@vitessce/config 2.0.3-beta.0 → 3.0.0

package/dist-tsc/VitessceConfig.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"VitessceConfig.d.ts","sourceRoot":"","sources":["../src/VitessceConfig.js"],"names":[],"mappings":"AAqMA;;;;;GAKG;AACH,kCAJe,CAAC,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,CAAC,KAE1E,yBAAyB,CAKrC;AAED;;;;;GAKG;AACH,kCAJe,CAAC,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,CAAC,KAE1E,yBAAyB,CAKrC;AAtND;;GAEG;AACH;IACE;;;;;;;;OAQG;IACH,iBAPW,MAAM,YAEN,MAAM,oCACN,MAAM,WAAO,IAAI,EAW3B;IANC;;;;;MAKC;IAGH;;OAEG;IACH,UAFa,MAAM,CAIlB;CACF;AAED;;GAEG;AACH;IACE;;;;;OAKG;IACH,iBAJW,MAAM,QACN,MAAM,eACN,MAAM,EAShB;IANC;;;;;MAKC;IAGH;;;;;;;;;;OAUG;IACH;QARoC,GAAG,EAA5B,MAAM,GAAC,SAAS;QACD,QAAQ,EAAvB,MAAM;QACmB,kBAAkB,EAA3C,MAAM,GAAC,SAAS;QACe,OAAO,EAAtC,MAAM,WAAO,SAAS;wBAGpB,qBAAqB,CA6BjC;IAED;;OAEG;IACH,UAFa,MAAM,CAOlB;CACF;AAED;;GAEG;AACH;IACE;;;;;;;;;OASG;IACH,uBARW,MAAM,sBACN,MAAM,KAEN,MAAM,KACN,MAAM,KACN,MAAM,KACN,MAAM,EAWhB;IARC;;;;;;;MAOC;IAGH;;;;;OAKG;IACH,yBAJe,+BAA+B,KAEjC,kBAAkB,CAQ9B;IAED;;;;;;;QAOI;IACJ,WANY,MAAM,KACN,MAAM,KACN,MAAM,KACN,MAAM,GACJ,kBAAkB,CAS/B;IAED;;;OAGG;IACH,sBAFa,kBAAkB,CAQ9B;IAED;;OAEG;IACH,UAFa,MAAM,CAIlB;CACF;AAED;;GAEG;AACH;IACE,wBAEC;IADC,WAAkB;CAErB;AAED;;GAEG;AACH;IACE,wBAEC;IADC,WAAkB;CAErB;AAwBD;;GAEG;AACH;IACE;;;;OAIG;IACH,mBAHW,MAAM,UACN,MAAM,EAMhB;IAHC,cAAkB;IAClB,eAAoB;IACpB,YAAkB;IAGpB;;;;OAIG;IACH,iBAHW,GAAG,GACD,+BAA+B,CAK3C;CACF;AAED;;GAEG;AACH;IAuNE;;;;;;OAMG;IACH,wBAJW,MAAM,GACJ,cAAc,CAiC1B;IA3PD;;;;;;OAMG;IACH;QAJ0B,aAAa,EAA5B,MAAM;QACS,IAAI,EAAnB,MAAM;QACmB,WAAW,EAApC,MAAM,GAAC,SAAS;uBAmC1B;IATC;;;;;;;;MAQC;IAGH;;;;;;;;OAQG;IACH,kBAPW,MAAM,gBACN,MAAM;QAEU,GAAG,EAAnB,MAAM;QAEJ,qBAAqB,CAWjC;IAED;;;;;;;;;;;;;OAaG;IACH,iBAZW,qBAAqB,aAErB,MAAM;QAEU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,OAAO,EAAvB,MAAM;QAEJ,kBAAkB,CAmC9B;IAED;;;;;OAKG;IACH,yBAHc,MAAM,KACP,+BAA+B,EAAE,CAmB7C;IAED;;;;;;;OAOG;IACH,iBANW,kBAAkB,EAAE,UACpB,MAAM,EAAE,YACR,GAAG,EAAE,GAEH,cAAc,CAe1B;IAED;;;;;OAKG;IACH,mBAJW,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,GAEpE,cAAc,CA0B1B;IAED;;;OAGG;IACH,UAFa,MAAM,CAmBlB;CAwCF"}

package/dist-tsc/VitessceConfig.test.d.ts

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

package/dist-tsc/VitessceConfig.test.d.ts.map

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

package/{dist → dist-tsc}/VitessceConfig.test.js

@@ -1,5 +1,5 @@
 import { CoordinationType } from '@vitessce/constants-internal';
-import { VitessceConfig, hconcat, vconcat, } from './VitessceConfig';
+import { VitessceConfig, hconcat, vconcat, } from './VitessceConfig.js';
 describe('src/api/VitessceConfig.js', () => {
     describe('VitessceConfig', () => {
         it('can be instantiated in the old way for backwards compatibility', () => {

package/dist-tsc/index.d.ts

@@ -0,0 +1,3 @@
+export { generateConfigs } from "./VitessceAutoConfig.js";
+export { VitessceConfig, vconcat, hconcat } from "./VitessceConfig.js";
+//# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.d.ts.map

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

package/dist-tsc/index.js

@@ -0,0 +1,2 @@
+export { VitessceConfig, vconcat, hconcat } from './VitessceConfig.js';
+export { generateConfigs } from './VitessceAutoConfig.js';

package/dist-tsc/utils.d.ts

@@ -0,0 +1,12 @@
+/**
+ * Generate a new scope name which does not
+ * conflict / overlap with a previous scope name.
+ * Really these just need to be unique within the coordination object.
+ * So in theory they could be String(Math.random()) or uuidv4() or something.
+ * However it may be good to make them more human-readable and memorable
+ * since eventually we will want to expose a UI to update the coordination.
+ * @param {string[]} prevScopes Previous scope names.
+ * @returns {string} The new scope name.
+ */
+export function getNextScope(prevScopes: string[]): string;
+//# sourceMappingURL=utils.d.ts.map

package/dist-tsc/utils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["../src/utils.js"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,yCAHW,MAAM,EAAE,GACN,MAAM,CAuClB"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/config",
-  "version": "2.0.3-beta.0",
+  "version": "3.0.0",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -8,17 +8,26 @@
     "url": "git+https://github.com/vitessce/vitessce.git"
   },
   "license": "MIT",
+  "type": "module",
   "main": "dist/index.js",
   "files": [
-    "dist"
+    "src",
+    "dist",
+    "dist-tsc"
   ],
   "dependencies": {
-    "@vitessce/constants-internal": "2.0.3-beta.0",
-    "@vitessce/utils": "2.0.3-beta.0"
+    "@vitessce/constants-internal": "3.0.0",
+    "@vitessce/utils": "3.0.0"
   },
   "scripts": {
-    "start": "tsc --watch",
-    "build": "tsc",
+    "bundle": "pnpm exec vite build -c ../../scripts/vite.config.js",
     "test": "pnpm exec vitest --run -r ../../ --dir ."
+  },
+  "module": "dist/index.js",
+  "exports": {
+    ".": {
+      "types": "./dist-tsc/index.d.ts",
+      "import": "./dist/index.js"
+    }
   }
 }

package/src/VitessceAutoConfig.js

@@ -0,0 +1,382 @@
+import { CoordinationType, FileType } from '@vitessce/constants-internal';
+import {
+  VitessceConfig,
+} from './VitessceConfig.js';
+
+
+class AbstractAutoConfig {
+  async composeViewsConfig() { /* eslint-disable-line class-methods-use-this */
+    throw new Error('The composeViewsConfig() method has not been implemented.');
+  }
+
+  async composeFileConfig() { /* eslint-disable-line class-methods-use-this */
+    throw new Error('The composeFileConfig() method has not been implemented.');
+  }
+}
+class OmeTiffAutoConfig extends AbstractAutoConfig {
+  constructor(fileUrl) {
+    super();
+    this.fileUrl = fileUrl;
+    this.fileType = FileType.RASTER_JSON;
+    this.fileName = fileUrl.split('/').at(-1);
+  }
+
+
+  async composeViewsConfig() { /* eslint-disable-line class-methods-use-this */
+    return [
+      ['description'],
+      ['spatial'],
+      ['layerController'],
+    ];
+  }
+
+  async composeFileConfig() {
+    return {
+      fileType: this.fileType,
+      options: {
+        images: [
+          {
+            metadata: {
+              isBitmask: false,
+            },
+            name: this.fileName,
+            type: 'ome-tiff',
+            url: this.fileUrl,
+          },
+        ],
+        schemaVersion: '0.0.2',
+        usePhysicalSizeScaling: false,
+      },
+    };
+  }
+}
+
+class OmeZarrAutoConfig extends AbstractAutoConfig {
+  constructor(fileUrl) {
+    super();
+    this.fileUrl = fileUrl;
+    this.fileType = FileType.RASTER_OME_ZARR;
+    this.fileName = fileUrl.split('/').at(-1);
+  }
+
+  async composeViewsConfig() { /* eslint-disable-line class-methods-use-this */
+    return [
+      ['description'],
+      ['spatial'],
+      ['layerController'],
+      ['status'],
+    ];
+  }
+
+  async composeFileConfig() {
+    return {
+      fileType: this.fileType,
+      type: 'raster',
+      url: this.fileUrl,
+    };
+  }
+}
+
+class AnndataZarrAutoConfig extends AbstractAutoConfig {
+  constructor(fileUrl) {
+    super();
+    this.fileUrl = fileUrl;
+    this.fileType = FileType.ANNDATA_ZARR;
+    this.fileName = fileUrl.split('/').at(-1);
+    this.metadataSummary = {};
+  }
+
+  async composeFileConfig() {
+    this.metadataSummary = await this.setMetadataSummary();
+
+    const options = {
+      obsEmbedding: [],
+      obsFeatureMatrix: {
+        path: 'X',
+      },
+    };
+
+    this.metadataSummary.obsm.forEach((key) => {
+      if (key.toLowerCase().includes(('obsm/x_segmentations'))) {
+        options.obsSegmentations = { path: key };
+      }
+      if (key.toLowerCase().includes(('obsm/x_spatial'))) {
+        options.obsLocations = { path: key };
+      }
+      if (key.toLowerCase().includes('obsm/x_umap')) {
+        options.obsEmbedding.push({ path: key, embeddingType: 'UMAP' });
+      }
+      if (key.toLowerCase().includes('obsm/x_tsne')) {
+        options.obsEmbedding.push({ path: key, embeddingType: 't-SNE' });
+      }
+      if (key.toLowerCase().includes('obsm/x_pca')) {
+        options.obsEmbedding.push({ path: key, embeddingType: 'PCA' });
+      }
+    });
+
+    const supportedObsSetsKeys = [
+      'cluster', 'subcluster', 'cell_type', 'leiden', 'louvain', 'disease', 'organism', 'self_reported_ethnicity', 'tissue', 'sex',
+    ];
+
+    this.metadataSummary.obs.forEach((key) => {
+      supportedObsSetsKeys.forEach((supportedKey) => {
+        if (key.toLowerCase() === ['obs', supportedKey].join('/')) {
+          if (!('obsSets' in options)) {
+            options.obsSets = [
+              {
+                name: 'Cell Type',
+                path: [key],
+              },
+            ];
+          } else {
+            options.obsSets[0].path.push(key);
+          }
+        }
+      });
+    });
+
+    return {
+      options,
+      fileType: this.fileType,
+      url: this.fileUrl,
+      coordinationValues: {
+        obsType: 'cell',
+        featureType: 'gene',
+        featureValueType: 'expression',
+      },
+    };
+  }
+
+  async composeViewsConfig() {
+    this.metadataSummary = await this.setMetadataSummary();
+
+    const views = [];
+
+    const hasCellSetData = this.metadataSummary.obs
+      .filter(key => key.toLowerCase().includes('cluster') || key.toLowerCase().includes('cell_type'));
+
+    if (hasCellSetData.length > 0) {
+      views.push(['obsSets']);
+    }
+
+    this.metadataSummary.obsm.forEach((key) => {
+      if (key.toLowerCase().includes('obsm/x_umap')) {
+        views.push(['scatterplot', { mapping: 'UMAP' }]);
+      }
+      if (key.toLowerCase().includes('obsm/x_tsne')) {
+        views.push(['scatterplot', { mapping: 't-SNE' }]);
+      }
+      if (key.toLowerCase().includes('obsm/x_pca')) {
+        views.push(['scatterplot', { mapping: 'PCA' }]);
+      }
+      if (key.toLowerCase().includes(('obsm/x_segmentations'))) {
+        views.push(['layerController']);
+      }
+      if (key.toLowerCase().includes(('obsm/x_spatial'))) {
+        views.push(['spatial']);
+      }
+    });
+
+    if (this.metadataSummary.X) {
+      views.push(['heatmap']);
+      views.push(['featureList']);
+    }
+
+    return views;
+  }
+
+  async setMetadataSummary() {
+    if (Object.keys(this.metadataSummary).length > 0) {
+      return this.metadataSummary;
+    }
+
+    const parseMetadataFile = (metadataFile) => {
+      if (!metadataFile.metadata) {
+        throw new Error('Could not generate config: .zmetadata file is not valid.');
+      }
+
+      const obsmKeys = Object.keys(metadataFile.metadata)
+        .filter(key => key.startsWith('obsm/X_'))
+        .map(key => key.split('/.zarray')[0]);
+
+      const obsKeysArr = Object.keys(metadataFile.metadata)
+        .filter(key => key.startsWith('obs/')).map(key => key.split('/.za')[0]);
+
+      function uniq(a) {
+        return a.sort().filter((item, pos, ary) => !pos || item !== ary[pos - 1]);
+      }
+      const obsKeys = uniq(obsKeysArr);
+
+      const X = Object.keys(metadataFile.metadata).filter(key => key.startsWith('X'));
+
+      const out = {
+        obsm: obsmKeys,
+        obs: obsKeys,
+        X: X.length > 0,
+      };
+
+      return out;
+    };
+
+    const metadataExtension = '.zmetadata';
+    const url = [this.fileUrl, metadataExtension].join('/');
+    return fetch(url).then((response) => {
+      if (response.ok) {
+        return response.json();
+      }
+      return Promise.reject(response);
+    })
+      .then(responseJson => parseMetadataFile(responseJson))
+      .catch((error) => {
+        if (error.status === 404) {
+          const errorMssg = `Could not generate config. File ${metadataExtension} not found in supplied file URL. Check docs for more explanation.`;
+          return Promise.reject(new Error(errorMssg));
+        }
+        return Promise.reject(error);
+      });
+  }
+}
+
+const configClasses = [
+  {
+    extensions: ['.ome.tif', '.ome.tiff', '.ome.tf2', '.ome.tf8'],
+    class: OmeTiffAutoConfig,
+  },
+  {
+    extensions: ['.h5ad.zarr', '.adata.zarr', '.anndata.zarr'],
+    class: AnndataZarrAutoConfig,
+  },
+  {
+    extensions: ['ome.zarr'],
+    class: OmeZarrAutoConfig,
+  },
+];
+
+function getFileType(url) {
+  const match = configClasses.find(obj => obj.extensions.filter(
+    ext => url.endsWith(ext),
+  ).length === 1);
+  if (!match) {
+    throw new Error(`Could not generate config for URL: ${url}. This file type is not supported.`);
+  }
+  return match.class;
+}
+
+function calculateCoordinates(viewsNumb) {
+  const rows = Math.ceil(Math.sqrt(viewsNumb));
+  const cols = Math.ceil(viewsNumb / rows);
+  const width = 12 / cols;
+  const height = 12 / rows;
+  const coords = [];
+
+  for (let i = 0; i < viewsNumb; i++) {
+    const row = Math.floor(i / cols);
+    const col = i % cols;
+    const x = col * width;
+    const y = row * height;
+    coords.push([x, y, width, height]);
+  }
+
+  return coords;
+}
+
+async function generateConfig(url, vc) {
+  let ConfigClassName;
+  try {
+    ConfigClassName = getFileType(url);
+  } catch (err) {
+    return Promise.reject(err);
+  }
+
+  const configInstance = new ConfigClassName(url);
+  let fileConfig;
+  let viewsConfig;
+  try {
+    fileConfig = await configInstance.composeFileConfig();
+    viewsConfig = await configInstance.composeViewsConfig();
+  } catch (error) {
+    console.error(error);
+    return Promise.reject(error);
+  }
+
+  const dataset = vc
+    .addDataset(configInstance.fileName)
+    .addFile(fileConfig);
+
+  let layerControllerView = false;
+  let spatialView = false;
+
+  const views = [];
+
+  viewsConfig.forEach((v) => {
+    const view = vc.addView(dataset, ...v);
+    if (v[0] === 'layerController') {
+      layerControllerView = view;
+    }
+    if (v[0] === 'spatial') {
+      spatialView = view;
+    }
+    // this piece of code can be removed once these props are added by default to layerController
+    // see this issue: https://github.com/vitessce/vitessce/issues/1454
+    if (v[0] === 'layerController' && configInstance instanceof OmeTiffAutoConfig) {
+      view.setProps({
+        disable3d: [],
+        disableChannelsIfRgbDetected: true,
+      });
+    }
+    // transpose the heatmap by default
+    if (v[0] === 'heatmap' && configInstance instanceof AnndataZarrAutoConfig) {
+      view.setProps({ transpose: true });
+    }
+
+    views.push(view);
+  });
+
+  if (layerControllerView && spatialView && configInstance instanceof AnndataZarrAutoConfig) {
+    const spatialSegmentationLayerValue = {
+      opacity: 1,
+      radius: 0,
+      visible: true,
+      stroked: false,
+    };
+
+    vc.linkViews(
+      [spatialView, layerControllerView],
+      [
+        CoordinationType.SPATIAL_ZOOM,
+        CoordinationType.SPATIAL_TARGET_X,
+        CoordinationType.SPATIAL_TARGET_Y,
+        CoordinationType.SPATIAL_SEGMENTATION_LAYER,
+      ],
+      [-5.5, 16000, 20000, spatialSegmentationLayerValue],
+    );
+  }
+
+  return views;
+}
+
+export async function generateConfigs(fileUrls) {
+  const vc = new VitessceConfig({
+    schemaVersion: '1.0.15',
+    name: 'An automatically generated config. Adjust values and add layout components if needed.',
+    description: 'Populate with text relevant to this visualisation.',
+  });
+
+  const allViews = [];
+
+  fileUrls.forEach((url) => {
+    allViews.push(generateConfig(url, vc));
+  });
+
+  return Promise.all(allViews).then((views) => {
+    const flattenedViews = views.flat();
+
+    const coord = calculateCoordinates(flattenedViews.length);
+
+    for (let i = 0; i < flattenedViews.length; i++) {
+      flattenedViews[i].setXYWH(...coord[i]);
+    }
+
+    return vc.toJSON();
+  });
+}