jbrowse-plugin-msaview 2.4.0 → 2.4.2

package/dist/utils/ncbiBlast.js

@@ -64,17 +64,16 @@ async function waitForRid({ rid, onProgress, baseUrl, }) {
             onProgress(`Re-checking BLAST status in... ${iter - i}`);
         }
         const res = await textfetch(`${baseUrl}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`);
-        const isWaiting = /\s+Status=WAITING/m.test(res);
-        const isFailed = /\s+Status=FAILED/m.test(res);
-        const isReady = /\s+Status=READY/m.test(res);
+        const statusMatch = /\s+Status=(\S+)/m.exec(res);
+        const status = statusMatch?.[1];
         const hasHits = /\s+ThereAreHits=yes/m.test(res);
-        if (isWaiting) {
+        if (status === 'WAITING') {
             continue;
         }
-        if (isFailed) {
+        if (status === 'FAILED') {
             throw new Error(`BLAST ${rid} failed`);
         }
-        if (isReady) {
+        if (status === 'READY') {
             if (hasHits) {
                 return true;
             }
@@ -82,6 +81,7 @@ async function waitForRid({ rid, onProgress, baseUrl, }) {
                 throw new Error('No hits found');
             }
         }
+        throw new Error(`BLAST ${rid} returned unexpected status: ${status ?? 'unknown'}`);
     }
 }
 //# sourceMappingURL=ncbiBlast.js.map

package/dist/utils/ncbiBlast.js.map

@@ -1 +1 @@
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package/dist/utils/taxonomyNames.js

@@ -101,9 +101,6 @@ export async function fetchTaxonomyInfo(taxids) {
                     result.set(taxid, { sciname: sci, commonName: name });
                     toCache.push({ taxid, sciname: sci, commonName: name });
                 }
-                else {
-                    toCache.push({ taxid, sciname: '', commonName: undefined });
-                }
             }
         }
         catch (error) {

package/dist/utils/taxonomyNames.js.map

@@ -1 +1 @@
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+{"version":3,"file":"taxonomyNames.js","sourceRoot":"","sources":["../../src/utils/taxonomyNames.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,KAAK,CAAA;AAE5B,MAAM,OAAO,GAAG,gCAAgC,CAAA;AAChD,MAAM,UAAU,GAAG,cAAc,CAAA;AACjC,MAAM,UAAU,GAAG,CAAC,CAAA;AAQpB,KAAK,UAAU,KAAK;IAClB,OAAO,MAAM,CAAC,OAAO,EAAE,UAAU,EAAE;QACjC,OAAO,CAAC,EAAE;YACR,IAAI,EAAE,CAAC,gBAAgB,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC7C,EAAE,CAAC,iBAAiB,CAAC,UAAU,CAAC,CAAA;YAClC,CAAC;YACD,EAAE,CAAC,iBAAiB,CAAC,UAAU,EAAE,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC,CAAA;QACxD,CAAC;KACF,CAAC,CAAA;AACJ,CAAC;AAED,KAAK,UAAU,mBAAmB,CAAC,MAAgB;IACjD,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,UAAU,EAAE,UAAU,CAAC,CAAA;IACjD,MAAM,OAAO,GAAG,MAAM,OAAO,CAAC,GAAG,CAC/B,MAAM,CAAC,GAAG,CACR,KAAK,CAAC,EAAE,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAwC,CACpE,CACF,CAAA;IACD,MAAM,EAAE,CAAC,IAAI,CAAA;IACb,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,KAAK,UAAU,iBAAiB,CAAC,OAAyB;IACxD,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,UAAU,EAAE,WAAW,CAAC,CAAA;IAClD,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,MAAM,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC3B,CAAC;IACD,MAAM,EAAE,CAAC,IAAI,CAAA;AACf,CAAC;AAOD,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,MAAgB;IAEhB,MAAM,MAAM,GAAG,IAAI,GAAG,EAAwB,CAAA;IAC9C,MAAM,cAAc,GAAa,EAAE,CAAA;IACnC,MAAM,aAAa,GAAG,MAAM,mBAAmB,CAAC,MAAM,CAAC,CAAA;IAEvD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACxB,MAAM,MAAM,GAAG,aAAa,CAAC,CAAC,CAAC,CAAA;QAC/B,IAAI,MAAM,EAAE,CAAC;YACX,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE;gBAChB,OAAO,EAAE,MAAM,CAAC,OAAO;gBACvB,UAAU,EAAE,MAAM,CAAC,UAAU;aAC9B,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,cAAc,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC;IACH,CAAC;IAED,IAAI,cAAc,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAChC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,SAAS,GAAG,GAAG,CAAA;IACrB,MAAM,OAAO,GAAqB,EAAE,CAAA;IAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,IAAI,SAAS,EAAE,CAAC;QAC1D,MAAM,KAAK,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,CAAA;QACpD,MAAM,QAAQ,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAEhC,IAAI,CAAC;YACH,MAAM,QAAQ,GAAG,MAAM,KAAK,CAC1B,4EAA4E,QAAQ,cAAc,CACnG,CAAA;YACD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;YAElC,iEAAiE;YACjE,uEAAuE;YACvE,2CAA2C;YAC3C,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAkB,CAAA;YAC1C,MAAM,UAAU,GAAG,kCAAkC,CAAA;YACrD,IAAI,KAAK,CAAA;YACT,OAAO,CAAC,KAAK,GAAG,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;gBAChD,MAAM,YAAY,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;gBACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,CAAA;gBAE5B,+DAA+D;gBAC/D,IAAI,KAAK,GAAG,CAAC,CAAA;gBACb,IAAI,MAAM,GAAG,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;gBACvC,OAAO,KAAK,GAAG,CAAC,IAAI,MAAM,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC;oBACzC,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,MAAM,CAAC,CAAA;oBACjD,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,EAAE,MAAM,CAAC,CAAA;oBACnD,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;wBACtB,MAAK;oBACP,CAAC;oBACD,IAAI,SAAS,KAAK,CAAC,CAAC,IAAI,SAAS,GAAG,UAAU,EAAE,CAAC;wBAC/C,KAAK,EAAE,CAAA;wBACP,MAAM,GAAG,SAAS,GAAG,CAAC,CAAA;oBACxB,CAAC;yBAAM,CAAC;wBACN,KAAK,EAAE,CAAA;wBACP,MAAM,GAAG,UAAU,GAAG,CAAC,CAAA;oBACzB,CAAC;gBACH,CAAC;gBAED,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAA;gBAC7C,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;gBAC3C,MAAM,YAAY,GAAG,QAAQ,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAA;gBACrD,MAAM,oBAAoB,GAAG,QAAQ,EAAE,QAAQ,CAAC,aAAa,CAAC,CAAA;gBAC9D,IAAI,CAAC,QAAQ,IAAI,CAAC,YAAY,IAAI,CAAC,oBAAoB,CAAC,EAAE,CAAC;oBACzD,QAAQ,CAAC,GAAG,CAAC,YAAY,EAAE,QAAQ,CAAC,CAAA;gBACtC,CAAC;YACH,CAAC;YAED,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE,CAAC;gBAC1B,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;gBACpC,IAAI,QAAQ,EAAE,CAAC;oBACb,MAAM,aAAa,GACjB,+CAA+C,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;oBAChE,MAAM,UAAU,GAAG,iCAAiC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;oBACnE,MAAM,OAAO,GAAG,yCAAyC,CAAC,IAAI,CAC5D,QAAQ,CACT,CAAA;oBACD,MAAM,IAAI,GAAG,aAAa,EAAE,CAAC,CAAC,CAAC,IAAI,UAAU,EAAE,CAAC,CAAC,CAAC,CAAA;oBAElD,MAAM,GAAG,GAAG,OAAO,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;oBAC9B,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE,EAAE,OAAO,EAAE,GAAG,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAA;oBACrD,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAA;gBACzD,CAAC;YACH,CAAC;QACH,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,OAAO,CAAC,KAAK,CAAC,gCAAgC,EAAE,KAAK,CAAC,CAAA;QACxD,CAAC;IACH,CAAC;IAED,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACvB,MAAM,iBAAiB,CAAC,OAAO,CAAC,CAAA;IAClC,CAAC;IAED,OAAO,MAAM,CAAA;AACf,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.4.0";
+export declare const version = "2.4.2";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '2.4.0';
+export const version = '2.4.2';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.4.0",
+  "version": "2.4.2",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {

package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx

@@ -24,14 +24,11 @@ const GenomeMouseoverHighlightRenderer = observer(function ({
   hovered,
 }: {
   model: LinearGenomeViewModel
-  hovered: { hoverPosition: unknown }
+  hovered: { hoverPosition: { coord: number; refName: string } }
 }) {
   const { classes } = useStyles()
   const { offsetPx } = model
-  const { coord, refName } = hovered.hoverPosition as {
-    coord: number
-    refName: string
-  }
+  const { coord, refName } = hovered.hoverPosition
 
   const s = model.bpToPx({ refName, coord: coord - 1 })
   const e = model.bpToPx({ refName, coord })

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -4,6 +4,7 @@ import { getSession } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
 import { hasHoverPosition, useStyles } from './util'
+import { getCanonicalRefName } from '../MsaViewPanel/util'
 
 import type { JBrowsePluginMsaViewModel } from '../MsaViewPanel/model'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -41,17 +42,16 @@ const MsaToGenomeHighlightRenderer = observer(function ({
 }) {
   const { classes } = useStyles()
   const { assemblyManager } = getSession(model)
-  const assembly = assemblyManager.get(model.assemblyNames[0]!)
   const { offsetPx } = model
 
-  if (!assembly) {
-    return null
-  }
-
   return (
     <>
       {highlights.map((r, idx) => {
-        const refName = assembly.getCanonicalRefName(r.refName) ?? r.refName
+        const refName = getCanonicalRefName({
+          assemblyManager,
+          assemblyNames: model.assemblyNames,
+          refName: r.refName,
+        })
         const s = model.bpToPx({ refName, coord: r.start })
         const e = model.bpToPx({ refName, coord: r.end })
         if (s && e) {

package/src/AddHighlightModel/util.ts

@@ -2,8 +2,13 @@ import { makeStyles } from 'tss-react/mui'
 
 export function hasHoverPosition(
   hovered: unknown,
-): hovered is { hoverPosition: unknown } {
-  return !!hovered && typeof hovered === 'object' && 'hoverPosition' in hovered
+): hovered is { hoverPosition: { coord: number; refName: string } } {
+  return (
+    !!hovered &&
+    typeof hovered === 'object' &&
+    'hoverPosition' in hovered &&
+    !!hovered.hoverPosition
+  )
 }
 
 export const useStyles = makeStyles()({

package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts

@@ -40,18 +40,24 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
     return this.refNamesP
   }
 
+  getMsaRegex() {
+    return new RegExp(this.getConf('msaRegex'))
+  }
+
+  refNameToMsaId(refName: string) {
+    return refName.split(this.getMsaRegex())[0]!
+  }
+
   async getMSAList() {
     const refNames = await this.getMSARefs()
-    const val = this.getConf('msaRegex')
-    const re = new RegExp(val)
-    const list = new Set(refNames.map(name => name.split(re)[0]!))
+    const list = new Set(refNames.map(name => this.refNameToMsaId(name)))
     return [...list]
   }
 
   async getMSA(id: string) {
     const adapter = await this.configure()
     const refNames = await adapter.getRefNames()
-    const rows = refNames.filter(refName => refName.startsWith(id))
+    const rows = refNames.filter(refName => this.refNameToMsaId(refName) === id)
     return firstValueFrom(
       adapter
         .getFeaturesInMultipleRegions(

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -42,8 +42,8 @@ export function loadStoredData(self: JBrowsePluginMsaViewModel) {
 }
 
 export function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel) {
-  const { rows, dataStoreId } = self
-  if (rows.length > 0 && !dataStoreId) {
+  const { rows, dataStoreId, isStoringData } = self
+  if (rows.length > 0 && !dataStoreId && !isStoringData) {
     if (self.msaFilehandle || self.treeFilehandle) {
       return
     }
@@ -52,6 +52,10 @@ export function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel) {
     const treeData = self.data.tree
 
     if (msaData || treeData) {
+      // mark as storing synchronously so re-runs of this autorun (e.g. when
+      // data observables change while the write is pending) don't kick off a
+      // duplicate write and leave an orphan IndexedDB entry
+      self.setIsStoringData(true)
       // eslint-disable-next-line @typescript-eslint/no-floating-promises
       ;(async () => {
         try {
@@ -66,6 +70,8 @@ export function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel) {
           }
         } catch (e) {
           console.error('Failed to store MSA data to IndexedDB:', e)
+        } finally {
+          self.setIsStoringData(false)
         }
       })()
     }

package/src/MsaViewPanel/model.ts

@@ -25,6 +25,7 @@ import {
   getProteinViews,
   ungappedToGappedPosition,
 } from './structureConnection'
+import { getCanonicalRefName } from './util'
 
 import type { ProteinView, StructureConnection } from './structureConnection'
 import type { MafRegion, MsaViewInitState } from './types'
@@ -137,6 +138,7 @@ export default function stateModelFactory() {
         progress: string
         error: unknown
         loadingStoredData: boolean
+        isStoringData: boolean
       } => ({
         /**
          * #volatile
@@ -154,6 +156,10 @@ export default function stateModelFactory() {
          * #volatile
          */
         loadingStoredData: false,
+        /**
+         * #volatile
+         */
+        isStoringData: false,
       }),
     )
 
@@ -333,6 +339,12 @@ export default function stateModelFactory() {
       setLoadingStoredData(arg: boolean) {
         self.loadingStoredData = arg
       },
+      /**
+       * #action
+       */
+      setIsStoringData(arg: boolean) {
+        self.isStoringData = arg
+      },
       /**
        * #action
        */
@@ -348,10 +360,11 @@ export default function stateModelFactory() {
         if (zoomToBaseLevel) {
           connectedView.navTo(r2)
         } else {
-          const r =
-            assemblyManager
-              .get(connectedView.assemblyNames[0]!)
-              ?.getCanonicalRefName(r2.refName) ?? r2.refName
+          const r = getCanonicalRefName({
+            assemblyManager,
+            assemblyNames: connectedView.assemblyNames,
+            refName: r2.refName,
+          })
           connectedView.centerAt(r2.start, r)
         }
       },

package/src/MsaViewPanel/util.ts

@@ -5,13 +5,38 @@ export function checkHovered(hovered: unknown): hovered is {
   hoverPosition: { coord: number; refName: string }
 } {
   return (
+    !!hovered &&
     typeof hovered === 'object' &&
-    hovered !== null &&
     'hoverFeature' in hovered &&
-    'hoverPosition' in hovered
+    'hoverPosition' in hovered &&
+    !!hovered.hoverPosition
   )
 }
 
+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/ncbiBlast.ts

@@ -121,25 +121,28 @@ async function waitForRid({
     const res = await textfetch(
       `${baseUrl}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
     )
-    const isWaiting = /\s+Status=WAITING/m.test(res)
-    const isFailed = /\s+Status=FAILED/m.test(res)
-    const isReady = /\s+Status=READY/m.test(res)
+    const statusMatch = /\s+Status=(\S+)/m.exec(res)
+    const status = statusMatch?.[1]
     const hasHits = /\s+ThereAreHits=yes/m.test(res)
 
-    if (isWaiting) {
+    if (status === 'WAITING') {
       continue
     }
 
-    if (isFailed) {
+    if (status === 'FAILED') {
       throw new Error(`BLAST ${rid} failed`)
     }
 
-    if (isReady) {
+    if (status === 'READY') {
       if (hasHits) {
         return true
       } else {
         throw new Error('No hits found')
       }
     }
+
+    throw new Error(
+      `BLAST ${rid} returned unexpected status: ${status ?? 'unknown'}`,
+    )
   }
 }

package/src/utils/taxonomyNames.ts

@@ -135,8 +135,6 @@ export async function fetchTaxonomyInfo(
           const sci = sciName?.[1] ?? ''
           result.set(taxid, { sciname: sci, commonName: name })
           toCache.push({ taxid, sciname: sci, commonName: name })
-        } else {
-          toCache.push({ taxid, sciname: '', commonName: undefined })
         }
       }
     } catch (error) {

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.4.0'
+export const version = '2.4.2'