.g., https://example.com/data.zarr)'); + return; + } + + // Proxy the request + await proxyRequest(req, res, targetUrl); + } catch (error) { + console.error('Error handling request:', error); + addCorsHeaders(res); + res.writeHead(500, { 'Content-Type': 'text/plain' }); + res.end('Internal Server Error'); + } +} + +/** + * Create a CORS proxy server + * @param {number} port - Port to listen on + * @returns {Promise} The HTTP server + */ +export function createProxyServer(port = 8081) { + const server = createServer(handleRequest); + + return new Promise((resolve, reject) => { + server.on('error', (err) => { + reject(err); + }); + + server.listen(port, () => { + resolve(server); + }); + }); +} + +/** + * Start a proxy server and return its base URL + * @param {number} port - Port to start on (will try next port if in use) + * @returns {Promise<{server: import('http').Server, baseUrl: string}>} + */ +export async function startProxyServer(port = 8081) { + try { + const server = await createProxyServer(port); + // Get the actual port (in case it was changed due to port conflict) + const actualPort = server.address()?.port || port; + const baseUrl = `http://localhost:${actualPort}`; + return { server, baseUrl }; + } catch (error) { + // If port is in use, try next port + if (error.code === 'EADDRINUSE') { + console.error(`Port ${port} is in use, trying ${port + 1}...`); + return startProxyServer(port + 1); + } + throw error; + } +} + +// If running as a standalone script, start the server +// Check if this file is being run directly (not imported) +const __filename = fileURLToPath(import.meta.url); +const isMainModule = process.argv[1] && resolve(process.argv[1]) === __filename; + +if (isMainModule) { + const server = await createProxyServer(PORT); + const actualPort = server.address()?.port || PORT; + + console.log(`CORS proxy server running at http://localhost:${actualPort}`); + console.log('\nUsage:'); + console.log(` GET http://localhost:${actualPort}/?url=`); + console.log(` Example: http://localhost:${actualPort}/?url=https://example.com/data.zarr/.zattrs`); + console.log('\nPress Ctrl+C to stop\n'); + + // Handle graceful shutdown + process.on('SIGINT', () => { + console.log('\nShutting down proxy server...'); + server.close(() => { + console.log('Proxy server stopped'); + process.exit(0); + }); + }); +} + diff --git a/scripts/test-server.js b/scripts/test-server.js new file mode 100755 index 0000000..448bee4 --- /dev/null +++ b/scripts/test-server.js @@ -0,0 +1,175 @@ +#!/usr/bin/env node +/** + * Simple static file server for serving test fixtures. + * + * Serves the test-fixtures directory so that fixtures can be accessed + * via HTTP URLs for testing with FetchStore. + */ + +import { createServer } from 'node:http'; +import { readFile, stat, readdir } from 'node:fs/promises'; +import { join, extname, resolve } from 'node:path'; +import { fileURLToPath } from 'node:url'; +import { dirname } from 'node:path'; + +const __filename = fileURLToPath(import.meta.url); +const __dirname = dirname(__filename); +const projectRoot = resolve(__dirname, '..'); +const fixturesDir = join(projectRoot, 'test-fixtures'); + +const PORT = process.env.PORT || 8080; + +/** + * Get MIME type for a file based on extension + */ +function getMimeType(filePath) { + const ext = extname(filePath).toLowerCase(); + const mimeTypes = { + '.json': 'application/json', + '.zarr': 'application/octet-stream', + '.zattrs': 'application/json', + '.zarray': 'application/json', + '.zgroup': 'application/json', + '.zmetadata': 'application/json', + '.html': 'text/html', + '.txt': 'text/plain', + }; + return mimeTypes[ext] || 'application/octet-stream'; +} + +/** + * Generate HTML directory listing + */ +/** + * Escape HTML special characters + */ +function escapeHtml(str) { + return str + .replace(/&/g, '&') + .replace(//g, '>') + .replace(/"/g, '"'); +} + +function generateDirectoryListing(files, currentPath, basePath) { + const items = files + .map((file) => { + const isDir = file.isDirectory; + const safeName = escapeHtml(file.name); + const href = `${currentPath}/${encodeURIComponent(file.name)}${isDir ? '/' : ''}`; + const icon = isDir ? '📁' : '📄'; + return `
  • ${icon} ${safeName}
    • `; + }) + .join('\n'); + + return ` + + + Test Fixtures - ${currentPath} + + + +

    Test Fixtures

    +

    Path: ${currentPath}

    +
      + ${items} +
    + +`; +} + +/** + * Handle HTTP request + */ +async function handleRequest(req, res) { + try { + // Remove query string and normalize path + const urlPath = new URL(req.url, `http://${req.headers.host}`).pathname; + + // Remove leading /test-fixtures if present (for cleaner URLs) + let filePath = urlPath.startsWith('/test-fixtures') + ? urlPath.slice('/test-fixtures'.length) + : urlPath; + + // Remove leading slash + filePath = filePath.startsWith('/') ? filePath.slice(1) : filePath; + + // Resolve to fixtures directory + const fullPath = join(fixturesDir, filePath); + + // Security: ensure path is within fixtures directory + if (!fullPath.startsWith(fixturesDir)) { + res.writeHead(403, { 'Content-Type': 'text/plain' }); + res.end('Forbidden'); + return; + } + + // Check if path exists + const stats = await stat(fullPath).catch(() => null); + + if (!stats) { + res.writeHead(404, { 'Content-Type': 'text/plain' }); + res.end('Not Found'); + return; + } + + // Handle directory listing + if (stats.isDirectory()) { + const files = await readdir(fullPath, { withFileTypes: true }); + const fileList = files.map((file) => ({ + name: file.name, + isDirectory: file.isDirectory(), + })); + + const html = generateDirectoryListing(fileList, urlPath, '/test-fixtures'); + res.writeHead(200, { 'Content-Type': 'text/html' }); + res.end(html); + return; + } + + // Serve file + const content = await readFile(fullPath); + const mimeType = getMimeType(fullPath); + + // Add CORS headers for cross-origin requests + res.writeHead(200, { + 'Content-Type': mimeType, + 'Access-Control-Allow-Origin': '*', + 'Access-Control-Allow-Methods': 'GET, HEAD, OPTIONS', + 'Access-Control-Allow-Headers': 'Range', + 'Content-Length': content.length, + }); + + res.end(content); + } catch (error) { + console.error('Error handling request:', error); + res.writeHead(500, { 'Content-Type': 'text/plain' }); + res.end('Internal Server Error'); + } +} + +// Create and start server +const server = createServer(handleRequest); + +server.listen(PORT, () => { + console.log(`Test fixture server running at http://localhost:${PORT}`); + console.log(`Serving fixtures from: ${fixturesDir}`); + console.log(`\nAccess fixtures at: http://localhost:${PORT}/test-fixtures/`); + console.log('Press Ctrl+C to stop\n'); +}); + +// Handle graceful shutdown +process.on('SIGINT', () => { + console.log('\nShutting down server...'); + server.close(() => { + console.log('Server stopped'); + process.exit(0); + }); +}); + diff --git a/scripts/validate-datasets-js.js b/scripts/validate-datasets-js.js new file mode 100755 index 0000000..eae463a --- /dev/null +++ b/scripts/validate-datasets-js.js @@ -0,0 +1,350 @@ +#!/usr/bin/env node +/** + * Validate spatialdata dataset compatibility with the JavaScript implementation. + * + * This script tests loading publicly available spatialdata datasets using the + * @spatialdata/core library in a Node.js environment (outside the browser). + */ + +import { readZarr } from '../packages/core/dist/index.js'; +import { writeFileSync } from 'node:fs'; +import { resolve } from 'node:path'; +import { startProxyServer } from './cors-proxy.js'; + +// Dataset definitions from https://spatialdata.scverse.org/en/stable/tutorials/notebooks/datasets/README.html +const DATASETS = [ + { + name: "Visium HD (Mouse intestin)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_hd_3.0.0_io.zarr/", + }, + { + name: "Visium (Breast cancer)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zarr/", + }, + { + name: "Xenium (Breast cancer - Rep1)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zarr/", + }, + { + name: "Xenium (Breast cancer - Rep2)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zarr/", + }, + { + name: "CyCIF (Lung adenocarcinoma)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr/", + }, + { + name: "MERFISH (Mouse brain)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr/", + }, + { + name: "MIBI-TOF (Colorectal carcinoma)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr/", + }, + { + name: "Imaging Mass Cytometry (Multiple cancers)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr/", + }, + { + name: "Molecular Cartography (Mouse Liver)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/mouse_liver.zarr", + }, + { + name: "SpaceM (Hepa/NIH3T3 cells)", + url: "https://s3.embl.de/spatialdata/spatialdata-sandbox/spacem_helanih3t3.zarr", + }, +]; + +/** + * Validate a single dataset + */ +async function validateDataset(dataset, proxyBaseUrl = null) { + const result = { + datasetName: dataset.name, + datasetUrl: dataset.url, + implementation: 'JavaScript (@spatialdata/core)', + success: false, + errorType: null, + errorMessage: null, + elements: null, + coordinateSystems: null, + }; + + try { + // Use proxy if provided + const url = proxyBaseUrl + ? `${proxyBaseUrl}/?url=${encodeURIComponent(dataset.url)}` + : dataset.url; + + // Try to read the dataset + const sdata = await readZarr(url); + + // Extract basic info + const elements = {}; + for (const elementType of ['images', 'labels', 'points', 'shapes', 'tables']) { + if (sdata[elementType]) { + elements[elementType] = Object.keys(sdata[elementType]); + } + } + + // Get coordinate systems + let coordinateSystems = null; + if (sdata.coordinateSystems) { + if (Array.isArray(sdata.coordinateSystems)) { + coordinateSystems = sdata.coordinateSystems; + } else { + coordinateSystems = [sdata.coordinateSystems]; + } + } + + result.success = true; + result.elements = elements; + result.coordinateSystems = coordinateSystems; + } catch (error) { + result.success = false; + result.errorType = error.constructor.name; + result.errorMessage = error.message; + + // Include stack trace for debugging + if (error.stack) { + result.stackTrace = error.stack.split('\n').slice(0, 5).join('\n'); + } + } + + return result; +} + +/** + * Generate a markdown table from validation results + */ +function generateMarkdownTable(results) { + const lines = []; + + lines.push('# SpatialData Dataset Compatibility Report (JavaScript)'); + lines.push(`\nGenerated: ${new Date().toISOString()}\n`); + lines.push('## Summary'); + lines.push(''); + + lines.push('| Dataset | Status | URL |'); + lines.push('|---------|--------|-----|'); + + for (const result of results) { + const status = result.success ? '✅' : '❌'; + const urlShort = result.datasetUrl.split('spatialdata-sandbox/')[1] || result.datasetUrl; + lines.push(`| ${result.datasetName} | ${status} | \`${urlShort}\` |`); + } + + lines.push(''); + lines.push('Legend: ✅ Success | ❌ Failed | ⏭️ Not tested'); + lines.push(''); + + // Add detailed error information + lines.push('## Detailed Results (JavaScript)'); + lines.push(''); + + for (const result of results) { + lines.push(`### ${result.datasetName}`); + lines.push(''); + + if (result.success) { + lines.push('**Status:** ✅ Success'); + lines.push(''); + + if (result.elements && Object.keys(result.elements).length > 0) { + lines.push('**Elements:**'); + for (const [elementType, items] of Object.entries(result.elements)) { + if (Array.isArray(items) && items.length > 0) { + lines.push(`- ${elementType}: ${items.join(', ')}`); + } else { + lines.push(`- ${elementType}: present`); + } + } + lines.push(''); + } + + if (result.coordinateSystems && result.coordinateSystems.length > 0) { + lines.push(`**Coordinate Systems:** ${result.coordinateSystems.join(', ')}`); + lines.push(''); + } + } else { + lines.push('**Status:** ❌ Failed'); + lines.push(''); + lines.push(`**Error Type:** \`${result.errorType}\``); + lines.push(''); + lines.push('**Error Message:**'); + lines.push('```'); + lines.push(result.errorMessage || 'No error message'); + lines.push('```'); + lines.push(''); + + if (result.stackTrace) { + lines.push('**Stack Trace:**'); + lines.push('```'); + lines.push(result.stackTrace); + lines.push('```'); + lines.push(''); + } + } + + lines.push('---'); + lines.push(''); + } + + return lines.join('\n'); +} + +/** + * Parse command line arguments + */ +function parseArgs() { + const args = { + dataset: null, + outputFormat: 'markdown', + outputFile: null, + }; + + for (let i = 2; i < process.argv.length; i++) { + const arg = process.argv[i]; + + if (arg === '--dataset' && i + 1 < process.argv.length) { + args.dataset = process.argv[++i]; + } else if (arg === '--output-format' && i + 1 < process.argv.length) { + args.outputFormat = process.argv[++i]; + } else if (arg === '--output-file' && i + 1 < process.argv.length) { + args.outputFile = process.argv[++i]; + } else if (arg === '--help') { + console.log(` +Usage: node validate-datasets-js.js [options] + +Options: + --dataset Test only dataset matching this name + --output-format Output format: markdown, csv, json (default: markdown) + --output-file Write output to file instead of stdout + --help Show this help message + +Note: The script automatically starts and manages a CORS proxy server for all requests. + `); + process.exit(0); + } + } + + return args; +} + +// Module-level variable to track proxy server for cleanup +let proxyServer = null; + +/** + * Main function + */ +async function main() { + const args = parseArgs(); + + // Filter datasets if specific one requested + let datasets = DATASETS; + if (args.dataset) { + datasets = DATASETS.filter(d => + d.name.toLowerCase().includes(args.dataset.toLowerCase()) + ); + + if (datasets.length === 0) { + console.error(`Error: No dataset matching '${args.dataset}' found`); + console.error('\nAvailable datasets:'); + for (const d of DATASETS) { + console.error(` - ${d.name}`); + } + process.exit(1); + } + } + + // Start proxy server automatically + console.error('Starting CORS proxy server...'); + let proxyBaseUrl = null; + try { + const proxy = await startProxyServer(); + proxyServer = proxy.server; + proxyBaseUrl = proxy.baseUrl; + console.error(`✓ Proxy server running at ${proxyBaseUrl}`); + console.error(''); + } catch (error) { + console.error(`Failed to start proxy server: ${error.message}`); + process.exit(1); + } + + // Run validation + console.error(`Validating ${datasets.length} dataset(s) with JavaScript implementation...\n`); + + const results = []; + let current = 0; + + for (const dataset of datasets) { + current++; + console.error(`[${current}/${datasets.length}] Testing ${dataset.name}...`); + + const result = await validateDataset(dataset, proxyBaseUrl); + results.push(result); + + const status = result.success ? '✅' : '❌'; + console.error(` ${status} ${dataset.name}`); + if (!result.success) { + console.error(` Error: ${result.errorType}`); + } + } + + console.error('\nValidation complete!\n'); + + // Generate output + let output; + if (args.outputFormat === 'markdown') { + output = generateMarkdownTable(results); + } else if (args.outputFormat === 'csv') { + // Simple CSV generation + const lines = ['Dataset Name,Dataset URL,Implementation,Success,Error Type,Error Message,Elements,Coordinate Systems']; + for (const r of results) { + const elements = r.elements ? JSON.stringify(r.elements).replace(/"/g, '""') : ''; + const cs = r.coordinateSystems ? JSON.stringify(r.coordinateSystems).replace(/"/g, '""') : ''; + const errorMsg = (r.errorMessage || '').replace(/"/g, '""'); + lines.push(`"${r.datasetName}","${r.datasetUrl}","${r.implementation}",${r.success},"${r.errorType || ''}","${errorMsg}","${elements}","${cs}"`); + } + output = lines.join('\n'); + } else if (args.outputFormat === 'json') { + output = JSON.stringify(results, null, 2); + } else { + console.error(`Unknown output format: ${args.outputFormat}`); + process.exit(1); + } + + // Write output + if (args.outputFile) { + writeFileSync(resolve(args.outputFile), output); + console.error(`Results written to: ${args.outputFile}`); + } else { + console.log(output); + } + + // Shutdown proxy server + console.error('\nShutting down proxy server...'); + await new Promise((resolve) => { + proxyServer.close(() => { + console.error('✓ Proxy server stopped'); + resolve(); + }); + }); +} + +main().catch(async error => { + console.error('Fatal error:', error); + + // Clean up proxy server if it was started + if (proxyServer) { + console.error('\nShutting down proxy server...'); + await new Promise((resolve) => { + proxyServer.close(() => { + console.error('✓ Proxy server stopped'); + resolve(); + }); + }); + } + + process.exit(1); +}); diff --git a/tests/integration/fixtures.test.ts b/tests/integration/fixtures.test.ts new file mode 100644 index 0000000..b37bb5f --- /dev/null +++ b/tests/integration/fixtures.test.ts @@ -0,0 +1,163 @@ +import { describe, expect, it, beforeAll } from 'vitest'; +import { readZarr } from '../../packages/core/src/store/index.js'; +import { execSync } from 'node:child_process'; +import { existsSync } from 'node:fs'; +import { join } from 'node:path'; +import { fileURLToPath } from 'node:url'; +import { dirname } from 'node:path'; + +const __filename = fileURLToPath(import.meta.url); +const __dirname = dirname(__filename); +const projectRoot = join(__dirname, '../..'); + +/** + * Ensure fixtures are generated for a specific version + */ +function ensureFixtures(version: string): string { + const fixturePath = join(projectRoot, 'test-fixtures', `v${version}`, 'blobs.zarr'); + + if (!existsSync(fixturePath)) { + console.log(`Fixtures not found for version ${version}, generating...`); + try { + execSync(`uv run python/scripts/generate_fixtures.py --version ${version}`, { + cwd: projectRoot, + stdio: 'inherit', + }); + } catch (error) { + throw new Error( + `Failed to generate fixtures for version ${version}. ` + + `Make sure uv is installed and spatialdata is available. Error: ${error}` + ); + } + } + + return fixturePath; +} + +// Test matrix for different spatialdata versions +const versions = ['0.5.0', '0.6.1', '0.7.0'] as const; + +describe.each(versions)('Integration Tests - spatialdata v%s', (version) => { + let fixturePath: string; + let fixtureUrl: string; + + beforeAll(() => { + fixturePath = ensureFixtures(version); + fixtureUrl = `http://localhost:8080/v${version}/blobs.zarr`; + }); + + it('should load spatialdata store', async () => { + // Note: This test requires the test server to be running + try { + const sdata = await readZarr(fixtureUrl); + expect(sdata).toBeDefined(); + expect(sdata.url).toBe(fixtureUrl); + } catch (error) { + // If FetchStore doesn't support file:// or server isn't running, + // we'll skip this test with a helpful message + if (error instanceof Error && error.message.includes('fetch')) { + console.warn( + 'Skipping integration test - test server not running. ' + + 'Start it with: pnpm test:server' + ); + return; + } + throw error; + } + }, 30000); // 30 second timeout for fixture generation + + it('should parse elements from store', async () => { + try { + const sdata = await readZarr(fixtureUrl); + + // Check that we can access parsed structure + expect(sdata.rootStore.tree).toBeDefined(); + + // The blobs dataset should have at least images + // We'll check what elements are available + const hasImages = sdata.images !== undefined && Object.keys(sdata.images).length > 0; + const hasPoints = sdata.points !== undefined && Object.keys(sdata.points).length > 0; + const hasShapes = sdata.shapes !== undefined && Object.keys(sdata.shapes).length > 0; + const hasLabels = sdata.labels !== undefined && Object.keys(sdata.labels).length > 0; + const hasTables = sdata.tables !== undefined && Object.keys(sdata.tables).length > 0; + + // At least one element type should be present + expect(hasImages || hasPoints || hasShapes || hasLabels || hasTables).toBe(true); + } catch (error) { + if (error instanceof Error && error.message.includes('fetch')) { + console.warn('Skipping test - test server not running'); + return; + } + throw error; + } + }, 30000); + + it('should resolve coordinate systems', async () => { + try { + const sdata = await readZarr(fixtureUrl); + + // Should be able to get coordinate systems + const coordinateSystems = sdata.coordinateSystems; + expect(Array.isArray(coordinateSystems)).toBe(true); + + // The blobs dataset should have at least one coordinate system + // ('global') + expect(coordinateSystems.length).toBeGreaterThan(0); + } catch (error) { + if (error instanceof Error && error.message.includes('fetch')) { + console.warn('Skipping test - test server not running'); + return; + } + throw error; + } + }, 30000); + + it('should have valid string representation', async () => { + try { + const sdata = await readZarr(fixtureUrl); + + const str = sdata.toString(); + expect(typeof str).toBe('string'); + expect(str.length).toBeGreaterThan(0); + expect(str).toContain('SpatialData object'); + expect(str).toContain(fixtureUrl); + } catch (error) { + if (error instanceof Error && error.message.includes('fetch')) { + console.warn('Skipping test - test server not running'); + return; + } + throw error; + } + }, 30000); +}); + +describe('Fixture Generation', () => { + it('should generate fixtures for all versions', () => { + const v050Path = join(projectRoot, 'test-fixtures', 'v0.5.0', 'blobs.zarr'); + const v061Path = join(projectRoot, 'test-fixtures', 'v0.6.1', 'blobs.zarr'); + const v070Path = join(projectRoot, 'test-fixtures', 'v0.7.0', 'blobs.zarr'); + + // Try to generate if missing + if (!existsSync(v050Path)) { + ensureFixtures('0.5.0'); + } else { + console.log('using existing fixture for 0.5.0'); + } + if (!existsSync(v061Path)) { + ensureFixtures('0.6.1'); + } else { + console.log('using existing fixture for 0.6.1'); + } + if (!existsSync(v070Path)) { + ensureFixtures('0.7.0'); + } else { + console.log('using existing fixture for 0.7.0'); + } + + // Check that directories exist (even if generation failed, we want to know) + expect(existsSync(join(projectRoot, 'test-fixtures', 'v0.5.0'))).toBe(true); + expect(existsSync(join(projectRoot, 'test-fixtures', 'v0.6.1'))).toBe(true); + expect(existsSync(join(projectRoot, 'test-fixtures', 'v0.7.0'))).toBe(true); + }, 90000); // 90 second timeout for generating all versions +}); + diff --git a/vitest.config.ts b/vitest.config.ts new file mode 100644 index 0000000..d176cbe --- /dev/null +++ b/vitest.config.ts @@ -0,0 +1,35 @@ +import { defineConfig } from 'vitest/config'; +import { dirname, resolve } from 'node:path'; +import { fileURLToPath } from 'node:url'; + +const __filename = fileURLToPath(import.meta.url); +// not strictly necessary as vite will provide this in config context +// but now I'm looking at it, adding this so there's less hidden magic. +const __dirname = dirname(__filename); + +export default defineConfig({ + test: { + globals: true, + environment: 'node', + include: [ + 'tests/**/*.test.ts', // Integration tests (run via test:integration) + 'packages/**/*.spec.ts', // Package unit tests (.spec.ts) + 'packages/**/*.spec.tsx', // Package unit tests for React (.spec.tsx) + ], + // Integration tests may need extra time for fixture generation hooks + hookTimeout: 60000, + coverage: { + provider: 'v8', + reporter: ['text', 'json', 'html'], + include: ['packages/**/*.ts'], + exclude: ['packages/**/*.test.ts', 'packages/**/dist/**'], + }, + }, + resolve: { + alias: { + '@spatialdata/core': resolve(__dirname, 'packages/core/src'), + '@spatialdata/zarrextra': resolve(__dirname, 'packages/zarrextra/src'), + }, + }, +}); +