Merge pull request #322 from BimberLab/25.3_fb_merge

Merge discvr-24.11 to discvr-25.3

Author: bbimber

jbrowse/package-lock.json

@@ -14,44 +14,45 @@
     "jb-pkg": "npm run prepareCli && npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli"
   },
   "dependencies": {
-    "@gmod/vcf": "^5.0.10",
-    "@jbrowse/core": "^2.15.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.15.0",
-    "@jbrowse/plugin-svg": "^2.15.0",
-    "@jbrowse/plugin-variants": "^2.15.0",
-    "@jbrowse/react-linear-genome-view": "^2.15.0",
-    "@labkey/api": "^1.35.0",
-    "@labkey/components": "^5.0.0",
-    "@mui/x-data-grid": "^7.0.0",
-    "@yao-pkg/pkg": "^5.12.0",
-    "assert": "^2.0.0",
+    "@gmod/vcf": "^6.0.9",
+    "@jbrowse/core": "^3.2.0",
+    "@jbrowse/product-core": "^3.2.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.2.0",
+    "@jbrowse/plugin-svg": "^3.2.0",
+    "@jbrowse/plugin-variants": "^3.2.0",
+    "@jbrowse/react-linear-genome-view2": "^3.2.0",
+    "@labkey/api": "^1.39.0",
+    "@labkey/components": "^6.32.2",
+    "@mui/x-data-grid": "^7.28.1",
+    "@yao-pkg/pkg": "^6.3.2",
+    "assert": "^2.1.0",
     "browserify-zlib": "^0.2.0",
     "buffer": "^6.0.3",
     "child_process": "^1.0.2",
     "fs": "^0.0.1-security",
-    "jquery": "^3.7.0",
-    "jspdf": "^2.5.1",
-    "jspdf-autotable": "^3.5.31",
-    "node-polyfill-webpack-plugin": "2.0.1",
+    "jquery": "^3.7.1",
+    "jspdf": "^3.0.0",
+    "jspdf-autotable": "^5.0.2",
+    "node-polyfill-webpack-plugin": "4.1.0",
     "path-browserify": "^1.0.1",
-    "react": "^18.0.0",
+    "react": "^18.3.0",
     "react-data-grid": "7.0.0-beta.46",
-    "react-dom": "^18.0.0",
-    "react-google-charts": "^4.0.1",
-    "react-select": "^5.8.0",
-    "regenerator-runtime": "^0.13.11",
+    "react-dom": "^18.3.0",
+    "react-google-charts": "^5.2.1",
+    "react-select": "^5.10.1",
+    "regenerator-runtime": "^0.14.1",
     "stream-browserify": "^3.0.0",
     "util": "^0.12.5",
-    "uuid": "^9.0.0",
+    "uuid": "^11.1.0",
     "vm-browserify": "^1.1.2"
   },
   "devDependencies": {
-    "@labkey/build": "^8.3.0",
-    "@types/jexl": "^2.3.1",
-    "@types/jquery": "^3.0.0",
+    "@labkey/build": "^8.4.0",
+    "@types/jexl": "^2.3.4",
+    "@types/jquery": "^3.5.32",
     "@types/node": "^20.14.11",
-    "@types/react": "^18.0.0",
-    "@types/react-dom": "^18.0.0",
+    "@types/react": "^18.3.0",
+    "@types/react-dom": "^18.3.0",
     "rimraf": "^6.0.1",
     "typescript": "^5.1.6"
   }

jbrowse/package.json

@@ -1,6 +1,6 @@
 import React, { useEffect, useState } from 'react';
 
-import { JBrowseLinearGenomeView, ViewModel } from '@jbrowse/react-linear-genome-view';
+import { JBrowseLinearGenomeView, ViewModel } from '@jbrowse/react-linear-genome-view2'
 import { createTheme } from '@mui/material/styles';
 import LogSession from './plugins/LogSession/index';
 import ExtendedVariantPlugin from './plugins/ExtendedVariantPlugin/index';

jbrowse/src/client/JBrowse/Browser/Browser.tsx

@@ -1,9 +1,8 @@
-import React from 'react';
-import ReactDOM from 'react-dom';
-
 import View from './Browser';
+import { createRoot } from 'react-dom/client';
+import React from 'react';
 
 // Need to wait for container element to be available in labkey wrapper before render
 window.addEventListener('DOMContentLoaded', (event) => {
-    ReactDOM.render(<View />, document.getElementById('app'))
+    createRoot(document.getElementById('app')).render(<View />)
 });

jbrowse/src/client/JBrowse/Browser/app.tsx

@@ -1,10 +1,8 @@
-import React from 'react';
-import ReactDOM from 'react-dom';
-
 import View from './Browser';
+import { createRoot } from 'react-dom/client';
+import React from 'react';
 
-const render = () => {
-    ReactDOM.render(<View />, document.getElementById('app'));
-};
-
-render();
+// Need to wait for container element to be available in labkey wrapper before render
+window.addEventListener('DOMContentLoaded', (event) => {
+    createRoot(document.getElementById('app')).render(<View />)
+}, true);

jbrowse/src/client/JBrowse/Browser/dev.tsx

@@ -27,7 +27,7 @@ export default class extends VcfTabixAdapter {
                 observer.next(v)
             })
             observer.complete()
-        }, opts.signal)
+        }, opts.stopToken)
     }
 
     private async getFeaturesAsArray(query: NoAssemblyRegion, opts: BaseOptions = {}) {

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVariantAdapter.ts

@@ -1,32 +1,14 @@
 import { VcfFeature } from '@jbrowse/plugin-variants'
-import VcfParser from '@gmod/vcf'
+import VcfParser, { Variant } from '@gmod/vcf';
 
 export default class ExtendedVcfFeature extends VcfFeature {
-    private readonly vcfParser: VcfParser
-
-    constructor(args: { variant: any; parser: VcfParser; id: string }) {
+    constructor(args: { variant: Variant; parser: VcfParser; id: string }) {
         args.variant = ExtendedVcfFeature.extractImpact(args.variant)
-        //args.variant = ExtendedVcfFeature.calculateVariableSamples(args.variant)
 
         super(args)
-
-        this.vcfParser = args.parser
-    }
-
-    public getInfoFieldMeta(propKey: string): VcfParser {
-        const map = this.vcfParser.getMetadata("INFO")
-
-        return map ? map[propKey] :  null
     }
 
-    static extractImpact(variant:  {
-        REF: string
-        POS: number
-        ALT: string[]
-        CHROM: string
-        INFO: any
-        ID: string[]
-    }) {
+    static extractImpact(variant: Variant) {
         // Only append if not present:
         if (variant.INFO["IMPACT"]) {
             return(variant);

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts

@@ -1,86 +1,158 @@
+import { TabixIndexedFile } from '@gmod/tabix'
+import VcfParser from '@gmod/vcf'
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
+  fetchAndMaybeUnzipText,
+  updateStatus,
+} from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature } from '@jbrowse/core/util'
-import { TabixIndexedFile } from '@gmod/tabix'
-import VcfParser from '@gmod/vcf'
+
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
+import type { Feature } from '@jbrowse/core/util'
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types'
 import { VcfFeature } from '@jbrowse/plugin-variants';
 
+function shorten2(name: string, max = 70) {
+  return name.length > max ? `${name.slice(0, max)}...` : name
+}
+
 export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
   private configured?: Promise<{
     vcf: TabixIndexedFile
     parser: VcfParser
   }>
 
-  private async configurePre() {
-    const pm = this.pluginManager
+  private async configurePre(_opts?: BaseOptions) {
     const vcfGzLocation = this.getConf('vcfGzLocation')
     const location = this.getConf(['index', 'location'])
     const indexType = this.getConf(['index', 'indexType'])
 
-    const filehandle = openLocation(vcfGzLocation, pm)
+    const filehandle = openLocation(vcfGzLocation, this.pluginManager)
     const isCSI = indexType === 'CSI'
     const vcf = new TabixIndexedFile({
       filehandle,
-      csiFilehandle: isCSI ? openLocation(location, pm) : undefined,
-      tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined,
-      chunkCacheSize: 50 * 2 ** 20
+      csiFilehandle: isCSI
+          ? openLocation(location, this.pluginManager)
+          : undefined,
+      tbiFilehandle: !isCSI
+          ? openLocation(location, this.pluginManager)
+          : undefined,
+      chunkCacheSize: 50 * 2 ** 20,
     })
 
-    const header = await vcf.getHeader()
     return {
       vcf,
-      parser: new VcfParser({ header }),
+      parser: new VcfParser({
+        header: await vcf.getHeader(),
+      }),
     }
   }
 
-  protected async configure() {
+  protected async configurePre2() {
     if (!this.configured) {
-      this.configured = this.configurePre().catch(e => {
+      this.configured = this.configurePre().catch((e: unknown) => {
         this.configured = undefined
         throw e
       })
     }
     return this.configured
   }
 
+  async configure(opts?: BaseOptions) {
+    const { statusCallback = () => {} } = opts || {}
+    return updateStatus('Downloading index', statusCallback, () =>
+        this.configurePre2(),
+    )
+  }
   public async getRefNames(opts: BaseOptions = {}) {
-    const { vcf } = await this.configure()
+    const { vcf } = await this.configure(opts)
     return vcf.getReferenceSequenceNames(opts)
   }
 
-  async getHeader() {
-    const { vcf } = await this.configure()
+  async getHeader(opts?: BaseOptions) {
+    const { vcf } = await this.configure(opts)
     return vcf.getHeader()
   }
 
-  async getMetadata() {
-    const { parser } = await this.configure()
+  async getMetadata(opts?: BaseOptions) {
+    const { parser } = await this.configure(opts)
     return parser.getMetadata()
   }
 
   public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
     return ObservableCreate<Feature>(async observer => {
       const { refName, start, end } = query
-      const { vcf, parser } = await this.configure()
-      await vcf.getLines(refName, start, end, {
-        lineCallback: (line, fileOffset) => {
-          observer.next(
-            new VcfFeature({
-              variant: parser.parseLine(line),
-              parser,
-              id: `${this.id}-vcf-${fileOffset}`,
-            }),
-          )
-        },
-        ...opts,
-      })
+      const { statusCallback = () => {} } = opts
+      const { vcf, parser } = await this.configure(opts)
+
+      await updateStatus('Downloading variants', statusCallback, () =>
+          vcf.getLines(refName, start, end, {
+            lineCallback: (line, fileOffset) => {
+              observer.next(
+                  new VcfFeature({
+                    variant: parser.parseLine(line),
+                    parser,
+                    id: `${this.id}-vcf-${fileOffset}`,
+                  }),
+              )
+            },
+            ...opts,
+          }),
+      )
       observer.complete()
-    }, opts.signal)
+    }, opts.stopToken)
+  }
+
+  async getSources() {
+    const conf = this.getConf('samplesTsvLocation')
+    if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
+      const { parser } = await this.configure()
+      return parser.samples.map(name => ({
+        name,
+      }))
+    } else {
+      const txt = await fetchAndMaybeUnzipText(
+          openLocation(conf, this.pluginManager),
+      )
+      const lines = txt.split(/\n|\r\n|\r/)
+      const header = lines[0]!.split('\t')
+      const { parser } = await this.configure()
+      const metadataLines = lines
+          .slice(1)
+          .filter(f => !!f)
+          .map(line => {
+            const [name, ...rest] = line.split('\t')
+            return {
+              ...Object.fromEntries(
+                  // force col 0 to be called name
+                  rest.map((c, idx) => [header[idx + 1]!, c] as const),
+              ),
+              name: name!,
+            }
+          })
+      const vcfSampleSet = new Set(parser.samples)
+      const metadataSet = new Set(metadataLines.map(r => r.name))
+      const metadataNotInVcfSamples = [...metadataSet].filter(
+          f => !vcfSampleSet.has(f),
+      )
+      const vcfSamplesNotInMetadata = [...vcfSampleSet].filter(
+          f => !metadataSet.has(f),
+      )
+      if (metadataNotInVcfSamples.length) {
+        console.warn(
+            `There are ${metadataNotInVcfSamples.length} samples in metadata file (${metadataLines.length} lines) not in VCF (${parser.samples.length} samples):`,
+            shorten2(metadataNotInVcfSamples.join(',')),
+        )
+      }
+      if (vcfSamplesNotInMetadata.length) {
+        console.warn(
+            `There are ${vcfSamplesNotInMetadata.length} samples in VCF file (${parser.samples.length} samples) not in metadata file (${metadataLines.length} lines):`,
+            shorten2(vcfSamplesNotInMetadata.map(m => m).join(',')),
+        )
+      }
+      return metadataLines.filter(f => vcfSampleSet.has(f.name))
+    }
   }
 
   public freeResources(/* { region } */): void {}

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/VcfTabixAdapter.ts

@@ -1,10 +1,10 @@
-import jexl from 'jexl';
 import { SvgFeatureRendererReactComponent } from '@jbrowse/plugin-svg';
 import { observer } from 'mobx-react';
 import React from 'react';
 import { deserializeFilters } from '../../InfoFilterWidget/filterUtil';
 import Diamond from './Diamond';
 import { passesInfoFilters, passesSampleFilters } from '../../../../../utils';
+import { VcfFeature } from '@jbrowse/plugin-variants';
 
 export function ExtendedVariantRendering(props) {
     const { features, rendererConfig } = props
@@ -17,11 +17,11 @@ export function ExtendedVariantRendering(props) {
 
     const sampleFilters = activeSamples.value ? activeSamples.value.split(',') : null
 
-    function diamondValidator(feature) {
+    function diamondValidator(feature: VcfFeature) {
         return feature.get('type') === "SNV";
     }
 
-    function isFeatureDisplayed(feature) {
+    function isFeatureDisplayed(feature: VcfFeature) {
         return passesInfoFilters(feature, expandedFilters) && passesSampleFilters(feature, sampleFilters)
     }
 

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/ExtendedVariantRendering.tsx

@@ -1,11 +1,9 @@
 import React from 'react';
-import ReactDOM from 'react-dom';
+import { createRoot } from 'react-dom/client';
 import { App } from '@labkey/api';
 
 import StandaloneSearch from '../StandaloneSearch';
 
 App.registerApp<any>('jbrowseSearchWebpart', (target: string, sessionId: string) => {
-    ReactDOM.render(
-        <StandaloneSearch sessionId={sessionId} />
-    , document.getElementById(target));
-});
+    createRoot(document.getElementById(target)).render(<StandaloneSearch sessionId={sessionId} />)
+});