npm - @jbrowse/plugin-legacy-jbrowse - Versions diffs - 2.5.0 → 2.6.1 - Mend

@jbrowse/plugin-legacy-jbrowse 2.5.0 → 2.6.1

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 (32) hide show

package/dist/JBrowse1Connection/jb1ConfigParse.js +1 -1
package/dist/JBrowse1Connection/jb1ConfigParse.js.map +1 -1
package/dist/JBrowse1Connection/jb1ToJb2.js +2 -2
package/dist/JBrowse1Connection/jb1ToJb2.js.map +1 -1
package/dist/JBrowse1Connection/model.d.ts +13 -1
package/dist/JBrowse1Connection/model.js +40 -18
package/dist/JBrowse1Connection/model.js.map +1 -1
package/dist/JBrowse1Connection/util.d.ts +1 -0
package/dist/JBrowse1Connection/util.js +4 -6
package/dist/JBrowse1Connection/util.js.map +1 -1
package/dist/NCListAdapter/NCListFeature.js +1 -2
package/dist/NCListAdapter/NCListFeature.js.map +1 -1
package/esm/JBrowse1Connection/jb1ConfigParse.js +1 -1
package/esm/JBrowse1Connection/jb1ConfigParse.js.map +1 -1
package/esm/JBrowse1Connection/jb1ToJb2.js +2 -2
package/esm/JBrowse1Connection/jb1ToJb2.js.map +1 -1
package/esm/JBrowse1Connection/model.d.ts +13 -1
package/esm/JBrowse1Connection/model.js +18 -19
package/esm/JBrowse1Connection/model.js.map +1 -1
package/esm/JBrowse1Connection/util.d.ts +1 -0
package/esm/JBrowse1Connection/util.js +4 -6
package/esm/JBrowse1Connection/util.js.map +1 -1
package/esm/NCListAdapter/NCListFeature.js +1 -2
package/esm/NCListAdapter/NCListFeature.js.map +1 -1
package/package.json +2 -2
package/src/JBrowse1Connection/jb1ConfigParse.ts +1 -1
package/src/JBrowse1Connection/jb1ToJb2.ts +2 -2
package/src/JBrowse1Connection/model.tsx +42 -50
package/src/JBrowse1Connection/util.ts +4 -6
package/src/JBrowse1TextSearchAdapter/HttpMap.test.ts +2 -2
package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.test.ts +1 -1
package/src/NCListAdapter/NCListFeature.ts +1 -2

package/dist/JBrowse1Connection/jb1ConfigParse.js CHANGED Viewed

@@ -58,7 +58,7 @@ function parse(text, url) {
                 }
                 // parse numbers if it looks numeric
                 else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
-                    parsedValue = parseFloat(value.replace(/,/g, ''));
+                    parsedValue = parseFloat(value.replaceAll(',', ''));
                 }
                 else {
                     parsedValue = value;

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

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

@@ -28,8 +28,8 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     }
     const resolveUrlTemplate = (urlTemplate) => {
         return new URL(urlTemplate, `${dataRoot}/`).href
-            .replace(/%7B/gi, '{')
-            .replace(/%7D/gi, '}');
+            .replaceAll(/%7B/gi, '{')
+            .replaceAll(/%7D/gi, '}');
     };
     const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
     if (storeClass) {

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

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

@@ -2,6 +2,18 @@ import PluginManager from '@jbrowse/core/PluginManager';
 export default function (pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        name: {
+            type: string;
+            defaultValue: string;
+            description: string;
+        };
+        assemblyNames: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
 } & {
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         dataDirLocation: {
@@ -49,5 +61,5 @@ export default function (pluginManager: PluginManager): import("mobx-state-tree"
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
     clear(): void;
 } & {
-    connect(): void;
+    connect(): Promise<void>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/JBrowse1Connection/model.js CHANGED Viewed

@@ -1,4 +1,27 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -7,9 +30,8 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const mobx_state_tree_1 = require("mobx-state-tree");
+// locals
 const configSchema_1 = __importDefault(require("./configSchema"));
-const jb1ConfigLoad_1 = require("./jb1ConfigLoad");
-const jb1ToJb2_1 = require("./jb1ToJb2");
 function default_1(pluginManager) {
     return mobx_state_tree_1.types
         .compose('JBrowse1Connection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types.model({
@@ -17,17 +39,19 @@ function default_1(pluginManager) {
         type: mobx_state_tree_1.types.literal('JBrowse1Connection'),
     }))
         .actions(self => ({
-        connect() {
-            const dataDirLocation = (0, configuration_1.readConfObject)(self.configuration, 'dataDirLocation');
+        async connect() {
+            var _a;
             const session = (0, util_1.getSession)(self);
-            (0, jb1ConfigLoad_1.fetchJb1)(dataDirLocation)
-                .then(config => {
-                var _a;
-                const assemblyName = (0, configuration_1.readConfObject)(self.configuration, 'assemblyNames')[0];
+            try {
+                const dataDirLocation = (0, configuration_1.getConf)(self, 'dataDirLocation');
+                const { fetchJb1 } = await Promise.resolve().then(() => __importStar(require('./jb1ConfigLoad')));
+                const { convertTrackConfig } = await Promise.resolve().then(() => __importStar(require('./jb1ToJb2')));
+                const config = await fetchJb1(dataDirLocation);
+                const assemblyName = (0, configuration_1.getConf)(self, 'assemblyNames')[0];
                 if (!assemblyName) {
                     throw new Error('assembly name required for JBrowse 1 connection');
                 }
-                const assemblyConf = session.assemblies.find(assembly => (0, configuration_1.readConfObject)(assembly, 'name') === assemblyName);
+                const assemblyConf = session.assemblies.find(a => (0, configuration_1.readConfObject)(a, 'name') === assemblyName);
                 if (!assemblyConf) {
                     throw new Error(`Assembly "${assemblyName}" not found`);
                 }
@@ -36,19 +60,17 @@ function default_1(pluginManager) {
                     'adapter',
                 ]);
                 // @ts-expect-error
-                const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => {
-                    const jb2Track = (0, jb1ToJb2_1.convertTrackConfig)(jb1Track, config.dataRoot || '', sequenceAdapter);
-                    // @ts-expect-error
-                    jb2Track.assemblyNames = [assemblyName];
-                    return jb2Track;
-                });
+                const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => ({
+                    ...convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter),
+                    assemblyNames: [assemblyName],
+                }));
                 self.setTrackConfs(jb2Tracks);
-            })
-                .catch(error => {
+            }
+            catch (error) {
                 console.error(error);
                 session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
                 session.breakConnection(self.configuration);
-            });
+            }
         },
     }));
 }

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

	@@ -1 +1 @@
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package/dist/JBrowse1Connection/util.d.ts CHANGED Viewed

@@ -8,6 +8,7 @@ type Obj = Record<string, any>;
 export declare function deepUpdate(a: Obj, b: Obj): Obj;
 /**
  * replace variables in a template string with values
+ *
  * @param template - String with variable names in curly brackets
  * e.g., `http://foo/{bar}?arg={baz.foo}`
  * @param fillWith - object with attribute-value mappings

package/dist/JBrowse1Connection/util.js CHANGED Viewed

@@ -31,6 +31,7 @@ function deepUpdate(a, b) {
 exports.deepUpdate = deepUpdate;
 /**
  * replace variables in a template string with values
+ *
  * @param template - String with variable names in curly brackets
  * e.g., `http://foo/{bar}?arg={baz.foo}`
  * @param fillWith - object with attribute-value mappings
@@ -39,14 +40,11 @@ exports.deepUpdate = deepUpdate;
  * e.g., 'htp://foo/someurl?arg=valueforbaz'
  */
 function fillTemplate(template, fillWith) {
-    return template.replace(/{([\s\w.]+)}/g, (match, varName) => {
-        varName = varName.replace(/\s+/g, ''); // remove all whitespace
+    return template.replaceAll(/{([\s\w.]+)}/g, (match, varName) => {
+        varName = varName.replaceAll(/\s+/g, '');
         const fill = (0, get_value_1.default)(fillWith, varName);
         if (fill !== undefined) {
-            if (typeof fill === 'function') {
-                return fill(varName);
-            }
-            return fill;
+            return typeof fill === 'function' ? fill(varName) : fill;
         }
         if (fillWith.callback) {
             // @ts-expect-error

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/util.ts"],"names":[],"mappings":";;;;;;AAAA,0DAAgC;AAGhC,8DAA8D;AAC9D,SAAgB,OAAO,CAAC,GAAQ;IAC9B,OAAO,GAAG,IAAI,GAAG,CAAC,KAAK,IAAI,OAAO,GAAG,CAAC,KAAK,KAAK,QAAQ,CAAA;AAC1D,CAAC;AAFD,0BAEC;AAED,8DAA8D;AAC9D,SAAgB,QAAQ,CAAC,GAAQ;IAC/B,OAAO,GAAG,IAAI,GAAG,CAAC,GAAG,IAAI,OAAO,GAAG,CAAC,GAAG,KAAK,QAAQ,CAAA;AACtD,CAAC;AAFD,4BAEC;AAOD,SAAgB,UAAU,CAAC,CAAM,EAAE,CAAM;IACvC,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE;QACjC,IACE,IAAI,IAAI,CAAC;YACT,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ;YAC3B,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ,EAC3B;YACA,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;SAC7B;aAAM,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,SAAS,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,SAAS,EAAE;YACzD,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;SAClB;KACF;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAbD,gCAaC;AAED;;;;;;;;;GASG;AACH,SAAgB,YAAY,CAAC,QAAgB,EAAE,QAAa;IAC1D,OAAO,QAAQ,CAAC,UAAU,CAAC,eAAe,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE;QAC7D,OAAO,GAAG,OAAO,CAAC,UAAU,CAAC,MAAM,EAAE,EAAE,CAAC,CAAA;QACxC,MAAM,IAAI,GAAG,IAAA,mBAAQ,EAAC,QAAQ,EAAE,OAAO,CAAC,CAAA;QACxC,IAAI,IAAI,KAAK,SAAS,EAAE;YACtB,OAAO,OAAO,IAAI,KAAK,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;SACzD;QACD,IAAI,QAAQ,CAAC,QAAQ,EAAE;YACrB,mBAAmB;YACnB,MAAM,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;YAC/C,IAAI,CAAC,KAAK,SAAS,EAAE;gBACnB,OAAO,CAAC,CAAA;aACT;SACF;QACD,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAhBD,oCAgBC;AAED;;;;;GAKG;AACH,8DAA8D;AAC9D,SAAgB,KAAK,CAAC,GAAQ;IAC5B,IACE,CAAC,GAAG;QACJ,OAAO,GAAG,KAAK,QAAQ;QACvB,MAAM,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,mBAAmB,EAC3D;QACA,+CAA+C;QAC/C,OAAO,GAAG,CAAA,CAAC,WAAW;KACvB;IACD,IAAI,GAAG,CAAC,QAAQ,IAAI,WAAW,IAAI,GAAG,EAAE;QACtC,WAAW;QACX,OAAO,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA,CAAC,OAAO;KACnC;IACD,IAAI,GAAG,YAAY,IAAI,EAAE;QACvB,OAAO;QACP,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC,CAAA,CAAC,OAAO;KACvC;IACD,IAAI,GAAG,YAAY,MAAM,EAAE;QACzB,SAAS;QACT,OAAO,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA,CAAC,SAAS;KACjC;IACD,IAAI,CAAC,CAAA;IACL,IAAI,CAAC,CAAA;IACL,IAAI,CAAC,CAAA;IACL,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE;QACtB,QAAQ;QACR,CAAC,GAAG,EAAE,CAAA;QACN,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,EAAE;YACtC,IAAI,CAAC,IAAI,GAAG,EAAE;gBACZ,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;aACrB;SACF;QACD,mDAAmD;QACnD,kCAAkC;QAClC,mBAAmB;QACnB,6DAA6D;KAC9D;SAAM;QACL,kBAAkB;QAClB,CAAC,GAAG,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAA;KACjD;IACD,OAAO,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,KAAK,CAAC,CAAA;AAC7B,CAAC;AAzCD,sBAyCC;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,SAAS,KAAK,CAAC,IAAS,EAAE,MAAW,EAAE,QAAkB;IACvD,IAAI,IAAI,CAAA;IACR,IAAI,CAAC,CAAA;IACL,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,IAAI,MAAM,EAAE;QACnB,uEAAuE;QACvE,wEAAwE;QACxE,sEAAsE;QACtE,gEAAgE;QAChE,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;QAChB,IACE,CAAC,CAAC,IAAI,IAAI,IAAI,CAAC;YACf,mBAAmB;YACnB,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,KAAK,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAC7D;YACA,IAAI,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;SACxC;KACF;IAED,OAAO,IAAI,CAAA,CAAC,SAAS;AACvB,CAAC"}

package/dist/NCListAdapter/NCListFeature.js CHANGED Viewed

@@ -23,8 +23,7 @@ class NCListFeature {
     jb1TagToJb2Tag(tag) {
         const t = tag.toLowerCase();
         // @ts-expect-error
-        const mapped = jb1ToJb2[t] || t;
-        return mapped;
+        return jb1ToJb2[t] || t;
     }
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     get(attrName) {

package/dist/NCListAdapter/NCListFeature.js.map CHANGED Viewed

	@@ -1 +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,MAAqB,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;~~AAlFD~~,~~gCAkFC~~"}
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,MAAqB,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,OAAO,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IACzB,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;AAjFD,gCAiFC"}

package/esm/JBrowse1Connection/jb1ConfigParse.js CHANGED Viewed

@@ -50,7 +50,7 @@ function parse(text, url) {
                 }
                 // parse numbers if it looks numeric
                 else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
-                    parsedValue = parseFloat(value.replace(/,/g, ''));
+                    parsedValue = parseFloat(value.replaceAll(',', ''));
                 }
                 else {
                     parsedValue = value;

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

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

@@ -25,8 +25,8 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     }
     const resolveUrlTemplate = (urlTemplate) => {
         return new URL(urlTemplate, `${dataRoot}/`).href
-            .replace(/%7B/gi, '{')
-            .replace(/%7D/gi, '}');
+            .replaceAll(/%7B/gi, '{')
+            .replaceAll(/%7D/gi, '}');
     };
     const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
     if (storeClass) {

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

	@@ -1 +1 @@
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package/esm/JBrowse1Connection/model.d.ts CHANGED Viewed

@@ -2,6 +2,18 @@ import PluginManager from '@jbrowse/core/PluginManager';
 export default function (pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        name: {
+            type: string;
+            defaultValue: string;
+            description: string;
+        };
+        assemblyNames: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
 } & {
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         dataDirLocation: {
@@ -49,5 +61,5 @@ export default function (pluginManager: PluginManager): import("mobx-state-tree"
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
     clear(): void;
 } & {
-    connect(): void;
+    connect(): Promise<void>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/JBrowse1Connection/model.js CHANGED Viewed

@@ -1,10 +1,9 @@
-import { ConfigurationReference, readConfObject, } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
 import { types } from 'mobx-state-tree';
+// locals
 import configSchema from './configSchema';
-import { fetchJb1 } from './jb1ConfigLoad';
-import { convertTrackConfig } from './jb1ToJb2';
 export default function (pluginManager) {
     return types
         .compose('JBrowse1Connection', BaseConnectionModelFactory(pluginManager), types.model({
@@ -12,17 +11,19 @@ export default function (pluginManager) {
         type: types.literal('JBrowse1Connection'),
     }))
         .actions(self => ({
-        connect() {
-            const dataDirLocation = readConfObject(self.configuration, 'dataDirLocation');
+        async connect() {
+            var _a;
             const session = getSession(self);
-            fetchJb1(dataDirLocation)
-                .then(config => {
-                var _a;
-                const assemblyName = readConfObject(self.configuration, 'assemblyNames')[0];
+            try {
+                const dataDirLocation = getConf(self, 'dataDirLocation');
+                const { fetchJb1 } = await import('./jb1ConfigLoad');
+                const { convertTrackConfig } = await import('./jb1ToJb2');
+                const config = await fetchJb1(dataDirLocation);
+                const assemblyName = getConf(self, 'assemblyNames')[0];
                 if (!assemblyName) {
                     throw new Error('assembly name required for JBrowse 1 connection');
                 }
-                const assemblyConf = session.assemblies.find(assembly => readConfObject(assembly, 'name') === assemblyName);
+                const assemblyConf = session.assemblies.find(a => readConfObject(a, 'name') === assemblyName);
                 if (!assemblyConf) {
                     throw new Error(`Assembly "${assemblyName}" not found`);
                 }
@@ -31,19 +32,17 @@ export default function (pluginManager) {
                     'adapter',
                 ]);
                 // @ts-expect-error
-                const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => {
-                    const jb2Track = convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter);
-                    // @ts-expect-error
-                    jb2Track.assemblyNames = [assemblyName];
-                    return jb2Track;
-                });
+                const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => ({
+                    ...convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter),
+                    assemblyNames: [assemblyName],
+                }));
                 self.setTrackConfs(jb2Tracks);
-            })
-                .catch(error => {
+            }
+            catch (error) {
                 console.error(error);
                 session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
                 session.breakConnection(self.configuration);
-            });
+            }
         },
     }));
 }

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

	@@ -1 +1 @@
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package/esm/JBrowse1Connection/util.d.ts CHANGED Viewed

@@ -8,6 +8,7 @@ type Obj = Record<string, any>;
 export declare function deepUpdate(a: Obj, b: Obj): Obj;
 /**
  * replace variables in a template string with values
+ *
  * @param template - String with variable names in curly brackets
  * e.g., `http://foo/{bar}?arg={baz.foo}`
  * @param fillWith - object with attribute-value mappings

package/esm/JBrowse1Connection/util.js CHANGED Viewed

@@ -22,6 +22,7 @@ export function deepUpdate(a, b) {
 }
 /**
  * replace variables in a template string with values
+ *
  * @param template - String with variable names in curly brackets
  * e.g., `http://foo/{bar}?arg={baz.foo}`
  * @param fillWith - object with attribute-value mappings
@@ -30,14 +31,11 @@ export function deepUpdate(a, b) {
  * e.g., 'htp://foo/someurl?arg=valueforbaz'
  */
 export function fillTemplate(template, fillWith) {
-    return template.replace(/{([\s\w.]+)}/g, (match, varName) => {
-        varName = varName.replace(/\s+/g, ''); // remove all whitespace
+    return template.replaceAll(/{([\s\w.]+)}/g, (match, varName) => {
+        varName = varName.replaceAll(/\s+/g, '');
         const fill = getValue(fillWith, varName);
         if (fill !== undefined) {
-            if (typeof fill === 'function') {
-                return fill(varName);
-            }
-            return fill;
+            return typeof fill === 'function' ? fill(varName) : fill;
         }
         if (fillWith.callback) {
             // @ts-expect-error

package/esm/JBrowse1Connection/util.js.map CHANGED Viewed

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

@@ -21,8 +21,7 @@ export default class NCListFeature {
     jb1TagToJb2Tag(tag) {
         const t = tag.toLowerCase();
         // @ts-expect-error
-        const mapped = jb1ToJb2[t] || t;
-        return mapped;
+        return jb1ToJb2[t] || t;
     }
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     get(attrName) {

package/esm/NCListAdapter/NCListFeature.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.5.0",
+  "version": "2.6.1",
   "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": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
 }

package/src/JBrowse1Connection/jb1ConfigParse.ts CHANGED Viewed

@@ -60,7 +60,7 @@ function parse(text: string, url: string): Config {
         }
         // parse numbers if it looks numeric
         else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
-          parsedValue = parseFloat(value.replace(/,/g, ''))
+          parsedValue = parseFloat(value.replaceAll(',', ''))
         } else {
           parsedValue = value
         }

package/src/JBrowse1Connection/jb1ToJb2.ts CHANGED Viewed

@@ -96,8 +96,8 @@ export function convertTrackConfig(
   const resolveUrlTemplate = (urlTemplate: string) => {
     return new URL(urlTemplate, `${dataRoot}/`).href
-      .replace(/%7B/gi, '{')
-      .replace(/%7D/gi, '}')
+      .replaceAll(/%7B/gi, '{')
+      .replaceAll(/%7D/gi, '}')
   }
   const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate)

package/src/JBrowse1Connection/model.tsx CHANGED Viewed

@@ -1,15 +1,15 @@
 import {
   ConfigurationReference,
+  getConf,
   readConfObject,
 } from '@jbrowse/core/configuration'
 import { getSession } from '@jbrowse/core/util'
+import PluginManager from '@jbrowse/core/PluginManager'
 import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'
 import { types } from 'mobx-state-tree'
-import configSchema from './configSchema'
-import { fetchJb1 } from './jb1ConfigLoad'
-import { convertTrackConfig } from './jb1ToJb2'
-import PluginManager from '@jbrowse/core/PluginManager'
+// locals
+import configSchema from './configSchema'
 export default function (pluginManager: PluginManager) {
   return types
@@ -23,55 +23,47 @@ export default function (pluginManager: PluginManager) {
     )
     .actions(self => ({
-      connect() {
-        const dataDirLocation = readConfObject(
-          self.configuration,
-          'dataDirLocation',
-        )
+      async connect() {
         const session = getSession(self)
-        fetchJb1(dataDirLocation)
-          .then(config => {
-            const assemblyName = readConfObject(
-              self.configuration,
-              'assemblyNames',
-            )[0]
-            if (!assemblyName) {
-              throw new Error('assembly name required for JBrowse 1 connection')
-            }
-            const assemblyConf = session.assemblies.find(
-              assembly => readConfObject(assembly, 'name') === assemblyName,
-            )
-            if (!assemblyConf) {
-              throw new Error(`Assembly "${assemblyName}" not found`)
-            }
-            const sequenceAdapter = readConfObject(assemblyConf, [
-              'sequence',
-              'adapter',
-            ])
-            // @ts-expect-error
-            const jb2Tracks = config.tracks?.map(jb1Track => {
-              const jb2Track = convertTrackConfig(
-                jb1Track,
-                config.dataRoot || '',
-                sequenceAdapter,
-              )
+        try {
+          const dataDirLocation = getConf(self, 'dataDirLocation')
+          const { fetchJb1 } = await import('./jb1ConfigLoad')
+          const { convertTrackConfig } = await import('./jb1ToJb2')
+          const config = await fetchJb1(dataDirLocation)
+          const assemblyName = getConf(self, 'assemblyNames')[0]
+          if (!assemblyName) {
+            throw new Error('assembly name required for JBrowse 1 connection')
+          }
+          const assemblyConf = session.assemblies.find(
+            a => readConfObject(a, 'name') === assemblyName,
+          )
+          if (!assemblyConf) {
+            throw new Error(`Assembly "${assemblyName}" not found`)
+          }
+          const sequenceAdapter = readConfObject(assemblyConf, [
+            'sequence',
+            'adapter',
+          ])
-              // @ts-expect-error
-              jb2Track.assemblyNames = [assemblyName]
-              return jb2Track
-            })
+          // @ts-expect-error
+          const jb2Tracks = config.tracks?.map(jb1Track => ({
+            ...convertTrackConfig(
+              jb1Track,
+              config.dataRoot || '',
+              sequenceAdapter,
+            ),
+            assemblyNames: [assemblyName],
+          }))
-            self.setTrackConfs(jb2Tracks)
-          })
-          .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.breakConnection(self.configuration)
-          })
+          self.setTrackConfs(jb2Tracks)
+        } 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.breakConnection(self.configuration)
+        }
       },
     }))
 }

package/src/JBrowse1Connection/util.ts CHANGED Viewed

@@ -33,6 +33,7 @@ export function deepUpdate(a: Obj, b: Obj): Obj {
 /**
  * replace variables in a template string with values
+ *
  * @param template - String with variable names in curly brackets
  * e.g., `http://foo/{bar}?arg={baz.foo}`
  * @param fillWith - object with attribute-value mappings
@@ -41,14 +42,11 @@ 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(/{([\s\w.]+)}/g, (match, varName: string): string => {
-    varName = varName.replace(/\s+/g, '') // remove all whitespace
+  return template.replaceAll(/{([\s\w.]+)}/g, (match, varName) => {
+    varName = varName.replaceAll(/\s+/g, '')
     const fill = getValue(fillWith, varName)
     if (fill !== undefined) {
-      if (typeof fill === 'function') {
-        return fill(varName)
-      }
-      return fill
+      return typeof fill === 'function' ? fill(varName) : fill
     }
     if (fillWith.callback) {
       // @ts-expect-error

package/src/JBrowse1TextSearchAdapter/HttpMap.test.ts CHANGED Viewed

@@ -7,7 +7,7 @@ import HttpMap from './HttpMap'
 test('read from meta', async () => {
   const rootTemplate = path
     .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
-    .replace(/\\/g, '\\\\')
+    .replaceAll('\\', '\\\\')
   jest.spyOn(global, 'fetch').mockImplementation(url => {
     const response = `${url}`.includes('names/meta.json') ? meta : {}
@@ -23,7 +23,7 @@ test('read from meta', async () => {
 test('get bucket contents', async () => {
   const rootTemplate = path
     .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
-    .replace(/\\/g, '\\\\')
+    .replaceAll('\\', '\\\\')
   const spy = jest.spyOn(global, 'fetch')
   spy.mockImplementation(url => {

package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.test.ts CHANGED Viewed

@@ -22,7 +22,7 @@ function mockFetch(url: RequestInfo | URL) {
 const rootTemplate = path
   .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
-  .replace(/\\/g, '\\\\')
+  .replaceAll('\\', '\\\\')
 test('search upper case', async () => {
   const spy = jest.spyOn(global, 'fetch')

package/src/NCListAdapter/NCListFeature.ts CHANGED Viewed

@@ -34,8 +34,7 @@ export default class NCListFeature implements Feature {
   jb1TagToJb2Tag(tag: string): string {
     const t = tag.toLowerCase()
     // @ts-expect-error
-    const mapped = jb1ToJb2[t] || t
-    return mapped
+    return jb1ToJb2[t] || t
   }
   // eslint-disable-next-line @typescript-eslint/no-explicit-any