@jbrowse/plugin-data-management 1.6.7 → 1.7.0

package/dist/ucsc-trackhub/configSchema.js

@@ -0,0 +1,30 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _models = require("@jbrowse/core/pluggableElementTypes/models");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('UCSCTrackHubConnection', {
+  hubTxtLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: 'http://mysite.com/path/to/hub.txt',
+      locationType: 'UriLocation'
+    },
+    description: 'location of the hub file (usually called hub.txt)'
+  },
+  assemblyNames: {
+    type: 'stringArray',
+    defaultValue: [],
+    description: 'optional list of genomes to import from this track hub, if empty all genomes will be imported'
+  }
+}, {
+  baseConfiguration: _models.baseConnectionConfig
+});
+
+exports["default"] = _default;

package/dist/ucsc-trackhub/index.js

@@ -0,0 +1,23 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema["default"];
+  }
+});
+Object.defineProperty(exports, "modelFactory", {
+  enumerable: true,
+  get: function get() {
+    return _model["default"];
+  }
+});
+
+var _model = _interopRequireDefault(require("./model"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));

package/dist/ucsc-trackhub/model.js

@@ -0,0 +1,130 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = UCSCTrackHubConnection;
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _models = require("@jbrowse/core/pluggableElementTypes/models");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _util = require("@jbrowse/core/util");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+var _ucscTrackHub = require("./ucscTrackHub");
+
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it["return"] != null) it["return"](); } finally { if (didErr) throw err; } } }; }
+
+function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
+
+function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
+
+function UCSCTrackHubConnection(pluginManager) {
+  return _mobxStateTree.types.compose('UCSCTrackHubConnection', (0, _models.BaseConnectionModelFactory)(pluginManager), _mobxStateTree.types.model({
+    configuration: (0, _configuration.ConfigurationReference)(_configSchema["default"]),
+    type: _mobxStateTree.types.literal('UCSCTrackHubConnection')
+  }).actions(function (self) {
+    return {
+      connect: function connect() {
+        var connectionName = (0, _configuration.getConf)(self, 'name');
+        var hubFileLocation = (0, _configuration.getConf)(self, 'hubTxtLocation');
+        var session = (0, _util.getSession)(self);
+        (0, _ucscTrackHub.fetchHubFile)(hubFileLocation).then(function (hubFile) {
+          var genomesFileLocation = hubFileLocation.uri ? {
+            uri: new URL(hubFile.get('genomesFile'), hubFileLocation.uri).href,
+            locationType: 'UriLocation'
+          } : {
+            localPath: hubFile.get('genomesFile'),
+            locationType: 'LocalPathLocation'
+          };
+          return Promise.all([hubFile, (0, _ucscTrackHub.fetchGenomesFile)(genomesFileLocation)]);
+        }).then(function (_ref) {
+          var _ref2 = (0, _slicedToArray2["default"])(_ref, 2),
+              hubFile = _ref2[0],
+              genomesFile = _ref2[1];
+
+          var trackDbData = [];
+
+          var _iterator = _createForOfIteratorHelper(genomesFile),
+              _step;
+
+          try {
+            var _loop = function _loop() {
+              var _step$value = (0, _slicedToArray2["default"])(_step.value, 2),
+                  genomeName = _step$value[0],
+                  genome = _step$value[1];
+
+              var assemblyNames = (0, _configuration.getConf)(self, 'assemblyNames');
+
+              if (assemblyNames.length > 0 && !assemblyNames.includes(genomeName)) {
+                return "break";
+              }
+
+              var assemblyConf = session.assemblies.find(function (assembly) {
+                return (0, _configuration.readConfObject)(assembly, 'name') === genomeName;
+              });
+
+              if (!assemblyConf) {
+                throw new Error("Cannot find assembly for \"".concat(genomeName, "\" from the genomes file for connection \"").concat(connectionName, "\""));
+              }
+
+              var trackDbFileLocation = hubFileLocation.uri ? {
+                uri: new URL(genome.get('trackDb'), new URL(hubFile.get('genomesFile'), hubFileLocation.uri)).href,
+                locationType: 'UriLocation'
+              } : {
+                localPath: genome.get('trackDb'),
+                locationType: 'LocalPathLocation'
+              };
+              trackDbData.push(Promise.all([trackDbFileLocation, (0, _ucscTrackHub.fetchTrackDbFile)(trackDbFileLocation), genomeName, assemblyConf]));
+            };
+
+            for (_iterator.s(); !(_step = _iterator.n()).done;) {
+              var _ret = _loop();
+
+              if (_ret === "break") break;
+            }
+          } catch (err) {
+            _iterator.e(err);
+          } finally {
+            _iterator.f();
+          }
+
+          return Promise.all([].concat(trackDbData));
+        }).then(function (trackDbData) {
+          var _iterator2 = _createForOfIteratorHelper(trackDbData),
+              _step2;
+
+          try {
+            for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
+              var _step2$value = (0, _slicedToArray2["default"])(_step2.value, 4),
+                  trackDbFileLocation = _step2$value[0],
+                  trackDbFile = _step2$value[1],
+                  genomeName = _step2$value[2],
+                  assemblyConf = _step2$value[3];
+
+              var sequenceAdapter = (0, _configuration.readConfObject)(assemblyConf, ['sequence', 'adapter']);
+              var tracks = (0, _ucscTrackHub.generateTracks)(trackDbFile, trackDbFileLocation, genomeName, sequenceAdapter);
+              self.addTrackConfs(tracks);
+            }
+          } catch (err) {
+            _iterator2.e(err);
+          } finally {
+            _iterator2.f();
+          }
+        })["catch"](function (error) {
+          console.error(error);
+          session.notify("There was a problem connecting to the UCSC Track Hub \"".concat(self.name, "\". Please make sure you have entered a valid hub.txt file. The error that was thrown is: \"").concat(error, "\""), 'error');
+          session.breakConnection(self.configuration);
+        });
+      }
+    };
+  }));
+}

package/dist/ucsc-trackhub/ucscAssemblies.js

@@ -0,0 +1,13 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+// These are the assemblies for which there is a sequence file located at
+// http://hgdownload.soe.ucsc.edu/goldenPath/${assemblyName}/bigZips/${assemblyName}.2bit
+// This list was generated by `getUcscAssemblies.js`
+var _default = "ailMel1\nallMis1\nanoCar1\nanoCar2\nanoGam1\nanoGam3\napiMel1\napiMel2\naplCal1\naptMan1\naquChr2\nbalAcu1\nbisBis1\nbosTau2\nbosTau3\nbosTau4\nbosTau6\nbosTau7\nbosTau8\nbraFlo1\ncaeJap1\ncaePb1\ncaePb2\ncaeRem2\ncaeRem3\ncalJac1\ncalJac3\ncalMil1\ncanFam1\ncanFam3\ncavPor3\ncb3\nce10\nce11\nce2\nce4\nce6\ncerSim1\nchlSab2\nchoHof1\nchrPic1\nci1\nci2\nci3\ncriGri1\ncriGriChoV1\ndanRer10\ndanRer11\ndanRer3\ndanRer4\ndanRer5\ndanRer6\ndanRer7\ndasNov3\ndipOrd1\ndm1\ndm2\ndm3\ndm6\ndp2\ndp3\ndroAna1\ndroAna2\ndroEre1\ndroGri1\ndroMoj1\ndroMoj2\ndroPer1\ndroSec1\ndroSim1\ndroVir1\ndroVir2\ndroYak1\ndroYak2\neboVir3\nechTel1\nechTel2\nequCab1\nequCab2\neriEur1\neriEur2\nfelCat3\nfelCat4\nfelCat5\nfelCat8\nfr1\nfr2\nfr3\ngadMor1\ngalGal2\ngalGal3\ngalGal4\ngalGal5\ngalGal6\ngalVar1\ngasAcu1\ngeoFor1\ngorGor3\ngorGor4\ngorGor5\nhetGla1\nhetGla2\nhg16\nhg18\nhg19\nhg38\nlatCha1\nloxAfr3\nmacEug2\nmacFas5\nmanPen1\nmelGal1\nmelGal5\nmelUnd1\nmicMur1\nmicMur2\nmm10\nmm7\nmm8\nmm9\nmonDom2\nmonDom4\nmonDom5\nmusFur1\nmyoLuc2\nnanPar1\nnasLar1\nnomLeu1\nnomLeu2\nnomLeu3\nochPri2\nochPri3\noreNil2\nornAna1\nornAna2\noryCun2\noryLat2\notoGar3\noviAri1\noviAri3\noviAri4\npanPan1\npanPan2\npanTro1\npanTro2\npanTro3\npanTro4\npanTro5\npanTro6\npapAnu2\npapHam1\npetMar1\npetMar2\nponAbe2\nponAbe3\npriPac1\nproCap1\npteVam1\nrheMac2\nrheMac3\nrheMac8\nrhiRox1\nrn4\nrn5\nrn6\nsacCer1\nsacCer2\nsacCer3\nsaiBol1\nsarHar1\nsorAra1\nsorAra2\nspeTri2\nstrPur1\nstrPur2\nsusScr11\nsusScr2\nsusScr3\ntaeGut1\ntaeGut2\ntarSyr1\ntarSyr2\ntetNig1\ntetNig2\nthaSir1\ntriMan1\ntupBel1\nturTru2\nventer1\nvicPac1\nvicPac2\nxenLae2\nxenTro1\nxenTro2\nxenTro3\nxenTro7\nxenTro9".split(/\r?\n/);
+
+exports["default"] = _default;