@vitessce/config 3.8.9 → 3.8.13

package/dist/index.js

@@ -41,11 +41,11 @@ function requirePluralize() {
   if (hasRequiredPluralize) return pluralize$1.exports;
   hasRequiredPluralize = 1;
   (function(module2, exports) {
-    (function(root2, pluralize2) {
+    (function(root, pluralize2) {
       if (typeof commonjsRequire === "function" && true && true) {
         module2.exports = pluralize2();
       } else {
-        root2.pluralize = pluralize2();
+        root.pluralize = pluralize2();
       }
     })(pluralize, function() {
       var pluralRules = [];
@@ -443,11 +443,11 @@ function requireLoglevel() {
   if (hasRequiredLoglevel) return loglevel$1.exports;
   hasRequiredLoglevel = 1;
   (function(module2) {
-    (function(root2, definition) {
+    (function(root, definition) {
       if (module2.exports) {
         module2.exports = definition();
       } else {
-        root2.log = definition();
+        root.log = definition();
       }
     })(loglevel, function() {
       var noop = function() {
@@ -2122,8 +2122,8 @@ function assert$1(expression, msg = "") {
   if (!expression)
     throw new Error(msg);
 }
-function resolve(root2, path) {
-  const base = typeof root2 === "string" ? new URL(root2) : root2;
+function resolve(root, path) {
+  const base = typeof root === "string" ? new URL(root) : root;
   if (!base.pathname.endsWith("/")) {
     base.pathname += "/";
   }
@@ -3070,9 +3070,6 @@ class Location {
     return new Location(this.store, decodeURIComponent(new URL(path, root2).pathname));
   }
 }
-function root(store) {
-  return new Location(store ?? /* @__PURE__ */ new Map());
-}
 class Group extends Location {
   constructor(store, path, metadata) {
     super(store, path);
@@ -4272,13 +4269,7 @@ class SpatialDataAutoConfig extends AbstractAutoConfig2 {
         };
       }
       if (relPath.match(/^(shapes)\/([^/]*)$/)) {
-        options.obsSpots = {
-          path: relPath,
-          coordinateSystem: firstCoordinateSystem
-        };
-      }
-      if (relPath.match(/^(points)\/([^/]*)$/)) {
-        options.obsPoints = {
+        options.obsSegmentations = {
           path: relPath,
           coordinateSystem: firstCoordinateSystem
         };
@@ -4292,21 +4283,6 @@ class SpatialDataAutoConfig extends AbstractAutoConfig2 {
             // region: null,
           };
         }
-        const hasObs = tableEls.find((el) => el.path === `${path}/obs`);
-        if (hasObs) {
-          const columnOrder = hasObs.attrs?.["column-order"];
-          options.obsSets = {
-            // region: null,
-            tablePath: relPath,
-            obsSets: columnOrder.map((c) => ({
-              // TODO: determine whether this column is string/categorical.
-              // TODO: determine whether this column contains too many
-              // categories to make sense to consider a cell set.
-              path: `${hasObs.path.substring(1)}/${c}`,
-              name: c
-            }))
-          };
-        }
       }
     });
     return options;
@@ -4461,8 +4437,19 @@ async function parsedUrlToZmetadata(parsedUrl) {
       store = await withConsolidated(initialStore, { metadataKey: "zmetadata" });
     }
     const contents = store.contents();
+    const consolidatedRoot = await open(store, { kind: "group" });
     promises = contents.map(async (value) => {
-      const item = await open(root(store).resolve(value.path));
+      let item;
+      try {
+        item = await open(
+          consolidatedRoot.resolve(value.path),
+          { kind: value.kind }
+        );
+      } catch {
+        item = {
+          attrs: {}
+        };
+      }
       return {
         ...value,
         attrs: item.attrs
@@ -4493,9 +4480,10 @@ async function parsedUrlToZmetadata(parsedUrl) {
       // Note: For spatialData, we assume the store is always consolidated.
       // TODO: throw error if spatialdata + not consolidated?
     ];
+    const storeRoot = await open(store, { kind: "group" });
     promises = keysToTry.map(async (k) => {
       try {
-        const item = await open(root(store).resolve(k));
+        const item = await open(storeRoot.resolve(k));
         return {
           path: k,
           kind: item.kind,

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

@@ -1 +1 @@
-{"version":3,"file":"generate-config-spatialdata.d.ts","sourceRoot":"","sources":["../src/generate-config-spatialdata.js"],"names":[],"mappings":"AAIA;IACE,iBA6FC;CAqCF;mCArIkC,8BAA8B"}
+{"version":3,"file":"generate-config-spatialdata.d.ts","sourceRoot":"","sources":["../src/generate-config-spatialdata.js"],"names":[],"mappings":"AAIA;IACE,iBAiGC;CAqCF;mCAzIkC,8BAA8B"}

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

@@ -36,20 +36,23 @@ export class SpatialDataAutoConfig extends AbstractAutoConfig {
             if (relPath.match(/^(shapes)\/([^/]*)$/)) {
                 // TODO: check if shapes are circles or polygons
                 // to determine which Vitessce data type to use.
-                options.obsSpots = {
+                options.obsSegmentations = {
                     path: relPath,
                     coordinateSystem: firstCoordinateSystem,
                 };
                 // TODO: check which table annotates these shapes.
             }
             // Handle point elements.
+            /* TODO: uncomment once points are more scalable
             if (relPath.match(/^(points)\/([^/]*)$/)) {
-                options.obsPoints = {
-                    path: relPath,
-                    coordinateSystem: firstCoordinateSystem,
-                };
-                // TODO: check which table annotates these shapes.
+              options.obsPoints = {
+                path: relPath,
+                coordinateSystem: firstCoordinateSystem,
+              };
+      
+              // TODO: check which table annotates these shapes.
             }
+            */
             // Handle table elements.
             if (relPath.match(/^(tables|table)\/([^/]*)$/)) {
                 // Identify all sub-paths within this table element.
@@ -63,22 +66,24 @@ export class SpatialDataAutoConfig extends AbstractAutoConfig {
                     };
                 }
                 // Check if the table contains an obs dataframe.
+                /* TODO: uncomment once logic for checking num. unique categories
                 const hasObs = tableEls.find(el => el.path === `${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 => ({
-                            // TODO: determine whether this column is string/categorical.
-                            // TODO: determine whether this column contains too many
-                            // categories to make sense to consider a cell set.
-                            path: `${hasObs.path.substring(1)}/${c}`,
-                            name: c,
-                        })),
-                    };
+                  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 => ({
+                      // TODO: determine whether this column is string/categorical.
+                      // TODO: determine whether this column contains too many
+                      // categories to make sense to consider a cell set.
+                      path: `${hasObs.path.substring(1)}/${c}`,
+                      name: c,
+                    })),
+                  };
                 }
+                */
             }
         });
         return options;

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

@@ -19,10 +19,14 @@ export function parseUrlsFromString(s: string): {
     fileType: string;
 }[];
 export function parsedUrlToZmetadata(parsedUrl: any): Promise<{
+    attrs: {};
+    path: import("zarrita").AbsolutePath;
+    kind: "array" | "group";
+}[] | ({
     path: string;
     kind: string;
     attrs: import("zarrita").Attributes;
-}[] | null>;
+} | null)[] | null>;
 /**
  *
  * @param {{ url, fileType, store }[]} parsedUrls

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

@@ -1 +1 @@
-{"version":3,"file":"generate-config.d.ts","sourceRoot":"","sources":["../src/generate-config.js"],"names":[],"mappings":"AA4GA;;;;GAIG;AACH,+BAHW,MAAM,EAAE,GACN;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,EAAE,CAoB/C;AAED;;;;;;GAMG;AACH,uCALW,MAAM,GAGJ;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAC,EAAE,CAK9C;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;+BAtR8B,qBAAqB"}
+{"version":3,"file":"generate-config.d.ts","sourceRoot":"","sources":["../src/generate-config.js"],"names":[],"mappings":"AA4GA;;;;GAIG;AACH,+BAHW,MAAM,EAAE,GACN;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,EAAE,CAoB/C;AAED;;;;;;GAMG;AACH,uCALW,MAAM,GAGJ;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAC,EAAE,CAK9C;AAGD;;;;;;;;oBA4FC;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;+BA5S8B,qBAAqB"}

package/dist-tsc/generate-config.js

@@ -1,6 +1,6 @@
 // TODO: ts-check
 import { FileType } from '@vitessce/constants-internal';
-import { withConsolidated, FetchStore, open as zarrOpen, root as zarrRoot } from 'zarrita';
+import { withConsolidated, FetchStore, open as zarrOpen } from 'zarrita';
 // eslint-disable-next-line import/no-unresolved
 import ZipFileStore from '@zarrita/storage/zip';
 import { transformEntriesForZipFileStore } from '@vitessce/zarr-utils';
@@ -149,8 +149,27 @@ export async function parsedUrlToZmetadata(parsedUrl) {
         }
         // Is consolidated.
         const contents = store.contents();
+        // Open all entries to get their attributes.
+        const consolidatedRoot = await zarrOpen(store, { kind: 'group' });
         promises = contents.map(async (value) => {
-            const item = await zarrOpen(zarrRoot(store).resolve(value.path));
+            let item;
+            try {
+                // Note: if `kind` is not provided,
+                // then zarrita must make extra network requests.
+                // TODO: open issue in Zarrita to avoid network requests for
+                // arrays that lack .zattrs (e.g., OME-NGFF multiscale arrays)
+                // (as determined from omission in consolidated metadata).
+                item = await zarrOpen(consolidatedRoot.resolve(value.path), { kind: value.kind });
+            }
+            catch {
+                // Opening can fail if the dtype is unsupported,
+                // since zarrita assumes string dtypes
+                // but Scanpy rank_genes_groups can result in recarrays
+                // that have an array of dtypes.
+                item = {
+                    attrs: {},
+                };
+            }
             return {
                 ...value,
                 attrs: item.attrs,
@@ -183,9 +202,10 @@ export async function parsedUrlToZmetadata(parsedUrl) {
             // Note: For spatialData, we assume the store is always consolidated.
             // TODO: throw error if spatialdata + not consolidated?
         ];
+        const storeRoot = await zarrOpen(store, { kind: 'group' });
         promises = keysToTry.map(async (k) => {
             try {
-                const item = await zarrOpen(zarrRoot(store).resolve(k));
+                const item = await zarrOpen(storeRoot.resolve(k));
                 return {
                     path: k,
                     kind: item.kind,

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

@@ -150,6 +150,13 @@ describe('generateConfig', () => {
             },
         ];
         const { config, stores } = await generateConfig(parsedUrls);
+        const configJson = config.toJSON();
+        // TODO: include all options in the test once implemented.
+        delete configJson.datasets[0].files[0].options.obsSegmentations;
+        delete configJson.datasets[0].files[0].options.obsSpots;
+        delete configJson.datasets[0].files[0].options.obsSets;
+        delete configJson.datasets[0].files[0].options.obsPoints;
+        // End TODO
         expect(config.toJSON().datasets[0].files).toEqual([
             {
                 url: './mouse_liver.spatialdata.json',
@@ -159,38 +166,9 @@ describe('generateConfig', () => {
                         path: 'images/raw_image',
                         coordinateSystem: 'global',
                     },
-                    obsSegmentations: {
-                        path: 'labels/segmentation_mask',
-                        coordinateSystem: 'global',
-                    },
-                    obsSpots: {
-                        // TODO: the test should be updated once fixed in the implementaiton,
-                        // since these are not circle shapes.
-                        path: 'shapes/nucleus_boundaries',
-                    },
                     obsFeatureMatrix: {
                         path: 'tables/table/X',
                     },
-                    obsPoints: {
-                        path: 'points/transcripts',
-                    },
-                    obsSets: {
-                        tablePath: 'tables/table',
-                        obsSets: [
-                            {
-                                path: 'tables/table/obs/cell_ID',
-                                name: 'cell_ID',
-                            },
-                            {
-                                path: 'tables/table/obs/fov_labels',
-                                name: 'fov_labels',
-                            },
-                            {
-                                path: 'tables/table/obs/annotation',
-                                name: 'annotation',
-                            },
-                        ],
-                    },
                 },
             },
         ]);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/config",
-  "version": "3.8.9",
+  "version": "3.8.13",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -18,10 +18,10 @@
   "dependencies": {
     "zarrita": "0.5.4",
     "@zarrita/storage": "0.1.3",
-    "@vitessce/constants-internal": "3.8.9",
-    "@vitessce/utils": "3.8.9",
-    "@vitessce/globals": "3.8.9",
-    "@vitessce/zarr-utils": "3.8.9"
+    "@vitessce/constants-internal": "3.8.13",
+    "@vitessce/globals": "3.8.13",
+    "@vitessce/zarr-utils": "3.8.13",
+    "@vitessce/utils": "3.8.13"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../scripts/vite.config.mjs",

package/src/generate-config-spatialdata.js

@@ -43,7 +43,7 @@ export class SpatialDataAutoConfig extends AbstractAutoConfig {
       if (relPath.match(/^(shapes)\/([^/]*)$/)) {
         // TODO: check if shapes are circles or polygons
         // to determine which Vitessce data type to use.
-        options.obsSpots = {
+        options.obsSegmentations = {
           path: relPath,
           coordinateSystem: firstCoordinateSystem,
         };
@@ -52,6 +52,7 @@ export class SpatialDataAutoConfig extends AbstractAutoConfig {
       }
 
       // Handle point elements.
+      /* TODO: uncomment once points are more scalable
       if (relPath.match(/^(points)\/([^/]*)$/)) {
         options.obsPoints = {
           path: relPath,
@@ -60,6 +61,7 @@ export class SpatialDataAutoConfig extends AbstractAutoConfig {
 
         // TODO: check which table annotates these shapes.
       }
+      */
 
       // Handle table elements.
       if (relPath.match(/^(tables|table)\/([^/]*)$/)) {
@@ -76,6 +78,7 @@ export class SpatialDataAutoConfig extends AbstractAutoConfig {
         }
 
         // Check if the table contains an obs dataframe.
+        /* TODO: uncomment once logic for checking num. unique categories
         const hasObs = tableEls.find(el => el.path === `${path}/obs`);
         if (hasObs) {
           const columnOrder = hasObs.attrs?.['column-order'];
@@ -92,6 +95,7 @@ export class SpatialDataAutoConfig extends AbstractAutoConfig {
             })),
           };
         }
+        */
       }
     });
 

package/src/generate-config.js

@@ -1,7 +1,7 @@
 // TODO: ts-check
 
 import { FileType } from '@vitessce/constants-internal';
-import { withConsolidated, FetchStore, open as zarrOpen, root as zarrRoot } from 'zarrita';
+import { withConsolidated, FetchStore, open as zarrOpen } from 'zarrita';
 // eslint-disable-next-line import/no-unresolved
 import ZipFileStore from '@zarrita/storage/zip';
 import { transformEntriesForZipFileStore } from '@vitessce/zarr-utils';
@@ -164,8 +164,29 @@ export async function parsedUrlToZmetadata(parsedUrl) {
     }
     // Is consolidated.
     const contents = store.contents();
+    // Open all entries to get their attributes.
+    const consolidatedRoot = await zarrOpen(store, { kind: 'group' });
     promises = contents.map(async (value) => {
-      const item = await zarrOpen(zarrRoot(store).resolve(value.path));
+      let item;
+      try {
+        // Note: if `kind` is not provided,
+        // then zarrita must make extra network requests.
+        // TODO: open issue in Zarrita to avoid network requests for
+        // arrays that lack .zattrs (e.g., OME-NGFF multiscale arrays)
+        // (as determined from omission in consolidated metadata).
+        item = await zarrOpen(
+          consolidatedRoot.resolve(value.path),
+          { kind: value.kind },
+        );
+      } catch {
+        // Opening can fail if the dtype is unsupported,
+        // since zarrita assumes string dtypes
+        // but Scanpy rank_genes_groups can result in recarrays
+        // that have an array of dtypes.
+        item = {
+          attrs: {},
+        };
+      }
       return {
         ...value,
         attrs: item.attrs,
@@ -198,9 +219,10 @@ export async function parsedUrlToZmetadata(parsedUrl) {
       // Note: For spatialData, we assume the store is always consolidated.
       // TODO: throw error if spatialdata + not consolidated?
     ];
+    const storeRoot = await zarrOpen(store, { kind: 'group' });
     promises = keysToTry.map(async (k) => {
       try {
-        const item = await zarrOpen(zarrRoot(store).resolve(k));
+        const item = await zarrOpen(storeRoot.resolve(k));
         return {
           path: k,
           kind: item.kind,

package/src/generate-config.test.js

@@ -163,6 +163,13 @@ describe('generateConfig', () => {
       },
     ];
     const { config, stores } = await generateConfig(parsedUrls);
+    const configJson = config.toJSON();
+    // TODO: include all options in the test once implemented.
+    delete configJson.datasets[0].files[0].options.obsSegmentations;
+    delete configJson.datasets[0].files[0].options.obsSpots;
+    delete configJson.datasets[0].files[0].options.obsSets;
+    delete configJson.datasets[0].files[0].options.obsPoints;
+    // End TODO
     expect(config.toJSON().datasets[0].files).toEqual([
       {
         url: './mouse_liver.spatialdata.json',
@@ -172,38 +179,9 @@ describe('generateConfig', () => {
             path: 'images/raw_image',
             coordinateSystem: 'global',
           },
-          obsSegmentations: {
-            path: 'labels/segmentation_mask',
-            coordinateSystem: 'global',
-          },
-          obsSpots: {
-            // TODO: the test should be updated once fixed in the implementaiton,
-            // since these are not circle shapes.
-            path: 'shapes/nucleus_boundaries',
-          },
           obsFeatureMatrix: {
             path: 'tables/table/X',
           },
-          obsPoints: {
-            path: 'points/transcripts',
-          },
-          obsSets: {
-            tablePath: 'tables/table',
-            obsSets: [
-              {
-                path: 'tables/table/obs/cell_ID',
-                name: 'cell_ID',
-              },
-              {
-                path: 'tables/table/obs/fov_labels',
-                name: 'fov_labels',
-              },
-              {
-                path: 'tables/table/obs/annotation',
-                name: 'annotation',
-              },
-            ],
-          },
         },
       },
     ]);