jbrowse-plugin-msaview 2.7.1 → 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/utils/useLocalStorage.d.ts

@@ -0,0 +1 @@
+export declare function useLocalStorage<T>(key: string, initialValue: T): readonly [T, (value: T) => void];

package/dist/utils/useLocalStorage.js

@@ -0,0 +1,29 @@
+import { useState } from 'react';
+// Vendored rather than imported from `@jbrowse/core/util`: that barrel is
+// host-provided, and a barrel split dropped this export, making the BLAST panel
+// throw "(0, PR.useLocalStorage) is not a function" on hosts built during that
+// window. Same failure mode as `defaultCodonTable`; keeping our own copy takes
+// this plugin out of the whack-a-mole.
+function readLocalStorage(key, initialValue) {
+    try {
+        const item = globalThis.localStorage.getItem(key);
+        return item === null ? initialValue : JSON.parse(item);
+    }
+    catch (error) {
+        console.error(error);
+        return initialValue;
+    }
+}
+export function useLocalStorage(key, initialValue) {
+    const [storedValue, setStoredValue] = useState(() => readLocalStorage(key, initialValue));
+    const setValue = (value) => {
+        setStoredValue(value);
+        try {
+            globalThis.localStorage.setItem(key, JSON.stringify(value));
+        }
+        catch (error) {
+            console.error(error);
+        }
+    };
+    return [storedValue, setValue];
+}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.7.1";
+export declare const version = "2.7.3";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.7.1';
+export const version = '2.7.3';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.7.1",
+  "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",
@@ -74,7 +74,9 @@
     "test:setup:version": "node scripts/test-versions.mjs setup",
     "test:versions": "node scripts/test-versions.mjs run",
     "test:version": "node scripts/test-versions.mjs run",
-    "preversion": "pnpm lint",
+    "host-compat": "node scripts/host-compat-probe.mjs --bundle dist/jbrowse-plugin-msaview.umd.production.min.js",
+    "check-ci": "node scripts/require-green-ci.mjs",
+    "preversion": "pnpm check-ci && pnpm lint && pnpm build && pnpm host-compat",
     "version": "node -e \"console.log('export const version = \\'' + require('./package.json').version + '\\'')\" > src/version.ts && git add src/version.ts",
     "postversion": "git push --follow-tags"
   }

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/NCBIBlastPanel.tsx

@@ -1,6 +1,5 @@
 import React, { useState } from 'react'
 
-import { useLocalStorage } from '@jbrowse/core/util'
 import SettingsIcon from '@mui/icons-material/Settings'
 import { IconButton } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
@@ -11,6 +10,7 @@ import NCBIBlastMethodSelector from './NCBIBlastMethodSelector'
 import NCBIBlastRIDPanel from './NCBIBlastRIDPanel'
 import NCBISettingsDialog from './NCBISettingsDialog'
 import { BASE_BLAST_URL } from './consts'
+import { useLocalStorage } from '../../../utils/useLocalStorage'
 
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 

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/LaunchMsaView/components/calculateProteinSequence.ts

@@ -1,35 +1,39 @@
-import {
-  dedupe,
-  defaultCodonTable,
-  generateCodonTable,
-  revcom,
-} from '@jbrowse/core/util'
+import { dedupe, revcom } from '@jbrowse/core/util'
+import { convertCodingSequenceToPeptides } from '@jbrowse/core/util/convertCodingSequenceToPeptides'
+
+import { getGeneticCode, parseTranslTable } from './geneticCodes'
 
 import type { Feat } from './types'
 import type { Feature } from '@jbrowse/core/util'
 
-// pure constant: the standard codon table never varies, so build it once rather
-// than on every translation (which runs on every panel re-render)
-const codonTable = generateCodonTable(defaultCodonTable)
-
-export function stitch(subfeats: Feat[], sequence: string) {
-  return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('')
-}
+// `@jbrowse/core/util/convertCodingSequenceToPeptides` is a deep path, so unlike
+// the `@jbrowse/core/util` barrel it is absent from ReExports and gets bundled
+// rather than resolved out of the host's JBrowseExports. That is what makes
+// reusing core's translation safe across every host a config names: this module
+// previously built its codon table at module scope from the barrel's
+// `defaultCodonTable`, and a core build that dropped that export turned it into
+// `Object.keys(undefined)` while the UMD was still evaluating -- the plugin
+// global was never assigned and PluginLoader error-paged the whole app.
 
 export function calculateProteinSequence({
   cds,
   sequence,
+  geneticCodeId,
 }: {
   cds: Feat[]
   sequence: string
+  geneticCodeId?: number
 }) {
-  const str = stitch(cds, sequence)
-  let protein = ''
-  for (let i = 0; i < str.length; i += 3) {
-    // use & symbol for undefined codon, or partial slice
-    protein += codonTable[str.slice(i, i + 3)] ?? '&'
-  }
-  return protein
+  // `starts` is deliberately not passed: @jbrowse/core 4.3.0's signature has no
+  // such parameter, so alternative initiators (GTG under table 11, ATA under
+  // table 2) render as their internal residue rather than M. Core main added it;
+  // pass it here when msaview's @jbrowse/core floor reaches that release.
+  const { codonTable } = getGeneticCode(geneticCodeId)
+  return convertCodingSequenceToPeptides({
+    cds,
+    sequence,
+    codonTable,
+  })
 }
 
 export function revlist(list: Feat[], seqlen: number) {
@@ -62,8 +66,19 @@ export function getProteinSequenceFromFeature({
     feat => `${feat.start}-${feat.end}`,
   )
 
+  // a mitochondrial gene declares e.g. transl_table=2, so it translates with
+  // NCBI table 2 rather than the standard code. GFF3 usually carries the
+  // attribute on the CDS rather than the transcript, so check both.
+  const cdsSubfeature = feature
+    .get('subfeatures')
+    ?.find((f: Feature) => f.get('type')?.toLowerCase() === 'cds')
+  const geneticCodeId =
+    parseTranslTable(feature.get('transl_table')) ??
+    parseTranslTable(cdsSubfeature?.get('transl_table'))
+
   return calculateProteinSequence({
     cds: strand === -1 ? revlist(cds, seq.length) : cds,
     sequence: strand === -1 ? revcom(seq) : seq,
+    geneticCodeId,
   })
 }