@jbrowse/plugin-legacy-jbrowse 2.12.0 → 2.12.2

package/dist/GuessNCList/index.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = GuessNCListF;
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function GuessNCListF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
@@ -17,4 +18,3 @@ function GuessNCListF(pluginManager) {
         };
     });
 }
-exports.default = GuessNCListF;

package/dist/JBrowse1Connection/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = JBrowse1ConnectionF;
 const ConnectionType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ConnectionType"));
 // locals
 const model_1 = __importDefault(require("./model"));
@@ -17,4 +18,3 @@ function JBrowse1ConnectionF(pluginManager) {
         url: '//jbrowse.org/',
     }));
 }
-exports.default = JBrowse1ConnectionF;

package/dist/JBrowse1Connection/jb1ConfigLoad.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseJb1 = exports.fetchConfigFile = exports.createFinalConfig = exports.fetchJb1 = void 0;
+exports.fetchJb1 = fetchJb1;
+exports.createFinalConfig = createFinalConfig;
+exports.fetchConfigFile = fetchConfigFile;
+exports.parseJb1 = parseJb1;
 const io_1 = require("@jbrowse/core/util/io");
 const jb1ConfigParse_1 = require("./jb1ConfigParse");
 const util_1 = require("./util");
@@ -69,7 +72,6 @@ baseConfigRoot = { uri: '', locationType: 'UriLocation' }) {
     }
     return createFinalConfig(newConfig);
 }
-exports.fetchJb1 = fetchJb1;
 async function createFinalConfig(baseConfig, defaults = configDefaults) {
     const configWithDefaults = (0, util_1.deepUpdate)((0, util_1.clone)(defaults), baseConfig);
     let finalConfig = await loadIncludes(configWithDefaults);
@@ -78,7 +80,6 @@ async function createFinalConfig(baseConfig, defaults = configDefaults) {
     validateConfig(finalConfig);
     return finalConfig;
 }
-exports.createFinalConfig = createFinalConfig;
 async function fetchConfigFile(location) {
     const result = await (0, io_1.openLocation)(location).readFile('utf8');
     if (isUriLocation(location)) {
@@ -89,14 +90,12 @@ async function fetchConfigFile(location) {
     }
     return parseJb1(result);
 }
-exports.fetchConfigFile = fetchConfigFile;
 function parseJb1(config, url = '') {
     if (config.trim().startsWith('{')) {
         return (0, jb1ConfigParse_1.parseJB1Json)(config, url);
     }
     return (0, jb1ConfigParse_1.parseJB1Conf)(config, url);
 }
-exports.parseJb1 = parseJb1;
 /**
  * Merges config object b into a. Properties in b override those in a.
  */

package/dist/JBrowse1Connection/jb1ConfigParse.js

@@ -3,7 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.regularizeConf = exports.parseJB1Conf = exports.parseJB1Json = void 0;
+exports.parseJB1Json = parseJB1Json;
+exports.parseJB1Conf = parseJB1Conf;
+exports.regularizeConf = regularizeConf;
 /* eslint no-cond-assign: ["error", "except-parens"] */
 const get_value_1 = __importDefault(require("get-value"));
 const set_value_1 = __importDefault(require("set-value"));
@@ -22,7 +24,6 @@ function parseJB1Json(config, url) {
     }
     return regularizeConf(config, url);
 }
-exports.parseJB1Json = parseJB1Json;
 function parseJB1Conf(config, url) {
     let parsedConf;
     try {
@@ -33,7 +34,6 @@ function parseJB1Conf(config, url) {
     }
     return regularizeConf(parsedConf, url);
 }
-exports.parseJB1Conf = parseJB1Conf;
 function isAlwaysArray(varName) {
     if (varName === 'include') {
         return true;
@@ -276,7 +276,6 @@ function regularizeConf(conf, url) {
     });
     return conf;
 }
-exports.regularizeConf = regularizeConf;
 /**
  * prefix class name with `root` if it contains no slashes
  * @param root - Prefix root

package/dist/JBrowse1Connection/jb1ToJb2.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createRefSeqsAdapter = exports.convertTrackConfig = void 0;
+exports.convertTrackConfig = convertTrackConfig;
+exports.createRefSeqsAdapter = createRefSeqsAdapter;
 const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
@@ -338,7 +339,6 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     }
     return jb2TrackConfig;
 }
-exports.convertTrackConfig = convertTrackConfig;
 function generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig) {
     const jb1Features = jb1TrackConfig.features || [];
     const jb2Features = jb1Features.map((feature) => {
@@ -400,7 +400,6 @@ async function createRefSeqsAdapter(refSeqs) {
     }
     throw new Error(`Could not determine adapter for JBrowse1 refSeqs: ${refSeqs.url || JSON.stringify(refSeqs)}`);
 }
-exports.createRefSeqsAdapter = createRefSeqsAdapter;
 function refSeqAdapterFromConfig(refSeqsData) {
     const features = refSeqsData.map((refSeq) => ({
         refName: refSeq.name,

package/dist/JBrowse1Connection/model.d.ts

@@ -43,28 +43,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
     type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
 }, {
-    connect(_arg: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>): void;
+    connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
 } & {
     afterAttach(): void;
-    addTrackConf(trackConf: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>): any;
-    addTrackConfs(trackConfs: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): any[];
-    setTrackConfs(trackConfs: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & 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>>;
+    addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
+    addTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): any[];
+    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): 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(): Promise<void>;

package/dist/JBrowse1Connection/model.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = stateModelFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
@@ -71,4 +72,3 @@ function stateModelFactory(pluginManager) {
         },
     }));
 }
-exports.default = stateModelFactory;

package/dist/JBrowse1Connection/util.js

@@ -3,18 +3,20 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clone = exports.fillTemplate = exports.deepUpdate = exports.isSource = exports.isTrack = void 0;
+exports.isTrack = isTrack;
+exports.isSource = isSource;
+exports.deepUpdate = deepUpdate;
+exports.fillTemplate = fillTemplate;
+exports.clone = clone;
 const get_value_1 = __importDefault(require("get-value"));
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function isTrack(arg) {
     return (arg === null || arg === void 0 ? void 0 : arg.label) && typeof arg.label === 'string';
 }
-exports.isTrack = isTrack;
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function isSource(arg) {
     return (arg === null || arg === void 0 ? void 0 : arg.url) && typeof arg.url === 'string';
 }
-exports.isSource = isSource;
 function deepUpdate(a, b) {
     for (const prop of Object.keys(b)) {
         if (prop in a &&
@@ -28,7 +30,6 @@ function deepUpdate(a, b) {
     }
     return a;
 }
-exports.deepUpdate = deepUpdate;
 /**
  * replace variables in a template string with values
  *
@@ -56,7 +57,6 @@ function fillTemplate(template, fillWith) {
         return match;
     });
 }
-exports.fillTemplate = fillTemplate;
 /**
  * Clones objects (including DOM nodes) and all children.
  * Warning: do not clone cyclic structures
@@ -105,7 +105,6 @@ function clone(src) {
     }
     return mixin(r, src, clone);
 }
-exports.clone = clone;
 /**
  * Copies/adds all properties of source to dest; returns dest.
  * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)

package/dist/JBrowse1TextSearchAdapter/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = JBrowse1TextSearchAdapterF;
 const TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
 // locals
 const JBrowse1TextSearchAdapter_1 = __importDefault(require("./JBrowse1TextSearchAdapter"));
@@ -15,4 +16,3 @@ function JBrowse1TextSearchAdapterF(pluginManager) {
         description: 'A JBrowse 1 text search adapter',
     }));
 }
-exports.default = JBrowse1TextSearchAdapterF;

package/dist/NCListAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = NCListAdapterF;
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const configSchema_1 = __importDefault(require("./configSchema"));
 function NCListAdapterF(pluginManager) {
@@ -36,4 +37,3 @@ function NCListAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./NCListAdapter'))).then(r => r.default),
     }));
 }
-exports.default = NCListAdapterF;

package/esm/JBrowse1Connection/model.d.ts

@@ -43,28 +43,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
     type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
 }, {
-    connect(_arg: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>): void;
+    connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
 } & {
     afterAttach(): void;
-    addTrackConf(trackConf: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>): any;
-    addTrackConfs(trackConfs: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): any[];
-    setTrackConfs(trackConfs: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & 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>>;
+    addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
+    addTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): any[];
+    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): 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(): Promise<void>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.12.0",
+  "version": "2.12.2",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
+  "gitHead": "1ec66736ce048a1637f52b7a7ef2eb02d956b771"
 }