jbrowse-plugin-msaview 2.7.2 → 2.7.3

package/dist/utils/blastCache.d.ts

@@ -29,6 +29,5 @@ export declare function saveBlastResult({ proteinSequence, blastDatabase, blastP
     transcriptName?: string;
     geneName?: string;
 }): Promise<CachedBlastResult>;
-export declare function getAllCachedResults(): Promise<any[]>;
+export declare function getAllCachedResults(): Promise<CachedBlastResult[]>;
 export declare function deleteCachedResult(id: string): Promise<void>;
-export declare function clearAllCachedResults(): Promise<void>;

package/dist/utils/blastCache.js

@@ -1,24 +1,15 @@
-import { openDB } from 'idb';
+import { createDbOpener } from './idb';
 const DB_NAME = 'jbrowse-msaview-blast-cache';
 const STORE_NAME = 'blast-results';
 const DB_VERSION = 2;
-let dbPromise;
-function getDB() {
-    dbPromise ??= openDB(DB_NAME, DB_VERSION, {
-        upgrade(db, oldVersion) {
-            if (oldVersion < 2 && db.objectStoreNames.contains(STORE_NAME)) {
-                db.deleteObjectStore(STORE_NAME);
-            }
-            if (!db.objectStoreNames.contains(STORE_NAME)) {
-                db.createObjectStore(STORE_NAME, { keyPath: 'id' });
-            }
-        },
-    }).catch((e) => {
-        dbPromise = undefined;
-        throw e;
-    });
-    return dbPromise;
-}
+const getDB = createDbOpener(DB_NAME, DB_VERSION, (db, oldVersion) => {
+    if (oldVersion < 2 && db.objectStoreNames.contains(STORE_NAME)) {
+        db.deleteObjectStore(STORE_NAME);
+    }
+    if (!db.objectStoreNames.contains(STORE_NAME)) {
+        db.createObjectStore(STORE_NAME, { keyPath: 'id' });
+    }
+});
 function createCacheKey(proteinSequence, blastDatabase, blastProgram, msaAlgorithm, transcriptId) {
     const idPart = transcriptId ? `:${transcriptId}` : '';
     // msaAlgorithm is part of the key because the stored msa/tree are produced by
@@ -57,7 +48,3 @@ export async function deleteCachedResult(id) {
     const db = await getDB();
     await db.delete(STORE_NAME, id);
 }
-export async function clearAllCachedResults() {
-    const db = await getDB();
-    await db.clear(STORE_NAME);
-}

package/dist/utils/domainCache.js

@@ -1,21 +1,12 @@
-import { openDB } from 'idb';
+import { createDbOpener } from './idb';
 const DB_NAME = 'jbrowse-msaview-domain-cache';
 const STORE_NAME = 'domains';
 const DB_VERSION = 1;
-let dbPromise;
-function getDB() {
-    dbPromise ??= openDB(DB_NAME, DB_VERSION, {
-        upgrade(db) {
-            if (!db.objectStoreNames.contains(STORE_NAME)) {
-                db.createObjectStore(STORE_NAME, { keyPath: 'accession' });
-            }
-        },
-    }).catch((e) => {
-        dbPromise = undefined;
-        throw e;
-    });
-    return dbPromise;
-}
+const getDB = createDbOpener(DB_NAME, DB_VERSION, db => {
+    if (!db.objectStoreNames.contains(STORE_NAME)) {
+        db.createObjectStore(STORE_NAME, { keyPath: 'accession' });
+    }
+});
 export async function getCachedDomains(accessions) {
     const db = await getDB();
     const tx = db.transaction(STORE_NAME, 'readonly');

package/dist/utils/idb.d.ts

@@ -0,0 +1,12 @@
+import type { DBSchema, IDBPDatabase, OpenDBCallbacks } from 'idb';
+/**
+ * Memoized `openDB` for a typed schema, shared by this plugin's caches.
+ *
+ * The connection promise is cached so callers share one connection, and dropped
+ * again if the open fails, so a later call retries instead of replaying the same
+ * rejection forever (IndexedDB is unavailable in some private-browsing modes).
+ *
+ * Passing a DBSchema is what keeps `get`/`getAll` from returning `any`: with an
+ * untyped database every cached record reaches the UI unchecked.
+ */
+export declare function createDbOpener<T extends DBSchema>(name: string, version: number, upgrade: OpenDBCallbacks<T>['upgrade']): () => Promise<IDBPDatabase<T>>;

package/dist/utils/idb.js

@@ -0,0 +1,21 @@
+import { openDB } from 'idb';
+/**
+ * Memoized `openDB` for a typed schema, shared by this plugin's caches.
+ *
+ * The connection promise is cached so callers share one connection, and dropped
+ * again if the open fails, so a later call retries instead of replaying the same
+ * rejection forever (IndexedDB is unavailable in some private-browsing modes).
+ *
+ * Passing a DBSchema is what keeps `get`/`getAll` from returning `any`: with an
+ * untyped database every cached record reaches the UI unchecked.
+ */
+export function createDbOpener(name, version, upgrade) {
+    let dbPromise;
+    return () => {
+        dbPromise ??= openDB(name, version, { upgrade }).catch((e) => {
+            dbPromise = undefined;
+            throw e;
+        });
+        return dbPromise;
+    };
+}

package/dist/utils/taxonomyNames.js

@@ -1,23 +1,15 @@
-import { openDB } from 'idb';
 import { efetchUrl } from './eutils';
+import { textfetch } from './fetch';
+import { createDbOpener } from './idb';
 const DB_NAME = 'jbrowse-msaview-taxonomy-cache';
 const STORE_NAME = 'common-names';
 const DB_VERSION = 2;
-let dbPromise;
-function getDB() {
-    dbPromise ??= openDB(DB_NAME, DB_VERSION, {
-        upgrade(db) {
-            if (db.objectStoreNames.contains(STORE_NAME)) {
-                db.deleteObjectStore(STORE_NAME);
-            }
-            db.createObjectStore(STORE_NAME, { keyPath: 'taxid' });
-        },
-    }).catch((e) => {
-        dbPromise = undefined;
-        throw e;
-    });
-    return dbPromise;
-}
+const getDB = createDbOpener(DB_NAME, DB_VERSION, db => {
+    if (db.objectStoreNames.contains(STORE_NAME)) {
+        db.deleteObjectStore(STORE_NAME);
+    }
+    db.createObjectStore(STORE_NAME, { keyPath: 'taxid' });
+});
 async function getCachedTaxonomies(taxids) {
     const db = await getDB();
     const tx = db.transaction(STORE_NAME, 'readonly');
@@ -59,8 +51,11 @@ export async function fetchTaxonomyInfo(taxids) {
         const batch = uncachedTaxids.slice(i, i + batchSize);
         const idsParam = batch.join(',');
         try {
-            const response = await fetch(efetchUrl({ db: 'taxonomy', id: idsParam, retmode: 'xml' }));
-            const text = await response.text();
+            // textfetch rather than a bare fetch: an NCBI 429/5xx returns an HTML
+            // error body that the regexes below silently find nothing in, so without
+            // the status check a throttled batch looks like "these taxa have no
+            // names" instead of reporting why
+            const text = await textfetch(efetchUrl({ db: 'taxonomy', id: idsParam, retmode: 'xml' }));
             // Build a map of taxid -> taxon block by finding Taxon elements.
             // Prefer entries with <LineageEx> (full top-level entries) over nested
             // entries inside another taxon's LineageEx

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.7.2";
+export declare const version = "2.7.3";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.7.2';
+export const version = '2.7.3';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.7.2",
+  "version": "2.7.3",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -51,7 +51,7 @@
     "puppeteer": "^25.3.0",
     "react": "^19.2.8",
     "react-dom": "^19.2.8",
-    "react-msaview": "^5.6.3",
+    "react-msaview": "^5.7.0",
     "rimraf": "^6.1.3",
     "rxjs": "^7.8.2",
     "serve": "^14.2.6",

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -23,14 +23,12 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({
   // The persistent click selection always shows. The hover codon is suppressed
   // while hovering the LGV — GenomeMouseoverHighlight handles the single-bp
   // display in that case, so we don't stack a wider codon band on top of it.
-  const clickHighlight = msaView?.connectedClickHighlight
-  const hoverHighlight = hasHoverPosition(hovered)
-    ? undefined
-    : msaView?.connectedHoverHighlight
-  const highlights = [clickHighlight, hoverHighlight].filter(
-    (r): r is { refName: string; start: number; end: number } =>
-      r !== undefined,
-  )
+  const highlights = [
+    ...(msaView?.connectedClickHighlights ?? []),
+    ...(hasHoverPosition(hovered)
+      ? []
+      : (msaView?.connectedHoverHighlights ?? [])),
+  ]
 
   return highlights.length ? (
     <MsaToGenomeHighlightRenderer model={model} highlights={highlights} />

package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx

@@ -117,7 +117,7 @@ const CachedBlastResults = observer(function ({
             }
           }}
         >
-          Clear All
+          Clear results for this gene
         </Button>
       </div>
       <List dense className={classes.resultList}>

package/src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts

@@ -1,7 +1,6 @@
 import useSWR from 'swr'
 
 import {
-  clearAllCachedResults,
   deleteCachedResult,
   getAllCachedResults,
 } from '../../../utils/blastCache'
@@ -30,8 +29,11 @@ export function useCachedBlastResults(geneIds: string[]) {
     )
   }
 
+  // deletes only what this hook listed, i.e. the results for these gene ids.
+  // The list the user is looking at is gene-scoped, so a store-wide clear here
+  // would silently throw away every other gene's cached alignments too
   const handleClearAll = async () => {
-    await clearAllCachedResults()
+    await Promise.all((results ?? []).map(r => deleteCachedResult(r.id)))
     await mutate([], false)
   }
 

package/src/MsaViewPanel/doLaunchBlast.ts

@@ -25,36 +25,29 @@ export async function doLaunchBlast({
   } = self.blastParams!
   const cleanedSeq = cleanProteinSequence(proteinSequence)
 
-  let hits
-  let rid: string
+  const onProgress = (arg: string) => {
+    self.setProgress(arg)
+  }
+
   if (existingRid) {
+    // publish it before the first poll so the view can link out to NCBI while
+    // the job is still running
     self.setRid(existingRid)
-    const result = await queryBlastFromRid({
-      rid: existingRid,
-      baseUrl,
-      onProgress: arg => {
-        self.setProgress(arg)
-      },
-    })
-    hits = result.hits
-    rid = result.rid
-  } else {
-    const result = await queryBlast({
-      query: cleanedSeq,
-      blastDatabase,
-      blastProgram,
-      baseUrl,
-      onProgress: arg => {
-        self.setProgress(arg)
-      },
-      onRid: r => {
-        self.setRid(r)
-      },
-    })
-    hits = result.hits
-    rid = result.rid
   }
 
+  const { hits, rid } = existingRid
+    ? await queryBlastFromRid({ rid: existingRid, baseUrl, onProgress })
+    : await queryBlast({
+        query: cleanedSeq,
+        blastDatabase,
+        blastProgram,
+        baseUrl,
+        onProgress,
+        onRid: r => {
+          self.setRid(r)
+        },
+      })
+
   self.setProgress('Fetching species taxonomy info...')
   const taxids = hits
     .map(h => h.description[0]?.taxid)
@@ -80,9 +73,7 @@ export async function doLaunchBlast({
   const result = await launchMSA({
     algorithm: msaAlgorithm,
     sequence: [`>QUERY\n${cleanedSeq}`, ...sequences].join('\n'),
-    onProgress: arg => {
-      self.setProgress(arg)
-    },
+    onProgress,
   })
 
   const treeMetadataJson = JSON.stringify(treeMetadata)

package/src/MsaViewPanel/genomeToMSA.test.ts

@@ -91,8 +91,9 @@ describe('genomeToMSA', () => {
 
       const result = genomeToMSA({ model })
 
-      // coord 1005 - start 1000 = ungapped position 5
-      expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 5)
+      // hover coord 1005 is 1-based, so the 0-based genome position is 1004,
+      // which is ungapped position 4 of a region starting at 1000
+      expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 4)
       expect(result).toBe(5)
     })
 
@@ -125,10 +126,11 @@ describe('genomeToMSA', () => {
     })
 
     test('returns undefined when hover coord is before mafRegion start', () => {
+      // 1-based coord 1000 is the 0-based base 999, one before the region
       mockGetSession.mockReturnValue({
         hovered: {
           hoverFeature: {},
-          hoverPosition: { coord: 999, refName: 'chr1' },
+          hoverPosition: { coord: 1000, refName: 'chr1' },
         },
       } as any)
 
@@ -153,10 +155,11 @@ describe('genomeToMSA', () => {
     })
 
     test('returns undefined when hover coord is at or after mafRegion end', () => {
+      // 1-based coord 1011 is the 0-based base 1010, one past the region
       mockGetSession.mockReturnValue({
         hovered: {
           hoverFeature: {},
-          hoverPosition: { coord: 1010, refName: 'chr1' },
+          hoverPosition: { coord: 1011, refName: 'chr1' },
         },
       } as any)
 
@@ -223,7 +226,9 @@ describe('genomeToMSA', () => {
       const model = {
         querySeqName: 'QUERY',
         transcriptToMsaMap: {
-          g2p: { 1005: 10 },
+          refName: 'chr1',
+          // g2p is keyed by 0-based genome position, the hover coord is 1-based
+          g2p: { 1004: 10 },
         },
         mafRegion: undefined,
         connectedView: { initialized: true },
@@ -236,6 +241,32 @@ describe('genomeToMSA', () => {
       expect(result).toBe(10)
     })
 
+    test('returns undefined when the hover is on another refName', () => {
+      // session.hovered is global, so a hover on an unrelated chromosome can
+      // carry a coordinate that happens to be a g2p key
+      mockGetSession.mockReturnValue({
+        hovered: {
+          hoverFeature: {},
+          hoverPosition: { coord: 1005, refName: 'chr2' },
+        },
+      } as any)
+
+      const mockSeqPosToVisibleCol = vi.fn()
+      const model = {
+        querySeqName: 'QUERY',
+        transcriptToMsaMap: {
+          refName: 'chr1',
+          g2p: { 1004: 10 },
+        },
+        mafRegion: undefined,
+        connectedView: { initialized: true },
+        seqPosToVisibleCol: mockSeqPosToVisibleCol,
+      } as any
+
+      expect(genomeToMSA({ model })).toBeUndefined()
+      expect(mockSeqPosToVisibleCol).not.toHaveBeenCalled()
+    })
+
     test('returns undefined when g2p has no mapping for coord', () => {
       mockGetSession.mockReturnValue({
         hovered: {
@@ -247,7 +278,8 @@ describe('genomeToMSA', () => {
       const model = {
         querySeqName: 'QUERY',
         transcriptToMsaMap: {
-          g2p: { 1000: 0 }, // No entry for 1005
+          refName: 'chr1',
+          g2p: { 1000: 0 }, // No entry for 1004
         },
         mafRegion: undefined,
         connectedView: { initialized: true },

package/src/MsaViewPanel/genomeToMSA.ts

@@ -12,22 +12,30 @@ export function genomeToMSA({ model }: { model: JBrowsePluginMsaViewModel }) {
     return undefined
   }
 
-  const { coord: hoverCoord, refName } = hovered.hoverPosition
+  const { coord, refName } = hovered.hoverPosition
+
+  // hoverPosition.coord is a 1-based display coordinate (core's pxToBp adds the
+  // +1), while g2p and mafRegion are keyed by 0-based genome position
+  const genomePos = coord - 1
 
   if (mafRegion) {
     if (
       refName !== mafRegion.refName ||
       !connectedView.assemblyNames.includes(mafRegion.assemblyName) ||
-      hoverCoord < mafRegion.start ||
-      hoverCoord >= mafRegion.end
+      genomePos < mafRegion.start ||
+      genomePos >= mafRegion.end
     ) {
       return undefined
     }
-    return model.seqPosToVisibleCol(querySeqName, hoverCoord - mafRegion.start)
+    return model.seqPosToVisibleCol(querySeqName, genomePos - mafRegion.start)
   }
 
-  if (transcriptToMsaMap) {
-    const seqPos = transcriptToMsaMap.g2p[hoverCoord]
+  // session.hovered is global -- set by whichever LinearGenomeView the cursor
+  // was last over, on any assembly -- so the refName gate is load bearing:
+  // without it the same numeric coordinate on an unrelated chromosome matches a
+  // g2p key and lights up a column for a different locus
+  if (refName === transcriptToMsaMap?.refName) {
+    const seqPos = transcriptToMsaMap.g2p[genomePos]
     if (seqPos !== undefined) {
       return model.seqPosToVisibleCol(querySeqName, seqPos)
     }

package/src/MsaViewPanel/model.ts

@@ -19,7 +19,10 @@ import {
   storeDataToIndexedDB,
   syncGenomeHoverToMsaColumn,
 } from './afterCreateAutoruns'
-import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
+import {
+  msaCoordToGenomeCoord,
+  msaCoordToGenomeRegions,
+} from './msaCoordToGenomeCoord'
 
 import type { MafRegion, MsaViewInitState } from './types'
 import type {
@@ -188,35 +191,37 @@ export default function stateModelFactory() {
     .views(self => ({
       /**
        * #getter
-       * Genome region under the current MSA hover column. Suppressed on the LGV
+       * Genome regions under the current MSA hover column. Suppressed on the LGV
        * while it's being hovered (GenomeMouseoverHighlight shows the crisp 1bp
        * marker there instead of this wider codon band).
        */
-      get connectedHoverHighlight(): IRegion | undefined {
+      get connectedHoverHighlights(): IRegion[] {
         const { mouseCol } = self
         return mouseCol === undefined
-          ? undefined
-          : msaCoordToGenomeCoord({ model: self, coord: mouseCol })
+          ? []
+          : msaCoordToGenomeRegions({ model: self, coord: mouseCol })
       },
       /**
        * #getter
-       * Genome region under the persistent MSA click selection. Shown
+       * Genome regions under the persistent MSA click selection. Shown
        * regardless of LGV hover, so hovering the genome doesn't hide it.
        */
-      get connectedClickHighlight(): IRegion | undefined {
+      get connectedClickHighlights(): IRegion[] {
         const { mouseClickCol } = self
         return mouseClickCol === undefined
-          ? undefined
-          : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
+          ? []
+          : msaCoordToGenomeRegions({ model: self, coord: mouseClickCol })
       },
       /**
        * #getter
+       * cross-plugin contract: jbrowse-plugin-mafviewer reads this off the view
+       * to draw the same highlights in its own display
        */
       get connectedHighlights(): IRegion[] {
         return [
-          this.connectedHoverHighlight,
-          this.connectedClickHighlight,
-        ].filter((r): r is IRegion => r !== undefined)
+          ...this.connectedHoverHighlights,
+          ...this.connectedClickHighlights,
+        ]
       },
     }))