@jbrowse/plugin-legacy-jbrowse 2.18.0 → 3.0.1

package/dist/GuessNCList/index.js

@@ -5,16 +5,14 @@ const tracks_1 = require("@jbrowse/core/util/tracks");
 function GuessNCListF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /trackData.jsonz?$/i;
-            const adapterName = 'NCListAdapter';
             const fileName = (0, tracks_1.getFileName)(file);
-            if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                return {
-                    type: adapterName,
+            return (/trackData.jsonz?$/i.test(fileName) && !adapterHint) ||
+                adapterHint === 'NCListAdapter'
+                ? {
+                    type: 'NCListAdapter',
                     rootUrlTemplate: file,
-                };
-            }
-            return adapterGuesser(file, index, adapterHint);
+                }
+                : adapterGuesser(file, index, adapterHint);
         };
     });
 }

package/dist/JBrowse1Connection/model.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/JBrowse1TextSearchAdapter/HttpMap.js

@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const buffer_1 = require("buffer");
 const crc32_1 = __importDefault(require("crc/crc32"));
 class HttpMap {
     constructor(args) {
@@ -60,7 +59,7 @@ class HttpMap {
         return '';
     }
     hash(data) {
-        return (0, crc32_1.default)(buffer_1.Buffer.from(data)).toString(16).toLowerCase().replace('-', 'n');
+        return (0, crc32_1.default)(data).toString(16).toLowerCase().replace('-', 'n');
     }
 }
 exports.default = HttpMap;

package/dist/JBrowse1TextSearchAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/NCListAdapter/NCListAdapter.js

@@ -7,7 +7,7 @@ const nclist_1 = __importDefault(require("@gmod/nclist"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const stopToken_1 = require("@jbrowse/core/util/stopToken");
-const generic_filehandle_1 = require("generic-filehandle");
+const generic_filehandle2_1 = require("generic-filehandle2");
 const NCListFeature_1 = __importDefault(require("./NCListFeature"));
 class NCListAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
@@ -18,7 +18,7 @@ class NCListAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         this.nclist = new nclist_1.default({
             baseUrl: '',
             urlTemplate: rootUrlTemplate.uri,
-            readFile: (url) => new generic_filehandle_1.RemoteFile(String(rootUrlTemplate.baseUri
+            readFile: (url) => new generic_filehandle2_1.RemoteFile(String(rootUrlTemplate.baseUri
                 ? new URL(url, rootUrlTemplate.baseUri).toString()
                 : url)).readFile(),
         });

package/dist/NCListAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -34,6 +44,9 @@ function NCListAdapterF(pluginManager) {
         name: 'NCListAdapter',
         displayName: 'NCList adapter',
         configSchema: configSchema_1.default,
+        adapterMetadata: {
+            category: 'Uncommon',
+        },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./NCListAdapter'))).then(r => r.default),
     }));
 }

package/esm/GuessNCList/index.js

@@ -2,16 +2,14 @@ import { getFileName } from '@jbrowse/core/util/tracks';
 export default function GuessNCListF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /trackData.jsonz?$/i;
-            const adapterName = 'NCListAdapter';
             const fileName = getFileName(file);
-            if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                return {
-                    type: adapterName,
+            return (/trackData.jsonz?$/i.test(fileName) && !adapterHint) ||
+                adapterHint === 'NCListAdapter'
+                ? {
+                    type: 'NCListAdapter',
                     rootUrlTemplate: file,
-                };
-            }
-            return adapterGuesser(file, index, adapterHint);
+                }
+                : adapterGuesser(file, index, adapterHint);
         };
     });
 }

package/esm/JBrowse1TextSearchAdapter/HttpMap.js

@@ -1,4 +1,3 @@
-import { Buffer } from 'buffer';
 import crc32 from 'crc/crc32';
 export default class HttpMap {
     constructor(args) {
@@ -55,6 +54,6 @@ export default class HttpMap {
         return '';
     }
     hash(data) {
-        return crc32(Buffer.from(data)).toString(16).toLowerCase().replace('-', 'n');
+        return crc32(data).toString(16).toLowerCase().replace('-', 'n');
     }
 }

package/esm/NCListAdapter/NCListAdapter.js

@@ -2,7 +2,7 @@ import NCListStore from '@gmod/nclist';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { checkStopToken } from '@jbrowse/core/util/stopToken';
-import { RemoteFile } from 'generic-filehandle';
+import { RemoteFile } from 'generic-filehandle2';
 import NCListFeature from './NCListFeature';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {

package/esm/NCListAdapter/index.js

@@ -5,6 +5,9 @@ export default function NCListAdapterF(pluginManager) {
         name: 'NCListAdapter',
         displayName: 'NCList adapter',
         configSchema,
+        adapterMetadata: {
+            category: 'Uncommon',
+        },
         getAdapterClass: () => import('./NCListAdapter').then(r => r.default),
     }));
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.18.0",
+  "version": "3.0.1",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -36,18 +36,16 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/nclist": "^1.0.3",
+    "@gmod/nclist": "^2.0.0",
+    "@jbrowse/core": "^3.0.1",
     "crc": "^4.0.0",
-    "generic-filehandle": "^3.0.0",
-    "get-value": "^3.0.1",
-    "set-value": "^4.0.1"
-  },
-  "peerDependencies": {
-    "@jbrowse/core": "^2.0.0",
+    "generic-filehandle2": "^1.0.0",
+    "get-value": "^3.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0"
+    "rxjs": "^7.0.0",
+    "set-value": "^4.0.1"
   },
   "publishConfig": {
     "access": "public"
@@ -55,5 +53,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
+  "gitHead": "aa2f1d1a89d2361c7fd1a93fe29506fa4554f5cc"
 }