@vitessce/config 4.0.4 → 4.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.js +1271 -824
- package/dist-tsc/generate-config-anndata.d.ts.map +1 -1
- package/dist-tsc/generate-config-anndata.js +3 -1
- package/dist-tsc/generate-config-anndata.js.map +1 -1
- package/dist-tsc/generate-config.d.ts +1 -9
- package/dist-tsc/generate-config.d.ts.map +1 -1
- package/dist-tsc/generate-config.js +3 -3
- package/dist-tsc/generate-config.js.map +1 -1
- package/dist-tsc/generate-config.test.js +2 -2
- package/dist-tsc/generate-config.test.js.map +1 -1
- package/package.json +7 -7
- package/src/generate-config-anndata.js +4 -1
- package/src/generate-config.js +9 -3
- package/src/generate-config.test.js +2 -2
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"generate-config-anndata.d.ts","sourceRoot":"","sources":["../src/generate-config-anndata.js"],"names":[],"mappings":"AAGA;IACE;;;MAsDC;
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{"version":3,"file":"generate-config-anndata.d.ts","sourceRoot":"","sources":["../src/generate-config-anndata.js"],"names":[],"mappings":"AAGA;IACE;;;MAsDC;CAmBF;mCA5EkC,8BAA8B"}
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@@ -61,7 +61,9 @@ export class AnnDataAutoConfig extends AbstractAutoConfig {
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}
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// eslint-disable-next-line class-methods-use-this
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addViews(vc, dataset, layoutOption) {
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64
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-
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64
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const geneList = vc.addView(dataset, 'featureList');
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65
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// Layout.
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vc.layout(geneList);
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}
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}
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//# sourceMappingURL=generate-config-anndata.js.map
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"generate-config-anndata.js","sourceRoot":"","sources":["../src/generate-config-anndata.js"],"names":[],"mappings":"AAAA,mCAAmC;AACnC,OAAO,EAAE,kBAAkB,EAAE,MAAM,8BAA8B,CAAC;AAElE,MAAM,OAAO,iBAAkB,SAAQ,kBAAkB;IACvD,UAAU;QACR,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAC;QAC3B,MAAM,OAAO,GAAG;YACd,YAAY,EAAE,EAAE;YAChB,OAAO,EAAE,EAAE;SACZ,CAAC;QAEF,SAAS,CAAC,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE;YACpC,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;YACrC,MAAM,OAAO,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;YAClC,0BAA0B;YAC1B,IAAI,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC/B,OAAO,CAAC,gBAAgB,GAAG;oBACzB,IAAI,EAAE,OAAO;oBAEb,mCAAmC;oBACnC,qEAAqE;oBACrE,8DAA8D;iBAC/D,CAAC;YACJ,CAAC;YAED,uBAAuB;YACvB,IAAI,CAAC,iBAAiB,EAAE,eAAe,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC7D,mDAAmD;gBACnD,OAAO,CAAC,YAAY,GAAG;oBACrB,IAAI,EAAE,OAAO;iBACd,CAAC;YACJ,CAAC;YAED,oBAAoB;YACpB,IAAI,CAAC,cAAc,EAAE,YAAY,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBACvD,OAAO,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,MAAM,EAAE,CAAC,CAAC;YACtE,CAAC;YACD,IAAI,CAAC,cAAc,EAAE,YAAY,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBACvD,OAAO,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,OAAO,EAAE,CAAC,CAAC;YACvE,CAAC;YACD,IAAI,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBACrD,OAAO,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,CAAC,CAAC;YACrE,CAAC;YAED,oBAAoB;YACpB,6EAA6E;YAC7E,MAAM,qBAAqB,GAAG;gBAC5B,SAAS,EAAE,UAAU,EAAE,YAAY,EAAE,WAAW,EAAE,UAAU;gBAC5D,QAAQ,EAAE,SAAS,EAAE,SAAS,EAAE,UAAU,EAAE,yBAAyB;gBACrE,QAAQ,EAAE,KAAK;aAChB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,QAAQ,OAAO,EAAE,CAAC,CAAC;YACpC,IAAI,qBAAqB,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC9C,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;gBACvC,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC;YAChD,CAAC;QACH,CAAC,CAAC,CAAC;QAEH,OAAO,OAAO,CAAC;IACjB,CAAC;IAED,QAAQ,CAAC,EAAE,EAAE,OAAO;QAClB,MAAM,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC;QAC/B,OAAO,CAAC,OAAO,CAAC;YACd,GAAG;YACH,QAAQ;YACR,OAAO,EAAE,IAAI,CAAC,UAAU,EAAE;YAC1B,6BAA6B;SAC9B,CAAC,CAAC;IACL,CAAC;IAED,kDAAkD;IAClD,QAAQ,CAAC,EAAE,EAAE,OAAO,EAAE,YAAY;QAChC,OAAO;
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1
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{"version":3,"file":"generate-config-anndata.js","sourceRoot":"","sources":["../src/generate-config-anndata.js"],"names":[],"mappings":"AAAA,mCAAmC;AACnC,OAAO,EAAE,kBAAkB,EAAE,MAAM,8BAA8B,CAAC;AAElE,MAAM,OAAO,iBAAkB,SAAQ,kBAAkB;IACvD,UAAU;QACR,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAC;QAC3B,MAAM,OAAO,GAAG;YACd,YAAY,EAAE,EAAE;YAChB,OAAO,EAAE,EAAE;SACZ,CAAC;QAEF,SAAS,CAAC,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE;YACpC,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;YACrC,MAAM,OAAO,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;YAClC,0BAA0B;YAC1B,IAAI,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC/B,OAAO,CAAC,gBAAgB,GAAG;oBACzB,IAAI,EAAE,OAAO;oBAEb,mCAAmC;oBACnC,qEAAqE;oBACrE,8DAA8D;iBAC/D,CAAC;YACJ,CAAC;YAED,uBAAuB;YACvB,IAAI,CAAC,iBAAiB,EAAE,eAAe,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC7D,mDAAmD;gBACnD,OAAO,CAAC,YAAY,GAAG;oBACrB,IAAI,EAAE,OAAO;iBACd,CAAC;YACJ,CAAC;YAED,oBAAoB;YACpB,IAAI,CAAC,cAAc,EAAE,YAAY,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBACvD,OAAO,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,MAAM,EAAE,CAAC,CAAC;YACtE,CAAC;YACD,IAAI,CAAC,cAAc,EAAE,YAAY,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBACvD,OAAO,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,OAAO,EAAE,CAAC,CAAC;YACvE,CAAC;YACD,IAAI,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBACrD,OAAO,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,CAAC,CAAC;YACrE,CAAC;YAED,oBAAoB;YACpB,6EAA6E;YAC7E,MAAM,qBAAqB,GAAG;gBAC5B,SAAS,EAAE,UAAU,EAAE,YAAY,EAAE,WAAW,EAAE,UAAU;gBAC5D,QAAQ,EAAE,SAAS,EAAE,SAAS,EAAE,UAAU,EAAE,yBAAyB;gBACrE,QAAQ,EAAE,KAAK;aAChB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,QAAQ,OAAO,EAAE,CAAC,CAAC;YACpC,IAAI,qBAAqB,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC9C,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;gBACvC,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC;YAChD,CAAC;QACH,CAAC,CAAC,CAAC;QAEH,OAAO,OAAO,CAAC;IACjB,CAAC;IAED,QAAQ,CAAC,EAAE,EAAE,OAAO;QAClB,MAAM,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC;QAC/B,OAAO,CAAC,OAAO,CAAC;YACd,GAAG;YACH,QAAQ;YACR,OAAO,EAAE,IAAI,CAAC,UAAU,EAAE;YAC1B,6BAA6B;SAC9B,CAAC,CAAC;IACL,CAAC;IAED,kDAAkD;IAClD,QAAQ,CAAC,EAAE,EAAE,OAAO,EAAE,YAAY;QAChC,MAAM,QAAQ,GAAG,EAAE,CAAC,OAAO,CAAC,OAAO,EAAE,aAAa,CAAC,CAAC;QAEpD,UAAU;QACV,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;IACtB,CAAC;CACF"}
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@@ -18,15 +18,7 @@ export function parseUrlsFromString(s: string): {
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url: string;
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fileType: string;
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}[];
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export function parsedUrlToZmetadata(parsedUrl: any): Promise<
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attrs: {};
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path: import("zarrita").AbsolutePath;
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kind: "array" | "group";
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}[] | ({
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path: string;
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kind: string;
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attrs: import("zarrita").Attributes;
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} | null)[] | null>;
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export function parsedUrlToZmetadata(parsedUrl: any): Promise<any[] | null>;
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/**
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*
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* @param {{ url, fileType, store }[]} parsedUrls
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{"version":3,"file":"generate-config.d.ts","sourceRoot":"","sources":["../src/generate-config.js"],"names":[],"mappings":"AAgHA;;;;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
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{"version":3,"file":"generate-config.d.ts","sourceRoot":"","sources":["../src/generate-config.js"],"names":[],"mappings":"AAgHA;;;;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,4EAkGC;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;+BAtT8B,qBAAqB"}
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@@ -1,6 +1,6 @@
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// TODO: ts-check
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import { FileType } from '@vitessce/constants-internal';
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import {
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import { withConsolidatedMetadata, extendStore, FetchStore, open as zarrOpen } from 'zarrita';
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// eslint-disable-next-line import/no-unresolved
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import ZipFileStore from '@zarrita/storage/zip';
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import { transformEntriesForZipFileStore } from '@vitessce/zarr-utils';
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@@ -144,12 +144,12 @@ export async function parsedUrlToZmetadata(parsedUrl) {
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let promises = [];
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try {
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try {
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store = await
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store = await extendStore(initialStore, s => withConsolidatedMetadata(s));
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}
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catch {
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// Try again with `zmetadata` rather than `.zmetadata`.
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// Reference: https://github.com/zarr-developers/zarr-python/issues/1121
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store = await
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store = await extendStore(initialStore, s => withConsolidatedMetadata(s, { metadataKey: 'zmetadata' }));
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}
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// Is consolidated.
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const contents = store.contents();
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{"version":3,"file":"generate-config.js","sourceRoot":"","sources":["../src/generate-config.js"],"names":[],"mappings":"AAAA,iBAAiB;AAEjB,OAAO,EAAE,QAAQ,EAAE,MAAM,8BAA8B,CAAC;AACxD,OAAO,EAAE,
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|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { describe, it, expect } from 'vitest';
|
|
2
2
|
import { createStoreFromMapContents } from '@vitessce/zarr-utils';
|
|
3
|
-
import {
|
|
3
|
+
import { withConsolidatedMetadata, extendStore } from 'zarrita';
|
|
4
4
|
import { parseUrlsFromString, parsedUrlToZmetadata, generateConfig } from './generate-config.js';
|
|
5
5
|
import spatialdataMouseLiverFixture from './json-fixtures/mouse_liver.spatialdata.json';
|
|
6
6
|
import anndataMouseLiverFixture from './json-fixtures/mouse_liver.anndata.json';
|
|
@@ -47,7 +47,7 @@ describe('generateConfig', () => {
|
|
|
47
47
|
});
|
|
48
48
|
it('store for SpatialData object supports withConsolidated', async () => {
|
|
49
49
|
const initialStore = createStoreFromMapContents(spatialdataMouseLiverFixture);
|
|
50
|
-
const store = await
|
|
50
|
+
const store = await extendStore(initialStore, s => withConsolidatedMetadata(s, { metadataKey: 'zmetadata' }));
|
|
51
51
|
expect(store.contents().length).toEqual(41);
|
|
52
52
|
});
|
|
53
53
|
it('parsed url to zmetadata for a SpatialData object', async () => {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"generate-config.test.js","sourceRoot":"","sources":["../src/generate-config.test.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAC9C,OAAO,EAAE,0BAA0B,EAAE,MAAM,sBAAsB,CAAC;AAClE,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"generate-config.test.js","sourceRoot":"","sources":["../src/generate-config.test.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAC9C,OAAO,EAAE,0BAA0B,EAAE,MAAM,sBAAsB,CAAC;AAClE,OAAO,EAAE,wBAAwB,EAAE,WAAW,EAAE,MAAM,SAAS,CAAC;AAChE,OAAO,EAAE,mBAAmB,EAAE,oBAAoB,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AACjG,OAAO,4BAA4B,MAAM,8CAA8C,CAAC;AACxF,OAAO,wBAAwB,MAAM,0CAA0C,CAAC;AAChF,OAAO,6BAA6B,MAAM,sCAAsC,CAAC;AACjF,OAAO,wCAAwC,MAAM,6CAA6C,CAAC;AAEnG,QAAQ,CAAC,gBAAgB,EAAE,GAAG,EAAE;IAC9B,EAAE,CAAC,aAAa,EAAE,GAAG,EAAE;QACrB,MAAM,EAAE,GAAG,sCAAsC,CAAC;QAClD,MAAM,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACtC;gBACE,GAAG,EAAE,sCAAsC;gBAC3C,QAAQ,EAAE,gBAAgB;aAC3B;SACF,CAAC,CAAC;QAEH,MAAM,EAAE,GAAG,gEAAgE,CAAC;QAC5E,MAAM,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACtC;gBACE,GAAG,EAAE,sCAAsC;gBAC3C,QAAQ,EAAE,2BAA2B;aACtC;SACF,CAAC,CAAC;QAEH,MAAM,EAAE,GAAG,yGAAyG,CAAC;QACrH,MAAM,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACtC;gBACE,GAAG,EAAE,sCAAsC;gBAC3C,QAAQ,EAAE,2BAA2B;aACtC;YACD;gBACE,GAAG,EAAE,6BAA6B;gBAClC,QAAQ,EAAE,cAAc;aACzB;SACF,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,+CAA+C,EAAE,KAAK,IAAI,EAAE;QAC7D,MAAM,SAAS,GAAG;YAChB,GAAG,EAAE,4BAA4B;YACjC,QAAQ,EAAE,cAAc;YACxB,KAAK,EAAE,0BAA0B,CAAC,wBAAwB,CAAC;SAC5D,CAAC;QACF,MAAM,SAAS,GAAG,MAAM,oBAAoB,CAAC,SAAS,CAAC,CAAC;QAExD,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;QACpC,MAAM,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,eAAe,CAAC,CAAC,CAAC;QAC7G,MAAM,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,EAAE,CAAC;IAC9D,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,wDAAwD,EAAE,KAAK,IAAI,EAAE;QACtE,MAAM,YAAY,GAAG,0BAA0B,CAAC,4BAA4B,CAAC,CAAC;QAC9E,MAAM,KAAK,GAAG,MAAM,WAAW,CAAC,YAAY,EAAE,CAAC,CAAC,EAAE,CAAC,wBAAwB,CAAC,CAAC,EAAE,EAAE,WAAW,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC;QAE9G,MAAM,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAC,MAAM,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;IAC9C,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,kDAAkD,EAAE,KAAK,IAAI,EAAE;QAChE,MAAM,SAAS,GAAG;YAChB,GAAG,EAAE,gCAAgC;YACrC,QAAQ,EAAE,kBAAkB;YAC5B,KAAK,EAAE,0BAA0B,CAAC,4BAA4B,CAAC;SAChE,CAAC;QACF,MAAM,SAAS,GAAG,MAAM,oBAAoB,CAAC,SAAS,CAAC,CAAC;QAExD,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QACrC,MAAM,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC;YACzC,GAAG;YACH,SAAS;YACT,mBAAmB;YACnB,qBAAqB;YACrB,qBAAqB;YACrB,SAAS;YACT,2BAA2B;YAC3B,6BAA6B;YAC7B,SAAS;YACT,qBAAqB;YACrB,SAAS;YACT,4BAA4B;YAC5B,SAAS;YACT,eAAe;YACf,iBAAiB;YACjB,sBAAsB;YACtB,yBAAyB;YACzB,wBAAwB;YACxB,sBAAsB;YACtB,mBAAmB;YACnB,0BAA0B;YAC1B,8BAA8B;YAC9B,yCAAyC;YACzC,oCAAoC;YACpC,2BAA2B;YAC3B,8BAA8B;YAC9B,yCAAyC;YACzC,oCAAoC;YACpC,oBAAoB;YACpB,4BAA4B;YAC5B,oBAAoB;YACpB,mBAAmB;YACnB,qCAAqC;YACrC,qCAAqC;YACrC,kDAAkD;YAClD,4CAA4C;YAC5C,gDAAgD;YAChD,mBAAmB;YACnB,0BAA0B;YAC1B,oBAAoB;YACpB,oBAAoB;SACrB,CAAC,CAAC;QACH,MAAM,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,EAAE,CAAC;IAC9D,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,+CAA+C,EAAE,KAAK,IAAI,EAAE;QAC7D,MAAM,SAAS,GAAG;YAChB,GAAG,EAAE,wBAAwB;YAC7B,QAAQ,EAAE,gBAAgB;YAC1B,KAAK,EAAE,0BAA0B,CAAC,6BAA6B,CAAC;SACjE,CAAC;QACF,MAAM,SAAS,GAAG,MAAM,oBAAoB,CAAC,SAAS,CAAC,CAAC;QAExD,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;QACpC,MAAM,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;QAClD,MAAM,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,EAAE,CAAC;IAC9D,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,oEAAoE,EAAE,KAAK,IAAI,EAAE;QAClF,MAAM,UAAU,GAAG;YACjB;gBACE,GAAG,EAAE,4BAA4B;gBACjC,QAAQ,EAAE,cAAc;gBACxB,KAAK,EAAE,0BAA0B,CAAC,wBAAwB,CAAC;aAC5D;SACF,CAAC;QACF,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,cAAc,CAAC,UAAU,CAAC,CAAC;QAC5D,MAAM,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC;YAChD;gBACE,GAAG,EAAE,4BAA4B;gBACjC,QAAQ,EAAE,cAAc;gBACxB,OAAO,EAAE;oBACP,YAAY,EAAE,EAAE;oBAChB,OAAO,EAAE,EAAE;oBACX,gBAAgB,EAAE;wBAChB,IAAI,EAAE,GAAG;qBACV;oBACD,YAAY,EAAE;wBACZ,IAAI,EAAE,cAAc;qBACrB;iBACF;aACF;SACF,CAAC,CAAC;QACH,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,4BAA4B,CAAC,CAAC,CAAC;IACtE,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,wEAAwE,EAAE,KAAK,IAAI,EAAE;QACtF,MAAM,UAAU,GAAG;YACjB;gBACE,GAAG,EAAE,gCAAgC;gBACrC,QAAQ,EAAE,kBAAkB;gBAC5B,KAAK,EAAE,0BAA0B,CAAC,4BAA4B,CAAC;aAChE;SACF,CAAC;QACF,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,cAAc,CAAC,UAAU,CAAC,CAAC;QAC5D,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC;QACnC,0DAA0D;QAC1D,OAAO,UAAU,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,gBAAgB,CAAC;QAChE,OAAO,UAAU,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC;QACxD,OAAO,UAAU,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC;QACvD,OAAO,UAAU,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC;QACzD,WAAW;QACX,MAAM,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC;YAChD;gBACE,GAAG,EAAE,gCAAgC;gBACrC,QAAQ,EAAE,kBAAkB;gBAC5B,OAAO,EAAE;oBACP,KAAK,EAAE;wBACL,IAAI,EAAE,kBAAkB;wBACxB,gBAAgB,EAAE,QAAQ;qBAC3B;oBACD,gBAAgB,EAAE;wBAChB,IAAI,EAAE,gBAAgB;qBACvB;iBACF;aACF;SACF,CAAC,CAAC;QACH,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,gCAAgC,CAAC,CAAC,CAAC;IAC1E,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,oEAAoE,EAAE,KAAK,IAAI,EAAE;QAClF,MAAM,UAAU,GAAG;YACjB;gBACE,GAAG,EAAE,wBAAwB;gBAC7B,QAAQ,EAAE,gBAAgB;gBAC1B,KAAK,EAAE,0BAA0B,CAAC,6BAA6B,CAAC;aACjE;SACF,CAAC;QACF,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,cAAc,CAAC,UAAU,CAAC,CAAC;QAC5D,MAAM,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC;YAChD;gBACE,GAAG,EAAE,wBAAwB;gBAC7B,QAAQ,EAAE,gBAAgB;aAC3B;SACF,CAAC,CAAC;QACH,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,wBAAwB,CAAC,CAAC,CAAC;IAClE,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,6FAA6F,EAAE,KAAK,IAAI,EAAE;QAC3G,MAAM,UAAU,GAAG;YACjB;gBACE,GAAG,EAAE,yCAAyC;gBAC9C,QAAQ,EAAE,gBAAgB;aAC3B;SACF,CAAC;QACF,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,cAAc,CAAC,UAAU,CAAC,CAAC;QAC5D,MAAM,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC;YAChD;gBACE,GAAG,EAAE,yCAAyC;gBAC9C,QAAQ,EAAE,gBAAgB;aAC3B;SACF,CAAC,CAAC;QACH,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;IAC1C,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,yEAAyE,EAAE,KAAK,IAAI,EAAE;QACvF,MAAM,UAAU,GAAG;YACjB;gBACE,GAAG,EAAE,wBAAwB;gBAC7B,QAAQ,EAAE,gBAAgB;gBAC1B,KAAK,EAAE,0BAA0B,CAAC,6BAA6B,CAAC;aACjE;YACD;gBACE,GAAG,EAAE,+BAA+B;gBACpC,QAAQ,EAAE,2BAA2B;gBACrC,KAAK,EAAE,0BAA0B,CAAC,wCAAwC,CAAC;aAC5E;SACF,CAAC;QACF,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,cAAc,CAAC,UAAU,CAAC,CAAC;QAC5D,MAAM,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC;YAChD;gBACE,GAAG,EAAE,wBAAwB;gBAC7B,QAAQ,EAAE,gBAAgB;aAC3B;YACD;gBACE,GAAG,EAAE,+BAA+B;gBACpC,QAAQ,EAAE,2BAA2B;aACtC;SACF,CAAC,CAAC;QACH,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC;YAClC,wBAAwB;YACxB,+BAA+B;SAChC,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@vitessce/config",
|
|
3
|
-
"version": "4.0.
|
|
3
|
+
"version": "4.0.5",
|
|
4
4
|
"author": "HIDIVE Lab at HMS",
|
|
5
5
|
"homepage": "http://vitessce.io",
|
|
6
6
|
"repository": {
|
|
@@ -16,13 +16,13 @@
|
|
|
16
16
|
"dist-tsc"
|
|
17
17
|
],
|
|
18
18
|
"dependencies": {
|
|
19
|
-
"zarrita": "0.
|
|
20
|
-
"@zarrita/storage": "0.
|
|
19
|
+
"zarrita": "0.7.5",
|
|
20
|
+
"@zarrita/storage": "0.2.0",
|
|
21
21
|
"fetch-jsonp": "^1.4.0",
|
|
22
|
-
"@vitessce/
|
|
23
|
-
"@vitessce/
|
|
24
|
-
"@vitessce/zarr-utils": "4.0.
|
|
25
|
-
"@vitessce/
|
|
22
|
+
"@vitessce/utils": "4.0.5",
|
|
23
|
+
"@vitessce/constants-internal": "4.0.5",
|
|
24
|
+
"@vitessce/zarr-utils": "4.0.5",
|
|
25
|
+
"@vitessce/globals": "4.0.5"
|
|
26
26
|
},
|
|
27
27
|
"scripts": {
|
|
28
28
|
"bundle": "pnpm exec vite build -c ../../scripts/vite.config.mjs",
|
|
@@ -70,6 +70,9 @@ export class AnnDataAutoConfig extends AbstractAutoConfig {
|
|
|
70
70
|
|
|
71
71
|
// eslint-disable-next-line class-methods-use-this
|
|
72
72
|
addViews(vc, dataset, layoutOption) {
|
|
73
|
-
|
|
73
|
+
const geneList = vc.addView(dataset, 'featureList');
|
|
74
|
+
|
|
75
|
+
// Layout.
|
|
76
|
+
vc.layout(geneList);
|
|
74
77
|
}
|
|
75
78
|
}
|
package/src/generate-config.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
// TODO: ts-check
|
|
2
2
|
|
|
3
3
|
import { FileType } from '@vitessce/constants-internal';
|
|
4
|
-
import {
|
|
4
|
+
import { withConsolidatedMetadata, extendStore, FetchStore, open as zarrOpen } from 'zarrita';
|
|
5
5
|
// eslint-disable-next-line import/no-unresolved
|
|
6
6
|
import ZipFileStore from '@zarrita/storage/zip';
|
|
7
7
|
import { transformEntriesForZipFileStore } from '@vitessce/zarr-utils';
|
|
@@ -160,11 +160,17 @@ export async function parsedUrlToZmetadata(parsedUrl) {
|
|
|
160
160
|
|
|
161
161
|
try {
|
|
162
162
|
try {
|
|
163
|
-
store = await
|
|
163
|
+
store = await extendStore(
|
|
164
|
+
initialStore,
|
|
165
|
+
s => withConsolidatedMetadata(s),
|
|
166
|
+
);
|
|
164
167
|
} catch {
|
|
165
168
|
// Try again with `zmetadata` rather than `.zmetadata`.
|
|
166
169
|
// Reference: https://github.com/zarr-developers/zarr-python/issues/1121
|
|
167
|
-
store = await
|
|
170
|
+
store = await extendStore(
|
|
171
|
+
initialStore,
|
|
172
|
+
s => withConsolidatedMetadata(s, { metadataKey: 'zmetadata' }),
|
|
173
|
+
);
|
|
168
174
|
}
|
|
169
175
|
// Is consolidated.
|
|
170
176
|
const contents = store.contents();
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { describe, it, expect } from 'vitest';
|
|
2
2
|
import { createStoreFromMapContents } from '@vitessce/zarr-utils';
|
|
3
|
-
import {
|
|
3
|
+
import { withConsolidatedMetadata, extendStore } from 'zarrita';
|
|
4
4
|
import { parseUrlsFromString, parsedUrlToZmetadata, generateConfig } from './generate-config.js';
|
|
5
5
|
import spatialdataMouseLiverFixture from './json-fixtures/mouse_liver.spatialdata.json';
|
|
6
6
|
import anndataMouseLiverFixture from './json-fixtures/mouse_liver.anndata.json';
|
|
@@ -53,7 +53,7 @@ describe('generateConfig', () => {
|
|
|
53
53
|
|
|
54
54
|
it('store for SpatialData object supports withConsolidated', async () => {
|
|
55
55
|
const initialStore = createStoreFromMapContents(spatialdataMouseLiverFixture);
|
|
56
|
-
const store = await
|
|
56
|
+
const store = await extendStore(initialStore, s => withConsolidatedMetadata(s, { metadataKey: 'zmetadata' }));
|
|
57
57
|
|
|
58
58
|
expect(store.contents().length).toEqual(41);
|
|
59
59
|
});
|