@jbrowse/plugin-legacy-jbrowse 2.4.0 → 2.4.2

package/esm/NCListAdapter/NCListFeature.js

@@ -14,13 +14,13 @@ export default class NCListFeature {
         throw new Error('not implemented');
     }
     jb2TagToJb1Tag(tag) {
-        // @ts-ignore
+        // @ts-expect-error
         const mapped = jb2ToJb1[tag] || tag;
         return mapped.toLowerCase();
     }
     jb1TagToJb2Tag(tag) {
         const t = tag.toLowerCase();
-        // @ts-ignore
+        // @ts-expect-error
         const mapped = jb1ToJb2[t] || t;
         return mapped;
     }

package/esm/NCListAdapter/NCListFeature.js.map

@@ -1 +1 @@
-{"version":3,"file":"NCListFeature.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListFeature.ts"],"names":[],"mappings":"AAKA,MAAM,QAAQ,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAA;AAEtC,MAAM,QAAQ,GAAG,EAAE,MAAM,EAAE,SAAS,EAAE,CAAA;AAEtC;;GAEG;AACH,MAAM,CAAC,OAAO,OAAO,aAAa;IAKhC,8DAA8D;IAC9D,YAAoB,SAAc,EAAE,MAAgB,EAAE,EAAW;QAA7C,cAAS,GAAT,SAAS,CAAK;QAChC,IAAI,CAAC,QAAQ,GAAG,EAAE,IAAI,SAAS,CAAC,EAAE,EAAE,CAAA;QACpC,IAAI,CAAC,YAAY,GAAG,MAAM,CAAA;IAC5B,CAAC;IAED,GAAG;QACD,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAA;IACpC,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,aAAa;QACb,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,IAAI,GAAG,CAAA;QACnC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,MAAM,CAAC,GAAG,GAAG,CAAC,WAAW,EAAE,CAAA;QAC3B,aAAa;QACb,MAAM,MAAM,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QAC/B,OAAO,MAAM,CAAA;IACf,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,QAAgB;QAClB,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,IAAI,IAAI,IAAI,QAAQ,KAAK,aAAa,EAAE;YACtC,8DAA8D;YAC9D,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,UAAe,EAAE,EAAE,CAAC,IAAI,aAAa,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC,CAAA;SAC1E;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED;;OAEG;IACH,IAAI;QACF,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAA;IACzE,CAAC;IAED;;OAEG;IACH,EAAE;QACA,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED;;OAEG;IACH,MAAM;QACJ,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;IAED;;OAEG;IACH,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;IAChC,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAA4B,EAAE,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE,EAAE,CAAA;QAC7D,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,OAAO,CAAC,CAAC,GAAW,EAAE,EAAE;YAC5C,MAAM,SAAS,GAAG,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;YACrC,IAAI,SAAS,KAAK,aAAa,EAAE;gBAC/B,IAAI,CAAC,WAAW,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAU,EAAE,EAAE;oBAClD,qEAAqE;oBACrE,OAAO,IAAI,aAAa,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,MAAM,EAAE,CAAA;gBAC5C,CAAC,CAAC,CAAA;aACH;iBAAM;gBACL,IAAI,CAAC,SAAS,CAAC,GAAG,KAAK,CAAA;aACxB;QACH,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
+{"version":3,"file":"NCListFeature.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListFeature.ts"],"names":[],"mappings":"AAKA,MAAM,QAAQ,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAA;AAEtC,MAAM,QAAQ,GAAG,EAAE,MAAM,EAAE,SAAS,EAAE,CAAA;AAEtC;;GAEG;AACH,MAAM,CAAC,OAAO,OAAO,aAAa;IAKhC,8DAA8D;IAC9D,YAAoB,SAAc,EAAE,MAAgB,EAAE,EAAW;QAA7C,cAAS,GAAT,SAAS,CAAK;QAChC,IAAI,CAAC,QAAQ,GAAG,EAAE,IAAI,SAAS,CAAC,EAAE,EAAE,CAAA;QACpC,IAAI,CAAC,YAAY,GAAG,MAAM,CAAA;IAC5B,CAAC;IAED,GAAG;QACD,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAA;IACpC,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,mBAAmB;QACnB,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,IAAI,GAAG,CAAA;QACnC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,MAAM,CAAC,GAAG,GAAG,CAAC,WAAW,EAAE,CAAA;QAC3B,mBAAmB;QACnB,MAAM,MAAM,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QAC/B,OAAO,MAAM,CAAA;IACf,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,QAAgB;QAClB,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,IAAI,IAAI,IAAI,QAAQ,KAAK,aAAa,EAAE;YACtC,8DAA8D;YAC9D,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,UAAe,EAAE,EAAE,CAAC,IAAI,aAAa,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC,CAAA;SAC1E;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED;;OAEG;IACH,IAAI;QACF,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAA;IACzE,CAAC;IAED;;OAEG;IACH,EAAE;QACA,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED;;OAEG;IACH,MAAM;QACJ,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;IAED;;OAEG;IACH,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;IAChC,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAA4B,EAAE,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE,EAAE,CAAA;QAC7D,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,OAAO,CAAC,CAAC,GAAW,EAAE,EAAE;YAC5C,MAAM,SAAS,GAAG,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;YACrC,IAAI,SAAS,KAAK,aAAa,EAAE;gBAC/B,IAAI,CAAC,WAAW,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAU,EAAE,EAAE;oBAClD,qEAAqE;oBACrE,OAAO,IAAI,aAAa,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,MAAM,EAAE,CAAA;gBAC5C,CAAC,CAAC,CAAA;aACH;iBAAM;gBACL,IAAI,CAAC,SAAS,CAAC,GAAG,KAAK,CAAA;aACxB;QACH,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.4.0",
+  "version": "2.4.2",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "78707a2bc3ba8489f26a590ef83f62ede945d048"
+  "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
 }

package/src/JBrowse1Connection/jb1ConfigLoad.ts

@@ -21,10 +21,13 @@ function isLocalPathLocation(
 }
 
 export async function fetchJb1(
+  // eslint-disable-next-line unicorn/no-object-as-default-parameter
   dataRoot: JBLocation = { uri: '', locationType: 'UriLocation' },
+  // eslint-disable-next-line unicorn/no-object-as-default-parameter
   baseConfig: Config = {
     include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf'],
   },
+  // eslint-disable-next-line unicorn/no-object-as-default-parameter
   baseConfigRoot: JBLocation = { uri: '', locationType: 'UriLocation' },
 ): Promise<Config> {
   const protocol = 'uri' in dataRoot ? 'uri' : 'localPath'
@@ -37,10 +40,7 @@ export async function fetchJb1(
     dataRootLocation = dataRoot.localPath
   }
   if (dataRootLocation.endsWith('/')) {
-    dataRootReg[protocol] = dataRootLocation.slice(
-      0,
-      dataRootLocation.length - 1,
-    )
+    dataRootReg[protocol] = dataRootLocation.slice(0, -1)
   }
   if (
     (isUriLocation(baseConfigRoot) && baseConfigRoot.uri) ||
@@ -55,16 +55,13 @@ export async function fetchJb1(
       baseConfigLocation = baseConfigRoot.localPath
     }
     if (baseConfigLocation.endsWith('/')) {
-      baseConfigLocation = baseConfigLocation.slice(
-        0,
-        baseConfigLocation.length - 1,
-      )
+      baseConfigLocation = baseConfigLocation.slice(0, -1)
     }
     let newConfig: Config = {}
     for (const conf of ['jbrowse.conf', 'jbrowse_conf.json']) {
       let fetchedConfig = null
       try {
-        // @ts-ignore
+        // @ts-expect-error
         fetchedConfig = await fetchConfigFile({
           [baseProtocol]: `${baseConfigLocation}/${conf}`,
         })
@@ -143,12 +140,12 @@ function mergeConfigs(a: Config | null, b: Config | null): Config | null {
     } else if (
       !noRecursiveMerge(prop) &&
       prop in a &&
-      // @ts-ignore
+      // @ts-expect-error
       typeof b[prop] === 'object' &&
-      // @ts-ignore
+      // @ts-expect-error
       typeof a[prop] === 'object'
     ) {
-      // @ts-ignore
+      // @ts-expect-error
       a[prop] = deepUpdate(a[prop], b[prop])
     } else if (prop === 'dataRoot') {
       if (
@@ -157,9 +154,9 @@ function mergeConfigs(a: Config | null, b: Config | null): Config | null {
       ) {
         a[prop] = b[prop]
       }
-      // @ts-ignore
+      // @ts-expect-error
     } else if (a[prop] === undefined || b[prop] !== undefined) {
-      // @ts-ignore
+      // @ts-expect-error
       a[prop] = b[prop]
     }
   }
@@ -284,7 +281,7 @@ function fillTemplates<T extends any>(subconfig: T, config: Config): T {
       sub[name] = fillTemplates(sub[name], config)
     }
   } else if (typeof subconfig === 'string') {
-    // @ts-ignore
+    // @ts-expect-error
     return fillTemplate(subconfig, config)
   }
 

package/src/JBrowse1Connection/jb1ConfigParse.ts

@@ -68,7 +68,7 @@ function parse(text: string, url: string): Config {
         if (!keyPath) {
           throw new Error(`Error parsing in section ${section.join(' - ')}`)
         }
-        const path = section.concat(keyPath).join('.')
+        const path = [...section, ...keyPath].join('.')
         if (operation === '+=') {
           let existing = getValue(data, path)
           if (existing) {
@@ -124,7 +124,7 @@ function parse(text: string, url: string): Config {
       recordVal()
       keyPath = match[1].trim().split(/\s*\.\s*/)
       ;[, , operation] = match
-      if (isAlwaysArray(section.concat(keyPath).join('.'))) {
+      if (isAlwaysArray([...section, ...keyPath].join('.'))) {
         operation = '+='
       }
       value = match[3].trim()
@@ -385,12 +385,9 @@ function synthesizeTrackStoreConfig(
   // defaults if it is not explicit in the configuration
   const { urlTemplate = '' } = trackConfig
 
-  let storeClass: string
-  if (trackConfig.storeClass) {
-    storeClass = regularizeClass('JBrowse/Store', trackConfig.storeClass)
-  } else {
-    storeClass = guessStoreClass(trackConfig, urlTemplate)
-  }
+  const storeClass = trackConfig.storeClass
+    ? regularizeClass('JBrowse/Store', trackConfig.storeClass)
+    : guessStoreClass(trackConfig, urlTemplate)
 
   if (!storeClass) {
     console.warn(
@@ -404,7 +401,7 @@ function synthesizeTrackStoreConfig(
 
   // if this is the first sequence store we see, and we have no refseqs store
   // defined explicitly, make this the refseqs store.
-  if (
+  storeConf.name =
     (storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||
       storeClass === 'JBrowse/Store/Sequence/IndexedFasta' ||
       storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta' ||
@@ -413,11 +410,8 @@ function synthesizeTrackStoreConfig(
       storeClass === 'JBrowse/Store/Sequence/TwoBit' ||
       trackConfig.useAsRefSeqStore) &&
     !(mainConf.stores && mainConf.stores.refseqs)
-  ) {
-    storeConf.name = 'refseqs'
-  } else {
-    storeConf.name = `store${objectHash(storeConf)}`
-  }
+      ? 'refseqs'
+      : `store${objectHash(storeConf)}`
   // record it
   if (!mainConf.stores) {
     mainConf.stores = {}

package/src/JBrowse1Connection/jb1ToJb2.ts

@@ -139,17 +139,15 @@ export function convertTrackConfig(
         cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },
         sequenceAdapter,
       }
-      if (jb1TrackConfig.craiUrlTemplate) {
-        adapter.craiLocation = {
-          uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
-          locationType: 'UriLocation',
-        }
-      } else {
-        adapter.craiLocation = {
-          uri: `${urlTemplate}.crai`,
-          locationType: 'UriLocation',
-        }
-      }
+      adapter.craiLocation = jb1TrackConfig.craiUrlTemplate
+        ? {
+            uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
+            locationType: 'UriLocation',
+          }
+        : {
+            uri: `${urlTemplate}.crai`,
+            locationType: 'UriLocation',
+          }
       return {
         ...jb2TrackConfig,
         type: 'AlignmentsTrack',
@@ -346,17 +344,15 @@ export function convertTrackConfig(
         type: 'IndexedFastaAdapter',
         fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
       }
-      if (jb1TrackConfig.faiUrlTemplate) {
-        adapter.faiLocation = {
-          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-          locationType: 'UriLocation',
-        }
-      } else {
-        adapter.faiLocation = {
-          uri: `${urlTemplate}.fai`,
-          locationType: 'UriLocation',
-        }
-      }
+      adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
+        ? {
+            uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+            locationType: 'UriLocation',
+          }
+        : {
+            uri: `${urlTemplate}.fai`,
+            locationType: 'UriLocation',
+          }
       return {
         ...jb2TrackConfig,
         type: 'SequenceTrack',
@@ -368,28 +364,24 @@ export function convertTrackConfig(
         type: 'BgzipFastaAdapter',
         fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
       }
-      if (jb1TrackConfig.faiUrlTemplate) {
-        adapter.faiLocation = {
-          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-          locationType: 'UriLocation',
-        }
-      } else {
-        adapter.faiLocation = {
-          uri: `${urlTemplate}.fai`,
-          locationType: 'UriLocation',
-        }
-      }
-      if (jb1TrackConfig.gziUrlTemplate) {
-        adapter.gziLocation = {
-          uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
-          locationType: 'UriLocation',
-        }
-      } else {
-        adapter.gziLocation = {
-          uri: `${urlTemplate}.gzi`,
-          locationType: 'UriLocation',
-        }
-      }
+      adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
+        ? {
+            uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+            locationType: 'UriLocation',
+          }
+        : {
+            uri: `${urlTemplate}.fai`,
+            locationType: 'UriLocation',
+          }
+      adapter.gziLocation = jb1TrackConfig.gziUrlTemplate
+        ? {
+            uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
+            locationType: 'UriLocation',
+          }
+        : {
+            uri: `${urlTemplate}.gzi`,
+            locationType: 'UriLocation',
+          }
       return {
         ...jb2TrackConfig,
         type: 'ReferenceSequenceTrack',

package/src/JBrowse1Connection/model.tsx

@@ -49,7 +49,7 @@ export default function (pluginManager: PluginManager) {
               'adapter',
             ])
 
-            // @ts-ignore
+            // @ts-expect-error
             const jb2Tracks = config.tracks?.map(jb1Track => {
               const jb2Track = convertTrackConfig(
                 jb1Track,
@@ -57,7 +57,7 @@ export default function (pluginManager: PluginManager) {
                 sequenceAdapter,
               )
 
-              // @ts-ignore
+              // @ts-expect-error
               jb2Track.assemblyNames = [assemblyName]
               return jb2Track
             })

package/src/JBrowse1Connection/util.ts

@@ -24,10 +24,7 @@ export function deepUpdate(a: Obj, b: Obj): Obj {
       typeof a[prop] === 'object'
     ) {
       deepUpdate(a[prop], b[prop])
-    } else if (
-      typeof a[prop] === 'undefined' ||
-      typeof b[prop] !== 'undefined'
-    ) {
+    } else if (a[prop] === undefined || b[prop] !== undefined) {
       a[prop] = b[prop]
     }
   }
@@ -44,27 +41,24 @@ export function deepUpdate(a: Obj, b: Obj): Obj {
  * e.g., 'htp://foo/someurl?arg=valueforbaz'
  */
 export function fillTemplate(template: string, fillWith: Obj): string {
-  return template.replace(
-    /\{([\w\s.]+)\}/g,
-    (match, varName: string): string => {
-      varName = varName.replace(/\s+/g, '') // remove all whitespace
-      const fill = getValue(fillWith, varName)
-      if (fill !== undefined) {
-        if (typeof fill === 'function') {
-          return fill(varName)
-        }
-        return fill
+  return template.replace(/{([\s\w.]+)}/g, (match, varName: string): string => {
+    varName = varName.replace(/\s+/g, '') // remove all whitespace
+    const fill = getValue(fillWith, varName)
+    if (fill !== undefined) {
+      if (typeof fill === 'function') {
+        return fill(varName)
       }
-      if (fillWith.callback) {
-        // @ts-ignore
-        const v = fillWith.callback.call(this, varName)
-        if (v !== undefined) {
-          return v
-        }
+      return fill
+    }
+    if (fillWith.callback) {
+      // @ts-expect-error
+      const v = fillWith.callback.call(this, varName)
+      if (v !== undefined) {
+        return v
       }
-      return match
-    },
-  )
+    }
+    return match
+  })
 }
 
 /**
@@ -146,7 +140,7 @@ function mixin(dest: Obj, source: Obj, copyFunc: Function): Obj {
     s = source[name]
     if (
       !(name in dest) ||
-      // @ts-ignore
+      // @ts-expect-error
       (dest[name] !== s && (!(name in empty) || empty[name] !== s))
     ) {
       dest[name] = copyFunc ? copyFunc(s) : s

package/src/JBrowse1TextSearchAdapter/HttpMap.ts

@@ -81,10 +81,10 @@ export default class HttpMap {
       while (hex.length < 8) {
         hex = `0${hex}`
       }
-      hex = hex.substr(8 - hashHexCharacters)
+      hex = hex.slice(8 - hashHexCharacters)
       const dirpath = []
       for (let i = 0; i < hex.length; i += 3) {
-        dirpath.push(hex.substring(i, i + 3))
+        dirpath.push(hex.slice(i, i + 3))
       }
       return `${dirpath.join('/')}.json${compress ? 'z' : ''}`
     }

package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.test.ts

@@ -6,50 +6,89 @@ import last from '../../test_data/names/f.json'
 import Adapter from './JBrowse1TextSearchAdapter'
 import configSchema from './configSchema'
 
-test('adapter can fetch files from names index', async () => {
-  function mockFetch(url: string): Promise<Response> {
-    let response = {}
-    if (url.includes('names/meta.json')) {
-      response = meta
-    }
-    if (url.includes('names/0.json')) {
-      response = first
-    }
-    if (url.includes('names/f.json')) {
-      response = last
-    }
-    return Promise.resolve(new Response(JSON.stringify(response)))
+function mockFetch(url: string) {
+  let response = {}
+  if (url.includes('names/meta.json')) {
+    response = meta
   }
+  if (url.includes('names/0.json')) {
+    response = first
+  }
+  if (url.includes('names/f.json')) {
+    response = last
+  }
+  return Promise.resolve(new Response(JSON.stringify(response)))
+}
 
-  const rootTemplate = path
-    .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
-    .replace(/\\/g, '\\\\')
+const rootTemplate = path
+  .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
+  .replace(/\\/g, '\\\\')
 
+test('search upper case', async () => {
   const spy = jest.spyOn(global, 'fetch')
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   spy.mockImplementation(mockFetch as any)
 
-  const urlPath = decodeURI(new URL(`file://${rootTemplate}`).href)
-  const args = {
-    type: 'JBrowse1TextSearchAdapter',
-    textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
-    namesIndexLocation: {
-      uri: urlPath,
-      locationType: 'UriLocation',
-    },
-  }
-  // create adapter
-  const adapter = new Adapter(configSchema.create(args))
-  // prefix search
+  const adapter = new Adapter(
+    configSchema.create({
+      type: 'JBrowse1TextSearchAdapter',
+      textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
+      namesIndexLocation: {
+        uri: decodeURI(new URL(`file://${rootTemplate}`).href),
+        locationType: 'UriLocation',
+      },
+    }),
+  )
+  const results = await adapter.searchIndex({
+    searchType: 'prefix',
+    queryString: 'Apple',
+  })
+  // check results are of type BaseResult for prefix search
+  expect(results.length).toBeGreaterThan(0)
+  expect(results[0] instanceof BaseResult).toBeTruthy()
+  expect(results[0].getLabel()).toEqual('Apple1')
+  expect(results[1].getLabel()).toEqual('Apple2')
+  expect(results[2].getLabel()).toEqual('Apple3')
+
+  // exact search
+  const results2 = await adapter.searchIndex({
+    searchType: 'exact',
+    queryString: 'Apple3',
+  })
+  // check results are of type location for exact search
+  expect(results2.length).toEqual(5)
+  expect(results2.length).toBeGreaterThan(0)
+  expect(results2[0] instanceof BaseResult).toBeTruthy()
+  expect(results2[0].getLabel()).toEqual('Apple3')
+  expect(results2[0].getLocation()).toEqual('ctgA:17399-23000')
+})
+
+test('search lower case', async () => {
+  const spy = jest.spyOn(global, 'fetch')
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  spy.mockImplementation(mockFetch as any)
+
+  const adapter = new Adapter(
+    configSchema.create({
+      type: 'JBrowse1TextSearchAdapter',
+      textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
+      namesIndexLocation: {
+        uri: decodeURI(new URL(`file://${rootTemplate}`).href),
+        locationType: 'UriLocation',
+      },
+    }),
+  )
   const results = await adapter.searchIndex({
     searchType: 'prefix',
     queryString: 'apple',
   })
   // check results are of type BaseResult for prefix search
+  expect(results.length).toBeGreaterThan(0)
   expect(results[0] instanceof BaseResult).toBeTruthy()
   expect(results[0].getLabel()).toEqual('Apple1')
   expect(results[1].getLabel()).toEqual('Apple2')
   expect(results[2].getLabel()).toEqual('Apple3')
+
   // exact search
   const results2 = await adapter.searchIndex({
     searchType: 'exact',
@@ -57,8 +96,8 @@ test('adapter can fetch files from names index', async () => {
   })
   // check results are of type location for exact search
   expect(results2.length).toEqual(5)
-  const test2 = results2[0]
-  expect(test2 instanceof BaseResult).toBeTruthy()
-  expect(test2.getLabel()).toEqual('Apple3')
-  expect(test2.getLocation()).toEqual('ctgA:17399-23000')
+  expect(results2.length).toBeGreaterThan(0)
+  expect(results2[0] instanceof BaseResult).toBeTruthy()
+  expect(results2[0].getLabel()).toEqual('Apple3')
+  expect(results2[0].getLocation()).toEqual('ctgA:17399-23000')
 })

package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.ts

@@ -4,9 +4,10 @@ import {
   BaseAdapter,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
-import { Instance } from 'mobx-state-tree'
-import { readConfObject } from '@jbrowse/core/configuration'
-import MyConfigSchema from './configSchema'
+import {
+  AnyConfigurationModel,
+  readConfObject,
+} from '@jbrowse/core/configuration'
 import HttpMap from './HttpMap'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
@@ -23,7 +24,8 @@ interface SearchResults {
 
 export type NamesIndexRecord = string | Array<string | number>
 
-//  Jbrowse1 text search adapter
+type IndexFile = Record<string, SearchResults>
+
 // Uses index built by generate-names.pl
 export default class JBrowse1TextSearchAdapter
   extends BaseAdapter
@@ -34,19 +36,15 @@ export default class JBrowse1TextSearchAdapter
   tracksNames?: string[]
 
   constructor(
-    config: Instance<typeof MyConfigSchema>,
+    config: AnyConfigurationModel,
     getSubAdapter?: getSubAdapterType,
     pluginManager?: PluginManager,
   ) {
     super(config, getSubAdapter, pluginManager)
-    const namesIndexLocation = readConfObject(config, 'namesIndexLocation')
-    if (!namesIndexLocation) {
-      throw new Error('must provide namesIndexLocation')
-    }
+    const namesIndex = readConfObject(config, 'namesIndexLocation')
+    const { baseUri, uri } = namesIndex
     this.httpMap = new HttpMap({
-      url: namesIndexLocation.baseUri
-        ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href
-        : namesIndexLocation.uri,
+      url: baseUri ? new URL(uri, baseUri).href : uri,
     })
   }
 
@@ -55,30 +53,31 @@ export default class JBrowse1TextSearchAdapter
    * else it returns empty
    * @param query - string query
    */
-  async loadIndexFile(query: string): Promise<Record<string, SearchResults>> {
+  async loadIndexFile(query: string): Promise<IndexFile> {
     return this.httpMap.getBucket(query)
   }
 
   async searchIndex(args: BaseArgs) {
     const { searchType, queryString } = args
     const tracks = this.tracksNames || (await this.httpMap.getTrackNames())
-    const entries = await this.loadIndexFile(queryString.toLowerCase())
-    if (entries[queryString]) {
-      return this.formatResults(entries[queryString], tracks, searchType)
-    }
-    return []
+    const str = queryString.toLowerCase()
+    const entries = await this.loadIndexFile(str)
+    return entries[str]
+      ? this.formatResults(entries[str], tracks, searchType)
+      : []
   }
   formatResults(results: SearchResults, tracks: string[], searchType?: string) {
     return [
       ...(searchType === 'exact'
         ? []
-        : results.prefix.map(result => {
-            return new BaseResult({
-              label: typeof result === 'object' ? result.name : result,
-              matchedAttribute: 'name',
-              matchedObject: { result: result },
-            })
-          })),
+        : results.prefix.map(
+            result =>
+              new BaseResult({
+                label: typeof result === 'object' ? result.name : result,
+                matchedAttribute: 'name',
+                matchedObject: { result: result },
+              }),
+          )),
       ...results.exact.map(result => {
         const name = result[0]
         const trackIndex = result[1]

package/src/NCListAdapter/NCListAdapter.test.ts

@@ -15,9 +15,9 @@ export function generateReadBuffer(
 }
 
 beforeEach(() => {
-  // @ts-ignore
+  // @ts-expect-error
   fetch.resetMocks()
-  // @ts-ignore
+  // @ts-expect-error
   fetch.mockResponse(
     generateReadBuffer(
       (url: string) =>

package/src/NCListAdapter/NCListFeature.ts

@@ -26,14 +26,14 @@ export default class NCListFeature implements Feature {
   }
 
   jb2TagToJb1Tag(tag: string): string {
-    // @ts-ignore
+    // @ts-expect-error
     const mapped = jb2ToJb1[tag] || tag
     return mapped.toLowerCase()
   }
 
   jb1TagToJb2Tag(tag: string): string {
     const t = tag.toLowerCase()
-    // @ts-ignore
+    // @ts-expect-error
     const mapped = jb1ToJb2[t] || t
     return mapped
   }