jbrowse-plugin-msaview 2.6.6 → 2.6.7

package/dist/utils/blastCache.js

@@ -2,8 +2,9 @@ import { openDB } from 'idb';
 const DB_NAME = 'jbrowse-msaview-blast-cache';
 const STORE_NAME = 'blast-results';
 const DB_VERSION = 2;
-async function getDB() {
-    return openDB(DB_NAME, DB_VERSION, {
+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);
@@ -12,15 +13,22 @@ async function getDB() {
                 db.createObjectStore(STORE_NAME, { keyPath: 'id' });
             }
         },
+    }).catch((e) => {
+        dbPromise = undefined;
+        throw e;
     });
+    return dbPromise;
 }
-function createCacheKey(proteinSequence, blastDatabase, blastProgram, transcriptId) {
+function createCacheKey(proteinSequence, blastDatabase, blastProgram, msaAlgorithm, transcriptId) {
     const idPart = transcriptId ? `:${transcriptId}` : '';
-    return `${blastDatabase}:${blastProgram}${idPart}:${proteinSequence}`;
+    // msaAlgorithm is part of the key because the stored msa/tree are produced by
+    // it — without it, re-running the same query under a different algorithm
+    // overwrites the earlier result and drops it from the history list
+    return `${blastDatabase}:${blastProgram}:${msaAlgorithm}${idPart}:${proteinSequence}`;
 }
 export async function saveBlastResult({ proteinSequence, blastDatabase, blastProgram, msaAlgorithm, msa, tree, treeMetadata, rid, geneId, transcriptId, transcriptName, geneName, }) {
     const db = await getDB();
-    const id = createCacheKey(proteinSequence, blastDatabase, blastProgram, transcriptId);
+    const id = createCacheKey(proteinSequence, blastDatabase, blastProgram, msaAlgorithm, transcriptId);
     const entry = {
         id,
         proteinSequence,

package/dist/utils/domainCache.js

@@ -2,14 +2,19 @@ import { openDB } from 'idb';
 const DB_NAME = 'jbrowse-msaview-domain-cache';
 const STORE_NAME = 'domains';
 const DB_VERSION = 1;
-async function getDB() {
-    return openDB(DB_NAME, DB_VERSION, {
+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;
 }
 export async function getCachedDomains(accessions) {
     const db = await getDB();

package/dist/utils/fetch.d.ts

@@ -2,5 +2,3 @@ export declare function handleFetch(url: string, args?: RequestInit): Promise<Re
 export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
 export declare function jsonfetch<T>(url: string, args?: RequestInit): Promise<T>;
 export declare function timeout(time: number): Promise<unknown>;
-export declare function fetchWithLocalStorageCache<T>(key: string, fetchFn: () => Promise<T>): Promise<T>;
-export declare function unzipfetch(url: string, arg?: RequestInit): Promise<any>;

package/dist/utils/fetch.js

@@ -1,4 +1,3 @@
-import { ungzip } from 'pako-esm2';
 export async function handleFetch(url, args) {
     const response = await fetch(url, args);
     if (!response.ok) {
@@ -17,23 +16,3 @@ export async function jsonfetch(url, args) {
 export function timeout(time) {
     return new Promise(res => setTimeout(res, time));
 }
-export async function fetchWithLocalStorageCache(key, fetchFn) {
-    const cachedData = localStorage.getItem(key);
-    if (cachedData) {
-        try {
-            return JSON.parse(cachedData);
-        }
-        catch (error) {
-            console.error(`Error parsing cached data for ${key}:`, error);
-            // Continue to fetch fresh data if parsing fails
-            localStorage.removeItem(key);
-        }
-    }
-    const data = await fetchFn();
-    localStorage.setItem(key, JSON.stringify(data));
-    return data;
-}
-export async function unzipfetch(url, arg) {
-    const res = await handleFetch(url, arg);
-    return ungzip(await res.arrayBuffer(), { to: 'string' });
-}

package/dist/utils/ncbiDomains.js

@@ -144,9 +144,16 @@ export async function fetchProteinDomains(accessions) {
         }));
         const parsed = parseCddDomains(xml);
         for (const acc of batch) {
-            const matches = parsed.get(acc) ?? [];
-            byAccession.set(acc, matches);
-            toCache.push({ accession: acc, matches });
+            // only cache accessions actually present in the response: a genuinely
+            // domain-less protein comes back as an empty array (cache it), but an
+            // accession the batch omitted comes back undefined — caching [] for it
+            // would permanently hide its domains on later loads (the domain cache
+            // never expires), so leave it uncached to be retried
+            const matches = parsed.get(acc);
+            if (matches !== undefined) {
+                byAccession.set(acc, matches);
+                toCache.push({ accession: acc, matches });
+            }
         }
     }
     if (toCache.length > 0) {

package/dist/utils/taxonomyNames.js

@@ -3,15 +3,20 @@ import { efetchUrl } from './eutils';
 const DB_NAME = 'jbrowse-msaview-taxonomy-cache';
 const STORE_NAME = 'common-names';
 const DB_VERSION = 2;
-async function getDB() {
-    return openDB(DB_NAME, DB_VERSION, {
+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;
 }
 async function getCachedTaxonomies(taxids) {
     const db = await getDB();

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.6.6";
+export declare const version = "2.6.7";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.6.6';
+export const version = '2.6.7';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.6.6",
+  "version": "2.6.7",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -20,7 +20,6 @@
     "@gmod/bgzf-filehandle": "^6.2.0",
     "g2p_mapper": "^2.1.5",
     "idb": "^8.0.3",
-    "pako-esm2": "^2.0.2",
     "react-msaview": "^5.5.0",
     "swr": "^2.4.2"
   },

package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts

@@ -56,7 +56,7 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
 
   async getMSA(id: string) {
     const adapter = await this.configure()
-    const refNames = await adapter.getRefNames()
+    const refNames = await this.getMSARefs()
     const rows = refNames.filter(refName => this.refNameToMsaId(refName) === id)
     return firstValueFrom(
       adapter

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

@@ -11,6 +11,7 @@ export function useCachedBlastResults(geneIds: string[]) {
   const {
     data: results,
     error,
+    isLoading,
     mutate,
   } = useSWR(
     `cached-blast-${geneIds.join(',')}`,
@@ -37,7 +38,7 @@ export function useCachedBlastResults(geneIds: string[]) {
   return {
     results: results ?? [],
     error,
-    isLoading: !results && !error,
+    isLoading,
     handleDelete,
     handleClearAll,
   }

package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx

@@ -70,7 +70,7 @@ const PreLoadedMSA = observer(function ({
     error: msaDataFetchError,
   } = useSWR(
     selectedId && selectedDataset && msaList
-      ? `${selectedDataset.datasetId}-${selectedId}-${msaList.length}-msa`
+      ? `${selectedDataset.datasetId}-${selectedId}-msa`
       : null,
     () =>
       fetchMSA({

package/src/LaunchMsaView/components/calculateProteinSequence.ts

@@ -8,6 +8,10 @@ import {
 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('')
 }
@@ -15,11 +19,9 @@ export function stitch(subfeats: Feat[], sequence: string) {
 export function calculateProteinSequence({
   cds,
   sequence,
-  codonTable,
 }: {
   cds: Feat[]
   sequence: string
-  codonTable: Record<string, string>
 }) {
   const str = stitch(cds, sequence)
   let protein = ''
@@ -63,6 +65,5 @@ export function getProteinSequenceFromFeature({
   return calculateProteinSequence({
     cds: strand === -1 ? revlist(cds, seq.length) : cds,
     sequence: strand === -1 ? revcom(seq) : seq,
-    codonTable: generateCodonTable(defaultCodonTable),
   })
 }

package/src/MsaViewPanel/msaDataStore.ts

@@ -12,15 +12,21 @@ interface StoredMsaData {
   timestamp: number
 }
 
-async function getDB() {
-  return openDB(DB_NAME, DB_VERSION, {
+let dbPromise: ReturnType<typeof openDB> | undefined
+
+function getDB() {
+  dbPromise ??= openDB(DB_NAME, DB_VERSION, {
     upgrade(db) {
       if (!db.objectStoreNames.contains(STORE_NAME)) {
         const store = db.createObjectStore(STORE_NAME, { keyPath: 'id' })
         store.createIndex('timestamp', 'timestamp', { unique: false })
       }
     },
+  }).catch((e: unknown) => {
+    dbPromise = undefined
+    throw e
   })
+  return dbPromise
 }
 
 export function generateDataStoreId() {

package/src/MsaViewPanel/util.ts

@@ -9,30 +9,6 @@ export function hasHoverPosition(
   )
 }
 
-interface AssemblyManagerLike {
-  get: (
-    name: string,
-  ) => { getCanonicalRefName: (r: string) => string | undefined } | undefined
-}
-
-export function getCanonicalRefName({
-  assemblyManager,
-  assemblyNames,
-  refName,
-}: {
-  assemblyManager: AssemblyManagerLike
-  assemblyNames: string[] | undefined
-  refName: string
-}) {
-  const assemblyName = assemblyNames?.[0]
-  if (assemblyName) {
-    return (
-      assemblyManager.get(assemblyName)?.getCanonicalRefName(refName) ?? refName
-    )
-  }
-  return refName
-}
-
 /**
  * Extracts UniProt ID from an AlphaFold URL
  * Examples:

package/src/utils/blastCache.ts

@@ -27,8 +27,10 @@ export interface CachedBlastResult {
   geneName?: string
 }
 
-async function getDB() {
-  return openDB(DB_NAME, DB_VERSION, {
+let dbPromise: ReturnType<typeof openDB> | undefined
+
+function getDB() {
+  dbPromise ??= openDB(DB_NAME, DB_VERSION, {
     upgrade(db, oldVersion) {
       if (oldVersion < 2 && db.objectStoreNames.contains(STORE_NAME)) {
         db.deleteObjectStore(STORE_NAME)
@@ -37,17 +39,25 @@ async function getDB() {
         db.createObjectStore(STORE_NAME, { keyPath: 'id' })
       }
     },
+  }).catch((e: unknown) => {
+    dbPromise = undefined
+    throw e
   })
+  return dbPromise
 }
 
 function createCacheKey(
   proteinSequence: string,
   blastDatabase: BlastDatabase,
   blastProgram: BlastProgram,
+  msaAlgorithm: MsaAlgorithm,
   transcriptId?: string,
 ) {
   const idPart = transcriptId ? `:${transcriptId}` : ''
-  return `${blastDatabase}:${blastProgram}${idPart}:${proteinSequence}`
+  // msaAlgorithm is part of the key because the stored msa/tree are produced by
+  // it — without it, re-running the same query under a different algorithm
+  // overwrites the earlier result and drops it from the history list
+  return `${blastDatabase}:${blastProgram}:${msaAlgorithm}${idPart}:${proteinSequence}`
 }
 
 export async function saveBlastResult({
@@ -82,6 +92,7 @@ export async function saveBlastResult({
     proteinSequence,
     blastDatabase,
     blastProgram,
+    msaAlgorithm,
     transcriptId,
   )
   const entry: CachedBlastResult = {

package/src/utils/domainCache.ts

@@ -11,14 +11,20 @@ interface CachedDomain {
   matches: DomainMatch[]
 }
 
-async function getDB() {
-  return openDB(DB_NAME, DB_VERSION, {
+let dbPromise: ReturnType<typeof openDB> | undefined
+
+function getDB() {
+  dbPromise ??= openDB(DB_NAME, DB_VERSION, {
     upgrade(db) {
       if (!db.objectStoreNames.contains(STORE_NAME)) {
         db.createObjectStore(STORE_NAME, { keyPath: 'accession' })
       }
     },
+  }).catch((e: unknown) => {
+    dbPromise = undefined
+    throw e
   })
+  return dbPromise
 }
 
 export async function getCachedDomains(accessions: string[]) {

package/src/utils/fetch.ts

@@ -1,5 +1,3 @@
-import { ungzip } from 'pako-esm2'
-
 export async function handleFetch(url: string, args?: RequestInit) {
   const response = await fetch(url, args)
 
@@ -25,29 +23,3 @@ export async function jsonfetch<T>(url: string, args?: RequestInit) {
 export function timeout(time: number) {
   return new Promise(res => setTimeout(res, time))
 }
-
-export async function fetchWithLocalStorageCache<T>(
-  key: string,
-  fetchFn: () => Promise<T>,
-): Promise<T> {
-  const cachedData = localStorage.getItem(key)
-
-  if (cachedData) {
-    try {
-      return JSON.parse(cachedData) as T
-    } catch (error) {
-      console.error(`Error parsing cached data for ${key}:`, error)
-      // Continue to fetch fresh data if parsing fails
-      localStorage.removeItem(key)
-    }
-  }
-
-  const data = await fetchFn()
-  localStorage.setItem(key, JSON.stringify(data))
-  return data
-}
-
-export async function unzipfetch(url: string, arg?: RequestInit) {
-  const res = await handleFetch(url, arg)
-  return ungzip(await res.arrayBuffer(), { to: 'string' })
-}

package/src/utils/ncbiDomains.ts

@@ -161,9 +161,16 @@ export async function fetchProteinDomains(accessions: string[]) {
     )
     const parsed = parseCddDomains(xml)
     for (const acc of batch) {
-      const matches = parsed.get(acc) ?? []
-      byAccession.set(acc, matches)
-      toCache.push({ accession: acc, matches })
+      // only cache accessions actually present in the response: a genuinely
+      // domain-less protein comes back as an empty array (cache it), but an
+      // accession the batch omitted comes back undefined — caching [] for it
+      // would permanently hide its domains on later loads (the domain cache
+      // never expires), so leave it uncached to be retried
+      const matches = parsed.get(acc)
+      if (matches !== undefined) {
+        byAccession.set(acc, matches)
+        toCache.push({ accession: acc, matches })
+      }
     }
   }
   if (toCache.length > 0) {

package/src/utils/taxonomyNames.ts

@@ -12,15 +12,21 @@ interface CachedTaxonomy {
   commonName?: string
 }
 
-async function getDB() {
-  return openDB(DB_NAME, DB_VERSION, {
+let dbPromise: ReturnType<typeof openDB> | undefined
+
+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: unknown) => {
+    dbPromise = undefined
+    throw e
   })
+  return dbPromise
 }
 
 async function getCachedTaxonomies(taxids: number[]) {

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.6.6'
+export const version = '2.6.7'

package/dist/LaunchMsaView/components/ManualMSALoader/fetchGeneList.d.ts

@@ -1 +0,0 @@
-export declare function fetchGeneList(): Promise<string[]>;

package/dist/LaunchMsaView/components/ManualMSALoader/fetchGeneList.js

@@ -1,11 +0,0 @@
-export async function fetchGeneList() {
-    const res = await fetch('https://jbrowse.org/demos/msaview/knownCanonical/list.txt');
-    if (!res.ok) {
-        throw new Error(`HTTP ${res.status} fetching list ${await res.text()}`);
-    }
-    const result = await res.text();
-    return result
-        .split('\n')
-        .map(f => f.trim())
-        .filter(f => !!f);
-}

package/src/LaunchMsaView/components/ManualMSALoader/fetchGeneList.ts

@@ -1,13 +0,0 @@
-export async function fetchGeneList() {
-  const res = await fetch(
-    'https://jbrowse.org/demos/msaview/knownCanonical/list.txt',
-  )
-  if (!res.ok) {
-    throw new Error(`HTTP ${res.status} fetching list ${await res.text()}`)
-  }
-  const result = await res.text()
-  return result
-    .split('\n')
-    .map(f => f.trim())
-    .filter(f => !!f)
-}