@jbrowse/plugin-data-management 1.6.9 → 1.7.0

package/dist/ucsc-trackhub/ucscTrackHub.js

@@ -0,0 +1,503 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.fetchGenomesFile = fetchGenomesFile;
+exports.fetchHubFile = fetchHubFile;
+exports.fetchTrackDbFile = fetchTrackDbFile;
+exports.generateTracks = generateTracks;
+Object.defineProperty(exports, "ucscAssemblies", {
+  enumerable: true,
+  get: function get() {
+    return _ucscAssemblies["default"];
+  }
+});
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _util = require("@jbrowse/core/util");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+var _ucscAssemblies = _interopRequireDefault(require("./ucscAssemblies"));
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+function fetchHubFile(_x) {
+  return _fetchHubFile.apply(this, arguments);
+}
+
+function _fetchHubFile() {
+  _fetchHubFile = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(hubFileLocation) {
+    var hubFileText, _yield$import, HubFile;
+
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            _context.prev = 0;
+            _context.next = 3;
+            return (0, _io.openLocation)(hubFileLocation).readFile('utf8');
+
+          case 3:
+            hubFileText = _context.sent;
+            _context.next = 6;
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('@gmod/ucsc-hub'));
+            });
+
+          case 6:
+            _yield$import = _context.sent;
+            HubFile = _yield$import.HubFile;
+            return _context.abrupt("return", new HubFile(hubFileText));
+
+          case 11:
+            _context.prev = 11;
+            _context.t0 = _context["catch"](0);
+            throw new Error("Not a valid hub.txt file, got error: '".concat(_context.t0, "'"));
+
+          case 14:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee, null, [[0, 11]]);
+  }));
+  return _fetchHubFile.apply(this, arguments);
+}
+
+function fetchGenomesFile(_x2) {
+  return _fetchGenomesFile.apply(this, arguments);
+}
+
+function _fetchGenomesFile() {
+  _fetchGenomesFile = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(genomesFileLocation) {
+    var genomesFileText, _yield$import2, GenomesFile;
+
+    return _regenerator["default"].wrap(function _callee2$(_context2) {
+      while (1) {
+        switch (_context2.prev = _context2.next) {
+          case 0:
+            _context2.next = 2;
+            return (0, _io.openLocation)(genomesFileLocation).readFile('utf8');
+
+          case 2:
+            genomesFileText = _context2.sent;
+            _context2.next = 5;
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('@gmod/ucsc-hub'));
+            });
+
+          case 5:
+            _yield$import2 = _context2.sent;
+            GenomesFile = _yield$import2.GenomesFile;
+            return _context2.abrupt("return", new GenomesFile(genomesFileText));
+
+          case 8:
+          case "end":
+            return _context2.stop();
+        }
+      }
+    }, _callee2);
+  }));
+  return _fetchGenomesFile.apply(this, arguments);
+}
+
+function fetchTrackDbFile(_x3) {
+  return _fetchTrackDbFile.apply(this, arguments);
+}
+
+function _fetchTrackDbFile() {
+  _fetchTrackDbFile = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(trackDbFileLocation) {
+    var text, _yield$import3, TrackDbFile;
+
+    return _regenerator["default"].wrap(function _callee3$(_context3) {
+      while (1) {
+        switch (_context3.prev = _context3.next) {
+          case 0:
+            _context3.next = 2;
+            return (0, _io.openLocation)(trackDbFileLocation).readFile('utf8');
+
+          case 2:
+            text = _context3.sent;
+            _context3.next = 5;
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('@gmod/ucsc-hub'));
+            });
+
+          case 5:
+            _yield$import3 = _context3.sent;
+            TrackDbFile = _yield$import3.TrackDbFile;
+            return _context3.abrupt("return", new TrackDbFile(text));
+
+          case 8:
+          case "end":
+            return _context3.stop();
+        }
+      }
+    }, _callee3);
+  }));
+  return _fetchTrackDbFile.apply(this, arguments);
+}
+
+function generateTracks(trackDb, trackDbFileLocation, assemblyName, sequenceAdapter) {
+  var tracks = [];
+  trackDb.forEach(function (track, trackName) {
+    var trackKeys = Array.from(track.keys());
+    var parentTrackKeys = ['superTrack', 'compositeTrack', 'container', 'view'];
+
+    if (trackKeys.some(function (key) {
+      return parentTrackKeys.includes(key);
+    })) {
+      return;
+    }
+
+    var parentTracks = [];
+    var currentTrackName = trackName;
+
+    do {
+      currentTrackName = trackDb.get(currentTrackName).get('parent');
+
+      if (currentTrackName) {
+        ;
+
+        var _currentTrackName$spl = currentTrackName.split(' ');
+
+        var _currentTrackName$spl2 = (0, _slicedToArray2["default"])(_currentTrackName$spl, 1);
+
+        currentTrackName = _currentTrackName$spl2[0];
+        parentTracks.push(trackDb.get(currentTrackName));
+      }
+    } while (currentTrackName);
+
+    parentTracks.reverse();
+    var categories = parentTracks.map(function (parentTrack) {
+      return parentTrack.get('shortLabel');
+    });
+    var res = makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter);
+    res.trackId = "ucsc-trackhub-".concat((0, _util.objectHash)(res));
+    res.assemblyNames = [assemblyName];
+    tracks.push(res);
+  });
+  return tracks;
+}
+
+function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter) {
+  var trackType = track.get('type');
+
+  if (!trackType) {
+    trackType = trackDb.get(track.get('parent')).get('type');
+  }
+
+  var baseTrackType = trackType.split(' ')[0];
+
+  if (baseTrackType === 'bam' && track.get('bigDataUrl').toLowerCase().endsWith('cram')) {
+    baseTrackType = 'cram';
+  }
+
+  var bigDataLocation;
+
+  if (trackDbFileLocation.uri) {
+    bigDataLocation = {
+      uri: new URL(track.get('bigDataUrl'), trackDbFileLocation.uri).href,
+      locationType: 'UriLocation'
+    };
+  } else {
+    bigDataLocation = {
+      localPath: track.get('bigDataUrl'),
+      locationType: 'LocalPathLocation'
+    };
+  }
+
+  var bigDataIndexLocation;
+
+  switch (baseTrackType) {
+    case 'bam':
+      if (trackDbFileLocation.uri) {
+        bigDataIndexLocation = track.get('bigDataIndex') ? {
+          uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri).href,
+          locationType: 'UriLocation'
+        } : {
+          uri: new URL("".concat(track.get('bigDataUrl'), ".bai"), trackDbFileLocation.uri).href,
+          locationType: 'UriLocation'
+        };
+      } else {
+        bigDataIndexLocation = track.get('bigDataIndex') ? {
+          localPath: track.get('bigDataIndex'),
+          locationType: 'LocalPathLocation'
+        } : {
+          localPath: "".concat(track.get('bigDataUrl'), ".bai"),
+          locationType: 'LocalPathLocation'
+        };
+      }
+
+      return {
+        type: 'AlignmentsTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BamAdapter',
+          bamLocation: bigDataLocation,
+          index: {
+            location: bigDataIndexLocation
+          }
+        }
+      };
+
+    case 'bed':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'bed5FloatScore':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'bedGraph':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'bedRnaElements':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'bigBarChart':
+      return {
+        type: 'FeatureTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer'
+        }
+      };
+
+    case 'bigBed':
+      return {
+        type: 'FeatureTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation
+        }
+      };
+
+    case 'bigGenePred':
+      return {
+        type: 'FeatureTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation
+        }
+      };
+
+    case 'bigChain':
+      return {
+        type: 'FeatureTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer'
+        }
+      };
+
+    case 'bigInteract':
+      return {
+        type: 'FeatureTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer'
+        }
+      };
+
+    case 'bigMaf':
+      return {
+        type: 'FeatureTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer'
+        }
+      };
+
+    case 'bigPsl':
+      return {
+        type: 'FeatureTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer'
+        }
+      };
+
+    case 'bigWig':
+      return {
+        type: 'QuantitativeTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigWigAdapter',
+          bigWigLocation: bigDataLocation
+        }
+      };
+
+    case 'broadPeak':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'coloredExon':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'cram':
+      if (trackDbFileLocation.uri) {
+        bigDataIndexLocation = track.get('bigDataIndex') ? {
+          uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri).href,
+          locationType: 'UriLocation'
+        } : {
+          uri: new URL("".concat(track.get('bigDataUrl'), ".crai"), trackDbFileLocation.uri).href,
+          locationType: 'UriLocation'
+        };
+      } else {
+        bigDataIndexLocation = track.get('bigDataIndex') ? {
+          localPath: track.get('bigDataIndex'),
+          locationType: 'LocalPathLocation'
+        } : {
+          localPath: "".concat(track.get('bigDataUrl'), ".crai"),
+          locationType: 'LocalPathLocation'
+        };
+      }
+
+      return {
+        type: 'AlignmentsTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'CramAdapter',
+          cramLocation: bigDataLocation,
+          craiLocation: bigDataIndexLocation,
+          sequenceAdapter: sequenceAdapter
+        }
+      };
+
+    case 'gvf':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'ld2':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'narrowPeak':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'bigNarrowPeak':
+      return {
+        type: 'FeatureTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation
+        }
+      };
+
+    case 'peptideMapping':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'vcfTabix':
+      if (trackDbFileLocation.uri) {
+        bigDataIndexLocation = track.get('bigDataIndex') ? {
+          uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri).href,
+          locationType: 'UriLocation'
+        } : {
+          uri: new URL("".concat(track.get('bigDataUrl'), ".tbi"), trackDbFileLocation.uri).href,
+          locationType: 'UriLocation'
+        };
+      } else {
+        bigDataIndexLocation = track.get('bigDataIndex') ? {
+          localPath: track.get('bigDataIndex'),
+          locationType: 'LocalPathLocation'
+        } : {
+          localPath: "".concat(track.get('bigDataUrl'), ".tbi"),
+          locationType: 'LocalPathLocation'
+        };
+      }
+
+      return {
+        type: 'VariantTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'VcfTabixAdapter',
+          vcfGzLocation: bigDataLocation,
+          index: {
+            location: bigDataIndexLocation
+          }
+        }
+      };
+
+    case 'wig':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'wigMaf':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    case 'hic':
+      return {
+        type: 'HicTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'HicAdapter',
+          hicLocation: bigDataLocation
+        }
+      };
+
+    case 'halSnake':
+      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+
+    default:
+      return (0, _tracks.generateUnknownTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+  }
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "1.6.9",
+  "version": "1.7.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -18,15 +18,12 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-data-management.esm.js",
-  "module": "dist/plugin-data-management.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
     "test": "cd ../..; jest plugins/data-management",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
@@ -56,5 +53,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f6c3d4edfadc26f7ac635a2fa7259f50f0c7e5e3"
+  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
 }

package/src/AddConnectionWidget/components/AddConnectionWidget.test.js

@@ -2,6 +2,7 @@ import { render, cleanup, fireEvent } from '@testing-library/react'
 import React from 'react'
 import { createTestSession } from '@jbrowse/web/src/rootModel'
 import AddConnectionWidget from './AddConnectionWidget'
+jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 
 window.fetch = jest.fn(() => new Promise(resolve => resolve()))
 

package/src/AddTrackWidget/components/AddTrackWidget.test.js

@@ -2,6 +2,7 @@ import React from 'react'
 import { render, cleanup, fireEvent } from '@testing-library/react'
 import { createTestSession } from '@jbrowse/web/src/rootModel'
 import AddTrackWidget from './AddTrackWidget'
+jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 
 describe('<AddTrackWidget />', () => {
   let session

package/src/AddTrackWidget/components/AddTrackWidget.tsx

@@ -47,7 +47,7 @@ function AddTrackWidget({ model }: { model: AddTrackModel }) {
   const classes = useStyles()
   const session = getSession(model)
   const { assembly, trackAdapter, trackData, trackName, trackType } = model
-  const [trackErrorMessage, setTrackErrorMessage] = useState<String>()
+  const [trackErrorMessage, setTrackErrorMessage] = useState<string>()
 
   function getStepContent(step: number) {
     switch (step) {

package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.js

@@ -3,6 +3,7 @@ import { createTheme, ThemeProvider } from '@material-ui/core/styles'
 import { cleanup, render } from '@testing-library/react'
 import React from 'react'
 import HierarchicalTrackSelector from './HierarchicalTrackSelector'
+jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 
 window.requestIdleCallback = cb => cb()
 window.cancelIdleCallback = () => {}

package/src/PluginStoreWidget/components/CustomPluginForm.tsx

@@ -132,7 +132,7 @@ function CustomPluginForm({
         <DialogContent className={classes.dialogContent}>
           <DialogContentText>
             Enter the name of the plugin and its URL. The name should match what
-            is defined in the plugin's build.
+            is defined in the plugin&apos;s build.
           </DialogContentText>
           <TextField
             id="umd-name-input"

package/src/PluginStoreWidget/components/InstalledPlugin.tsx

@@ -19,8 +19,10 @@ import LockIcon from '@material-ui/icons/Lock'
 
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSession } from '@jbrowse/core/util'
-import { BasePlugin } from '@jbrowse/core/util/types'
-import { isSessionWithSessionPlugins } from '@jbrowse/core/util/types'
+import {
+  BasePlugin,
+  isSessionWithSessionPlugins,
+} from '@jbrowse/core/util/types'
 import { PluginStoreModel } from '../model'
 
 const useStyles = makeStyles(() => ({

package/src/PluginStoreWidget/components/PluginCard.tsx

@@ -3,8 +3,10 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import { observer } from 'mobx-react'
 import { getEnv, getParent } from 'mobx-state-tree'
 import { getSession } from '@jbrowse/core/util'
-import { JBrowsePlugin } from '@jbrowse/core/util/types'
-import { isSessionWithSessionPlugins } from '@jbrowse/core/util/types'
+import {
+  JBrowsePlugin,
+  isSessionWithSessionPlugins,
+} from '@jbrowse/core/util/types'
 import {
   Card,
   CardActions,

package/src/PluginStoreWidget/components/PluginStoreWidget.test.js

@@ -4,6 +4,7 @@ import { render, cleanup, fireEvent, waitFor } from '@testing-library/react'
 import { createTestSession } from '@jbrowse/web/src/rootModel'
 
 import PluginStoreWidget from './PluginStoreWidget'
+jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 
 const plugins = {
   plugins: [

package/src/PluginStoreWidget/model.test.js

@@ -1,4 +1,5 @@
 import { createTestSession } from '@jbrowse/web/src/rootModel'
+jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 
 describe('PluginStoreModel', () => {
   it('filters plugins correctly', () => {

package/src/SetDefaultSession/SetDefaultSession.tsx

@@ -32,9 +32,10 @@ const SetDefaultSession = observer(
         <DialogTitle>Set default session</DialogTitle>
         <DialogContent>
           <Typography>
-            Select "Set current session as default" to make your current session
-            saved to the config file. You can also hit "Clear default session",
-            which would remove the default session from the config.
+            Select &quot;Set current session as default&quot; to make your
+            current session saved to the config file. You can also hit
+            &quot;Clear default session&quot;, which would remove the default
+            session from the config.
           </Typography>
         </DialogContent>
         <DialogActions>