@vitessce/config 3.0.0 → 3.0.1

package/dist/index.js

@@ -15751,41 +15751,91 @@ class AnndataZarrAutoConfig extends AbstractAutoConfig {
     }
     return views;
   }
+  async setMetadataSummaryWithZmetadata(response) {
+    const metadataFile = await response.json();
+    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"));
+    return {
+      // Array of keys in obsm that are found by the fetches above
+      obsm: obsmKeys,
+      // Array of keys in obs that are found by the fetches above
+      obs: obsKeys,
+      // Boolean indicating whether the X array was found by the fetches above
+      X: X.length > 0
+    };
+  }
+  async setMetadataSummaryWithoutZmetadata() {
+    const knownMetadataFileSuffixes = [
+      "/obsm/X_pca/.zarray",
+      "/obsm/X_umap/.zarray",
+      "/obsm/X_tsne/.zarray",
+      "/obsm/X_spatial/.zarray",
+      "/obsm/X_segmentations/.zarray",
+      "/obs/.zattrs",
+      "/X/.zarray"
+    ];
+    const getObsmKey = (url) => {
+      const obsmKeyStartIndex = `${this.fileUrl}/`.length;
+      const obsmKeyEndIndex = url.length - "/.zarray".length;
+      return url.substring(obsmKeyStartIndex, obsmKeyEndIndex);
+    };
+    const promises = knownMetadataFileSuffixes.map((suffix) => fetch(`${this.fileUrl}${suffix}`));
+    const fetchResults = await Promise.all(promises);
+    const okFetchResults = fetchResults.filter((j) => j.ok);
+    const metadataSummary = {
+      // Array of keys in obsm that are found by the fetches above
+      obsm: [],
+      // Array of keys in obs that are found by the fetches above
+      obs: [],
+      // Boolean indicating whether the X array was found by the fetches above
+      X: false
+    };
+    const obsPromiseResult = okFetchResults.find(
+      (r) => r.url === `${this.fileUrl}/obs/.zattrs`
+    );
+    const isObsValid = (obsAttr) => Object.keys(obsAttr).includes("column-order") && Object.keys(obsAttr).includes("encoding-version") && Object.keys(obsAttr).includes("encoding-type") && obsAttr["encoding-type"] === "dataframe" && (obsAttr["encoding-version"] === "0.1.0" || obsAttr["encoding-version"] === "0.2.0");
+    if (obsPromiseResult) {
+      const obsAttrs = await obsPromiseResult.json();
+      if (isObsValid(obsAttrs)) {
+        obsAttrs["column-order"].forEach((key) => metadataSummary.obs.push(`obs/${key}`));
+      } else {
+        throw new Error("Could not generate config: /obs/.zattrs file is not valid.");
+      }
+    }
+    okFetchResults.forEach((r) => {
+      if (r.url.startsWith(`${this.fileUrl}/obsm`)) {
+        const obsmKey = getObsmKey(r.url);
+        if (obsmKey) {
+          metadataSummary.obsm.push(obsmKey);
+        }
+      } else if (r.url.startsWith(`${this.fileUrl}/X`)) {
+        metadataSummary.X = true;
+      }
+    });
+    return metadataSummary;
+  }
   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 this.setMetadataSummaryWithZmetadata(response);
       }
-      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));
+      if (response.status === 404) {
+        return this.setMetadataSummaryWithoutZmetadata();
       }
-      return Promise.reject(error);
+      throw new Error(`Could not generate config: ${response.statusText}`);
     });
   }
 }

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

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

package/dist-tsc/VitessceAutoConfig.js

@@ -160,46 +160,101 @@ class AnndataZarrAutoConfig extends AbstractAutoConfig {
         }
         return views;
     }
+    async setMetadataSummaryWithZmetadata(response) {
+        const metadataFile = await response.json();
+        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'));
+        return {
+            // Array of keys in obsm that are found by the fetches above
+            obsm: obsmKeys,
+            // Array of keys in obs that are found by the fetches above
+            obs: obsKeys,
+            // Boolean indicating whether the X array was found by the fetches above
+            X: X.length > 0,
+        };
+    }
+    async setMetadataSummaryWithoutZmetadata() {
+        const knownMetadataFileSuffixes = [
+            '/obsm/X_pca/.zarray',
+            '/obsm/X_umap/.zarray',
+            '/obsm/X_tsne/.zarray',
+            '/obsm/X_spatial/.zarray',
+            '/obsm/X_segmentations/.zarray',
+            '/obs/.zattrs',
+            '/X/.zarray',
+        ];
+        const getObsmKey = (url) => {
+            // Get the substring "X_pca" from a URL like
+            // http://example.com/foo/adata.zarr/obsm/X_pca/.zarray
+            const obsmKeyStartIndex = `${this.fileUrl}/`.length;
+            const obsmKeyEndIndex = url.length - '/.zarray'.length;
+            return url.substring(obsmKeyStartIndex, obsmKeyEndIndex);
+        };
+        const promises = knownMetadataFileSuffixes.map(suffix => fetch(`${this.fileUrl}${suffix}`));
+        const fetchResults = await Promise.all(promises);
+        const okFetchResults = fetchResults.filter(j => j.ok);
+        const metadataSummary = {
+            // Array of keys in obsm that are found by the fetches above
+            obsm: [],
+            // Array of keys in obs that are found by the fetches above
+            obs: [],
+            // Boolean indicating whether the X array was found by the fetches above
+            X: false,
+        };
+        const obsPromiseResult = okFetchResults.find(r => r.url === (`${this.fileUrl}/obs/.zattrs`));
+        const isObsValid = obsAttr => Object.keys(obsAttr).includes('column-order')
+            && Object.keys(obsAttr).includes('encoding-version')
+            && Object.keys(obsAttr).includes('encoding-type')
+            && obsAttr['encoding-type'] === 'dataframe'
+            && (obsAttr['encoding-version'] === '0.1.0' || obsAttr['encoding-version'] === '0.2.0');
+        if (obsPromiseResult) {
+            const obsAttrs = await obsPromiseResult.json();
+            if (isObsValid(obsAttrs)) {
+                obsAttrs['column-order'].forEach(key => metadataSummary.obs.push(`obs/${key}`));
+            }
+            else {
+                throw new Error('Could not generate config: /obs/.zattrs file is not valid.');
+            }
+        }
+        okFetchResults
+            .forEach((r) => {
+            if (r.url.startsWith(`${this.fileUrl}/obsm`)) {
+                const obsmKey = getObsmKey(r.url);
+                if (obsmKey) {
+                    metadataSummary.obsm.push(obsmKey);
+                }
+            }
+            else if (r.url.startsWith(`${this.fileUrl}/X`)) {
+                metadataSummary.X = true;
+            }
+        });
+        return metadataSummary;
+    }
     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 this.setMetadataSummaryWithZmetadata(response);
             }
-            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));
+            if (response.status === 404) {
+                return this.setMetadataSummaryWithoutZmetadata();
             }
-            return Promise.reject(error);
+            throw new Error(`Could not generate config: ${response.statusText}`);
         });
     }
 }

package/dist-tsc/VitessceAutoConfig.test.js

@@ -1,3 +1,4 @@
+import { describe, it, expect } from 'vitest';
 import { generateConfigs } from './VitessceAutoConfig.js';
 describe('src/VitessceAutoConfig.js', () => {
     it('generates config for OME-TIFF file correctly', async () => {
@@ -150,7 +151,7 @@ describe('src/VitessceAutoConfig.js', () => {
         expect(config).toEqual(expectedConfig);
     });
     it('generates config for Anndata-ZARR file correctly', async () => {
-        const urls = ['http://localhost:51204/@fixtures/zarr/partials/.anndata.zarr'];
+        const urls = ['http://localhost:4204/@fixtures/zarr/partials/.anndata.zarr'];
         const expectedName = urls[0].split('/').at(-1);
         const expectedConfig = {
             version: '1.0.15',
@@ -258,7 +259,7 @@ describe('src/VitessceAutoConfig.js', () => {
         expect(config).toEqual(expectedConfig);
     });
     it('generates empty config for Anndata-ZARR file with empty .zmetadata', async () => {
-        const urls = ['http://localhost:51204/@fixtures/zarr/partials/emptymeta.h5ad.zarr'];
+        const urls = ['http://localhost:4204/@fixtures/zarr/partials/emptymeta.h5ad.zarr'];
         const expectedName = urls[0].split('/').at(-1);
         const expectedConfig = {
             version: '1.0.15',
@@ -299,8 +300,13 @@ describe('src/VitessceAutoConfig.js', () => {
         expect(config).toEqual(expectedConfig);
     });
     it('raises an error for Anndata-ZARR file with misconfigured .zmetadata', async () => {
-        const urls = ['http://localhost:51204/@fixtures/zarr/partials/invalidmeta.adata.zarr'];
-        await generateConfigs(urls).catch(e => expect(e.message).toContain('Could not generate config: .zmetadata file is not valid.'));
+        const urls = ['http://localhost:4204/@fixtures/zarr/partials/invalidmeta.adata.zarr'];
+        // References:
+        // - https://vitest.dev/api/expect.html#tothrowerror
+        // - https://vitest.dev/api/expect.html#rejects
+        await expect(() => generateConfigs(urls))
+            .rejects
+            .toThrowError('Could not generate config: .zmetadata file is not valid.');
     });
     it('generates config for multiple files correctly', async () => {
         const urls = ['somefile.ome.tif', 'anoterfile.ome.zarr'];
@@ -431,12 +437,77 @@ describe('src/VitessceAutoConfig.js', () => {
         const config = await generateConfigs(urls);
         expect(config).toEqual(expectedConfig);
     });
-    it('raises an Error when .zmetadata file not present in folder', async () => {
-        const urls = ['http://localhost:51204/@fixtures/zarr/partials/invalid.adata.zarr'];
-        await generateConfigs(urls).catch(e => expect(e.message).toContain('Could not generate config. File .zmetadata not found in supplied file URL'));
+    it('Does the parsing when .zmetadata file not present in folder', async () => {
+        const urls = ['http://localhost:4204/@fixtures/zarr/anndata-0.8/anndata-csr.adata.zarr'];
+        const expectedName = urls[0].split('/').at(-1);
+        const expectedConfig = {
+            version: '1.0.15',
+            name: 'An automatically generated config. Adjust values and add layout components if needed.',
+            description: 'Populate with text relevant to this visualisation.',
+            datasets: [
+                {
+                    uid: 'A',
+                    name: expectedName,
+                    files: [
+                        {
+                            url: urls[0],
+                            fileType: 'anndata.zarr',
+                            coordinationValues: {
+                                obsType: 'cell',
+                                featureType: 'gene',
+                                featureValueType: 'expression',
+                            },
+                            options: {
+                                obsEmbedding: [
+                                    {
+                                        path: 'obsm/X_umap',
+                                        embeddingType: 'UMAP',
+                                    },
+                                ],
+                                obsFeatureMatrix: {
+                                    path: 'X',
+                                },
+                                obsSets: [
+                                    {
+                                        name: 'Cell Type',
+                                        path: [
+                                            'obs/leiden',
+                                        ],
+                                    },
+                                ],
+                            },
+                        },
+                    ],
+                },
+            ],
+            coordinationSpace: {
+                dataset: {
+                    A: 'A',
+                },
+                embeddingType: {
+                    A: 'UMAP',
+                },
+            },
+            layout: [
+                {
+                    component: 'scatterplot',
+                    coordinationScopes: {
+                        dataset: 'A',
+                        embeddingType: 'A',
+                    },
+                    x: 0,
+                    y: 0,
+                    w: 12,
+                    h: 12,
+                },
+            ],
+            initStrategy: 'auto',
+        };
+        const config = await generateConfigs(urls);
+        expect(config).toEqual(expectedConfig);
     });
     it('raises an error when URL with unsupported file format is passed', async () => {
-        const urls = ['http://localhost:51204/@fixtures/zarr/anndata-0.7/somefile.zarr'];
+        const urls = ['http://localhost:4204/@fixtures/zarr/anndata-0.7/somefile.zarr'];
         await generateConfigs(urls).catch(e => expect(e.message).toContain('This file type is not supported.'));
     });
 });

package/dist-tsc/VitessceConfig.test.js

@@ -1,3 +1,4 @@
+import { describe, it, expect } from 'vitest';
 import { CoordinationType } from '@vitessce/constants-internal';
 import { VitessceConfig, hconcat, vconcat, } from './VitessceConfig.js';
 describe('src/api/VitessceConfig.js', () => {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/config",
-  "version": "3.0.0",
+  "version": "3.0.1",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -16,12 +16,12 @@
     "dist-tsc"
   ],
   "dependencies": {
-    "@vitessce/constants-internal": "3.0.0",
-    "@vitessce/utils": "3.0.0"
+    "@vitessce/constants-internal": "3.0.1",
+    "@vitessce/utils": "3.0.1"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../scripts/vite.config.js",
-    "test": "pnpm exec vitest --run -r ../../ --dir ."
+    "test": "pnpm exec vitest --run"
   },
   "module": "dist/index.js",
   "exports": {

package/src/VitessceAutoConfig.js

@@ -185,55 +185,118 @@ class AnndataZarrAutoConfig extends AbstractAutoConfig {
     return views;
   }
 
-  async setMetadataSummary() {
-    if (Object.keys(this.metadataSummary).length > 0) {
-      return this.metadataSummary;
+  async setMetadataSummaryWithZmetadata(response) { /* eslint-disable-line class-methods-use-this */
+    const metadataFile = await response.json();
+    if (!metadataFile.metadata) {
+      throw new Error('Could not generate config: .zmetadata file is not valid.');
     }
 
-    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 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]);
 
-      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);
 
-      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'));
+
+    return {
+      // Array of keys in obsm that are found by the fetches above
+      obsm: obsmKeys,
+      // Array of keys in obs that are found by the fetches above
+      obs: obsKeys,
+      // Boolean indicating whether the X array was found by the fetches above
+      X: X.length > 0,
+    };
+  }
 
-      const X = Object.keys(metadataFile.metadata).filter(key => key.startsWith('X'));
+  async setMetadataSummaryWithoutZmetadata() {
+    const knownMetadataFileSuffixes = [
+      '/obsm/X_pca/.zarray',
+      '/obsm/X_umap/.zarray',
+      '/obsm/X_tsne/.zarray',
+      '/obsm/X_spatial/.zarray',
+      '/obsm/X_segmentations/.zarray',
+      '/obs/.zattrs',
+      '/X/.zarray',
+    ];
 
-      const out = {
-        obsm: obsmKeys,
-        obs: obsKeys,
-        X: X.length > 0,
-      };
+    const getObsmKey = (url) => {
+      // Get the substring "X_pca" from a URL like
+      // http://example.com/foo/adata.zarr/obsm/X_pca/.zarray
+      const obsmKeyStartIndex = `${this.fileUrl}/`.length;
+      const obsmKeyEndIndex = url.length - '/.zarray'.length;
+      return url.substring(obsmKeyStartIndex, obsmKeyEndIndex);
+    };
 
-      return out;
+    const promises = knownMetadataFileSuffixes.map(suffix => fetch(`${this.fileUrl}${suffix}`));
+
+    const fetchResults = await Promise.all(promises);
+    const okFetchResults = fetchResults.filter(j => j.ok);
+    const metadataSummary = {
+      // Array of keys in obsm that are found by the fetches above
+      obsm: [],
+      // Array of keys in obs that are found by the fetches above
+      obs: [],
+      // Boolean indicating whether the X array was found by the fetches above
+      X: false,
     };
 
+    const obsPromiseResult = okFetchResults.find(
+      r => r.url === (`${this.fileUrl}/obs/.zattrs`),
+    );
+
+    const isObsValid = obsAttr => Object.keys(obsAttr).includes('column-order')
+      && Object.keys(obsAttr).includes('encoding-version')
+      && Object.keys(obsAttr).includes('encoding-type')
+      && obsAttr['encoding-type'] === 'dataframe'
+      && (obsAttr['encoding-version'] === '0.1.0' || obsAttr['encoding-version'] === '0.2.0');
+
+    if (obsPromiseResult) {
+      const obsAttrs = await obsPromiseResult.json();
+      if (isObsValid(obsAttrs)) {
+        obsAttrs['column-order'].forEach(key => metadataSummary.obs.push(`obs/${key}`));
+      } else {
+        throw new Error('Could not generate config: /obs/.zattrs file is not valid.');
+      }
+    }
+
+    okFetchResults
+      .forEach((r) => {
+        if (r.url.startsWith(`${this.fileUrl}/obsm`)) {
+          const obsmKey = getObsmKey(r.url);
+          if (obsmKey) {
+            metadataSummary.obsm.push(obsmKey);
+          }
+        } else if (r.url.startsWith(`${this.fileUrl}/X`)) {
+          metadataSummary.X = true;
+        }
+      });
+
+    return metadataSummary;
+  }
+
+  async setMetadataSummary() {
+    if (Object.keys(this.metadataSummary).length > 0) {
+      return this.metadataSummary;
+    }
+
     const metadataExtension = '.zmetadata';
     const url = [this.fileUrl, metadataExtension].join('/');
     return fetch(url).then((response) => {
       if (response.ok) {
-        return response.json();
+        return this.setMetadataSummaryWithZmetadata(response);
       }
-      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);
-      });
+      if (response.status === 404) {
+        return this.setMetadataSummaryWithoutZmetadata();
+      }
+      throw new Error(`Could not generate config: ${response.statusText}`);
+    });
   }
 }
 

package/src/VitessceAutoConfig.test.js

@@ -1,3 +1,4 @@
+import { describe, it, expect } from 'vitest';
 import { generateConfigs } from './VitessceAutoConfig.js';
 
 describe('src/VitessceAutoConfig.js', () => {
@@ -155,7 +156,7 @@ describe('src/VitessceAutoConfig.js', () => {
   });
 
   it('generates config for Anndata-ZARR file correctly', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/partials/.anndata.zarr'];
+    const urls = ['http://localhost:4204/@fixtures/zarr/partials/.anndata.zarr'];
     const expectedName = urls[0].split('/').at(-1);
     const expectedConfig = {
       version: '1.0.15',
@@ -264,7 +265,7 @@ describe('src/VitessceAutoConfig.js', () => {
   });
 
   it('generates empty config for Anndata-ZARR file with empty .zmetadata', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/partials/emptymeta.h5ad.zarr'];
+    const urls = ['http://localhost:4204/@fixtures/zarr/partials/emptymeta.h5ad.zarr'];
     const expectedName = urls[0].split('/').at(-1);
     const expectedConfig = {
       version: '1.0.15',
@@ -307,11 +308,14 @@ describe('src/VitessceAutoConfig.js', () => {
   });
 
   it('raises an error for Anndata-ZARR file with misconfigured .zmetadata', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/partials/invalidmeta.adata.zarr'];
+    const urls = ['http://localhost:4204/@fixtures/zarr/partials/invalidmeta.adata.zarr'];
 
-    await generateConfigs(urls).catch(
-      e => expect(e.message).toContain('Could not generate config: .zmetadata file is not valid.'),
-    );
+    // References:
+    // - https://vitest.dev/api/expect.html#tothrowerror
+    // - https://vitest.dev/api/expect.html#rejects
+    await expect(() => generateConfigs(urls))
+      .rejects
+      .toThrowError('Could not generate config: .zmetadata file is not valid.');
   });
 
   it('generates config for multiple files correctly', async () => {
@@ -447,16 +451,79 @@ describe('src/VitessceAutoConfig.js', () => {
   });
 
 
-  it('raises an Error when .zmetadata file not present in folder', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/partials/invalid.adata.zarr'];
+  it('Does the parsing when .zmetadata file not present in folder', async () => {
+    const urls = ['http://localhost:4204/@fixtures/zarr/anndata-0.8/anndata-csr.adata.zarr'];
+    const expectedName = urls[0].split('/').at(-1);
+    const expectedConfig = {
+      version: '1.0.15',
+      name: 'An automatically generated config. Adjust values and add layout components if needed.',
+      description: 'Populate with text relevant to this visualisation.',
+      datasets: [
+        {
+          uid: 'A',
+          name: expectedName,
+          files: [
+            {
+              url: urls[0],
+              fileType: 'anndata.zarr',
+              coordinationValues: {
+                obsType: 'cell',
+                featureType: 'gene',
+                featureValueType: 'expression',
+              },
+              options: {
+                obsEmbedding: [
+                  {
+                    path: 'obsm/X_umap',
+                    embeddingType: 'UMAP',
+                  },
+                ],
+                obsFeatureMatrix: {
+                  path: 'X',
+                },
+                obsSets: [
+                  {
+                    name: 'Cell Type',
+                    path: [
+                      'obs/leiden',
+                    ],
+                  },
+                ],
+              },
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+        },
+        embeddingType: {
+          A: 'UMAP',
+        },
+      },
+      layout: [
+        {
+          component: 'scatterplot',
+          coordinationScopes: {
+            dataset: 'A',
+            embeddingType: 'A',
+          },
+          x: 0,
+          y: 0,
+          w: 12,
+          h: 12,
+        },
+      ],
+      initStrategy: 'auto',
+    };
 
-    await generateConfigs(urls).catch(
-      e => expect(e.message).toContain('Could not generate config. File .zmetadata not found in supplied file URL'),
-    );
+    const config = await generateConfigs(urls);
+    expect(config).toEqual(expectedConfig);
   });
 
   it('raises an error when URL with unsupported file format is passed', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/anndata-0.7/somefile.zarr'];
+    const urls = ['http://localhost:4204/@fixtures/zarr/anndata-0.7/somefile.zarr'];
 
     await generateConfigs(urls).catch(
       e => expect(e.message).toContain('This file type is not supported.'),

package/src/VitessceConfig.test.js

@@ -1,3 +1,4 @@
+import { describe, it, expect } from 'vitest';
 import { CoordinationType } from '@vitessce/constants-internal';
 import {
   VitessceConfig,