@jbrowse/plugin-data-management 1.7.11 → 2.0.0

package/dist/ucsc-trackhub/model.js

@@ -1,130 +1,152 @@
 "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);
-        });
-      }
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __values = (this && this.__values) || function(o) {
+    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
+    if (m) return m.call(o);
+    if (o && typeof o.length === "number") return {
+        next: function () {
+            if (o && i >= o.length) o = void 0;
+            return { value: o && o[i++], done: !o };
+        }
     };
-  }));
-}
+    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+var configuration_1 = require("@jbrowse/core/configuration");
+var util_1 = require("@jbrowse/core/util");
+var mobx_state_tree_1 = require("mobx-state-tree");
+var configSchema_1 = __importDefault(require("./configSchema"));
+var ucscTrackHub_1 = require("./ucscTrackHub");
+function UCSCTrackHubConnection(pluginManager) {
+    return mobx_state_tree_1.types.compose('UCSCTrackHubConnection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types
+        .model({
+        configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
+        type: mobx_state_tree_1.types.literal('UCSCTrackHubConnection'),
+    })
+        .actions(function (self) { return ({
+        connect: function () {
+            var connectionName = (0, configuration_1.getConf)(self, 'name');
+            var hubFileLocation = (0, configuration_1.getConf)(self, 'hubTxtLocation');
+            var session = (0, util_1.getSession)(self);
+            (0, ucscTrackHub_1.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_1.fetchGenomesFile)(genomesFileLocation),
+                ]);
+            })
+                .then(function (_a) {
+                var e_1, _b;
+                var _c = __read(_a, 2), hubFile = _c[0], genomesFile = _c[1];
+                var trackDbData = [];
+                var _loop_1 = function (genomeName, genome) {
+                    var assemblyNames = (0, configuration_1.getConf)(self, 'assemblyNames');
+                    if (assemblyNames.length > 0 &&
+                        !assemblyNames.includes(genomeName)) {
+                        return "break";
+                    }
+                    var assemblyConf = session.assemblies.find(function (assembly) { return (0, configuration_1.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_1.fetchTrackDbFile)(trackDbFileLocation),
+                        genomeName,
+                        assemblyConf,
+                    ]));
+                };
+                try {
+                    for (var genomesFile_1 = __values(genomesFile), genomesFile_1_1 = genomesFile_1.next(); !genomesFile_1_1.done; genomesFile_1_1 = genomesFile_1.next()) {
+                        var _d = __read(genomesFile_1_1.value, 2), genomeName = _d[0], genome = _d[1];
+                        var state_1 = _loop_1(genomeName, genome);
+                        if (state_1 === "break")
+                            break;
+                    }
+                }
+                catch (e_1_1) { e_1 = { error: e_1_1 }; }
+                finally {
+                    try {
+                        if (genomesFile_1_1 && !genomesFile_1_1.done && (_b = genomesFile_1.return)) _b.call(genomesFile_1);
+                    }
+                    finally { if (e_1) throw e_1.error; }
+                }
+                return Promise.all(__spreadArray([], __read(trackDbData), false));
+            })
+                .then(function (trackDbData) {
+                var e_2, _a;
+                try {
+                    for (var trackDbData_1 = __values(trackDbData), trackDbData_1_1 = trackDbData_1.next(); !trackDbData_1_1.done; trackDbData_1_1 = trackDbData_1.next()) {
+                        var _b = __read(trackDbData_1_1.value, 4), trackDbFileLocation = _b[0], trackDbFile = _b[1], genomeName = _b[2], assemblyConf = _b[3];
+                        var sequenceAdapter = (0, configuration_1.readConfObject)(assemblyConf, [
+                            'sequence',
+                            'adapter',
+                        ]);
+                        var tracks = (0, ucscTrackHub_1.generateTracks)(trackDbFile, trackDbFileLocation, genomeName, sequenceAdapter);
+                        self.addTrackConfs(tracks);
+                    }
+                }
+                catch (e_2_1) { e_2 = { error: e_2_1 }; }
+                finally {
+                    try {
+                        if (trackDbData_1_1 && !trackDbData_1_1.done && (_a = trackDbData_1.return)) _a.call(trackDbData_1);
+                    }
+                    finally { if (e_2) throw e_2.error; }
+                }
+            })
+                .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);
+            });
+        },
+    }); }));
+}
+exports.default = UCSCTrackHubConnection;
+//# sourceMappingURL=model.js.map

package/dist/ucsc-trackhub/model.js.map

@@ -0,0 +1 @@
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package/dist/ucsc-trackhub/ucscAssemblies.js

@@ -1,13 +1,7 @@
 "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;
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.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/);
+//# sourceMappingURL=ucscAssemblies.js.map

package/dist/ucsc-trackhub/ucscAssemblies.js.map

@@ -0,0 +1 @@
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