@jbrowse/plugin-legacy-jbrowse 1.7.9 → 2.0.0

package/esm/NCListAdapter/NCListFeature.d.ts

@@ -0,0 +1,31 @@
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+/**
+ * wrapper to adapt nclist features to act like jbrowse 2 features
+ */
+export default class NCListFeature implements Feature {
+    private ncFeature;
+    private parentHandle?;
+    private uniqueId;
+    constructor(ncFeature: any, parent?: Feature, id?: string);
+    set(): void;
+    jb2TagToJb1Tag(tag: string): string;
+    jb1TagToJb2Tag(tag: string): string;
+    get(attrName: string): any;
+    /**
+     * Get an array listing which data keys are present in this feature.
+     */
+    tags(): string[];
+    /**
+     * Get the unique ID of this feature.
+     */
+    id(): string;
+    /**
+     * Get this feature's parent feature, or undefined if none.
+     */
+    parent(): Feature | undefined;
+    /**
+     * Get an array of child features, or undefined if none.
+     */
+    children(): Feature[] | undefined;
+    toJSON(): SimpleFeatureSerialized;
+}

package/esm/NCListAdapter/NCListFeature.js

@@ -0,0 +1,78 @@
+const jb2ToJb1 = { refName: 'seq_id' };
+const jb1ToJb2 = { seq_id: 'refName' };
+/**
+ * wrapper to adapt nclist features to act like jbrowse 2 features
+ */
+export default class NCListFeature {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    constructor(ncFeature, parent, id) {
+        this.ncFeature = ncFeature;
+        this.uniqueId = id || ncFeature.id();
+        this.parentHandle = parent;
+    }
+    set() {
+        throw new Error('not implemented');
+    }
+    jb2TagToJb1Tag(tag) {
+        // @ts-ignore
+        const mapped = jb2ToJb1[tag] || tag;
+        return mapped.toLowerCase();
+    }
+    jb1TagToJb2Tag(tag) {
+        const t = tag.toLowerCase();
+        // @ts-ignore
+        const mapped = jb1ToJb2[t] || t;
+        return mapped;
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    get(attrName) {
+        const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName));
+        if (attr && attrName === 'subfeatures') {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return attr.map((subfeature) => new NCListFeature(subfeature, this));
+        }
+        return attr;
+    }
+    /**
+     * Get an array listing which data keys are present in this feature.
+     */
+    tags() {
+        return this.ncFeature.tags().map((t) => this.jb1TagToJb2Tag(t));
+    }
+    /**
+     * Get the unique ID of this feature.
+     */
+    id() {
+        return this.uniqueId;
+    }
+    /**
+     * Get this feature's parent feature, or undefined if none.
+     */
+    parent() {
+        return this.parentHandle;
+    }
+    /**
+     * Get an array of child features, or undefined if none.
+     */
+    children() {
+        return this.get('subfeatures');
+    }
+    toJSON() {
+        const data = { uniqueId: this.id() };
+        this.ncFeature.tags().forEach((tag) => {
+            const mappedTag = this.jb1TagToJb2Tag(tag);
+            const value = this.ncFeature.get(tag);
+            if (mappedTag === 'subfeatures') {
+                data.subfeatures = (value || []).map((f) => {
+                    // note: was new NCListFeature(f, `${this.id()}-${i}`, this).toJSON()
+                    return new NCListFeature(f, this).toJSON();
+                });
+            }
+            else {
+                data[mappedTag] = value;
+            }
+        });
+        return data;
+    }
+}
+//# sourceMappingURL=NCListFeature.js.map

package/esm/NCListAdapter/NCListFeature.js.map

@@ -0,0 +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,MAAM,CAAC,OAAO,OAAO,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,aAAa;QACb,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,aAAa;QACb,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"}

package/esm/NCListAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/NCListAdapter/configSchema.js

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('NCListAdapter', {
+    rootUrlTemplate: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my/{refseq}/trackData.json',
+            locationType: 'UriLocation',
+        },
+    },
+    refNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'List of refNames used by the NCList used for aliasing',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/NCListAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/NCListAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,eAAe,EAAE;QACf,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,qCAAqC;YAC1C,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,uDAAuD;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/NCListAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/NCListAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/NCListAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/NCListAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class LegacyJBrowsePlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,50 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType';
+import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType';
+import Plugin from '@jbrowse/core/Plugin';
+import { configSchema as ncListAdapterConfigSchema } from './NCListAdapter';
+import { AdapterClass as JBrowse1TextSearchAdapterClass, configSchema as jbrowse1AdapterConfigSchema, } from './JBrowse1TextSeachAdapter';
+import { getFileName } from '@jbrowse/core/util/tracks';
+import { configSchema as jbrowse1ConfigSchema, modelFactory as jbrowse1ModelFactory, } from './JBrowse1Connection';
+export default class LegacyJBrowsePlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'LegacyJBrowsePlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'NCListAdapter',
+            configSchema: ncListAdapterConfigSchema,
+            getAdapterClass: () => import('./NCListAdapter/NCListAdapter').then(r => r.default),
+        }));
+        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,
+                        rootUrlTemplate: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType({
+            name: 'JBrowse1TextSearchAdapter',
+            configSchema: jbrowse1AdapterConfigSchema,
+            AdapterClass: JBrowse1TextSearchAdapterClass,
+            description: 'A JBrowse 1 text search adapter',
+        }));
+        pluginManager.addConnectionType(() => new ConnectionType({
+            name: 'JBrowse1Connection',
+            configSchema: jbrowse1ConfigSchema,
+            stateModel: jbrowse1ModelFactory(pluginManager),
+            displayName: 'JBrowse 1 Data',
+            description: 'A JBrowse 1 data directory',
+            url: '//jbrowse.org/',
+        }));
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,qBAAqB,MAAM,2DAA2D,CAAA;AAC7F,OAAO,cAAc,MAAM,oDAAoD,CAAA;AAC/E,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAAE,YAAY,IAAI,yBAAyB,EAAE,MAAM,iBAAiB,CAAA;AAC3E,OAAO,EACL,YAAY,IAAI,8BAA8B,EAC9C,YAAY,IAAI,2BAA2B,GAC5C,MAAM,4BAA4B,CAAA;AACnC,OAAO,EAAkB,WAAW,EAAE,MAAM,2BAA2B,CAAA;AAEvE,OAAO,EACL,YAAY,IAAI,oBAAoB,EACpC,YAAY,IAAI,oBAAoB,GACrC,MAAM,sBAAsB,CAAA;AAE7B,MAAM,CAAC,OAAO,OAAO,mBAAoB,SAAQ,MAAM;IAAvD;;QACE,SAAI,GAAG,qBAAqB,CAAA;IAwD9B,CAAC;IAtDC,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;YACd,IAAI,EAAE,eAAe;YACrB,YAAY,EAAE,yBAAyB;YACvC,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,+BAA+B,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SAC/D,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,oBAAoB,CAAA;gBACvC,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,eAAe,EAAE,IAAI;qBACtB,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,wBAAwB,CACpC,GAAG,EAAE,CACH,IAAI,qBAAqB,CAAC;YACxB,IAAI,EAAE,2BAA2B;YACjC,YAAY,EAAE,2BAA2B;YACzC,YAAY,EAAE,8BAA8B;YAC5C,WAAW,EAAE,iCAAiC;SAC/C,CAAC,CACL,CAAA;QAED,aAAa,CAAC,iBAAiB,CAC7B,GAAG,EAAE,CACH,IAAI,cAAc,CAAC;YACjB,IAAI,EAAE,oBAAoB;YAC1B,YAAY,EAAE,oBAAoB;YAClC,UAAU,EAAE,oBAAoB,CAAC,aAAa,CAAC;YAC/C,WAAW,EAAE,gBAAgB;YAC7B,WAAW,EAAE,4BAA4B;YACzC,GAAG,EAAE,gBAAgB;SACtB,CAAC,CACL,CAAA;IACH,CAAC;CACF"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "1.7.9",
+  "version": "2.0.0",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -20,17 +20,21 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/legacy-jbrowse",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
-    "postbuild": "tsc --build tsconfig.build.json"
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
@@ -42,11 +46,16 @@
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
-    "mobx-state-tree": "3.14.1",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "rxjs": "^6.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "a6504c385d703ce6e755d05652ef659ffe28c864"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
 }

package/dist/JBrowse1TextSeachAdapter/HttpMap.test.js

@@ -1,118 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _path = _interopRequireDefault(require("path"));
-
-var _meta = _interopRequireDefault(require("../../test_data/names/meta.json"));
-
-var _ = _interopRequireDefault(require("../../test_data/names/0.json"));
-
-var _f = _interopRequireDefault(require("../../test_data/names/f.json"));
-
-var _HttpMap = _interopRequireDefault(require("./HttpMap"));
-
-describe('test JBrowse1 hash implementation', function () {
-  test('read from meta', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    var mockFetch, rootTemplate, spy, hashMap;
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            mockFetch = function _mockFetch(url) {
-              var response = {};
-
-              if (url.includes('names/meta.json')) {
-                response = _meta.default;
-              }
-
-              return Promise.resolve(new Response(JSON.stringify(response)));
-            };
-
-            rootTemplate = _path.default.join(__dirname, '..', '..', '..', '..', 'test_data', 'names').replace(/\\/g, '\\\\');
-            spy = jest.spyOn(global, 'fetch'); // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-            spy.mockImplementation(mockFetch);
-            hashMap = new _HttpMap.default({
-              url: rootTemplate
-            });
-            _context.next = 7;
-            return hashMap.getBucket('apple');
-
-          case 7:
-            _context.t0 = expect;
-            _context.next = 10;
-            return hashMap.getHashHexCharacters();
-
-          case 10:
-            _context.t1 = _context.sent;
-            (0, _context.t0)(_context.t1).toBe(1);
-            _context.t2 = expect;
-            _context.next = 15;
-            return hashMap.getCompress();
-
-          case 15:
-            _context.t3 = _context.sent;
-            (0, _context.t2)(_context.t3).toBe(0);
-
-          case 17:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  })));
-  test('get bucket contents', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-    var mockFetch, rootTemplate, spy, hashMap;
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            mockFetch = function _mockFetch2(url) {
-              var response = {};
-
-              if (url.includes('names/meta.json')) {
-                response = _meta.default;
-              }
-
-              if (url.includes('names/0.json')) {
-                response = _.default;
-              }
-
-              if (url.includes('names/f.json')) {
-                response = _f.default;
-              }
-
-              return Promise.resolve(new Response(JSON.stringify(response)));
-            };
-
-            rootTemplate = _path.default.join(__dirname, '..', '..', '..', '..', 'test_data', 'names').replace(/\\/g, '\\\\');
-            spy = jest.spyOn(global, 'fetch'); // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-            spy.mockImplementation(mockFetch);
-            hashMap = new _HttpMap.default({
-              url: rootTemplate
-            });
-            _context2.next = 7;
-            return hashMap.getBucket('apple');
-
-          case 7:
-            expect(spy).toHaveBeenLastCalledWith("".concat(rootTemplate, "/0.json"));
-            _context2.next = 10;
-            return hashMap.getBucket('apple3');
-
-          case 10:
-            expect(spy).toHaveBeenLastCalledWith("".concat(rootTemplate, "/f.json"));
-
-          case 11:
-          case "end":
-            return _context2.stop();
-        }
-      }
-    }, _callee2);
-  })));
-});

package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.test.js

@@ -1,98 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _BaseResults = _interopRequireDefault(require("@jbrowse/core/TextSearch/BaseResults"));
-
-var _path = _interopRequireDefault(require("path"));
-
-var _meta = _interopRequireDefault(require("../../test_data/names/meta.json"));
-
-var _ = _interopRequireDefault(require("../../test_data/names/0.json"));
-
-var _f = _interopRequireDefault(require("../../test_data/names/f.json"));
-
-var _JBrowse1TextSearchAdapter = _interopRequireDefault(require("./JBrowse1TextSearchAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch files from names index', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var mockFetch, rootTemplate, spy, urlPath, args, adapter, results, results2, test2;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          mockFetch = function _mockFetch(url) {
-            var response = {};
-
-            if (url.includes('names/meta.json')) {
-              response = _meta.default;
-            }
-
-            if (url.includes('names/0.json')) {
-              response = _.default;
-            }
-
-            if (url.includes('names/f.json')) {
-              response = _f.default;
-            }
-
-            return Promise.resolve(new Response(JSON.stringify(response)));
-          };
-
-          rootTemplate = _path.default.join(__dirname, '..', '..', '..', '..', 'test_data', 'names').replace(/\\/g, '\\\\');
-          spy = jest.spyOn(global, 'fetch'); // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-          spy.mockImplementation(mockFetch);
-          urlPath = decodeURI(new URL("file://".concat(rootTemplate)).href);
-          args = {
-            type: 'JBrowse1TextSearchAdapter',
-            textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
-            namesIndexLocation: {
-              uri: urlPath,
-              locationType: 'UriLocation'
-            }
-          }; // create adapter
-
-          adapter = new _JBrowse1TextSearchAdapter.default(_configSchema.default.create(args)); // prefix search
-
-          _context.next = 9;
-          return adapter.searchIndex({
-            searchType: 'prefix',
-            queryString: 'apple'
-          });
-
-        case 9:
-          results = _context.sent;
-          // check results are of type BaseResult for prefix search
-          expect(results[0] instanceof _BaseResults.default).toBeTruthy();
-          expect(results[0].getLabel()).toEqual('Apple1');
-          expect(results[1].getLabel()).toEqual('Apple2');
-          expect(results[2].getLabel()).toEqual('Apple3'); // exact search
-
-          _context.next = 16;
-          return adapter.searchIndex({
-            searchType: 'exact',
-            queryString: 'apple3'
-          });
-
-        case 16:
-          results2 = _context.sent;
-          // check results are of type location for exact search
-          expect(results2.length).toEqual(5);
-          test2 = results2[0];
-          expect(test2 instanceof _BaseResults.default).toBeTruthy();
-          expect(test2.getLabel()).toEqual('Apple3');
-          expect(test2.getLocation()).toEqual('ctgA:17399-23000');
-
-        case 22:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/NCListAdapter/NCListAdapter.test.js

@@ -1,108 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _fs = require("fs");
-
-var _path = _interopRequireDefault(require("path"));
-
-var _url = require("url");
-
-var _operators = require("rxjs/operators");
-
-var _NCListAdapter = _interopRequireDefault(require("./NCListAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
-
-function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
-
-function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
-
-test('adapter can fetch features from ensembl_genes test set', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var rootTemplate, args, adapter, features, featuresArray, featuresJsonArray, _iterator, _step, feature;
-
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          rootTemplate = _path.default.join(__dirname, '..', '..', 'test_data', 'ensembl_genes', '{refseq}', 'trackData.json').replace(/\\/g, '\\\\');
-          _context.next = 3;
-          return _fs.promises.stat(rootTemplate.replace('{refseq}', '21'));
-
-        case 3:
-          // will throw if doesnt exist
-          args = {
-            refNames: [],
-            rootUrlTemplate: {
-              uri: decodeURI(new _url.URL("file://".concat(rootTemplate)).href),
-              locationType: 'UriLocation'
-            }
-          };
-          adapter = new _NCListAdapter.default(_configSchema.default.create(args));
-          features = adapter.getFeatures({
-            assemblyName: 'volvox',
-            refName: '21',
-            start: 34960388,
-            end: 35960388
-          });
-          _context.next = 8;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 8:
-          featuresArray = _context.sent;
-          expect(featuresArray[0].get('refName')).toBe('21');
-          expect(featuresArray[0].id()).toBe("test-21,0,0,19,22,0");
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.length).toEqual(94);
-          _iterator = _createForOfIteratorHelper(featuresJsonArray);
-
-          try {
-            for (_iterator.s(); !(_step = _iterator.n()).done;) {
-              feature = _step.value;
-              expect(feature).toMatchSnapshot({
-                uniqueId: expect.any(String)
-              });
-            }
-          } catch (err) {
-            _iterator.e(err);
-          } finally {
-            _iterator.f();
-          }
-
-          _context.t0 = expect;
-          _context.next = 18;
-          return adapter.hasDataForRefName('ctgA');
-
-        case 18:
-          _context.t1 = _context.sent;
-          (0, _context.t0)(_context.t1).toBe(false);
-          _context.t2 = expect;
-          _context.next = 23;
-          return adapter.hasDataForRefName('21');
-
-        case 23:
-          _context.t3 = _context.sent;
-          (0, _context.t2)(_context.t3).toBe(true);
-          _context.t4 = expect;
-          _context.next = 28;
-          return adapter.hasDataForRefName('20');
-
-        case 28:
-          _context.t5 = _context.sent;
-          (0, _context.t4)(_context.t5).toBe(false);
-
-        case 30:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/declare.d.js

@@ -1 +0,0 @@
-"use strict";

package/dist/index.test.js

@@ -1,44 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _ = _interopRequireDefault(require("."));
-
-test('plugin in a stock JBrowse', function () {
-  var originalConsoleWarn = console.warn;
-  console.warn = jest.fn();
-  var pluginManager = new _PluginManager.default([new _.default()]);
-  pluginManager.createPluggableElements();
-  pluginManager.configure();
-  console.warn = originalConsoleWarn;
-  expect(function () {
-    return pluginManager.addPlugin(new _.default());
-  }).toThrow(/JBrowse already configured, cannot add plugins/);
-  var NCListAdapter = pluginManager.getAdapterType('NCListAdapter');
-  var config = NCListAdapter.configSchema.create({
-    type: 'NCListAdapter'
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-});
-test('test creating a text search adapter', function () {
-  console.warn = jest.fn();
-  var pluginManager = new _PluginManager.default([new _.default()]);
-  pluginManager.createPluggableElements();
-  pluginManager.configure();
-  var JB1TextSearchAdapter = pluginManager.getTextSearchAdapterType('JBrowse1TextSearchAdapter');
-  var config = JB1TextSearchAdapter.configSchema.create({
-    type: 'JBrowse1TextSearchAdapter',
-    textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
-    namesIndexLocation: {
-      uri: 'names/',
-      locationType: 'UriLocation'
-    },
-    tracks: [],
-    assemblies: []
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-});