@jbrowse/plugin-legacy-jbrowse 1.6.9 → 1.7.3

package/dist/JBrowse1Connection/jb1ToJb2.js

@@ -0,0 +1,556 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.convertTrackConfig = convertTrackConfig;
+exports.createRefSeqsAdapter = createRefSeqsAdapter;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _io = require("@jbrowse/core/util/io");
+
+var _util = require("@jbrowse/core/util");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+
+function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
+  var jb2TrackConfig = {
+    trackId: (0, _util.objectHash)(jb1TrackConfig),
+    name: jb1TrackConfig.key || jb1TrackConfig.label
+  };
+  var description = jb1TrackConfig.metadata && (jb1TrackConfig.metadata.description || jb1TrackConfig.metadata.Description);
+
+  if (description) {
+    jb2TrackConfig.description = description;
+  }
+
+  var category = jb1TrackConfig.category || jb1TrackConfig.metadata && jb1TrackConfig.metadata.category;
+  jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
+  var storeClass = jb1TrackConfig.storeClass;
+
+  if (!jb1TrackConfig.urlTemplate) {
+    if (!(storeClass && storeClass.endsWith('FromConfig'))) {
+      var trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
+      console.warn("Could not import JBrowse1 track \"".concat(trackIdentifier, "\" because it does not have a \"urlTemplate\" or is not a \"FromConfig\" track"));
+      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
+    }
+
+    return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig);
+  }
+
+  var resolveUrlTemplate = function resolveUrlTemplate(urlTemplate) {
+    return new URL(urlTemplate, "".concat(dataRoot, "/")).href.replace(/%7B/gi, '{').replace(/%7D/gi, '}');
+  };
+
+  var urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
+
+  if (storeClass) {
+    if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {
+      var adapter = {
+        type: 'BamAdapter',
+        bamLocation: {
+          uri: urlTemplate,
+          locationType: 'UriLocation'
+        }
+      };
+
+      if (jb1TrackConfig.baiUrlTemplate) {
+        adapter.index = {
+          location: {
+            uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),
+            locationType: 'UriLocation'
+          }
+        };
+      } else if (jb1TrackConfig.csiUrlTemplate) {
+        adapter.index = {
+          location: {
+            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+            locationType: 'UriLocation'
+          },
+          indexType: 'CSI'
+        };
+      } else {
+        adapter.index = {
+          location: {
+            uri: "".concat(urlTemplate, ".bai"),
+            locationType: 'UriLocation'
+          }
+        };
+      }
+
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'AlignmentsTrack',
+        adapter: adapter
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {
+      var _adapter = {
+        type: 'CramAdapter',
+        cramLocation: {
+          uri: urlTemplate,
+          locationType: 'UriLocation'
+        },
+        sequenceAdapter: sequenceAdapter
+      };
+
+      if (jb1TrackConfig.craiUrlTemplate) {
+        _adapter.craiLocation = {
+          uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
+          locationType: 'UriLocation'
+        };
+      } else {
+        _adapter.craiLocation = {
+          uri: "".concat(urlTemplate, ".crai"),
+          locationType: 'UriLocation'
+        };
+      }
+
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'AlignmentsTrack',
+        adapter: _adapter
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'FeatureTrack',
+        adapter: {
+          type: 'NCListAdapter',
+          rootUrlTemplate: {
+            uri: urlTemplate,
+            locationType: 'UriLocation'
+          }
+        }
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' || storeClass === 'JBrowse/Store/BigWig') {
+      if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+        jb2TrackConfig.defaultRendering = 'xyplot';
+      } else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
+        jb2TrackConfig.defaultRendering = 'density';
+      }
+
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'QuantitativeTrack',
+        adapter: {
+          type: 'BigWigAdapter',
+          bigWigLocation: {
+            uri: urlTemplate,
+            locationType: 'UriLocation'
+          }
+        }
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {
+      var _adapter2 = {
+        type: 'VcfTabixAdapter',
+        vcfGzLocation: {
+          uri: urlTemplate,
+          locationType: 'UriLocation'
+        }
+      };
+
+      if (jb1TrackConfig.tbiUrlTemplate) {
+        _adapter2.index = {
+          location: {
+            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
+            locationType: 'UriLocation'
+          }
+        };
+      } else if (jb1TrackConfig.csiUrlTemplate) {
+        _adapter2.index = {
+          location: {
+            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+            locationType: 'UriLocation'
+          },
+          indexType: 'CSI'
+        };
+      } else {
+        _adapter2.index = {
+          location: {
+            uri: "".concat(urlTemplate, ".tbi"),
+            locationType: 'UriLocation'
+          }
+        };
+      }
+
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'VariantTrack',
+        adapter: _adapter2
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {
+      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "VCFTribble (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
+      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "GFF3 (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'FeatureTrack',
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: {
+            uri: urlTemplate,
+            locationType: 'UriLocation'
+          }
+        }
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {
+      var _adapter3 = {
+        type: 'Gff3TabixAdapter',
+        gffGzLocation: {
+          uri: urlTemplate,
+          locationType: 'UriLocation'
+        }
+      };
+
+      if (jb1TrackConfig.tbiUrlTemplate) {
+        _adapter3.index = {
+          location: {
+            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
+            locationType: 'UriLocation'
+          }
+        };
+      } else if (jb1TrackConfig.csiUrlTemplate) {
+        _adapter3.index = {
+          location: {
+            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+            locationType: 'UriLocation'
+          },
+          indexType: 'CSI'
+        };
+      } else {
+        _adapter3.index = {
+          location: {
+            uri: "".concat(urlTemplate, ".tbi"),
+            locationType: 'UriLocation'
+          }
+        };
+      }
+
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'FeatureTrack',
+        adapter: _adapter3
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/BED') {
+      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "BED (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {
+      var _adapter4 = {
+        type: 'BedTabixAdapter',
+        bedGzLocation: {
+          uri: urlTemplate,
+          locationType: 'UriLocation'
+        }
+      };
+
+      if (jb1TrackConfig.tbiUrlTemplate) {
+        _adapter4.index = {
+          location: {
+            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
+            locationType: 'UriLocation'
+          }
+        };
+      } else if (jb1TrackConfig.csiUrlTemplate) {
+        _adapter4.index = {
+          location: {
+            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+            locationType: 'UriLocation'
+          },
+          indexType: 'CSI'
+        };
+      } else {
+        _adapter4.index = {
+          location: {
+            uri: "".concat(urlTemplate, ".tbi"),
+            locationType: 'UriLocation'
+          }
+        };
+      }
+
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'FeatureTrack',
+        adapter: _adapter4
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
+      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "GTF (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' || storeClass === 'JBrowse/Store/Sequence/StaticChunked') {
+      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "StaticChunked (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {
+      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "UnindexedFasta (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {
+      var _adapter5 = {
+        type: 'IndexedFastaAdapter',
+        fastaLocation: {
+          uri: urlTemplate,
+          locationType: 'UriLocation'
+        }
+      };
+
+      if (jb1TrackConfig.faiUrlTemplate) {
+        _adapter5.faiLocation = {
+          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+          locationType: 'UriLocation'
+        };
+      } else {
+        _adapter5.faiLocation = {
+          uri: "".concat(urlTemplate, ".fai"),
+          locationType: 'UriLocation'
+        };
+      }
+
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'SequenceTrack',
+        adapter: _adapter5
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {
+      var _adapter6 = {
+        type: 'BgzipFastaAdapter',
+        fastaLocation: {
+          uri: urlTemplate,
+          locationType: 'UriLocation'
+        }
+      };
+
+      if (jb1TrackConfig.faiUrlTemplate) {
+        _adapter6.faiLocation = {
+          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+          locationType: 'UriLocation'
+        };
+      } else {
+        _adapter6.faiLocation = {
+          uri: "".concat(urlTemplate, ".fai"),
+          locationType: 'UriLocation'
+        };
+      }
+
+      if (jb1TrackConfig.gziUrlTemplate) {
+        _adapter6.gziLocation = {
+          uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
+          locationType: 'UriLocation'
+        };
+      } else {
+        _adapter6.gziLocation = {
+          uri: "".concat(urlTemplate, ".gzi"),
+          locationType: 'UriLocation'
+        };
+      }
+
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'ReferenceSequenceTrack',
+        adapter: _adapter6
+      });
+    }
+
+    if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {
+      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
+        type: 'ReferenceSequenceTrack',
+        adapter: {
+          type: 'TwoBitAdapter',
+          twoBitLocation: {
+            uri: urlTemplate,
+            locationType: 'UriLocation'
+          }
+        }
+      });
+    }
+  } // If we don't recogize the store class, make a best effort to guess by file type
+
+
+  jb2TrackConfig.adapter = (0, _tracks.guessAdapter)({
+    uri: urlTemplate,
+    locationType: 'UriLocation'
+  }, undefined, urlTemplate);
+
+  if (!jb2TrackConfig.adapter) {
+    throw new Error('Could not determine adapter');
+  }
+
+  if (jb2TrackConfig.adapter.type === _tracks.UNSUPPORTED) {
+    return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
+  }
+
+  if (jb2TrackConfig.adapter.type === _tracks.UNKNOWN) {
+    return (0, _tracks.generateUnknownTrackConf)(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
+  }
+
+  jb2TrackConfig.type = (0, _tracks.guessTrackType)(jb2TrackConfig.adapter.type);
+
+  if (jb2TrackConfig.type === 'QuantitativeTrack') {
+    if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+      jb2TrackConfig.defaultRendering = 'xyplot';
+    } else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
+      jb2TrackConfig.defaultRendering = 'density';
+    }
+  }
+
+  return jb2TrackConfig;
+}
+
+function generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig) {
+  var jb1Features = jb1TrackConfig.features || [];
+  var jb2Features = jb1Features.map(function (feature) {
+    var jb2Feature = JSON.parse(JSON.stringify(feature));
+    jb2Feature.refName = feature.seq_id;
+    jb2Feature.uniqueId = "".concat(feature.seq_id, ":").concat(feature.start, "-").concat(feature.end, ":").concat(feature.name || '');
+    return jb2Feature;
+  });
+  jb2TrackConfig.adapter = {
+    type: 'FromConfigAdapter',
+    features: jb2Features
+  };
+  jb2TrackConfig.type = 'FeatureTrack';
+  return jb2TrackConfig;
+}
+
+function createRefSeqsAdapter(_x) {
+  return _createRefSeqsAdapter.apply(this, arguments);
+}
+
+function _createRefSeqsAdapter() {
+  _createRefSeqsAdapter = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(refSeqs) {
+    var refSeqsJson, refSeqsData;
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            if (typeof refSeqs === 'string') {
+              // assume refSeqs is a url if it is string
+              refSeqs = {
+                url: refSeqs
+              };
+            } // check refseq urls
+
+
+            if (!refSeqs.url) {
+              _context.next = 15;
+              break;
+            }
+
+            if (!refSeqs.url.match(/.fai$/)) {
+              _context.next = 4;
+              break;
+            }
+
+            return _context.abrupt("return", {
+              type: 'IndexedFastaAdapter',
+              fastaLocation: {
+                uri: refSeqs.url.slice(0, -4),
+                locationType: 'UriLocation'
+              },
+              faiLocation: {
+                uri: refSeqs.url,
+                locationType: 'UriLocation'
+              }
+            });
+
+          case 4:
+            if (!refSeqs.url.match(/.2bit$/)) {
+              _context.next = 6;
+              break;
+            }
+
+            return _context.abrupt("return", {
+              type: 'TwoBitAdapter',
+              twoBitLocation: {
+                uri: refSeqs.url,
+                locationType: 'UriLocation'
+              }
+            });
+
+          case 6:
+            if (!refSeqs.url.match(/.fa$/)) {
+              _context.next = 8;
+              break;
+            }
+
+            throw new Error('Unindexed FASTA adapter not available');
+
+          case 8:
+            if (!refSeqs.url.match(/.sizes/)) {
+              _context.next = 10;
+              break;
+            }
+
+            throw new Error('chromosome SIZES adapter not available');
+
+          case 10:
+            _context.next = 12;
+            return (0, _io.openLocation)({
+              uri: refSeqs.url,
+              locationType: 'UriLocation'
+            }).readFile('utf8');
+
+          case 12:
+            refSeqsJson = _context.sent;
+            refSeqsData = JSON.parse(refSeqsJson);
+            return _context.abrupt("return", refSeqAdapterFromConfig(refSeqsData));
+
+          case 15:
+            if (!('data' in refSeqs)) {
+              _context.next = 17;
+              break;
+            }
+
+            return _context.abrupt("return", refSeqAdapterFromConfig(refSeqs.data || []));
+
+          case 17:
+            throw new Error("Could not determine adapter for JBrowse1 refSeqs: ".concat(refSeqs.url || JSON.stringify(refSeqs)));
+
+          case 18:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  }));
+  return _createRefSeqsAdapter.apply(this, arguments);
+}
+
+function refSeqAdapterFromConfig(refSeqsData) {
+  var features = refSeqsData.map(function (refSeq) {
+    return {
+      refName: refSeq.name,
+      uniqueId: refSeq.name,
+      start: refSeq.start,
+      end: refSeq.end
+    };
+  });
+  return {
+    type: 'FromConfigAdapter',
+    features: features
+  };
+}

package/dist/JBrowse1Connection/model.d.ts

@@ -1,4 +1,15 @@
-export default function _default(pluginManager: any): import("mobx-state-tree").IModelType<import("mobx-state-tree").ModelProperties & {
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
-    type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
-}, any, any, any>;
+export default function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
+    name: import("mobx-state-tree").ISimpleType<string>;
+    tracks: import("mobx-state-tree").IArrayType<any>;
+} & {
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
+}, {
+    afterAttach(): void;
+    addTrackConf(trackConf: any): any;
+    addTrackConfs(trackConfs: any): any[];
+    setTrackConfs(trackConfs: any): import("mobx-state-tree").IMSTArray<any> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<any>>;
+    clear(): void;
+} & {
+    connect(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/JBrowse1Connection/model.js

@@ -0,0 +1,58 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = _default;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _util = require("@jbrowse/core/util");
+
+var _models = require("@jbrowse/core/pluggableElementTypes/models");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+var _jb1ConfigLoad = require("./jb1ConfigLoad");
+
+var _jb1ToJb = require("./jb1ToJb2");
+
+function _default(pluginManager) {
+  return _mobxStateTree.types.compose('JBrowse1Connection', (0, _models.BaseConnectionModelFactory)(pluginManager), _mobxStateTree.types.model({
+    configuration: (0, _configuration.ConfigurationReference)(_configSchema["default"]),
+    type: _mobxStateTree.types.literal('JBrowse1Connection')
+  }).actions(function (self) {
+    return {
+      connect: function connect() {
+        var dataDirLocation = (0, _configuration.readConfObject)(self.configuration, 'dataDirLocation');
+        var session = (0, _util.getSession)(self);
+        (0, _jb1ConfigLoad.fetchJb1)(dataDirLocation).then(function (config) {
+          var assemblyName = (0, _configuration.readConfObject)(self.configuration, 'assemblyNames')[0];
+
+          if (!assemblyName) {
+            throw new Error('assembly name required for JBrowse 1 connection');
+          }
+
+          var assemblyConf = session.assemblies.find(function (assembly) {
+            return (0, _configuration.readConfObject)(assembly, 'name') === assemblyName;
+          });
+          var sequenceAdapter = (0, _configuration.readConfObject)(assemblyConf, ['sequence', 'adapter']);
+          var jb2Tracks = config.tracks.map(function (jb1Track) {
+            var jb2Track = (0, _jb1ToJb.convertTrackConfig)(jb1Track, config.dataRoot, sequenceAdapter);
+            jb2Track.assemblyNames = [assemblyName];
+            return jb2Track;
+          });
+          self.setTrackConfs(jb2Tracks);
+        })["catch"](function (error) {
+          console.error(error);
+          session.notify("There was a problem connecting to the JBrowse 1 data directory \"".concat(self.name, "\". Please make sure you have entered a valid location. The error that was thrown is: \"").concat(error, "\""), 'error');
+          session.breakConnection(self.configuration);
+        });
+      }
+    };
+  }));
+}