@jbrowse/plugin-legacy-jbrowse 2.10.2 → 2.11.0

package/dist/JBrowse1Connection/jb1ConfigParse.js

@@ -293,10 +293,11 @@ function regularizeClass(root, className) {
     return className;
 }
 function guessStoreClass(trackConfig, urlTemplate) {
+    var _a, _b;
     if (!trackConfig) {
         return '';
     }
-    if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {
+    if ((_a = trackConfig.type) === null || _a === void 0 ? void 0 : _a.includes('/FixedImage')) {
         return `JBrowse/Store/TiledImage/Fixed${trackConfig.backendVersion === 0 ? '_v0' : ''}`;
     }
     if (/\.jsonz?$/i.test(urlTemplate)) {
@@ -338,7 +339,7 @@ function guessStoreClass(trackConfig, urlTemplate) {
     if (/\.2bit$/i.test(urlTemplate)) {
         return 'JBrowse/Store/SeqFeature/TwoBit';
     }
-    if (trackConfig.type && trackConfig.type.endsWith('/Sequence')) {
+    if ((_b = trackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('/Sequence')) {
         return 'JBrowse/Store/Sequence/StaticChunked';
     }
     return '';

package/dist/JBrowse1Connection/jb1ToJb2.js

@@ -5,7 +5,7 @@ const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
-    var _a;
+    var _a, _b, _c, _d, _e;
     const jb2TrackConfig = {
         trackId: (0, util_1.objectHash)(jb1TrackConfig),
         name: jb1TrackConfig.key || jb1TrackConfig.label,
@@ -19,7 +19,7 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
     const { storeClass } = jb1TrackConfig;
     if (!jb1TrackConfig.urlTemplate) {
-        if (!(storeClass && storeClass.endsWith('FromConfig'))) {
+        if (!(storeClass === null || storeClass === void 0 ? void 0 : storeClass.endsWith('FromConfig'))) {
             const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
             console.warn(`Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`);
             return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
@@ -99,11 +99,10 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
             storeClass === 'JBrowse/Store/BigWig') {
-            if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+            if ((_b = jb1TrackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('XYPlot')) {
                 jb2TrackConfig.defaultRendering = 'xyplot';
             }
-            else if (jb1TrackConfig.type &&
-                jb1TrackConfig.type.endsWith('Density')) {
+            else if ((_c = jb1TrackConfig.type) === null || _c === void 0 ? void 0 : _c.endsWith('Density')) {
                 jb2TrackConfig.defaultRendering = 'density';
             }
             return {
@@ -330,10 +329,10 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     }
     jb2TrackConfig.type = (0, tracks_1.guessTrackType)(jb2TrackConfig.adapter.type);
     if (jb2TrackConfig.type === 'QuantitativeTrack') {
-        if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+        if ((_d = jb1TrackConfig.type) === null || _d === void 0 ? void 0 : _d.endsWith('XYPlot')) {
             jb2TrackConfig.defaultRendering = 'xyplot';
         }
-        else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
+        else if ((_e = jb1TrackConfig.type) === null || _e === void 0 ? void 0 : _e.endsWith('Density')) {
             jb2TrackConfig.defaultRendering = 'density';
         }
     }

package/dist/JBrowse1Connection/model.js

@@ -65,7 +65,7 @@ function default_1(pluginManager) {
             }
             catch (error) {
                 console.error(error);
-                session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
+                session.notifyError(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, error);
                 (_b = session.breakConnection) === null || _b === void 0 ? void 0 : _b.call(session, self.configuration);
             }
         },

package/esm/JBrowse1Connection/jb1ConfigParse.js

@@ -284,10 +284,11 @@ function regularizeClass(root, className) {
     return className;
 }
 function guessStoreClass(trackConfig, urlTemplate) {
+    var _a, _b;
     if (!trackConfig) {
         return '';
     }
-    if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {
+    if ((_a = trackConfig.type) === null || _a === void 0 ? void 0 : _a.includes('/FixedImage')) {
         return `JBrowse/Store/TiledImage/Fixed${trackConfig.backendVersion === 0 ? '_v0' : ''}`;
     }
     if (/\.jsonz?$/i.test(urlTemplate)) {
@@ -329,7 +330,7 @@ function guessStoreClass(trackConfig, urlTemplate) {
     if (/\.2bit$/i.test(urlTemplate)) {
         return 'JBrowse/Store/SeqFeature/TwoBit';
     }
-    if (trackConfig.type && trackConfig.type.endsWith('/Sequence')) {
+    if ((_b = trackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('/Sequence')) {
         return 'JBrowse/Store/Sequence/StaticChunked';
     }
     return '';

package/esm/JBrowse1Connection/jb1ToJb2.js

@@ -2,7 +2,7 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { objectHash } from '@jbrowse/core/util';
 import { generateUnknownTrackConf, generateUnsupportedTrackConf, guessAdapter, guessTrackType, UNKNOWN, UNSUPPORTED, } from '@jbrowse/core/util/tracks';
 export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
-    var _a;
+    var _a, _b, _c, _d, _e;
     const jb2TrackConfig = {
         trackId: objectHash(jb1TrackConfig),
         name: jb1TrackConfig.key || jb1TrackConfig.label,
@@ -16,7 +16,7 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
     const { storeClass } = jb1TrackConfig;
     if (!jb1TrackConfig.urlTemplate) {
-        if (!(storeClass && storeClass.endsWith('FromConfig'))) {
+        if (!(storeClass === null || storeClass === void 0 ? void 0 : storeClass.endsWith('FromConfig'))) {
             const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
             console.warn(`Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`);
             return generateUnsupportedTrackConf(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
@@ -96,11 +96,10 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
             storeClass === 'JBrowse/Store/BigWig') {
-            if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+            if ((_b = jb1TrackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('XYPlot')) {
                 jb2TrackConfig.defaultRendering = 'xyplot';
             }
-            else if (jb1TrackConfig.type &&
-                jb1TrackConfig.type.endsWith('Density')) {
+            else if ((_c = jb1TrackConfig.type) === null || _c === void 0 ? void 0 : _c.endsWith('Density')) {
                 jb2TrackConfig.defaultRendering = 'density';
             }
             return {
@@ -327,10 +326,10 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     }
     jb2TrackConfig.type = guessTrackType(jb2TrackConfig.adapter.type);
     if (jb2TrackConfig.type === 'QuantitativeTrack') {
-        if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+        if ((_d = jb1TrackConfig.type) === null || _d === void 0 ? void 0 : _d.endsWith('XYPlot')) {
             jb2TrackConfig.defaultRendering = 'xyplot';
         }
-        else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
+        else if ((_e = jb1TrackConfig.type) === null || _e === void 0 ? void 0 : _e.endsWith('Density')) {
             jb2TrackConfig.defaultRendering = 'density';
         }
     }

package/esm/JBrowse1Connection/model.js

@@ -37,7 +37,7 @@ export default function (pluginManager) {
             }
             catch (error) {
                 console.error(error);
-                session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
+                session.notifyError(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, error);
                 (_b = session.breakConnection) === null || _b === void 0 ? void 0 : _b.call(session, self.configuration);
             }
         },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.10.2",
+  "version": "2.11.0",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
   },
   "dependencies": {
     "@gmod/nclist": "^0.2.1",
-    "buffer-crc32": "^0.2.13",
+    "buffer-crc32": "^1.0.0",
     "generic-filehandle": "^3.0.0",
     "get-value": "^3.0.1",
     "set-value": "^4.0.1"
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
+  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
 }