@jbrowse/plugin-trix 3.7.0 → 4.0.1

package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.js

@@ -20,6 +20,9 @@ function shorten(str, term, w = 15) {
             (tidx + term.length < str.length ? '...' : '');
 }
 export default class TrixTextSearchAdapter extends BaseAdapter {
+    indexingAttributes;
+    trixJs;
+    tracksNames;
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const ixFilePath = readConfObject(config, 'ixFilePath');

package/esm/TrixTextSearchAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const TrixTextSearchAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     ixFilePath: {
         type: string;
         defaultValue: {
@@ -30,5 +30,5 @@ declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configu
         defaultValue: never[];
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
 export default TrixTextSearchAdapter;

package/esm/index.js

@@ -1,11 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
 import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType';
-import configSchema from './TrixTextSearchAdapter/configSchema';
+import configSchema from "./TrixTextSearchAdapter/configSchema.js";
 export default class TrixPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'TrixPlugin';
-    }
+    name = 'TrixPlugin';
     install(pluginManager) {
         pluginManager.addTextSearchAdapterType(() => {
             return new TextSearchAdapterType({
@@ -13,7 +10,7 @@ export default class TrixPlugin extends Plugin {
                 displayName: 'Trix text search adapter',
                 configSchema,
                 description: 'Trix text search adapter',
-                getAdapterClass: () => import('./TrixTextSearchAdapter/TrixTextSearchAdapter').then(d => d.default),
+                getAdapterClass: () => import("./TrixTextSearchAdapter/TrixTextSearchAdapter.js").then(d => d.default),
             });
         });
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-trix",
-  "version": "3.7.0",
+  "version": "4.0.1",
   "description": "JBrowse 2 trix text search adapter",
   "keywords": [
     "jbrowse",
@@ -15,42 +15,33 @@
     "directory": "plugins/trix"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/trix",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "peerDependencies": {
     "react": ">=18.0.0"
   },
   "dependencies": {
-    "@gmod/trix": "^3.0.2",
-    "@jbrowse/core": "^3.7.0",
-    "@mui/material": "^7.0.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0"
+    "@gmod/trix": "^3.0.4",
+    "@jbrowse/core": "^4.0.1"
   },
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/trix",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.d.ts

@@ -1,14 +0,0 @@
-import Trix from '@gmod/trix';
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { BaseTextSearchAdapter, BaseTextSearchArgs } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export default class TrixTextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
-    indexingAttributes?: string[];
-    trixJs: Trix;
-    tracksNames?: string[];
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]>;
-}

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js

@@ -1,73 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const trix_1 = __importDefault(require("@gmod/trix"));
-const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
-const configuration_1 = require("@jbrowse/core/configuration");
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const io_1 = require("@jbrowse/core/util/io");
-function decodeURIComponentNoThrow(uri) {
-    try {
-        return decodeURIComponent(uri);
-    }
-    catch (e) {
-        return uri;
-    }
-}
-function shorten(str, term, w = 15) {
-    const tidx = str.toLowerCase().indexOf(term);
-    return str.length < 40
-        ? str
-        : (Math.max(0, tidx - w) > 0 ? '...' : '') +
-            str.slice(Math.max(0, tidx - w), tidx + term.length + w).trim() +
-            (tidx + term.length < str.length ? '...' : '');
-}
-class TrixTextSearchAdapter extends BaseAdapter_1.BaseAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        const ixFilePath = (0, configuration_1.readConfObject)(config, 'ixFilePath');
-        const ixxFilePath = (0, configuration_1.readConfObject)(config, 'ixxFilePath');
-        if (!ixFilePath) {
-            throw new Error('must provide out.ix');
-        }
-        if (!ixxFilePath) {
-            throw new Error('must provide out.ixx');
-        }
-        this.trixJs = new trix_1.default((0, io_1.openLocation)(ixxFilePath, pluginManager), (0, io_1.openLocation)(ixFilePath, pluginManager), 1500);
-    }
-    async searchIndex(args) {
-        const query = args.queryString.toLowerCase();
-        const strs = query.split(' ');
-        const results = await this.trixJs.search(query);
-        const formatted = results
-            .filter(([, data]) => strs.every(r => decodeURIComponentNoThrow(data).toLowerCase().includes(r)))
-            .map(([term, data]) => {
-            const result = JSON.parse(data.replaceAll('|', ','));
-            const [loc, trackId, ...rest] = result.map(record => decodeURIComponentNoThrow(record));
-            const labelFieldIdx = rest.findIndex(elt => !!elt);
-            const contextIdx = rest
-                .map(elt => elt.toLowerCase())
-                .findIndex(f => f.includes(term.toLowerCase()));
-            const labelField = rest[labelFieldIdx];
-            const contextField = rest[contextIdx];
-            const context = contextIdx !== -1 ? shorten(contextField, term) : undefined;
-            const label = shorten(labelField, term);
-            const displayString = !context || label.toLowerCase() === context.toLowerCase()
-                ? label
-                : `${label} (${context})`;
-            return new BaseResults_1.default({
-                locString: loc,
-                label: labelField,
-                displayString,
-                matchedObject: result.map(record => decodeURIComponent(record)),
-                trackId,
-            });
-        });
-        return args.searchType === 'exact'
-            ? formatted.filter(r => r.getLabel().toLowerCase() === args.queryString.toLowerCase())
-            : formatted;
-    }
-}
-exports.default = TrixTextSearchAdapter;

package/dist/TrixTextSearchAdapter/configSchema.d.ts

@@ -1,34 +0,0 @@
-declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    ixFilePath: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    ixxFilePath: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    metaFilePath: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    tracks: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
-export default TrixTextSearchAdapter;

package/dist/TrixTextSearchAdapter/configSchema.js

@@ -1,56 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const TrixTextSearchAdapter = (0, configuration_1.ConfigurationSchema)('TrixTextSearchAdapter', {
-    ixFilePath: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: 'out.ix',
-            locationType: 'UriLocation',
-        },
-    },
-    ixxFilePath: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: 'out.ixx',
-            locationType: 'UriLocation',
-        },
-    },
-    metaFilePath: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: 'meta.json',
-            locationType: 'UriLocation',
-        },
-    },
-    tracks: {
-        type: 'stringArray',
-        defaultValue: [],
-        description: 'List of tracks covered by text search adapter',
-    },
-    assemblyNames: {
-        type: 'stringArray',
-        defaultValue: [],
-        description: 'List of assemblies covered by text search adapter',
-    },
-}, {
-    explicitlyTyped: true,
-    explicitIdentifier: 'textSearchAdapterId',
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                ixFilePath: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                ixxFilePath: {
-                    uri: `${snap.uri}x`,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = TrixTextSearchAdapter;

package/dist/index.d.ts

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

package/dist/index.js

@@ -1,59 +0,0 @@
-"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 () {
-    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 };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
-const configSchema_1 = __importDefault(require("./TrixTextSearchAdapter/configSchema"));
-class TrixPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'TrixPlugin';
-    }
-    install(pluginManager) {
-        pluginManager.addTextSearchAdapterType(() => {
-            return new TextSearchAdapterType_1.default({
-                name: 'TrixTextSearchAdapter',
-                displayName: 'Trix text search adapter',
-                configSchema: configSchema_1.default,
-                description: 'Trix text search adapter',
-                getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./TrixTextSearchAdapter/TrixTextSearchAdapter'))).then(d => d.default),
-            });
-        });
-    }
-}
-exports.default = TrixPlugin;