jbrowse-plugin-msaview 2.2.8 → 2.3.2

package/dist/utils/msa.js

@@ -1,65 +1,27 @@
 import { textfetch, timeout } from './fetch';
 const base = `https://www.ebi.ac.uk/Tools/services/rest`;
-async function runClustalOmega({ sequence, onProgress, }) {
-    const jobId = await textfetch(`${base}/clustalo/run`, {
-        method: 'POST',
-        body: new URLSearchParams({
-            email: 'colin.diesh@gmail.com',
-            sequence,
-        }),
-    });
-    await wait({ jobId, algorithm: 'clustalo', onProgress });
-    return {
-        msa: await textfetch(`${base}/clustalo/result/${jobId}/aln-clustal_num`),
-        tree: await textfetch(`${base}/clustalo/result/${jobId}/phylotree`),
-    };
-}
-async function runMuscle({ sequence, onProgress, }) {
-    const jobId = await textfetch(`${base}/muscle/run`, {
-        method: 'POST',
-        body: new URLSearchParams({
-            email: 'colin.diesh@gmail.com',
-            format: 'clw',
-            tree: 'tree1',
-            sequence,
-        }),
-    });
-    await wait({ jobId, algorithm: 'muscle', onProgress });
-    return {
-        msa: await textfetch(`${base}/muscle/result/${jobId}/fa`),
-        tree: await textfetch(`${base}/muscle/result/${jobId}/phylotree`),
-    };
-}
-async function runKalign({ sequence, onProgress, }) {
-    const jobId = await textfetch(`${base}/kalign/run`, {
-        method: 'POST',
-        body: new URLSearchParams({
-            email: 'colin.diesh@gmail.com',
-            stype: 'protein',
-            sequence,
-        }),
-    });
-    await wait({ jobId, algorithm: 'kalign', onProgress });
-    return {
-        msa: await textfetch(`${base}/kalign/result/${jobId}/fa`),
-        tree: await textfetch(`${base}/kalign/result/${jobId}/phylotree`),
-    };
-}
-async function runMafft({ sequence, onProgress, }) {
-    const jobId = await textfetch(`${base}/mafft/run`, {
-        method: 'POST',
-        body: new URLSearchParams({
-            email: 'colin.diesh@gmail.com',
-            stype: 'protein',
-            sequence,
-        }),
-    });
-    await wait({ jobId, algorithm: 'mafft', onProgress });
-    return {
-        msa: await textfetch(`${base}/mafft/result/${jobId}/fa`),
-        tree: await textfetch(`${base}/mafft/result/${jobId}/phylotree`),
-    };
-}
+const algorithms = {
+    clustalo: {
+        params: { email: 'colin.diesh@gmail.com' },
+        msaResult: 'aln-clustal_num',
+        treeResult: 'phylotree',
+    },
+    muscle: {
+        params: { email: 'colin.diesh@gmail.com', format: 'clw', tree: 'tree1' },
+        msaResult: 'fa',
+        treeResult: 'phylotree',
+    },
+    kalign: {
+        params: { email: 'colin.diesh@gmail.com', stype: 'protein' },
+        msaResult: 'fa',
+        treeResult: 'phylotree',
+    },
+    mafft: {
+        params: { email: 'colin.diesh@gmail.com', stype: 'protein' },
+        msaResult: 'fa',
+        treeResult: 'phylotree',
+    },
+};
 async function wait({ onProgress, jobId, algorithm, }) {
     // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     while (true) {
@@ -77,23 +39,19 @@ async function wait({ onProgress, jobId, algorithm, }) {
     }
 }
 export async function launchMSA({ algorithm, sequence, onProgress, }) {
-    onProgress(`Launching ${algorithm} MSA...`);
-    switch (algorithm) {
-        case 'clustalo': {
-            return runClustalOmega({ sequence, onProgress });
-        }
-        case 'muscle': {
-            return runMuscle({ sequence, onProgress });
-        }
-        case 'kalign': {
-            return runKalign({ sequence, onProgress });
-        }
-        case 'mafft': {
-            return runMafft({ sequence, onProgress });
-        }
-        default: {
-            throw new Error('unknown algorithm');
-        }
+    const config = algorithms[algorithm];
+    if (!config) {
+        throw new Error(`unknown algorithm: ${algorithm}`);
     }
+    onProgress(`Launching ${algorithm} MSA...`);
+    const jobId = await textfetch(`${base}/${algorithm}/run`, {
+        method: 'POST',
+        body: new URLSearchParams({ ...config.params, sequence }),
+    });
+    await wait({ jobId, algorithm, onProgress });
+    return {
+        msa: await textfetch(`${base}/${algorithm}/result/${jobId}/${config.msaResult}`),
+        tree: await textfetch(`${base}/${algorithm}/result/${jobId}/${config.treeResult}`),
+    };
 }
 //# sourceMappingURL=msa.js.map

package/dist/utils/msa.js.map

@@ -1 +1 @@
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+{"version":3,"file":"msa.js","sourceRoot":"","sources":["../../src/utils/msa.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAE5C,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAExD,MAAM,UAAU,GAOZ;IACF,QAAQ,EAAE;QACR,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE;QAC1C,SAAS,EAAE,iBAAiB;QAC5B,UAAU,EAAE,WAAW;KACxB;IACD,MAAM,EAAE;QACN,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,EAAE,OAAO,EAAE;QACxE,SAAS,EAAE,IAAI;QACf,UAAU,EAAE,WAAW;KACxB;IACD,MAAM,EAAE;QACN,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE,KAAK,EAAE,SAAS,EAAE;QAC5D,SAAS,EAAE,IAAI;QACf,UAAU,EAAE,WAAW;KACxB;IACD,KAAK,EAAE;QACL,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE,KAAK,EAAE,SAAS,EAAE;QAC5D,SAAS,EAAE,IAAI;QACf,UAAU,EAAE,WAAW;KACxB;CACF,CAAA;AAED,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,EACL,SAAS,GAKV;IACC,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;YACnB,UAAU,CAAC,gCAAgC,EAAE,GAAG,CAAC,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,EAAE,CAAC,CAAA;QAEtE,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;YAC1B,MAAK;QACP,CAAC;aAAM,IAAI,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;YACtC,MAAM,IAAI,KAAK,CAAC,wBAAwB,KAAK,EAAE,CAAC,CAAA;QAClD,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,EAC9B,SAAS,EACT,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,MAAM,GAAG,UAAU,CAAC,SAAS,CAAC,CAAA;IACpC,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,sBAAsB,SAAS,EAAE,CAAC,CAAA;IACpD,CAAC;IAED,UAAU,CAAC,aAAa,SAAS,SAAS,CAAC,CAAA;IAE3C,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,IAAI,SAAS,MAAM,EAAE;QACxD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,QAAQ,EAAE,CAAC;KAC1D,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,CAAC,CAAA;IAC5C,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAClB,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAC3D;QACD,IAAI,EAAE,MAAM,SAAS,CACnB,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,IAAI,MAAM,CAAC,UAAU,EAAE,CAC5D;KACF,CAAA;AACH,CAAC"}

package/dist/utils/ncbiBlast.js

@@ -21,16 +21,7 @@ export async function queryBlast({ query, blastDatabase, blastProgram, baseUrl,
         baseUrl,
     });
     onRid(rid);
-    await waitForRid({
-        rid,
-        onProgress,
-        baseUrl,
-    });
-    const ret = await jsonfetch(`${baseUrl}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);
-    return {
-        rid,
-        hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
-    };
+    return queryBlastFromRid({ rid, baseUrl, onProgress });
 }
 async function initialQuery({ query, blastProgram, blastDatabase, baseUrl, }) {
     const res = await textfetch(baseUrl, {

package/dist/utils/ncbiBlast.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ncbiBlast.js","sourceRoot":"","sources":["../../src/utils/ncbiBlast.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAIvD,MAAM,CAAC,KAAK,UAAU,iBAAiB,CAAC,EACtC,GAAG,EACH,OAAO,EACP,UAAU,GAKX;IACC,UAAU,CAAC,kCAAkC,GAAG,KAAK,CAAC,CAAA;IACtD,MAAM,UAAU,CAAC;QACf,GAAG;QACH,UAAU;QACV,OAAO;KACR,CAAC,CAAA;IACF,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,OAAO,gBAAgB,GAAG,8CAA8C,CAC5E,CAAA;IACD,OAAO;QACL,GAAG;QACH,IAAI,EAAE,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,IAAI,EAAE;KAC5D,CAAA;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,UAAU,CAAC,EAC/B,KAAK,EACL,aAAa,EACb,YAAY,EACZ,OAAO,EACP,UAAU,EACV,KAAK,GAQN;IACC,UAAU,CAAC,6BAA6B,CAAC,CAAA;IACzC,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,YAAY,CAAC;QACjC,KAAK;QACL,aAAa;QACb,YAAY;QACZ,OAAO;KACR,CAAC,CAAA;IACF,KAAK,CAAC,GAAG,CAAC,CAAA;IACV,OAAO,iBAAiB,CAAC,EAAE,GAAG,EAAE,OAAO,EAAE,UAAU,EAAE,CAAC,CAAA;AACxD,CAAC;AAED,KAAK,UAAU,YAAY,CAAC,EAC1B,KAAK,EACL,YAAY,EACZ,aAAa,EACb,OAAO,GAMR;IACC,MAAM,GAAG,GAAG,MAAM,SAAS,CAAC,OAAO,EAAE;QACnC,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,GAAG,EAAE,KAAK;YACV,OAAO,EAAE,YAAY,KAAK,cAAc,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,YAAY;YAClE,QAAQ,EAAE,aAAa;YACvB,KAAK,EAAE,KAAK;YACZ,GAAG,CAAC,aAAa,KAAK,kBAAkB;gBACtC,CAAC,CAAC;oBACE,YAAY,EAAE,IAAI;oBAClB,OAAO,EAAE,wBAAwB;iBAClC;gBACH,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,YAAY,KAAK,cAAc;gBACjC,CAAC,CAAC,EAAE,cAAc,EAAE,YAAY,EAAE;gBAClC,CAAC,CAAC,EAAE,CAAC;SACR,CAAC;KACH,CAAC,CAAA;IAEF,4EAA4E;IAC5E,qEAAqE;IACrE,8DAA8D;IAC9D,MAAM,GAAG,GAAG,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IAC9C,MAAM,IAAI,GAAG,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IAEhD,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,MAAM,IAAI,KAAK,CAAC,sCAAsC,CAAC,CAAA;IACzD,CAAC;IACD,OAAO;QACL,GAAG;QACH,IAAI;KACL,CAAA;AACH,CAAC;AAED,KAAK,UAAU,UAAU,CAAC,EACxB,GAAG,EACH,UAAU,EACV,OAAO,GAKR;IACC,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,CAAC;YAC9B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;YACnB,UAAU,CAAC,kCAAkC,IAAI,GAAG,CAAC,EAAE,CAAC,CAAA;QAC1D,CAAC;QAED,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,OAAO,yCAAyC,GAAG,EAAE,CACzD,CAAA;QACD,MAAM,SAAS,GAAG,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC9C,MAAM,OAAO,GAAG,kBAAkB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,OAAO,GAAG,sBAAsB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAEhD,IAAI,SAAS,EAAE,CAAC;YACd,SAAQ;QACV,CAAC;QAED,IAAI,QAAQ,EAAE,CAAC;YACb,MAAM,IAAI,KAAK,CAAC,SAAS,GAAG,SAAS,CAAC,CAAA;QACxC,CAAC;QAED,IAAI,OAAO,EAAE,CAAC;YACZ,IAAI,OAAO,EAAE,CAAC;gBACZ,OAAO,IAAI,CAAA;YACb,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.2.8";
+export declare const version = "2.2.11";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '2.2.8';
+export const version = '2.2.11';
 //# sourceMappingURL=version.js.map

package/dist/version.js.map

@@ -1 +1 @@
-{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,OAAO,CAAA"}
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,QAAQ,CAAA"}

package/package.json

@@ -1,7 +1,11 @@
 {
-  "version": "2.2.8",
+  "version": "2.3.2",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-plugin-msaview.git"
+  },
   "keywords": [
     "jbrowse",
     "jbrowse2"
@@ -26,51 +30,50 @@
     "test:versions": "node scripts/test-versions.mjs run",
     "test:version": "node scripts/test-versions.mjs run",
     "prepack": "yarn build",
-    "prepublishOnly": "node -e \"console.log('export const version = \\'' + require('./package.json').version + '\\'')\" > src/version.ts && git add -A src && git diff --cached --quiet || git commit -m '[skip ci] Bump version.ts'",
-    "preversion": "yarn lint",
-    "postversion": "git push --follow-tags"
+    "postversion": "node -e \"console.log('export const version = \\'' + require('./package.json').version + '\\'')\" > src/version.ts && git add -A src && git diff --cached --quiet || git commit -m '[skip ci] Bump version.ts' && git push --follow-tags",
+    "preversion": "yarn lint"
   },
   "dependencies": {
     "@emotion/styled": "^11.14.1",
     "g2p_mapper": "^2.0.0",
     "idb": "^8.0.3",
-    "pako-esm2": "^2.0.0",
-    "react-msaview": "^5.0.6",
-    "swr": "^2.3.8"
+    "pako-esm2": "^2.0.2",
+    "react-msaview": "^5.0.13",
+    "swr": "^2.4.1"
   },
   "devDependencies": {
     "@emotion/react": "^11.14.0",
-    "@eslint/js": "^9.39.2",
+    "@eslint/js": "^9.39.4",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
-    "@jbrowse/core": "^4.1.3",
-    "@jbrowse/mobx-state-tree": "^5.4.2",
-    "@jbrowse/plugin-linear-genome-view": "^4.1.3",
-    "@mui/icons-material": "^7.3.7",
-    "@mui/material": "^7.3.7",
-    "@mui/system": "^7.3.7",
-    "@mui/x-data-grid": "^8.24.0",
-    "@types/node": "^25.1.0",
-    "@types/react": "^19.2.10",
-    "esbuild": "^0.27.2",
-    "eslint": "^9.39.2",
+    "@jbrowse/core": "^4.1.15",
+    "@jbrowse/mobx-state-tree": "^5.6.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.1.15",
+    "@mui/icons-material": "^7.3.10",
+    "@mui/material": "^7.3.10",
+    "@mui/system": "^7.3.10",
+    "@mui/x-data-grid": "^8.28.2",
+    "@types/node": "^25.6.0",
+    "@types/react": "^19.2.14",
+    "esbuild": "^0.28.0",
+    "eslint": "^9.39.4",
     "eslint-plugin-import": "^2.32.0",
     "eslint-plugin-react": "^7.37.5",
     "eslint-plugin-react-hooks": "^7.0.1",
-    "eslint-plugin-react-refresh": "^0.4.26",
-    "eslint-plugin-unicorn": "^62.0.0",
+    "eslint-plugin-react-refresh": "^0.5.2",
+    "eslint-plugin-unicorn": "^64.0.0",
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
-    "prettier": "^3.7.4",
+    "prettier": "^3.8.2",
     "pretty-bytes": "^7.1.0",
-    "puppeteer": "^24.36.1",
-    "react": "^19.2.4",
-    "react-dom": "^19.2.4",
-    "rimraf": "^6.1.2",
+    "puppeteer": "^24.40.0",
+    "react": "^19.2.5",
+    "react-dom": "^19.2.5",
+    "rimraf": "^6.1.3",
     "rxjs": "^7.8.2",
-    "serve": "^14.2.5",
+    "serve": "^14.2.6",
     "tss-react": "^4.9.20",
-    "typescript": "^5.9.3",
-    "typescript-eslint": "^8.54.0",
-    "vitest": "^4.0.16"
+    "typescript": "^6.0.2",
+    "typescript-eslint": "^8.58.2",
+    "vitest": "^4.1.4"
   }
 }

package/src/AddHighlightModel/index.tsx

@@ -1,10 +1,10 @@
 import React from 'react'
 
-import PluginManager from '@jbrowse/core/PluginManager'
 import { getSession } from '@jbrowse/core/util'
 
 import HighlightComponents from './HighlightComponents'
 
+import type PluginManager from '@jbrowse/core/PluginManager'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 export default function AddHighlightComponentsModelF(

package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts

@@ -1,10 +1,9 @@
 import { readConfObject } from '@jbrowse/core/configuration'
-import {
-  BaseAdapter,
-  BaseFeatureDataAdapter,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { firstValueFrom, toArray } from 'rxjs'
 
+import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
+
 export default class BgzipFastaMsaAdapter extends BaseAdapter {
   configureP: Promise<BaseFeatureDataAdapter> | undefined
 

package/src/BgzipFastaMsaAdapter/configSchema.ts

@@ -1,6 +1,7 @@
-import PluginManager from '@jbrowse/core/PluginManager'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
+import type PluginManager from '@jbrowse/core/PluginManager'
+
 export default function configSchemaF(pluginManager: PluginManager) {
   const base = pluginManager.getAdapterType('BgzipFastaAdapter')
   return ConfigurationSchema(

package/src/BgzipFastaMsaAdapter/index.ts

@@ -1,8 +1,9 @@
-import PluginManager from '@jbrowse/core/PluginManager'
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
 
 import configSchemaF from './configSchema'
 
+import type PluginManager from '@jbrowse/core/PluginManager'
+
 export default function BgzipFastaMsaAdapterF(pluginManager: PluginManager) {
   return pluginManager.addAdapterType(() => {
     return new AdapterType({

package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx

@@ -1,12 +1,7 @@
 import React, { useState } from 'react'
 
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
-import {
-  AbstractTrackModel,
-  Feature,
-  getContainingView,
-  getSession,
-} from '@jbrowse/core/util'
+import { getContainingView, getSession } from '@jbrowse/core/util'
 import { Button, DialogActions, DialogContent, Link } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
@@ -17,6 +12,7 @@ import { getGeneDisplayName } from '../../util'
 import TranscriptSelector from '../TranscriptSelector'
 import { useTranscriptSelection } from '../useTranscriptSelection'
 
+import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 const useStyles = makeStyles()({

package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts

@@ -1,7 +1,8 @@
 import { gatherSequencesFromTree } from './gatherSequencesFromTree'
-import { TreeNode } from './types'
 import { fetchWithLocalStorageCache, jsonfetch, textfetch } from './util'
 
+import type { TreeNode } from './types'
+
 const base = 'https://rest.ensembl.org'
 
 export async function geneTreeFetcher(id2: string) {

package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx

@@ -2,7 +2,7 @@ import React, { useState } from 'react'
 
 import { readConfObject } from '@jbrowse/core/configuration'
 import { Dialog } from '@jbrowse/core/ui'
-import { AbstractTrackModel, Feature, getSession } from '@jbrowse/core/util'
+import { getSession } from '@jbrowse/core/util'
 import { Tab, Tabs } from '@mui/material'
 
 import EnsemblGeneTree from './EnsemblGeneTree/EnsemblGeneTree'
@@ -12,6 +12,7 @@ import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel'
 import TabPanel from './TabPanel'
 
 import type { Dataset } from './PreLoadedMSA/types'
+import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 
 export default function LaunchMsaViewDialog({
   handleClose,

package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx

@@ -1,13 +1,7 @@
 import React, { useState } from 'react'
 
 import { ErrorMessage, FileSelector } from '@jbrowse/core/ui'
-import {
-  AbstractTrackModel,
-  Feature,
-  FileLocation,
-  getContainingView,
-  getSession,
-} from '@jbrowse/core/util'
+import { getContainingView, getSession } from '@jbrowse/core/util'
 import {
   Alert,
   Button,
@@ -27,6 +21,11 @@ import { getGeneDisplayName } from '../../util'
 import TranscriptSelector from '../TranscriptSelector'
 import { useTranscriptSelection } from '../useTranscriptSelection'
 
+import type {
+  AbstractTrackModel,
+  Feature,
+  FileLocation,
+} from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 const useStyles = makeStyles()({

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

@@ -1,5 +1,8 @@
-import { AbstractSessionModel, Feature, FileLocation } from '@jbrowse/core/util'
-
+import type {
+  AbstractSessionModel,
+  Feature,
+  FileLocation,
+} from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 export function launchView({

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

@@ -1,6 +1,7 @@
 import React, { useEffect, useMemo, useState } from 'react'
 
-import { Feature, getContainingView } from '@jbrowse/core/util'
+import { ErrorMessage } from '@jbrowse/core/ui'
+import { getContainingView } from '@jbrowse/core/util'
 import DeleteIcon from '@mui/icons-material/Delete'
 import {
   Button,
@@ -19,22 +20,12 @@ import {
   deleteCachedResult,
   getAllCachedResults,
 } from '../../../utils/blastCache'
+import { getGeneIdentifiers } from '../../util'
 
 import type { CachedBlastResult } from '../../../utils/blastCache'
-import type { AbstractTrackModel } from '@jbrowse/core/util'
+import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
-function getGeneIdentifiers(feature: Feature): string[] {
-  const ids = [
-    feature.id(),
-    feature.get('id'),
-    feature.get('name'),
-    feature.get('gene_id'),
-    feature.get('gene_name'),
-  ].filter((id): id is string => !!id)
-  return [...new Set(ids)]
-}
-
 function getResultDisplayName(result: CachedBlastResult): string {
   const parts = []
   if (result.geneName) {
@@ -60,6 +51,7 @@ const CachedBlastResults = observer(function ({
 }) {
   const [results, setResults] = useState<CachedBlastResult[]>([])
   const [loading, setLoading] = useState(true)
+  const [error, setError] = useState<unknown>()
   const view = getContainingView(model) as LinearGenomeViewModel
 
   const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature])
@@ -73,18 +65,27 @@ const CachedBlastResults = observer(function ({
         setLoading(false)
       } catch (e) {
         console.error(e)
+        setError(e)
       }
     })()
   }, [geneIds])
 
   const handleDelete = async (id: string) => {
-    await deleteCachedResult(id)
-    setResults(r => r.filter(result => result.id !== id))
+    try {
+      await deleteCachedResult(id)
+      setResults(r => r.filter(result => result.id !== id))
+    } catch (e) {
+      setError(e)
+    }
   }
 
   const handleClearAll = async () => {
-    await clearAllCachedResults()
-    setResults([])
+    try {
+      await clearAllCachedResults()
+      setResults([])
+    } catch (e) {
+      setError(e)
+    }
   }
 
   const handleUseCached = (cached: CachedBlastResult) => {
@@ -96,6 +97,10 @@ const CachedBlastResults = observer(function ({
     handleClose()
   }
 
+  if (error) {
+    return <ErrorMessage error={error} />
+  }
+
   if (loading) {
     return <Typography>Loading cached results...</Typography>
   }