@jbrowse/plugin-sequence 1.7.6 → 1.7.9

package/dist/BgzipFastaAdapter/configSchema.js

@@ -22,6 +22,14 @@ var _default = (0, _configuration.ConfigurationSchema)('BgzipFastaAdapter', {
       locationType: 'UriLocation'
     }
   },
+  metadataLocation: {
+    description: 'Optional metadata file',
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/fa.metadata.yaml',
+      locationType: 'UriLocation'
+    }
+  },
   gziLocation: {
     type: 'fileLocation',
     defaultValue: {

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -1,12 +1,13 @@
 import { IndexedFasta } from '@gmod/indexedfasta';
 import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { Feature } from '@jbrowse/core/util';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends BaseSequenceAdapter {
     protected fasta: IndexedFasta;
+    protected header?: Promise<string>;
     private seqCache;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<string[]>;
@@ -15,6 +16,7 @@ export default class extends BaseSequenceAdapter {
         start: number;
         end: number;
     }[]>;
+    getHeader(): Promise<string | null>;
     getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -33,9 +33,7 @@ var _io = require("@jbrowse/core/util/io");
 
 var _rxjs = require("@jbrowse/core/util/rxjs");
 
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _configuration = require("@jbrowse/core/configuration");
+var _util = require("@jbrowse/core/util");
 
 var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
 
@@ -60,6 +58,7 @@ var _default = /*#__PURE__*/function (_BaseSequenceAdapter) {
     (0, _classCallCheck2.default)(this, _default);
     _this = _super.call(this, config, getSubAdapter, pluginManager);
     (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "fasta", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "header", void 0);
     (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "seqCache", new _abortablePromiseCache.default({
       cache: new _QuickLRU.default({
         maxSize: 200
@@ -91,8 +90,11 @@ var _default = /*#__PURE__*/function (_BaseSequenceAdapter) {
         return fill;
       }()
     }));
-    var fastaLocation = (0, _configuration.readConfObject)(config, 'fastaLocation');
-    var faiLocation = (0, _configuration.readConfObject)(config, 'faiLocation');
+
+    var fastaLocation = _this.getConf('fastaLocation');
+
+    var faiLocation = _this.getConf('faiLocation');
+
     var fastaOpts = {
       fasta: (0, _io.openLocation)(fastaLocation, _this.pluginManager),
       fai: (0, _io.openLocation)(faiLocation, _this.pluginManager)
@@ -142,26 +144,75 @@ var _default = /*#__PURE__*/function (_BaseSequenceAdapter) {
 
       return getRegions;
     }()
+  }, {
+    key: "getHeader",
+    value: function () {
+      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+        var _this2 = this;
+
+        var loc;
+        return _regenerator.default.wrap(function _callee3$(_context3) {
+          while (1) {
+            switch (_context3.prev = _context3.next) {
+              case 0:
+                if (!this.header) {
+                  _context3.next = 2;
+                  break;
+                }
+
+                return _context3.abrupt("return", this.header);
+
+              case 2:
+                loc = this.getConf('metadataLocation');
+
+                if (!(loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml')) {
+                  _context3.next = 5;
+                  break;
+                }
+
+                return _context3.abrupt("return", null);
+
+              case 5:
+                this.header = (0, _io.openLocation)(loc).readFile('utf8').catch(function (e) {
+                  _this2.header = undefined;
+                  throw e;
+                });
+                return _context3.abrupt("return", this.header);
+
+              case 7:
+              case "end":
+                return _context3.stop();
+            }
+          }
+        }, _callee3, this);
+      }));
+
+      function getHeader() {
+        return _getHeader.apply(this, arguments);
+      }
+
+      return getHeader;
+    }()
   }, {
     key: "getFeatures",
     value: function getFeatures(region, opts) {
-      var _this2 = this;
+      var _this3 = this;
 
       var refName = region.refName,
           start = region.start,
           end = region.end;
       return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(observer) {
+        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(observer) {
           var size, regionEnd, chunks, chunkSize, s, e, chunkStart, r, seq;
-          return _regenerator.default.wrap(function _callee3$(_context3) {
+          return _regenerator.default.wrap(function _callee4$(_context4) {
             while (1) {
-              switch (_context3.prev = _context3.next) {
+              switch (_context4.prev = _context4.next) {
                 case 0:
-                  _context3.next = 2;
-                  return _this2.fasta.getSequenceSize(refName, opts);
+                  _context4.next = 2;
+                  return _this3.fasta.getSequenceSize(refName, opts);
 
                 case 2:
-                  size = _context3.sent;
+                  size = _context4.sent;
                   regionEnd = size !== undefined ? Math.min(size, end) : end;
                   chunks = [];
                   chunkSize = 128000;
@@ -174,17 +225,17 @@ var _default = /*#__PURE__*/function (_BaseSequenceAdapter) {
                       start: chunkStart,
                       end: chunkStart + chunkSize
                     };
-                    chunks.push(_this2.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
+                    chunks.push(_this3.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
                   }
 
-                  _context3.next = 11;
+                  _context4.next = 11;
                   return Promise.all(chunks);
 
                 case 11:
-                  seq = _context3.sent.join('').slice(start - s).slice(0, end - start);
+                  seq = _context4.sent.join('').slice(start - s).slice(0, end - start);
 
                   if (seq) {
-                    observer.next(new _simpleFeature.default({
+                    observer.next(new _util.SimpleFeature({
                       id: "".concat(refName, " ").concat(start, "-").concat(regionEnd),
                       data: {
                         refName: refName,
@@ -199,10 +250,10 @@ var _default = /*#__PURE__*/function (_BaseSequenceAdapter) {
 
                 case 14:
                 case "end":
-                  return _context3.stop();
+                  return _context4.stop();
               }
             }
-          }, _callee3);
+          }, _callee4);
         }));
 
         return function (_x4) {

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.test.js

@@ -13,7 +13,7 @@ var _IndexedFastaAdapter = _interopRequireDefault(require("./IndexedFastaAdapter
 var _configSchema = _interopRequireDefault(require("./configSchema"));
 
 test('adapter can fetch sequence from volvox.fa', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, features, featuresArray, features2, featuresArray2, features3, featuresArray3;
+  var adapter, features, featuresArray, features2, featuresArray2, features3, data, featuresArray3;
   return _regenerator.default.wrap(function _callee$(_context) {
     while (1) {
       switch (_context.prev = _context.next) {
@@ -26,6 +26,10 @@ test('adapter can fetch sequence from volvox.fa', /*#__PURE__*/(0, _asyncToGener
             faiLocation: {
               localPath: require.resolve('../../test_data/volvox.fa.fai'),
               locationType: 'LocalPathLocation'
+            },
+            metadataLocation: {
+              localPath: require.resolve('../../test_data/hello.txt'),
+              locationType: 'LocalPathLocation'
             }
           }));
           features = adapter.getFeatures({
@@ -56,13 +60,19 @@ test('adapter can fetch sequence from volvox.fa', /*#__PURE__*/(0, _asyncToGener
             end: 20000
           });
           _context.next = 14;
-          return features3.pipe((0, _operators.toArray)()).toPromise();
+          return adapter.getHeader();
 
         case 14:
+          data = _context.sent;
+          expect(data === null || data === void 0 ? void 0 : data.trim()).toBe('hello world');
+          _context.next = 18;
+          return features3.pipe((0, _operators.toArray)()).toPromise();
+
+        case 18:
           featuresArray3 = _context.sent;
           expect(featuresArray3).toMatchSnapshot();
 
-        case 16:
+        case 20:
         case "end":
           return _context.stop();
       }

package/dist/IndexedFastaAdapter/configSchema.js

@@ -21,6 +21,14 @@ var _default = (0, _configuration.ConfigurationSchema)('IndexedFastaAdapter', {
       uri: '/path/to/seq.fa.fai',
       locationType: 'UriLocation'
     }
+  },
+  metadataLocation: {
+    description: 'Optional metadata file',
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/fa.metadata.yaml',
+      locationType: 'UriLocation'
+    }
   }
 }, {
   explicitlyTyped: true

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "1.7.6",
+  "version": "1.7.9",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -53,5 +53,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "dbd73f99714e395cf20877d5e05d26855857a0e3"
+  "gitHead": "a6504c385d703ce6e755d05652ef659ffe28c864"
 }

package/src/BgzipFastaAdapter/configSchema.ts

@@ -14,6 +14,14 @@ export default ConfigurationSchema(
         locationType: 'UriLocation',
       },
     },
+    metadataLocation: {
+      description: 'Optional metadata file',
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/fa.metadata.yaml',
+        locationType: 'UriLocation',
+      },
+    },
     gziLocation: {
       type: 'fileLocation',
       defaultValue: {

package/src/IndexedFastaAdapter/IndexedFastaAdapter.test.ts

@@ -13,6 +13,10 @@ test('adapter can fetch sequence from volvox.fa', async () => {
         localPath: require.resolve('../../test_data/volvox.fa.fai'),
         locationType: 'LocalPathLocation',
       },
+      metadataLocation: {
+        localPath: require.resolve('../../test_data/hello.txt'),
+        locationType: 'LocalPathLocation',
+      },
     }),
   )
 
@@ -40,6 +44,9 @@ test('adapter can fetch sequence from volvox.fa', async () => {
     end: 20000,
   })
 
+  const data = await adapter.getHeader()
+  expect(data?.trim()).toBe('hello world')
+
   const featuresArray3 = await features3.pipe(toArray()).toPromise()
   expect(featuresArray3).toMatchSnapshot()
 })

package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts

@@ -6,9 +6,8 @@ import {
 import { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
+import { SimpleFeature, Feature } from '@jbrowse/core/util'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import AbortablePromiseCache from 'abortable-promise-cache'
 import LRU from '@jbrowse/core/util/QuickLRU'
 import PluginManager from '@jbrowse/core/PluginManager'
@@ -17,6 +16,8 @@ import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 export default class extends BaseSequenceAdapter {
   protected fasta: IndexedFasta
 
+  protected header?: Promise<string>
+
   private seqCache = new AbortablePromiseCache({
     cache: new LRU({ maxSize: 200 }),
     fill: async (
@@ -34,8 +35,8 @@ export default class extends BaseSequenceAdapter {
     pluginManager?: PluginManager,
   ) {
     super(config, getSubAdapter, pluginManager)
-    const fastaLocation = readConfObject(config, 'fastaLocation')
-    const faiLocation = readConfObject(config, 'faiLocation')
+    const fastaLocation = this.getConf('fastaLocation')
+    const faiLocation = this.getConf('faiLocation')
     const fastaOpts = {
       fasta: openLocation(fastaLocation as FileLocation, this.pluginManager),
       fai: openLocation(faiLocation as FileLocation, this.pluginManager),
@@ -57,6 +58,26 @@ export default class extends BaseSequenceAdapter {
     }))
   }
 
+  public async getHeader() {
+    if (this.header) {
+      return this.header
+    }
+    const loc = this.getConf('metadataLocation')
+
+    if (loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml') {
+      return null
+    }
+
+    this.header = openLocation(loc)
+      .readFile('utf8')
+      .catch(e => {
+        this.header = undefined
+        throw e
+      })
+
+    return this.header
+  }
+
   public getFeatures(region: NoAssemblyRegion, opts?: BaseOptions) {
     const { refName, start, end } = region
     return ObservableCreate<Feature>(async observer => {

package/src/IndexedFastaAdapter/configSchema.ts

@@ -11,6 +11,14 @@ export default ConfigurationSchema(
       type: 'fileLocation',
       defaultValue: { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' },
     },
+    metadataLocation: {
+      description: 'Optional metadata file',
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/fa.metadata.yaml',
+        locationType: 'UriLocation',
+      },
+    },
   },
   { explicitlyTyped: true },
 )