@vitessce/biomarker-select 3.5.1 → 3.5.3

package/dist-tsc/default-async-functions.d.ts

@@ -20,6 +20,27 @@ export function autocompleteFeature({ queryClient }: {
 export function transformFeature({ queryClient }: {
     queryClient: QueryClient;
 }, node: KgNode, targetModality: TargetModalityType): Promise<KgNode[]>;
+/**
+ * @satisfies {GetAlternativeTermsFunc}
+ * @param {object} ctx
+ * @param {QueryClient} ctx.queryClient
+ * @param {string} curie
+ * @returns {Promise<string[]>} A list of curie strings.
+ */
+export function getAlternativeTerms({ queryClient }: {
+    queryClient: QueryClient;
+}, curie: string): Promise<string[]>;
+/**
+ * @satisfies {GetTermMappingFunc}
+ * @param {object} ctx
+ * @param {QueryClient} ctx.queryClient
+ * @param {string} keyCuriePrefix
+ * @param {string} valCuriePrefix
+ * @returns {Promise<Map<string, string>>} A mapping between curie strings.
+ */
+export function getTermMapping({ queryClient }: {
+    queryClient: QueryClient;
+}, keyCuriePrefix: string, valCuriePrefix: string): Promise<Map<string, string>>;
 import type { QueryClient } from '@tanstack/react-query';
 import type { TargetModalityType } from '@vitessce/types';
 import type { KgNode } from '@vitessce/types';

package/dist-tsc/default-async-functions.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"default-async-functions.d.ts","sourceRoot":"","sources":["../src/default-async-functions.js"],"names":[],"mappings":"AA4GA;;;;;;;GAOG;AACH,qDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,WAAQ,MAAM,kBACN,IAAI,GAAG,kBAAkB,GACvB,OAAO,CAAC,MAAM,EAAE,CAAC,CAiB7B;AAeD;;;;;;;GAOG;AACH,kDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,QAAQ,MAAM,kBACN,kBAAkB,GAChB,OAAO,CAAC,MAAM,EAAE,CAAC,CAkC7B;iCAlLsD,uBAAuB;wCADyB,iBAAiB;4BAAjB,iBAAiB"}
+{"version":3,"file":"default-async-functions.d.ts","sourceRoot":"","sources":["../src/default-async-functions.js"],"names":[],"mappings":"AAqHA;;;;;;;GAOG;AACH,qDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,WAAQ,MAAM,kBACN,IAAI,GAAG,kBAAkB,GACvB,OAAO,CAAC,MAAM,EAAE,CAAC,CAiB7B;AAeD;;;;;;;GAOG;AACH,kDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,QAAQ,MAAM,kBACN,kBAAkB,GAChB,OAAO,CAAC,MAAM,EAAE,CAAC,CAkC7B;AAED;;;;;;GAMG;AACH,qDAJG;IAAyB,WAAW,EAA5B,WAAW;CACnB,SAAQ,MAAM,GACJ,OAAO,CAAC,MAAM,EAAE,CAAC,CA2B7B;AAED;;;;;;;GAOG;AACH,gDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,kBAAQ,MAAM,kBACN,MAAM,GACJ,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAoBxC;iCAzPsD,uBAAuB;wCADsE,iBAAiB;4BAAjB,iBAAiB"}

package/dist-tsc/default-async-functions.js

@@ -4,9 +4,10 @@
 import { csvParse } from 'd3-dsv';
 // eslint-disable-next-line import/no-unresolved
 import Fuse from 'fuse.js/basic';
-/** @import { KgNode, KgEdge, TargetModalityType, AutocompleteFeatureFunc, TransformFeatureFunc } from '@vitessce/types' */
+/** @import { KgNode, KgEdge, TargetModalityType, AutocompleteFeatureFunc, TransformFeatureFunc, GetAlternativeTermsFunc, GetTermMappingFunc } from '@vitessce/types' */
 /** @import { QueryClient, QueryFunctionContext } from '@tanstack/react-query' */
 const KG_BASE_URL = 'https://storage.googleapis.com/vitessce-demo-data/enrichr-kg-september-2023';
+const ENSG_TO_GENE_SYMBOL_URL = 'https://vitessce-resources.s3.us-east-2.amazonaws.com/genes_filtered.json';
 /**
  * @returns {Promise<KgNode[]>}
  */
@@ -55,6 +56,13 @@ function loadPathwayNodes() {
         }));
     });
 }
+/**
+ * @returns {Promise<Record<string,string>>}
+ */
+function loadEnsgToGeneSymbolMapping() {
+    return fetch(ENSG_TO_GENE_SYMBOL_URL)
+        .then(res => res.json());
+}
 // Parent app can pass in queryClient
 // (to every async function) so that functions can call .fetchQuery
 // Reference: https://tanstack.com/query/latest/docs/reference/QueryClient#queryclientfetchquery
@@ -166,3 +174,58 @@ export async function transformFeature({ queryClient }, node, targetModality) {
     // TODO: handle other target modalities
     return [];
 }
+/**
+ * @satisfies {GetAlternativeTermsFunc}
+ * @param {object} ctx
+ * @param {QueryClient} ctx.queryClient
+ * @param {string} curie
+ * @returns {Promise<string[]>} A list of curie strings.
+ */
+export async function getAlternativeTerms({ queryClient }, curie) {
+    // Reference: https://registry.identifiers.org/registry/ensembl
+    // Currently, we only map Ensembl gene IDs to gene symbols,
+    // using our own JSON file.
+    // In the future, we can expand this functionality.
+    const inputIsEnsemblGeneId = curie.toUpperCase().startsWith('ENSEMBL:ENSG');
+    if (inputIsEnsemblGeneId) {
+        const idMapping = await queryClient.fetchQuery({
+            queryKey: ['ensgToGeneSymbolMapping'],
+            staleTime: Infinity,
+            queryFn: loadEnsgToGeneSymbolMapping,
+        });
+        // In our current JSON file, the ENSG IDs are not prefixed with 'ENSEMBL:'.
+        const ensemblId = curie.split(':')[1];
+        let geneSymbol = idMapping?.[ensemblId];
+        if (geneSymbol) {
+            if (!geneSymbol.toUpperCase().startsWith('HGNC:')) {
+                // In our current JSON file, the gene symbols are not prefixed with 'HGNC:'.
+                geneSymbol = `HGNC:${geneSymbol}`;
+            }
+            return [geneSymbol];
+        }
+    }
+    return [];
+}
+/**
+ * @satisfies {GetTermMappingFunc}
+ * @param {object} ctx
+ * @param {QueryClient} ctx.queryClient
+ * @param {string} keyCuriePrefix
+ * @param {string} valCuriePrefix
+ * @returns {Promise<Map<string, string>>} A mapping between curie strings.
+ */
+export async function getTermMapping({ queryClient }, keyCuriePrefix, valCuriePrefix) {
+    if ((keyCuriePrefix.toUpperCase() === 'ENSEMBL' && valCuriePrefix.toUpperCase() === 'HGNC')
+        || (keyCuriePrefix.toUpperCase() === 'HGNC' && valCuriePrefix.toUpperCase() === 'ENSEMBL')) {
+        const idMapping = await queryClient.fetchQuery({
+            queryKey: ['ensgToGeneSymbolMapping'],
+            staleTime: Infinity,
+            queryFn: loadEnsgToGeneSymbolMapping,
+        });
+        const isReversed = (keyCuriePrefix.toUpperCase() === 'HGNC');
+        return new Map(Object.entries(idMapping).map(([key, value]) => (isReversed
+            ? ([`HGNC:${value}`, `ENSEMBL:${key}`])
+            : ([`ENSEMBL:${key}`, `HGNC:${value}`]))));
+    }
+    throw new Error(`Mapping between ${keyCuriePrefix} and ${valCuriePrefix} is not yet implemented.`);
+}

package/dist-tsc/index.d.ts

@@ -1,3 +1,3 @@
 export { BiomarkerSelectSubscriber } from "./BiomarkerSelectSubscriber.js";
-export { autocompleteFeature, transformFeature } from "./default-async-functions.js";
+export { autocompleteFeature, transformFeature, getAlternativeTerms, getTermMapping } from "./default-async-functions.js";
 //# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.js

@@ -1,2 +1,2 @@
 export { BiomarkerSelectSubscriber } from './BiomarkerSelectSubscriber.js';
-export { autocompleteFeature, transformFeature, } from './default-async-functions.js';
+export { autocompleteFeature, transformFeature, getAlternativeTerms, getTermMapping, } from './default-async-functions.js';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/biomarker-select",
-  "version": "3.5.1",
+  "version": "3.5.3",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -24,9 +24,9 @@
     "react-window": "^1.8.10",
     "fuse.js": "^7.0.0",
     "d3-dsv": "^1.1.1",
-    "@vitessce/constants-internal": "3.5.1",
-    "@vitessce/vit-s": "3.5.1",
-    "@vitessce/types": "3.5.1"
+    "@vitessce/constants-internal": "3.5.3",
+    "@vitessce/vit-s": "3.5.3",
+    "@vitessce/types": "3.5.3"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^5.16.4",

package/src/default-async-functions.js

@@ -5,10 +5,11 @@ import { csvParse } from 'd3-dsv';
 // eslint-disable-next-line import/no-unresolved
 import Fuse from 'fuse.js/basic';
 
-/** @import { KgNode, KgEdge, TargetModalityType, AutocompleteFeatureFunc, TransformFeatureFunc } from '@vitessce/types' */
+/** @import { KgNode, KgEdge, TargetModalityType, AutocompleteFeatureFunc, TransformFeatureFunc, GetAlternativeTermsFunc, GetTermMappingFunc } from '@vitessce/types' */
 /** @import { QueryClient, QueryFunctionContext } from '@tanstack/react-query' */
 
 const KG_BASE_URL = 'https://storage.googleapis.com/vitessce-demo-data/enrichr-kg-september-2023';
+const ENSG_TO_GENE_SYMBOL_URL = 'https://vitessce-resources.s3.us-east-2.amazonaws.com/genes_filtered.json';
 
 /**
  * @returns {Promise<KgNode[]>}
@@ -61,6 +62,14 @@ function loadPathwayNodes() {
     });
 }
 
+/**
+ * @returns {Promise<Record<string,string>>}
+ */
+function loadEnsgToGeneSymbolMapping() {
+  return fetch(ENSG_TO_GENE_SYMBOL_URL)
+    .then(res => res.json());
+}
+
 // Parent app can pass in queryClient
 // (to every async function) so that functions can call .fetchQuery
 // Reference: https://tanstack.com/query/latest/docs/reference/QueryClient#queryclientfetchquery
@@ -185,3 +194,65 @@ export async function transformFeature({ queryClient }, node, targetModality) {
   // TODO: handle other target modalities
   return [];
 }
+
+/**
+ * @satisfies {GetAlternativeTermsFunc}
+ * @param {object} ctx
+ * @param {QueryClient} ctx.queryClient
+ * @param {string} curie
+ * @returns {Promise<string[]>} A list of curie strings.
+ */
+export async function getAlternativeTerms({ queryClient }, curie) {
+  // Reference: https://registry.identifiers.org/registry/ensembl
+  // Currently, we only map Ensembl gene IDs to gene symbols,
+  // using our own JSON file.
+  // In the future, we can expand this functionality.
+  const inputIsEnsemblGeneId = curie.toUpperCase().startsWith('ENSEMBL:ENSG');
+
+  if (inputIsEnsemblGeneId) {
+    const idMapping = await queryClient.fetchQuery({
+      queryKey: ['ensgToGeneSymbolMapping'],
+      staleTime: Infinity,
+      queryFn: loadEnsgToGeneSymbolMapping,
+    });
+    // In our current JSON file, the ENSG IDs are not prefixed with 'ENSEMBL:'.
+    const ensemblId = curie.split(':')[1];
+    let geneSymbol = idMapping?.[ensemblId];
+    if (geneSymbol) {
+      if (!geneSymbol.toUpperCase().startsWith('HGNC:')) {
+        // In our current JSON file, the gene symbols are not prefixed with 'HGNC:'.
+        geneSymbol = `HGNC:${geneSymbol}`;
+      }
+      return [geneSymbol];
+    }
+  }
+  return [];
+}
+
+/**
+ * @satisfies {GetTermMappingFunc}
+ * @param {object} ctx
+ * @param {QueryClient} ctx.queryClient
+ * @param {string} keyCuriePrefix
+ * @param {string} valCuriePrefix
+ * @returns {Promise<Map<string, string>>} A mapping between curie strings.
+ */
+export async function getTermMapping({ queryClient }, keyCuriePrefix, valCuriePrefix) {
+  if (
+    (keyCuriePrefix.toUpperCase() === 'ENSEMBL' && valCuriePrefix.toUpperCase() === 'HGNC')
+    || (keyCuriePrefix.toUpperCase() === 'HGNC' && valCuriePrefix.toUpperCase() === 'ENSEMBL')
+  ) {
+    const idMapping = await queryClient.fetchQuery({
+      queryKey: ['ensgToGeneSymbolMapping'],
+      staleTime: Infinity,
+      queryFn: loadEnsgToGeneSymbolMapping,
+    });
+    const isReversed = (keyCuriePrefix.toUpperCase() === 'HGNC');
+    return new Map(Object.entries(idMapping).map(([key, value]) => (
+      isReversed
+        ? ([`HGNC:${value}`, `ENSEMBL:${key}`])
+        : ([`ENSEMBL:${key}`, `HGNC:${value}`])
+    )));
+  }
+  throw new Error(`Mapping between ${keyCuriePrefix} and ${valCuriePrefix} is not yet implemented.`);
+}

package/src/index.js

@@ -2,4 +2,6 @@ export { BiomarkerSelectSubscriber } from './BiomarkerSelectSubscriber.js';
 export {
   autocompleteFeature,
   transformFeature,
+  getAlternativeTerms,
+  getTermMapping,
 } from './default-async-functions.js';