npm - @jbrowse/plugin-legacy-jbrowse - Versions diffs - 2.3.4 → 2.4.1 - Mend

@jbrowse/plugin-legacy-jbrowse 2.3.4 → 2.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (45) hide show

package/dist/JBrowse1Connection/jb1ConfigLoad.js CHANGED Viewed

@@ -10,9 +10,15 @@ function isUriLocation(location) {
 function isLocalPathLocation(location) {
     return location.localPath !== undefined;
 }
-async function fetchJb1(dataRoot = { uri: '', locationType: 'UriLocation' }, baseConfig = {
+async function fetchJb1(
+// eslint-disable-next-line unicorn/no-object-as-default-parameter
+dataRoot = { uri: '', locationType: 'UriLocation' },
+// eslint-disable-next-line unicorn/no-object-as-default-parameter
+baseConfig = {
     include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf'],
-}, baseConfigRoot = { uri: '', locationType: 'UriLocation' }) {
+},
+// eslint-disable-next-line unicorn/no-object-as-default-parameter
+baseConfigRoot = { uri: '', locationType: 'UriLocation' }) {
     const protocol = 'uri' in dataRoot ? 'uri' : 'localPath';
     const dataRootReg = JSON.parse(JSON.stringify(dataRoot));
     let dataRootLocation = '';
@@ -23,7 +29,7 @@ async function fetchJb1(dataRoot = { uri: '', locationType: 'UriLocation' }, bas
         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) ||
         (isLocalPathLocation(baseConfigRoot) && baseConfigRoot.localPath)) {
@@ -36,13 +42,13 @@ async function fetchJb1(dataRoot = { uri: '', locationType: 'UriLocation' }, bas
             baseConfigLocation = baseConfigRoot.localPath;
         }
         if (baseConfigLocation.endsWith('/')) {
-            baseConfigLocation = baseConfigLocation.slice(0, baseConfigLocation.length - 1);
+            baseConfigLocation = baseConfigLocation.slice(0, -1);
         }
         let newConfig = {};
         for (const conf of ['jbrowse.conf', 'jbrowse_conf.json']) {
             let fetchedConfig = null;
             try {
-                // @ts-ignore
+                // @ts-expect-error
                 fetchedConfig = await fetchConfigFile({
                     [baseProtocol]: `${baseConfigLocation}/${conf}`,
                 });
@@ -114,11 +120,11 @@ function mergeConfigs(a, b) {
         }
         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] = (0, util_1.deepUpdate)(a[prop], b[prop]);
         }
         else if (prop === 'dataRoot') {
@@ -126,10 +132,10 @@ function mergeConfigs(a, b) {
                 (a[prop] === 'data' && b[prop] !== undefined)) {
                 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];
         }
     }
@@ -234,7 +240,7 @@ function fillTemplates(subconfig, config) {
         }
     }
     else if (typeof subconfig === 'string') {
-        // @ts-ignore
+        // @ts-expect-error
         return (0, util_1.fillTemplate)(subconfig, config);
     }
     return subconfig;

package/dist/JBrowse1Connection/jb1ConfigLoad.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/JBrowse1Connection/jb1ConfigParse.js CHANGED Viewed

@@ -66,7 +66,7 @@ function parse(text, url) {
                 if (!keyPath) {
                     throw new Error(`Error parsing in section ${section.join(' - ')}`);
                 }
-                const path = section.concat(keyPath).join('.');
+                const path = [...section, ...keyPath].join('.');
                 if (operation === '+=') {
                     let existing = (0, get_value_1.default)(data, path);
                     if (existing) {
@@ -113,7 +113,7 @@ function parse(text, url) {
             recordVal();
             keyPath = match[1].trim().split(/\s*\.\s*/);
             [, , operation] = match;
-            if (isAlwaysArray(section.concat(keyPath).join('.'))) {
+            if (isAlwaysArray([...section, ...keyPath].join('.'))) {
                 operation = '+=';
             }
             value = match[3].trim();
@@ -347,13 +347,9 @@ function synthesizeTrackStoreConfig(mainConf, trackConfig) {
     // figure out what data store class to use with the track, applying some
     // defaults if it is not explicit in the configuration
     const { urlTemplate = '' } = trackConfig;
-    let storeClass;
-    if (trackConfig.storeClass) {
-        storeClass = regularizeClass('JBrowse/Store', trackConfig.storeClass);
-    }
-    else {
-        storeClass = guessStoreClass(trackConfig, urlTemplate);
-    }
+    const storeClass = trackConfig.storeClass
+        ? regularizeClass('JBrowse/Store', trackConfig.storeClass)
+        : guessStoreClass(trackConfig, urlTemplate);
     if (!storeClass) {
         console.warn(`Unable to determine an appropriate data store to use with track '${trackConfig.label}', please explicitly specify a storeClass in the configuration.`);
         return;
@@ -362,19 +358,17 @@ function synthesizeTrackStoreConfig(mainConf, trackConfig) {
     const storeConf = { ...trackConfig, type: storeClass };
     // if this is the first sequence store we see, and we have no refseqs store
     // defined explicitly, make this the refseqs store.
-    if ((storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||
-        storeClass === 'JBrowse/Store/Sequence/IndexedFasta' ||
-        storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta' ||
-        storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta' ||
-        storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||
-        storeClass === 'JBrowse/Store/Sequence/TwoBit' ||
-        trackConfig.useAsRefSeqStore) &&
-        !(mainConf.stores && mainConf.stores.refseqs)) {
-        storeConf.name = 'refseqs';
-    }
-    else {
-        storeConf.name = `store${(0, util_1.objectHash)(storeConf)}`;
-    }
+    storeConf.name =
+        (storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||
+            storeClass === 'JBrowse/Store/Sequence/IndexedFasta' ||
+            storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta' ||
+            storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta' ||
+            storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||
+            storeClass === 'JBrowse/Store/Sequence/TwoBit' ||
+            trackConfig.useAsRefSeqStore) &&
+            !(mainConf.stores && mainConf.stores.refseqs)
+            ? 'refseqs'
+            : `store${(0, util_1.objectHash)(storeConf)}`;
     // record it
     if (!mainConf.stores) {
         mainConf.stores = {};

package/dist/JBrowse1Connection/jb1ConfigParse.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/JBrowse1Connection/jb1ToJb2.js CHANGED Viewed

@@ -72,18 +72,15 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
                 cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },
                 sequenceAdapter,
             };
-            if (jb1TrackConfig.craiUrlTemplate) {
-                adapter.craiLocation = {
+            adapter.craiLocation = jb1TrackConfig.craiUrlTemplate
+                ? {
                     uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
                     locationType: 'UriLocation',
-                };
-            }
-            else {
-                adapter.craiLocation = {
+                }
+                : {
                     uri: `${urlTemplate}.crai`,
                     locationType: 'UriLocation',
                 };
-            }
             return {
                 ...jb2TrackConfig,
                 type: 'AlignmentsTrack',
@@ -265,18 +262,15 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
                 type: 'IndexedFastaAdapter',
                 fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
             };
-            if (jb1TrackConfig.faiUrlTemplate) {
-                adapter.faiLocation = {
+            adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
+                ? {
                     uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
                     locationType: 'UriLocation',
-                };
-            }
-            else {
-                adapter.faiLocation = {
+                }
+                : {
                     uri: `${urlTemplate}.fai`,
                     locationType: 'UriLocation',
                 };
-            }
             return {
                 ...jb2TrackConfig,
                 type: 'SequenceTrack',
@@ -288,30 +282,24 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
                 type: 'BgzipFastaAdapter',
                 fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
             };
-            if (jb1TrackConfig.faiUrlTemplate) {
-                adapter.faiLocation = {
+            adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
+                ? {
                     uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
                     locationType: 'UriLocation',
-                };
-            }
-            else {
-                adapter.faiLocation = {
+                }
+                : {
                     uri: `${urlTemplate}.fai`,
                     locationType: 'UriLocation',
                 };
-            }
-            if (jb1TrackConfig.gziUrlTemplate) {
-                adapter.gziLocation = {
+            adapter.gziLocation = jb1TrackConfig.gziUrlTemplate
+                ? {
                     uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
                     locationType: 'UriLocation',
-                };
-            }
-            else {
-                adapter.gziLocation = {
+                }
+                : {
                     uri: `${urlTemplate}.gzi`,
                     locationType: 'UriLocation',
                 };
-            }
             return {
                 ...jb2TrackConfig,
                 type: 'ReferenceSequenceTrack',

package/dist/JBrowse1Connection/jb1ToJb2.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/JBrowse1Connection/model.js CHANGED Viewed

@@ -35,10 +35,10 @@ function default_1(pluginManager) {
                     'sequence',
                     'adapter',
                 ]);
-                // @ts-ignore
+                // @ts-expect-error
                 const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => {
                     const jb2Track = (0, jb1ToJb2_1.convertTrackConfig)(jb1Track, config.dataRoot || '', sequenceAdapter);
-                    // @ts-ignore
+                    // @ts-expect-error
                     jb2Track.assemblyNames = [assemblyName];
                     return jb2Track;
                 });

package/dist/JBrowse1Connection/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/model.tsx"],"names":[],"mappings":";;;;;AAAA,+DAGoC;AACpC,6CAA+C;AAC/C,uEAAuF;AACvF,qDAAuC;AACvC,kEAAyC;AAEzC,mDAA0C;AAC1C,yCAA+C;AAG/C,mBAAyB,aAA4B;IACnD,OAAO,uBAAK;SACT,OAAO,CACN,oBAAoB,EACpB,IAAA,mCAA0B,EAAC,aAAa,CAAC,EACzC,uBAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,IAAA,sCAAsB,EAAC,sBAAY,CAAC;QACnD,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;KAC1C,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,OAAO;YACL,MAAM,eAAe,GAAG,IAAA,8BAAc,EACpC,IAAI,CAAC,aAAa,EAClB,iBAAiB,CAClB,CAAA;YACD,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAA,wBAAQ,EAAC,eAAe,CAAC;iBACtB,IAAI,CAAC,MAAM,CAAC,EAAE;;gBACb,MAAM,YAAY,GAAG,IAAA,8BAAc,EACjC,IAAI,CAAC,aAAa,EAClB,eAAe,CAChB,CAAC,CAAC,CAAC,CAAA;gBACJ,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;iBACnE;gBACD,MAAM,YAAY,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAC1C,QAAQ,CAAC,EAAE,CAAC,IAAA,8BAAc,EAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,YAAY,CAC9D,CAAA;gBACD,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,aAAa,CAAC,CAAA;iBACxD;gBACD,MAAM,eAAe,GAAG,IAAA,8BAAc,EAAC,YAAY,EAAE;oBACnD,UAAU;oBACV,SAAS;iBACV,CAAC,CAAA;gBAEF,~~aAAa~~;~~gBACb~~,MAAM,SAAS,GAAG,MAAA,MAAM,CAAC,MAAM,0CAAE,GAAG,CAAC,QAAQ,CAAC,EAAE;oBAC9C,MAAM,QAAQ,GAAG,IAAA,6BAAkB,EACjC,QAAQ,EACR,MAAM,CAAC,QAAQ,IAAI,EAAE,EACrB,eAAe,CAChB,CAAA;oBAED,~~aAAa~~;~~oBACb~~,QAAQ,CAAC,aAAa,GAAG,CAAC,YAAY,CAAC,CAAA;oBACvC,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBAEF,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC,CAAA;YAC/B,CAAC,CAAC;iBACD,KAAK,CAAC,KAAK,CAAC,EAAE;gBACb,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACpB,OAAO,CAAC,MAAM,CACZ,mEAAmE,IAAI,CAAC,IAAI,yFAAyF,KAAK,GAAG,EAC7K,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;YAC7C,CAAC,CAAC,CAAA;QACN,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AA/DD,4BA+DC"}
1	+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/model.tsx"],"names":[],"mappings":";;;;;AAAA,+DAGoC;AACpC,6CAA+C;AAC/C,uEAAuF;AACvF,qDAAuC;AACvC,kEAAyC;AAEzC,mDAA0C;AAC1C,yCAA+C;AAG/C,mBAAyB,aAA4B;IACnD,OAAO,uBAAK;SACT,OAAO,CACN,oBAAoB,EACpB,IAAA,mCAA0B,EAAC,aAAa,CAAC,EACzC,uBAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,IAAA,sCAAsB,EAAC,sBAAY,CAAC;QACnD,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;KAC1C,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,OAAO;YACL,MAAM,eAAe,GAAG,IAAA,8BAAc,EACpC,IAAI,CAAC,aAAa,EAClB,iBAAiB,CAClB,CAAA;YACD,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAA,wBAAQ,EAAC,eAAe,CAAC;iBACtB,IAAI,CAAC,MAAM,CAAC,EAAE;;gBACb,MAAM,YAAY,GAAG,IAAA,8BAAc,EACjC,IAAI,CAAC,aAAa,EAClB,eAAe,CAChB,CAAC,CAAC,CAAC,CAAA;gBACJ,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;iBACnE;gBACD,MAAM,YAAY,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAC1C,QAAQ,CAAC,EAAE,CAAC,IAAA,8BAAc,EAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,YAAY,CAC9D,CAAA;gBACD,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,aAAa,CAAC,CAAA;iBACxD;gBACD,MAAM,eAAe,GAAG,IAAA,8BAAc,EAAC,YAAY,EAAE;oBACnD,UAAU;oBACV,SAAS;iBACV,CAAC,CAAA;gBAEF,mBAAmB;gBACnB,MAAM,SAAS,GAAG,MAAA,MAAM,CAAC,MAAM,0CAAE,GAAG,CAAC,QAAQ,CAAC,EAAE;oBAC9C,MAAM,QAAQ,GAAG,IAAA,6BAAkB,EACjC,QAAQ,EACR,MAAM,CAAC,QAAQ,IAAI,EAAE,EACrB,eAAe,CAChB,CAAA;oBAED,mBAAmB;oBACnB,QAAQ,CAAC,aAAa,GAAG,CAAC,YAAY,CAAC,CAAA;oBACvC,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBAEF,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC,CAAA;YAC/B,CAAC,CAAC;iBACD,KAAK,CAAC,KAAK,CAAC,EAAE;gBACb,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACpB,OAAO,CAAC,MAAM,CACZ,mEAAmE,IAAI,CAAC,IAAI,yFAAyF,KAAK,GAAG,EAC7K,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;YAC7C,CAAC,CAAC,CAAA;QACN,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AA/DD,4BA+DC"}

package/dist/JBrowse1Connection/util.js CHANGED Viewed

@@ -22,8 +22,7 @@ function deepUpdate(a, b) {
             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];
         }
     }
@@ -40,7 +39,7 @@ exports.deepUpdate = deepUpdate;
  * e.g., 'htp://foo/someurl?arg=valueforbaz'
  */
 function fillTemplate(template, fillWith) {
-    return template.replace(/\{([\w\s.]+)\}/g, (match, varName) => {
+    return template.replace(/{([\s\w.]+)}/g, (match, varName) => {
         varName = varName.replace(/\s+/g, ''); // remove all whitespace
         const fill = (0, get_value_1.default)(fillWith, varName);
         if (fill !== undefined) {
@@ -50,7 +49,7 @@ function fillTemplate(template, fillWith) {
             return fill;
         }
         if (fillWith.callback) {
-            // @ts-ignore
+            // @ts-expect-error
             const v = fillWith.callback.call(this, varName);
             if (v !== undefined) {
                 return v;
@@ -137,7 +136,7 @@ function mixin(dest, source, copyFunc) {
         // toString() method that source inherited from Object.prototype
         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/dist/JBrowse1Connection/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/JBrowse1TextSearchAdapter/HttpMap.js CHANGED Viewed

@@ -75,10 +75,10 @@ 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/dist/JBrowse1TextSearchAdapter/HttpMap.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"HttpMap.js","sourceRoot":"","sources":["../../src/JBrowse1TextSearchAdapter/HttpMap.ts"],"names":[],"mappings":";;;;;AAAA;;;GAGG;AACH,gEAAgC;AAEhC,MAAqB,OAAO;IAG1B,YAAY,IAAqB;QAC/B,qCAAqC;QACrC,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,GAAG,CAAA;IAC7D,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,QAAQ;QACZ,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;QAC7C,MAAM,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAC9C,MAAM,iBAAiB,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,GAAG,CAAC,CAAC,CAAA;QACvD,OAAO,EAAE,iBAAiB,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAA;IAChD,CAAC;IAED,KAAK,CAAC,oBAAoB;QACxB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAClC,OAAO,IAAI,CAAC,iBAAiB,CAAA;IAC/B,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAClC,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAClC,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,GAAG,CAAC,GAAW;QACnB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,CAAA;QACxC,OAAO,MAAM,CAAC,GAAG,CAAC,CAAA;IACpB,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,SAAS,CAAC,GAAW;QACzB,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAClC,MAAM,YAAY,GAAG,MAAM,IAAI,CAAC,YAAY,CAAC,WAAW,CAAC,CAAA;QACzD,OAAO,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAA;IACpC,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,QAAQ,CAAC,EAAU;QACvB,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,IAAI,CAAC,GAAG,GAAG,EAAE,EAAE,CAAC,CAAA;QAChD,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,QAAQ,QAAQ,CAAC,MAAM,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAC,CAAA;SAClE;QACD,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;IACxB,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,YAAY,CAAC,GAAW;QAC5B,qDAAqD;QACrD,MAAM,iBAAiB,GAAG,MAAM,IAAI,CAAC,oBAAoB,EAAE,CAAA;QAC3D,IAAI,iBAAiB,EAAE;YACrB,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,EAAE,CAAA;YACzC,OAAO,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE;gBACrB,GAAG,GAAG,IAAI,GAAG,EAAE,CAAA;aAChB;YACD,GAAG,GAAG,GAAG,CAAC,~~MAAM~~,CAAC,CAAC,GAAG,iBAAiB,CAAC,CAAA;~~YACvC~~,MAAM,OAAO,GAAG,EAAE,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;gBACtC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,~~SAAS~~,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;~~aACtC~~;YACD,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,QAAQ,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAA;SACzD;QACD,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,CAAC,IAAY;QACf,OAAO,IAAA,sBAAK,EAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;aAC5B,QAAQ,CAAC,KAAK,CAAC;aACf,WAAW,EAAE;aACb,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IACtB,CAAC;CACF;AA7FD,0BA6FC"}
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package/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts CHANGED Viewed

@@ -1,7 +1,6 @@
 import { BaseTextSearchAdapter, BaseArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { Instance } from 'mobx-state-tree';
-import MyConfigSchema from './configSchema';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import HttpMap from './HttpMap';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
@@ -16,16 +15,17 @@ interface SearchResults {
     exact: [string, number, string, string, number, number][];
 }
 export type NamesIndexRecord = string | Array<string | number>;
+type IndexFile = Record<string, SearchResults>;
 export default class JBrowse1TextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
     httpMap: HttpMap;
     tracksNames?: string[];
-    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     /**
      * Returns the contents of the file containing the query if it exists
      * else it returns empty
      * @param query - string query
      */
-    loadIndexFile(query: string): Promise<Record<string, SearchResults>>;
+    loadIndexFile(query: string): Promise<IndexFile>;
     searchIndex(args: BaseArgs): Promise<BaseResult[]>;
     formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];
     freeResources(): void;

package/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js CHANGED Viewed

@@ -7,19 +7,14 @@ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
 const configuration_1 = require("@jbrowse/core/configuration");
 const HttpMap_1 = __importDefault(require("./HttpMap"));
-//  Jbrowse1 text search adapter
 // Uses index built by generate-names.pl
 class JBrowse1TextSearchAdapter extends BaseAdapter_1.BaseAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
-        const namesIndexLocation = (0, configuration_1.readConfObject)(config, 'namesIndexLocation');
-        if (!namesIndexLocation) {
-            throw new Error('must provide namesIndexLocation');
-        }
+        const namesIndex = (0, configuration_1.readConfObject)(config, 'namesIndexLocation');
+        const { baseUri, uri } = namesIndex;
         this.httpMap = new HttpMap_1.default({
-            url: namesIndexLocation.baseUri
-                ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href
-                : namesIndexLocation.uri,
+            url: baseUri ? new URL(uri, baseUri).href : uri,
         });
     }
     /**
@@ -33,23 +28,21 @@ class JBrowse1TextSearchAdapter extends BaseAdapter_1.BaseAdapter {
     async searchIndex(args) {
         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, tracks, searchType) {
         return [
             ...(searchType === 'exact'
                 ? []
-                : results.prefix.map(result => {
-                    return new BaseResults_1.default({
-                        label: typeof result === 'object' ? result.name : result,
-                        matchedAttribute: 'name',
-                        matchedObject: { result: result },
-                    });
-                })),
+                : results.prefix.map(result => new BaseResults_1.default({
+                    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/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/NCListAdapter/NCListFeature.js CHANGED Viewed

@@ -16,13 +16,13 @@ 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;
     }