@jbrowse/plugin-rdf 3.7.0 → 4.0.1

package/esm/SPARQLAdapter/SPARQLAdapter.d.ts

@@ -1,11 +1,11 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type MyConfigSchema from './configSchema';
+import type MyConfigSchema from './configSchema.ts';
 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';
+import type { Instance } from '@jbrowse/mobx-state-tree';
 export default class SPARQLAdapter extends BaseFeatureDataAdapter {
     private endpoint;
     private queryTemplate;

package/esm/SPARQLAdapter/SPARQLAdapter.js

@@ -4,6 +4,12 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import format from 'string-template';
 export default class SPARQLAdapter extends BaseFeatureDataAdapter {
+    endpoint;
+    queryTemplate;
+    refNamesQueryTemplate;
+    additionalQueryParams;
+    configRefNames;
+    refNames;
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         this.endpoint = readConfObject(config, 'endpoint').uri;
@@ -137,7 +143,9 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
                             break;
                         }
                         if (subfeature.subfeatures) {
-                            subfeatures.push(...subfeature.subfeatures);
+                            for (const sf of subfeature.subfeatures) {
+                                subfeatures.push(sf);
+                            }
                         }
                     }
                     if (!found) {

package/esm/SPARQLAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const _default: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     endpoint: {
         type: string;
         defaultValue: {
@@ -27,5 +27,5 @@ declare const _default: import("@jbrowse/core/configuration/configurationSchema"
         defaultValue: never[];
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default _default;

package/esm/SPARQLAdapter/index.js

@@ -1,5 +1,5 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function SPARQLAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'SPARQLAdapter',
@@ -8,6 +8,6 @@ export default function SPARQLAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Uncommon',
         },
-        getAdapterClass: () => import('./SPARQLAdapter').then(r => r.default),
+        getAdapterClass: () => import("./SPARQLAdapter.js").then(r => r.default),
     }));
 }

package/esm/index.js

@@ -1,11 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { getFileName } from '@jbrowse/core/util/tracks';
-import SPARQLAdapterF from './SPARQLAdapter';
+import SPARQLAdapterF from "./SPARQLAdapter/index.js";
 export default class RdfPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'RdfPlugin';
-    }
+    name = 'RdfPlugin';
     install(pluginManager) {
         SPARQLAdapterF(pluginManager);
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-rdf",
-  "version": "3.7.0",
+  "version": "4.0.1",
   "description": "JBrowse 2 RDF resources",
   "keywords": [
     "jbrowse",
@@ -15,39 +15,33 @@
     "directory": "plugins/rdf"
   },
   "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/rdf",
-    "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"
-  },
   "dependencies": {
-    "@jbrowse/core": "^3.7.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0",
-    "string-template": "^1.0.0"
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "mobx": "^6.15.0",
+    "rxjs": "^7.8.2",
+    "string-template": "^1.0.0",
+    "@jbrowse/core": "^4.0.1"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/rdf",
+    "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/SPARQLAdapter/SPARQLAdapter.d.ts

@@ -1,23 +0,0 @@
-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;
-    private refNamesQueryTemplate;
-    private additionalQueryParams;
-    private configRefNames;
-    private refNames;
-    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    private querySparql;
-    private resultsToRefNames;
-    private resultsToFeatures;
-    hasDataForRefName(refName: string, opts?: BaseOptions): Promise<boolean>;
-}

package/dist/SPARQLAdapter/SPARQLAdapter.js

@@ -1,168 +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 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"));
-class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        this.endpoint = (0, configuration_1.readConfObject)(config, 'endpoint').uri;
-        this.queryTemplate = (0, configuration_1.readConfObject)(config, 'queryTemplate');
-        this.additionalQueryParams = (0, configuration_1.readConfObject)(config, 'additionalQueryParams');
-        this.refNamesQueryTemplate = (0, configuration_1.readConfObject)(config, 'refNamesQueryTemplate');
-        this.configRefNames = (0, configuration_1.readConfObject)(config, 'refNames');
-    }
-    async getRefNames(opts) {
-        if (this.refNames) {
-            return this.refNames;
-        }
-        if (this.refNamesQueryTemplate) {
-            const queryTemplate = encodeURIComponent(this.refNamesQueryTemplate);
-            const results = await this.querySparql(queryTemplate, opts);
-            this.refNames = this.resultsToRefNames(results);
-        }
-        else {
-            this.refNames = this.configRefNames;
-        }
-        return this.refNames;
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const filledTemplate = encodeURIComponent((0, string_template_1.default)(this.queryTemplate, query));
-            const { refName } = query;
-            const results = await this.querySparql(filledTemplate, opts);
-            const features = this.resultsToFeatures(results, refName);
-            for (const feature of features) {
-                observer.next(feature);
-            }
-            observer.complete();
-        }, opts.stopToken);
-    }
-    async querySparql(query, _opts) {
-        let additionalQueryParams = '';
-        if (this.additionalQueryParams.length) {
-            additionalQueryParams = `&${this.additionalQueryParams.join('&')}`;
-        }
-        const url = `${this.endpoint}?query=${query}${additionalQueryParams}`;
-        const response = await fetch(url, {
-            headers: {
-                accept: 'application/json,application/sparql-results+json',
-            },
-        });
-        return response.json();
-    }
-    resultsToRefNames(response) {
-        const rows = response.results.bindings || [];
-        const fields = response.head.vars;
-        if (!fields.includes('refName')) {
-            throw new Error('"refName" not found in refNamesQueryTemplate response');
-        }
-        return rows.map(row => row.refName.value);
-    }
-    resultsToFeatures(results, refName) {
-        const rows = results.results.bindings || [];
-        const fields = results.head.vars;
-        const requiredFields = ['start', 'end', 'uniqueId'];
-        for (const requiredField of requiredFields) {
-            if (!fields.includes(requiredField)) {
-                console.error(`Required field ${requiredField} missing from feature data`);
-            }
-        }
-        const seenFeatures = {};
-        for (const row of rows) {
-            const rawData = [{}];
-            for (let field of fields) {
-                if (field in row) {
-                    const { value } = row[field];
-                    let idx = 0;
-                    while (field.startsWith('sub_')) {
-                        field = field.slice(4);
-                        idx += 1;
-                    }
-                    while (idx > rawData.length - 1) {
-                        rawData.push({});
-                    }
-                    rawData[idx][field] = value;
-                }
-            }
-            for (const [idx, rd] of rawData.entries()) {
-                const { uniqueId, start, end, strand } = rd;
-                if (idx < rawData.length - 1) {
-                    rawData[idx + 1].parentUniqueId = uniqueId;
-                }
-                seenFeatures[uniqueId] = {
-                    data: {
-                        ...rd,
-                        uniqueId: uniqueId,
-                        refName,
-                        start: Number.parseInt(start, 10),
-                        end: Number.parseInt(end, 10),
-                        strand: Number.parseInt(strand, 10) || 0,
-                    },
-                };
-            }
-        }
-        for (const [uniqueId, f] of Object.entries(seenFeatures)) {
-            const pid = f.data.parentUniqueId;
-            f.data.parentUniqueId = undefined;
-            if (pid) {
-                const p = seenFeatures[pid];
-                if (p) {
-                    if (!p.data.subfeatures) {
-                        p.data.subfeatures = [];
-                    }
-                    p.data.subfeatures.push({
-                        ...f.data,
-                        uniqueId,
-                    });
-                    delete seenFeatures[uniqueId];
-                }
-                else {
-                    const subfeatures = Object.values(seenFeatures)
-                        .map(sf => sf.data.subfeatures)
-                        .filter(sf => !!sf)
-                        .flat();
-                    let found = false;
-                    for (const subfeature of subfeatures) {
-                        if (subfeature.uniqueId === pid) {
-                            if (!subfeature.subfeatures) {
-                                subfeature.subfeatures = [];
-                            }
-                            subfeature.subfeatures.push({
-                                ...f.data,
-                                uniqueId,
-                            });
-                            delete seenFeatures[uniqueId];
-                            found = true;
-                            break;
-                        }
-                        if (subfeature.subfeatures) {
-                            subfeatures.push(...subfeature.subfeatures);
-                        }
-                    }
-                    if (!found) {
-                        console.error(`Could not find parentID ${pid}`);
-                    }
-                }
-            }
-        }
-        return Object.keys(seenFeatures).map(seenFeature => new simpleFeature_1.default({
-            ...seenFeatures[seenFeature].data,
-            uniqueId: seenFeature,
-            subfeatures: seenFeatures[seenFeature].data.subfeatures,
-        }));
-    }
-    async hasDataForRefName(refName, opts = {}) {
-        const refNames = await this.getRefNames(opts);
-        if (refNames.length && !refNames.includes(refName)) {
-            return false;
-        }
-        return true;
-    }
-}
-exports.default = SPARQLAdapter;

package/dist/SPARQLAdapter/configSchema.d.ts

@@ -1,31 +0,0 @@
-declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    endpoint: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-        description: string;
-    };
-    queryTemplate: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    refNamesQueryTemplate: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    refNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-    additionalQueryParams: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default _default;

package/dist/SPARQLAdapter/configSchema.js

@@ -1,33 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('SPARQLAdapter', {
-    endpoint: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: 'https://somesite.com/sparql',
-            locationType: 'UriLocation',
-        },
-        description: 'URL of the SPARQL endpoint',
-    },
-    queryTemplate: {
-        type: 'text',
-        defaultValue: '',
-        description: 'SPARQL query where {start} {end} and {refName} will get replaced for each call',
-    },
-    refNamesQueryTemplate: {
-        type: 'text',
-        defaultValue: '',
-        description: 'SPARQL query that returns the possible refNames in a ?refName column',
-    },
-    refNames: {
-        type: 'stringArray',
-        defaultValue: [],
-        description: 'Possible refNames used by the SPARQL endpoint (ignored if "refNamesQueryTemplate" is provided)',
-    },
-    additionalQueryParams: {
-        type: 'stringArray',
-        defaultValue: [],
-        description: 'Additional parameters to add to the query, e.g. "format=JSON"',
-    },
-}, { explicitlyTyped: true });

package/dist/SPARQLAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function SPARQLAdapterF(pluginManager: PluginManager): void;

package/dist/SPARQLAdapter/index.js

@@ -1,52 +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 });
-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

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

package/dist/index.js

@@ -1,32 +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 Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-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) {
-        (0, SPARQLAdapter_1.default)(pluginManager);
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\/sparql$/i;
-                const adapterName = 'SPARQLAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        endpoint: file,
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-    }
-}
-exports.default = RdfPlugin;