@jbrowse/plugin-rdf 2.17.0 → 3.0.0

package/dist/SPARQLAdapter/SPARQLAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type MyConfigSchema from './configSchema';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import type { Instance } from 'mobx-state-tree';
 export default class SPARQLAdapter extends BaseFeatureDataAdapter {
     private endpoint;
     private queryTemplate;

package/dist/SPARQLAdapter/SPARQLAdapter.js

@@ -3,11 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const string_template_1 = __importDefault(require("string-template"));
-const configuration_1 = require("@jbrowse/core/configuration");
 class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -17,7 +17,7 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         this.refNamesQueryTemplate = (0, configuration_1.readConfObject)(config, 'refNamesQueryTemplate');
         this.configRefNames = (0, configuration_1.readConfObject)(config, 'refNames');
     }
-    async getRefNames(opts = {}) {
+    async getRefNames(opts) {
         if (this.refNames) {
             return this.refNames;
         }
@@ -36,21 +36,23 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             const filledTemplate = encodeURIComponent((0, string_template_1.default)(this.queryTemplate, query));
             const { refName } = query;
             const results = await this.querySparql(filledTemplate, opts);
-            this.resultsToFeatures(results, refName).forEach(feature => {
+            const features = this.resultsToFeatures(results, refName);
+            for (const feature of features) {
                 observer.next(feature);
-            });
+            }
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    async querySparql(query, opts) {
+    async querySparql(query, _opts) {
         let additionalQueryParams = '';
         if (this.additionalQueryParams.length) {
             additionalQueryParams = `&${this.additionalQueryParams.join('&')}`;
         }
-        const signal = opts === null || opts === void 0 ? void 0 : opts.signal;
-        const response = await fetch(`${this.endpoint}?query=${query}${additionalQueryParams}`, {
-            headers: { accept: 'application/json,application/sparql-results+json' },
-            signal,
+        const url = `${this.endpoint}?query=${query}${additionalQueryParams}`;
+        const response = await fetch(url, {
+            headers: {
+                accept: 'application/json,application/sparql-results+json',
+            },
         });
         return response.json();
     }
@@ -105,7 +107,6 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 };
             });
         });
-        // resolve subfeatures, keeping only top-level features in seenFeatures
         for (const [uniqueId, f] of Object.entries(seenFeatures)) {
             const pid = f.data.parentUniqueId;
             f.data.parentUniqueId = undefined;
@@ -163,6 +164,6 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return true;
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = SPARQLAdapter;

package/dist/SPARQLAdapter/index.d.ts

@@ -1,2 +1,2 @@
-export { default as AdapterClass } from './SPARQLAdapter';
-export { default as configSchema } from './configSchema';
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function SPARQLAdapterF(pluginManager: PluginManager): void;

package/dist/SPARQLAdapter/index.js

@@ -1,10 +1,52 @@
 "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 });
-exports.configSchema = exports.AdapterClass = void 0;
-var SPARQLAdapter_1 = require("./SPARQLAdapter");
-Object.defineProperty(exports, "AdapterClass", { enumerable: true, get: function () { return __importDefault(SPARQLAdapter_1).default; } });
-var configSchema_1 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+exports.default = SPARQLAdapterF;
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+const configSchema_1 = __importDefault(require("./configSchema"));
+function SPARQLAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
+        name: 'SPARQLAdapter',
+        displayName: 'SPARQL adapter',
+        configSchema: configSchema_1.default,
+        adapterMetadata: {
+            category: 'Uncommon',
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SPARQLAdapter'))).then(r => r.default),
+    }));
+}

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class RdfPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -3,22 +3,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const SPARQLAdapter_1 = require("./SPARQLAdapter");
 const tracks_1 = require("@jbrowse/core/util/tracks");
+const SPARQLAdapter_1 = __importDefault(require("./SPARQLAdapter"));
 class RdfPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
         this.name = 'RdfPlugin';
     }
     install(pluginManager) {
-        pluginManager.addAdapterType(() => new AdapterType_1.default({
-            name: 'SPARQLAdapter',
-            displayName: 'SPARQL adapter',
-            configSchema: SPARQLAdapter_1.configSchema,
-            AdapterClass: SPARQLAdapter_1.AdapterClass,
-        }));
+        (0, SPARQLAdapter_1.default)(pluginManager);
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
             return (file, index, adapterHint) => {
                 const regexGuess = /\/sparql$/i;

package/esm/SPARQLAdapter/SPARQLAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type MyConfigSchema from './configSchema';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import type { Instance } from 'mobx-state-tree';
 export default class SPARQLAdapter extends BaseFeatureDataAdapter {
     private endpoint;
     private queryTemplate;

package/esm/SPARQLAdapter/SPARQLAdapter.js

@@ -1,8 +1,8 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import format from 'string-template';
-import { readConfObject } from '@jbrowse/core/configuration';
 export default class SPARQLAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -12,7 +12,7 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
         this.refNamesQueryTemplate = readConfObject(config, 'refNamesQueryTemplate');
         this.configRefNames = readConfObject(config, 'refNames');
     }
-    async getRefNames(opts = {}) {
+    async getRefNames(opts) {
         if (this.refNames) {
             return this.refNames;
         }
@@ -31,21 +31,23 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
             const filledTemplate = encodeURIComponent(format(this.queryTemplate, query));
             const { refName } = query;
             const results = await this.querySparql(filledTemplate, opts);
-            this.resultsToFeatures(results, refName).forEach(feature => {
+            const features = this.resultsToFeatures(results, refName);
+            for (const feature of features) {
                 observer.next(feature);
-            });
+            }
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    async querySparql(query, opts) {
+    async querySparql(query, _opts) {
         let additionalQueryParams = '';
         if (this.additionalQueryParams.length) {
             additionalQueryParams = `&${this.additionalQueryParams.join('&')}`;
         }
-        const signal = opts === null || opts === void 0 ? void 0 : opts.signal;
-        const response = await fetch(`${this.endpoint}?query=${query}${additionalQueryParams}`, {
-            headers: { accept: 'application/json,application/sparql-results+json' },
-            signal,
+        const url = `${this.endpoint}?query=${query}${additionalQueryParams}`;
+        const response = await fetch(url, {
+            headers: {
+                accept: 'application/json,application/sparql-results+json',
+            },
         });
         return response.json();
     }
@@ -100,7 +102,6 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
                 };
             });
         });
-        // resolve subfeatures, keeping only top-level features in seenFeatures
         for (const [uniqueId, f] of Object.entries(seenFeatures)) {
             const pid = f.data.parentUniqueId;
             f.data.parentUniqueId = undefined;
@@ -158,5 +159,5 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
         }
         return true;
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/SPARQLAdapter/index.d.ts

@@ -1,2 +1,2 @@
-export { default as AdapterClass } from './SPARQLAdapter';
-export { default as configSchema } from './configSchema';
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function SPARQLAdapterF(pluginManager: PluginManager): void;

package/esm/SPARQLAdapter/index.js

@@ -1,2 +1,13 @@
-export { default as AdapterClass } from './SPARQLAdapter';
-export { default as configSchema } from './configSchema';
+import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
+import configSchema from './configSchema';
+export default function SPARQLAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'SPARQLAdapter',
+        displayName: 'SPARQL adapter',
+        configSchema,
+        adapterMetadata: {
+            category: 'Uncommon',
+        },
+        getAdapterClass: () => import('./SPARQLAdapter').then(r => r.default),
+    }));
+}

package/esm/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class RdfPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,19 +1,13 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import Plugin from '@jbrowse/core/Plugin';
-import { AdapterClass as SPARQLAdapterClass, configSchema as sparqlAdapterConfigSchema, } from './SPARQLAdapter';
 import { getFileName } from '@jbrowse/core/util/tracks';
+import SPARQLAdapterF from './SPARQLAdapter';
 export default class RdfPlugin extends Plugin {
     constructor() {
         super(...arguments);
         this.name = 'RdfPlugin';
     }
     install(pluginManager) {
-        pluginManager.addAdapterType(() => new AdapterType({
-            name: 'SPARQLAdapter',
-            displayName: 'SPARQL adapter',
-            configSchema: sparqlAdapterConfigSchema,
-            AdapterClass: SPARQLAdapterClass,
-        }));
+        SPARQLAdapterF(pluginManager);
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
             return (file, index, adapterHint) => {
                 const regexGuess = /\/sparql$/i;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-rdf",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 RDF resources",
   "keywords": [
     "jbrowse",
@@ -51,5 +51,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }