@vitessce/config 3.6.3 → 3.6.4

package/dist-tsc/generate-config-anndata.d.ts

@@ -0,0 +1,8 @@
+export class AnnDataAutoConfig extends AbstractAutoConfig {
+    getOptions(): {
+        obsEmbedding: never[];
+        obsSets: never[];
+    };
+}
+import { AbstractAutoConfig } from './generate-config-helpers.js';
+//# sourceMappingURL=generate-config-anndata.d.ts.map

package/dist-tsc/generate-config-anndata.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"generate-config-anndata.d.ts","sourceRoot":"","sources":["../src/generate-config-anndata.js"],"names":[],"mappings":"AAGA;IACE;;;MAsDC;CAgBF;mCAzEkC,8BAA8B"}

package/dist-tsc/generate-config-anndata.js

@@ -0,0 +1,66 @@
+/* eslint-disable no-unused-vars */
+import { AbstractAutoConfig } from './generate-config-helpers.js';
+export class AnnDataAutoConfig extends AbstractAutoConfig {
+    getOptions() {
+        const { zmetadata } = this;
+        const options = {
+            obsEmbedding: [],
+            obsSets: [],
+        };
+        zmetadata.forEach(({ path, attrs }) => {
+            const lowerPath = path.toLowerCase();
+            const relPath = path.substring(1);
+            // Gene expression matrix.
+            if (['/x'].includes(lowerPath)) {
+                options.obsFeatureMatrix = {
+                    path: relPath,
+                    // TODO: Also check the shape of X.
+                    // If X is very large, try to initialize initial-filtering properties
+                    // (will require that /var contains a boolean column however.)
+                };
+            }
+            // Spatial coordinates.
+            if (['/obsm/x_spatial', '/obsm/spatial'].includes(lowerPath)) {
+                // TODO: use obsSpots instead of obsLocations here?
+                options.obsLocations = {
+                    path: relPath,
+                };
+            }
+            // Embedding arrays.
+            if (['/obsm/x_umap', '/obsm/umap'].includes(lowerPath)) {
+                options.obsEmbedding.push({ path: relPath, embeddingType: 'UMAP' });
+            }
+            if (['/obsm/x_tsne', '/obsm/tsne'].includes(lowerPath)) {
+                options.obsEmbedding.push({ path: relPath, embeddingType: 't-SNE' });
+            }
+            if (['/obsm/x_pca', '/obsm/pca'].includes(lowerPath)) {
+                options.obsEmbedding.push({ path: relPath, embeddingType: 'PCA' });
+            }
+            // Cell set columns.
+            // TODO: use all categorical/string columns of obs instead of this fixed set?
+            const supportedObsSetsPaths = [
+                'cluster', 'clusters', 'subcluster', 'cell_type', 'celltype',
+                'leiden', 'louvain', 'disease', 'organism', 'self_reported_ethnicity',
+                'tissue', 'sex',
+            ].map(colname => `/obs/${colname}`);
+            if (supportedObsSetsPaths.includes(lowerPath)) {
+                const name = relPath.split('/').at(-1);
+                options.obsSets.push({ path: relPath, name });
+            }
+        });
+        return options;
+    }
+    addFiles(vc, dataset) {
+        const { url, fileType } = this;
+        dataset.addFile({
+            url,
+            fileType,
+            options: this.getOptions(),
+            // TODO: coordination values?
+        });
+    }
+    // eslint-disable-next-line class-methods-use-this
+    addViews(vc, layoutOption) {
+        // TODO
+    }
+}

package/dist-tsc/generate-config-helpers.d.ts

@@ -0,0 +1,9 @@
+export class AbstractAutoConfig {
+    constructor(parsedStore: any);
+    url: any;
+    fileType: any;
+    zmetadata: any;
+    addFiles(vc: any, dataset: any): void;
+    addViews(vc: any, layoutOption: any): void;
+}
+//# sourceMappingURL=generate-config-helpers.d.ts.map

package/dist-tsc/generate-config-helpers.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"generate-config-helpers.d.ts","sourceRoot":"","sources":["../src/generate-config-helpers.js"],"names":[],"mappings":"AACA;IACE,8BAKC;IAHC,SAAc;IACd,cAAwB;IACxB,eAA0B;IAI5B,sCAEC;IAGD,2CAEC;CACF"}

package/dist-tsc/generate-config-helpers.js

@@ -0,0 +1,17 @@
+/* eslint-disable no-unused-vars */
+export class AbstractAutoConfig {
+    constructor(parsedStore) {
+        const { url, fileType, zmetadata } = parsedStore;
+        this.url = url;
+        this.fileType = fileType;
+        this.zmetadata = zmetadata;
+    }
+    // eslint-disable-next-line class-methods-use-this
+    addFiles(vc, dataset) {
+        throw new Error('The addFiles() method has not been implemented.');
+    }
+    // eslint-disable-next-line class-methods-use-this
+    addViews(vc, layoutOption) {
+        throw new Error('The addViews() method has not been implemented.');
+    }
+}

package/dist-tsc/generate-config-ome.d.ts

@@ -0,0 +1,4 @@
+export class OmeAutoConfig extends AbstractAutoConfig {
+}
+import { AbstractAutoConfig } from './generate-config-helpers.js';
+//# sourceMappingURL=generate-config-ome.d.ts.map

package/dist-tsc/generate-config-ome.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"generate-config-ome.d.ts","sourceRoot":"","sources":["../src/generate-config-ome.js"],"names":[],"mappings":"AAKA;CAeC;mCAnBkC,8BAA8B"}

package/dist-tsc/generate-config-ome.js

@@ -0,0 +1,19 @@
+/* eslint-disable no-unused-vars */
+import { AbstractAutoConfig } from './generate-config-helpers.js';
+// TODO: split into separate classes for OME-TIFF and OME-Zarr?
+// TODO: split into separate classes for image and obsSegmentations?
+export class OmeAutoConfig extends AbstractAutoConfig {
+    addFiles(vc, dataset) {
+        const { url, fileType } = this;
+        dataset.addFile({
+            url,
+            fileType,
+            // TODO: options?
+            // TODO: coordination values?
+        });
+    }
+    // eslint-disable-next-line class-methods-use-this
+    addViews(vc, layoutOption) {
+        // TODO
+    }
+}

package/dist-tsc/generate-config-spatialdata.d.ts

@@ -0,0 +1,5 @@
+export class SpatialDataAutoConfig extends AbstractAutoConfig {
+    getOptions(): {};
+}
+import { AbstractAutoConfig } from './generate-config-helpers.js';
+//# sourceMappingURL=generate-config-spatialdata.d.ts.map

package/dist-tsc/generate-config-spatialdata.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"generate-config-spatialdata.d.ts","sourceRoot":"","sources":["../src/generate-config-spatialdata.js"],"names":[],"mappings":"AAGA;IACE,iBAgFC;CAgBF;mCAnGkC,8BAA8B"}

package/dist-tsc/generate-config-spatialdata.js

@@ -0,0 +1,87 @@
+/* eslint-disable no-unused-vars */
+import { AbstractAutoConfig } from './generate-config-helpers.js';
+export class SpatialDataAutoConfig extends AbstractAutoConfig {
+    getOptions() {
+        const { zmetadata } = this;
+        const options = {};
+        const availableElements = zmetadata.filter(({ path }) => {
+            const relPath = path.substring(1);
+            return relPath.match(/^(tables|table|images|labels|shapes|points)\/([^/]*)$/);
+        });
+        availableElements.forEach(({ path, attrs }) => {
+            const relPath = path.substring(1);
+            const firstCoordinateSystem = attrs
+                ?.multiscales?.[0]
+                ?.coordinateTransformations?.[0]
+                ?.output?.name;
+            // Handle image elements.
+            if (relPath.match(/^(images)\/([^/]*)$/)) {
+                options.image = {
+                    path: relPath,
+                    coordinateSystem: firstCoordinateSystem,
+                    // TODO: support a fileUid property in the schema?
+                };
+            }
+            // Handle labels elements.
+            if (relPath.match(/^(labels)\/([^/]*)$/)) {
+                options.labels = {
+                    path: relPath,
+                    coordinateSystem: firstCoordinateSystem,
+                    // TODO: support a fileUid property in the schema?
+                };
+                // TODO: check which table annotates these labels.
+            }
+            // Handle shapes elements.
+            if (relPath.match(/^(shapes)\/([^/]*)$/)) {
+                // TODO: check if shapes are circles or polygons
+                // to determine which Vitessce data type to use.
+                options.obsSpots = {
+                    path: relPath,
+                    coordinateSystem: firstCoordinateSystem,
+                };
+                // TODO: check which table annotates these shapes.
+            }
+            // Handle table elements.
+            if (relPath.match(/^(tables|table)\/([^/]*)$/)) {
+                // Identify all sub-paths within this table element.
+                const tableEls = zmetadata.filter(({ path: subpath }) => subpath.startsWith(path));
+                // Check if the table contains an X array.
+                const hasX = tableEls.find(el => el.path === `${path}/X`);
+                if (hasX) {
+                    options.obsFeatureMatrix = {
+                        path: hasX.path.substring(1),
+                        // region: null,
+                    };
+                }
+                // Check if the table contains an obs dataframe.
+                const hasObs = tableEls.find(el => el.path === `${path}/obs`);
+                if (hasObs) {
+                    const columnOrder = hasObs.attrs?.['column-order'];
+                    // Use the columns of this dataframe to configure the obsSets.
+                    options.obsSets = {
+                        // region: null,
+                        tablePath: relPath,
+                        obsSets: columnOrder.map(c => ({
+                            path: `${hasObs.path.substring(1)}/${c}`,
+                            name: c,
+                        })),
+                    };
+                }
+            }
+        });
+        return options;
+    }
+    addFiles(vc, dataset) {
+        const { url, fileType } = this;
+        dataset.addFile({
+            url,
+            fileType,
+            options: this.getOptions(),
+            // TODO: coordination values?
+        });
+    }
+    // eslint-disable-next-line class-methods-use-this
+    addViews(vc, layoutOption) {
+        // TODO
+    }
+}

package/dist-tsc/generate-config.d.ts

@@ -0,0 +1,41 @@
+/**
+ *
+ * @param {string} s A single string, like this
+ * `http://example.com/my_zarr.zarr#anndata.zarr;
+ * http://example.com/my_tiff.ome.tif`
+ * @returns {{ url: string, fileType: string}[]} The URLs with file types.
+ */
+export function parseUrls(s: string): {
+    url: string;
+    fileType: string;
+}[];
+export function parsedUrlToZmetadata(parsedUrl: any): Promise<{
+    path: string;
+    kind: string;
+    attrs: import("zarrita").Attributes;
+}[] | null>;
+/**
+ *
+ * @param {{ url, fileType, store }[]} parsedUrls
+ * @return {string[]} The layoutOptions.
+ */
+export function parsedUrlsToLayoutOptions(parsedUrls: {
+    url: any;
+    fileType: any;
+    store: any;
+}[]): string[];
+/**
+ *
+ * @param {{ url, fileType, store }[]} parsedUrls
+ * @param {string|null} layoutOption
+ */
+export function generateConfig(parsedUrls: {
+    url: any;
+    fileType: any;
+    store: any;
+}[], layoutOption?: string | null): Promise<{
+    config: VitessceConfig;
+    stores: any;
+}>;
+import { VitessceConfig } from './VitessceConfig.js';
+//# sourceMappingURL=generate-config.d.ts.map

package/dist-tsc/generate-config.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"generate-config.d.ts","sourceRoot":"","sources":["../src/generate-config.js"],"names":[],"mappings":"AAgGA;;;;;;GAMG;AACH,6BALW,MAAM,GAGJ;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAC,EAAE,CAqB9C;AAGD;;;;YAsEC;AAED;;;;GAIG;AACH,sDAHW;IAAE,GAAG,MAAC;IAAC,QAAQ,MAAC;IAAC,KAAK,MAAA;CAAE,EAAE,GACzB,MAAM,EAAE,CAOnB;AAED;;;;GAIG;AACH,2CAHW;IAAE,GAAG,MAAC;IAAC,QAAQ,MAAC;IAAC,KAAK,MAAA;CAAE,EAAE,iBAC1B,MAAM,GAAC,IAAI;;;GAoDrB;+BArQ8B,qBAAqB"}

package/dist-tsc/generate-config.js

@@ -0,0 +1,241 @@
+// TODO: ts-check
+import { FileType } from '@vitessce/constants-internal';
+import { withConsolidated, FetchStore, ZipFileStore, open as zarrOpen, root as zarrRoot } from 'zarrita';
+import { VitessceConfig } from './VitessceConfig.js';
+// Classes for different types of objects
+import { AnnDataAutoConfig } from './generate-config-anndata.js';
+import { SpatialDataAutoConfig } from './generate-config-spatialdata.js';
+import { OmeAutoConfig } from './generate-config-ome.js';
+const fileTypeToExtensions = {
+    [FileType.IMAGE_OME_TIFF]: ['.ome.tif', '.ome.tiff', '.ome.tf2', '.ome.tf8'],
+    [FileType.IMAGE_OME_ZARR]: ['.ome.zarr'],
+    [FileType.IMAGE_OME_ZARR_ZIP]: ['.ome.zarr.zip'],
+    [FileType.ANNDATA_ZARR]: ['.ad.zarr', '.h5ad.zarr', '.adata.zarr', '.anndata.zarr'],
+    [FileType.ANNDATA_ZARR_ZIP]: ['.ad.zarr.zip', '.h5ad.zarr.zip', '.adata.zarr.zip', '.anndata.zarr.zip'],
+    // TODO: how to handle h5ad-based AnnData (since needs reference JSON file).
+    // Perhaps just assume one H5AD+one JSON (or .ref.json) file correspond to each other?
+    [FileType.SPATIALDATA_ZARR]: ['.sd.zarr', '.sdata.zarr', '.spatialdata.zarr'],
+    [FileType.SPATIALDATA_ZARR_ZIP]: ['.sd.zarr.zip', '.sdata.zarr.zip', '.spatialdata.zarr.zip'],
+};
+const fileTypeToClass = {
+    // OME-TIFF
+    [FileType.IMAGE_OME_TIFF]: OmeAutoConfig,
+    [FileType.OBS_SEGMENTATIONS_OME_TIFF]: OmeAutoConfig,
+    // OME-Zarr
+    [FileType.IMAGE_OME_ZARR]: OmeAutoConfig,
+    [FileType.IMAGE_OME_ZARR_ZIP]: OmeAutoConfig,
+    [FileType.OBS_SEGMENTATIONS_OME_ZARR]: OmeAutoConfig,
+    [FileType.OBS_SEGMENTATIONS_OME_ZARR_ZIP]: OmeAutoConfig,
+    // AnnData
+    [FileType.ANNDATA_ZARR]: AnnDataAutoConfig,
+    [FileType.ANNDATA_ZARR_ZIP]: AnnDataAutoConfig,
+    // SpatialData
+    [FileType.SPATIALDATA_ZARR]: SpatialDataAutoConfig,
+    [FileType.SPATIALDATA_ZARR_ZIP]: SpatialDataAutoConfig,
+};
+// This list contains file types that can be mapped to a regular Zarr store
+// (e.g., FetchStore or ZipStore).
+const ZARR_FILETYPES = [
+    FileType.ANNDATA_ZARR,
+    FileType.ANNDATA_ZARR_ZIP,
+    FileType.SPATIALDATA_ZARR,
+    FileType.SPATIALDATA_ZARR_ZIP,
+    FileType.IMAGE_OME_ZARR,
+    FileType.IMAGE_OME_ZARR_ZIP,
+    FileType.OBS_SEGMENTATIONS_OME_ZARR,
+    FileType.OBS_SEGMENTATIONS_OME_ZARR_ZIP,
+];
+function urlToFileType(url) {
+    const match = Object.entries(fileTypeToExtensions).find(
+    // eslint-disable-next-line no-unused-vars
+    ([fileType, extensions]) => extensions.some(ext => url.endsWith(ext)));
+    if (match) {
+        return match[0];
+    }
+    throw new Error('The file extension contained in the URL did not map to a supported fileType.');
+}
+/**
+ *
+ * @param {{ fileType, url }} parsedUrl
+ * @returns {Readable}
+ */
+function getStore(parsedUrl) {
+    const { fileType, url } = parsedUrl;
+    if (!ZARR_FILETYPES.includes(fileType)) {
+        return null;
+    }
+    return fileType.endsWith('.zip')
+        ? ZipFileStore.fromUrl(url)
+        : new FetchStore(url);
+}
+/**
+ * Ensure that each object { url, fileType, [store] }
+ * contains a `store`.
+ * @param {object[]} parsedUrls
+ * @returns {object[]}
+ */
+function ensureStores(parsedUrls) {
+    return parsedUrls.map((parsedUrl) => {
+        if (parsedUrl.store) {
+            return parsedUrl;
+        }
+        const store = getStore(parsedUrl);
+        return {
+            ...parsedUrl,
+            store,
+        };
+    });
+}
+/**
+ *
+ * @param {string} s A single string, like this
+ * `http://example.com/my_zarr.zarr#anndata.zarr;
+ * http://example.com/my_tiff.ome.tif`
+ * @returns {{ url: string, fileType: string}[]} The URLs with file types.
+ */
+export function parseUrls(s) {
+    const urlsWithHashes = s.split(';');
+    return urlsWithHashes.map((urlWithHash) => {
+        const parts = urlWithHash.split('#');
+        if (parts.length === 1) {
+            const [url] = parts;
+            return {
+                url,
+                fileType: urlToFileType(url),
+            };
+        }
+        if (parts.length === 2) {
+            const [url, fileType] = parts;
+            return {
+                url,
+                fileType,
+            };
+        }
+        throw new Error('Only expected zero or one # character per URL, but received more.');
+    });
+}
+export async function parsedUrlToZmetadata(parsedUrl) {
+    const { store: initialStore } = parsedUrl;
+    if (!initialStore) {
+        return null;
+    }
+    let store;
+    let promises = [];
+    try {
+        try {
+            store = await withConsolidated(initialStore);
+        }
+        catch {
+            // Try again with `zmetadata` rather than `.zmetadata`.
+            // Reference: https://github.com/zarr-developers/zarr-python/issues/1121
+            store = await withConsolidated(initialStore, { metadataKey: 'zmetadata' });
+        }
+        // Is consolidated.
+        const contents = store.contents();
+        promises = contents.map(async (value) => {
+            const item = await zarrOpen(zarrRoot(store).resolve(value.path));
+            return {
+                ...value,
+                attrs: item.attrs,
+            };
+        });
+    }
+    catch {
+        store = initialStore;
+        // Is not consolidated.
+        const keysToTry = [
+            // Note: OME-NGFF metadata is stored in the root attrs.
+            '/',
+            // AnnData keys
+            '/X',
+            '/layers',
+            '/obs',
+            '/var',
+            '/obsm',
+            '/obsm/spatial',
+            '/obsm/X_spatial',
+            '/obsm/pca',
+            '/obsm/X_pca',
+            '/obsm/tsne',
+            '/obsm/X_tsne',
+            '/obsm/umap',
+            '/obsm/X_umap',
+            // TODO: second round of getting metadata for
+            // columns listed in /obs and /var .attrs['column-order'] ?
+            // SpatialData keys
+            // Note: For spatialData, we assume the store is always consolidated.
+            // TODO: throw error if spatialdata + not consolidated?
+        ];
+        promises = keysToTry.map(async (k) => {
+            try {
+                const item = await zarrOpen(zarrRoot(store).resolve(k));
+                return {
+                    path: k,
+                    kind: item.kind,
+                    attrs: item.attrs,
+                };
+            }
+            catch {
+                return null;
+            }
+        });
+    }
+    return (await Promise.all(promises))
+        .filter(entry => entry !== null);
+}
+/**
+ *
+ * @param {{ url, fileType, store }[]} parsedUrls
+ * @return {string[]} The layoutOptions.
+ */
+export function parsedUrlsToLayoutOptions(parsedUrls) {
+    // eslint-disable-next-line no-unused-vars
+    const parsedStores = ensureStores(parsedUrls);
+    // TODO: implement
+}
+/**
+ *
+ * @param {{ url, fileType, store }[]} parsedUrls
+ * @param {string|null} layoutOption
+ */
+export async function generateConfig(parsedUrls, layoutOption = null) {
+    // Map each URL to a Zarr store.
+    const parsedStores = ensureStores(parsedUrls);
+    // Obtain Zarr consolidated_metadata for each store.
+    const zmetadataStores = await Promise.all(parsedStores.map(async (parsedStore) => ({
+        ...parsedStore,
+        zmetadata: await parsedUrlToZmetadata(parsedStore),
+    })));
+    // Create configuration instance.
+    const vc = new VitessceConfig({
+        schemaVersion: '1.0.17',
+        name: 'Automatically-generated configuration.',
+        // TODO: write a description based on what is known
+        // (fileType(s) and maybe layoutOption).
+        description: 'Populate with a description of this visualization.',
+    });
+    // Create datasets.
+    // TODO: cases in which more than one dataset should be created?
+    const dataset = vc.addDataset('Main dataset');
+    zmetadataStores.forEach((parsedStore) => {
+        const { fileType } = parsedStore;
+        const AutoConfigClass = fileTypeToClass[fileType];
+        const autoConfig = new AutoConfigClass(parsedStore);
+        autoConfig.addFiles(vc, dataset);
+        // TODO: add all files, then add all views (in two separate loops)?
+        autoConfig.addViews(vc, layoutOption);
+    });
+    const stores = Object.fromEntries(
+    // Here, we use `parsedUrls` rather than `parsedStores`
+    // so that we do not provide more stores than intended
+    // (i.e., we do not provide stores which were solely created
+    // to obtain zmetadata).
+    parsedUrls
+        .filter(d => d.store)
+        .map(d => ([d.url, d.store])));
+    // Return both the config and the `stores` url-to-store dict.
+    return {
+        config: vc,
+        stores,
+    };
+}

package/dist-tsc/generate-config.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=generate-config.test.d.ts.map

package/dist-tsc/generate-config.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"generate-config.test.d.ts","sourceRoot":"","sources":["../src/generate-config.test.js"],"names":[],"mappings":""}