@jbrowse/core 1.4.4 → 1.5.3

package/assemblyManager/assembly.js

@@ -60,12 +60,12 @@ var refNameColors = ['rgb(153, 102, 0)', 'rgb(102, 102, 0)', 'rgb(153, 153, 30)'
 
 function loadRefNameMap(_x, _x2, _x3, _x4) {
   return _loadRefNameMap.apply(this, arguments);
-}
+} // Valid refName pattern from https://samtools.github.io/hts-specs/SAMv1.pdf
+
 
 function _loadRefNameMap() {
   _loadRefNameMap = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(assembly, adapterConf, options, signal) {
-    var sessionId, refNames, refNameMap, refNameAliases, reversed, _i, _Object$entries, _Object$entries$_i, canonicalName, adapterName;
-
+    var sessionId, refNames, refNameAliases, refNameMap, reversed;
     return _regenerator.default.wrap(function _callee4$(_context4) {
       while (1) {
         switch (_context4.prev = _context4.next) {
@@ -90,39 +90,34 @@ function _loadRefNameMap() {
 
           case 5:
             refNames = _context4.sent;
-            refNameMap = {};
             refNameAliases = assembly.refNameAliases;
 
             if (refNameAliases) {
-              _context4.next = 10;
+              _context4.next = 9;
               break;
             }
 
             throw new Error("error loading assembly ".concat(assembly.name, "'s refNameAliases"));
 
-          case 10:
-            refNames.forEach(function (refName) {
-              checkRefName(refName);
-              var canon = assembly.getCanonicalRefName(refName);
-
-              if (canon) {
-                refNameMap[canon] = refName;
-              }
-            }); // make the reversed map too
-
-            reversed = {};
-
-            for (_i = 0, _Object$entries = Object.entries(refNameMap); _i < _Object$entries.length; _i++) {
-              _Object$entries$_i = (0, _slicedToArray2.default)(_Object$entries[_i], 2), canonicalName = _Object$entries$_i[0], adapterName = _Object$entries$_i[1];
-              reversed[adapterName] = canonicalName;
-            }
-
+          case 9:
+            refNameMap = Object.fromEntries(refNames.map(function (name) {
+              checkRefName(name);
+              return [assembly.getCanonicalRefName(name), name];
+            })); // make the reversed map too
+
+            reversed = Object.fromEntries(Object.entries(refNameMap).map(function (_ref2) {
+              var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
+                  canonicalName = _ref3[0],
+                  adapterName = _ref3[1];
+
+              return [adapterName, canonicalName];
+            }));
             return _context4.abrupt("return", {
               forwardMap: refNameMap,
               reverseMap: reversed
             });
 
-          case 14:
+          case 12:
           case "end":
             return _context4.stop();
         }
@@ -133,7 +128,6 @@ function _loadRefNameMap() {
 }
 
 function checkRefName(refName) {
-  // Valid refName pattern from https://samtools.github.io/hts-specs/SAMv1.pdf
   if (!refName.match(/[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*/)) {
     throw new Error("Encountered invalid refName: \"".concat(refName, "\""));
   }
@@ -175,12 +169,13 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
     return {
       error: undefined,
       regions: undefined,
-      refNameAliases: undefined
+      refNameAliases: undefined,
+      cytobands: undefined
     };
   }).views(function (self) {
     return {
       get initialized() {
-        return Boolean(self.refNameAliases);
+        return !!self.refNameAliases;
       },
 
       get name() {
@@ -192,7 +187,7 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       },
 
       hasName: function hasName(name) {
-        return this.name === name || this.aliases.includes(name);
+        return this.allAliases.includes(name);
       },
 
       get allAliases() {
@@ -200,7 +195,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       },
 
       get refNames() {
-        return self.regions && self.regions.map(function (region) {
+        var _self$regions;
+
+        return (_self$regions = self.regions) === null || _self$regions === void 0 ? void 0 : _self$regions.map(function (region) {
           return region.refName;
         });
       },
@@ -259,14 +256,15 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       setLoading: function setLoading() {},
       setLoaded: function setLoaded(_ref) {
         var adapterRegionsWithAssembly = _ref.adapterRegionsWithAssembly,
-            refNameAliases = _ref.refNameAliases;
+            refNameAliases = _ref.refNameAliases,
+            cytobands = _ref.cytobands;
         this.setRegions(adapterRegionsWithAssembly);
         this.setRefNameAliases(refNameAliases);
+        this.setCytobands(cytobands);
       },
-      setError: function setError(error) {
-        if (!(0, _mobxStateTree.getParent)(self, 3).isAssemblyEditing) {
-          self.error = error;
-        }
+      setError: function setError(e) {
+        console.error(e);
+        self.error = e;
       },
       setRegions: function setRegions(regions) {
         self.regions = regions;
@@ -274,6 +272,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       setRefNameAliases: function setRefNameAliases(refNameAliases) {
         self.refNameAliases = refNameAliases;
       },
+      setCytobands: function setCytobands(cytobands) {
+        self.cytobands = cytobands;
+      },
       afterAttach: function afterAttach() {
         (0, _util.makeAbortableReaction)( // eslint-disable-next-line @typescript-eslint/no-explicit-any
         self, // @ts-ignore
@@ -299,7 +300,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
           adapterConf: adapterConf,
           self: self,
           options: rest
-        }, signal, statusCallback);
+        }, // signal intentionally not passed here, fixes issues like #2221.
+        // alternative fix #2540 was proposed but non-working currently
+        undefined, statusCallback);
       },
 
       /**
@@ -372,17 +375,21 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
 function makeLoadAssemblyData(pluginManager) {
   return function (self) {
     if (self.configuration) {
-      var _self$configuration$r;
-
       // use full configuration instead of snapshot of the config, the
       // rpcManager normally receives a snapshot but we bypass rpcManager here
       // to avoid spinning up a webworker
-      var sequenceAdapterConfig = self.configuration.sequence.adapter;
-      var refNameAliasesAdapterConfig = (_self$configuration$r = self.configuration.refNameAliases) === null || _self$configuration$r === void 0 ? void 0 : _self$configuration$r.adapter;
+      var _self$configuration = self.configuration,
+          sequence = _self$configuration.sequence,
+          refNameAliases = _self$configuration.refNameAliases,
+          cytobands = _self$configuration.cytobands;
+      var sequenceAdapterConfig = sequence.adapter;
+      var refNameAliasesAdapterConfig = refNameAliases === null || refNameAliases === void 0 ? void 0 : refNameAliases.adapter;
+      var cytobandAdapterConfig = cytobands === null || cytobands === void 0 ? void 0 : cytobands.adapter;
       return {
         sequenceAdapterConfig: sequenceAdapterConfig,
         assemblyName: self.name,
         refNameAliasesAdapterConfig: refNameAliasesAdapterConfig,
+        cytobandAdapterConfig: cytobandAdapterConfig,
         pluginManager: pluginManager
       };
     }
@@ -397,7 +404,7 @@ function loadAssemblyReaction(_x5, _x6) {
 
 function _loadAssemblyReaction() {
   _loadAssemblyReaction = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(props, signal) {
-    var sequenceAdapterConfig, assemblyName, refNameAliasesAdapterConfig, pluginManager, dataAdapterType, AdapterClass, getAdapterClass, CLASS, adapter, adapterRegions, adapterRegionsWithAssembly, refNameAliases, refAliasAdapterType, RefAdapterClass, getRefAdapterClass, REFCLASS, refNameAliasAdapter, refNameAliasesList;
+    var sequenceAdapterConfig, assemblyName, refNameAliasesAdapterConfig, cytobandAdapterConfig, pluginManager, adapterRegions, adapterRegionsWithAssembly, refNameAliases, aliases, cytobands;
     return _regenerator.default.wrap(function _callee5$(_context5) {
       while (1) {
         switch (_context5.prev = _context5.next) {
@@ -410,109 +417,48 @@ function _loadAssemblyReaction() {
             return _context5.abrupt("return");
 
           case 2:
-            sequenceAdapterConfig = props.sequenceAdapterConfig, assemblyName = props.assemblyName, refNameAliasesAdapterConfig = props.refNameAliasesAdapterConfig, pluginManager = props.pluginManager;
-            dataAdapterType = pluginManager.getAdapterType(sequenceAdapterConfig.type);
-            AdapterClass = dataAdapterType.AdapterClass, getAdapterClass = dataAdapterType.getAdapterClass;
-            _context5.t0 = AdapterClass;
-
-            if (_context5.t0) {
-              _context5.next = 10;
-              break;
-            }
+            sequenceAdapterConfig = props.sequenceAdapterConfig, assemblyName = props.assemblyName, refNameAliasesAdapterConfig = props.refNameAliasesAdapterConfig, cytobandAdapterConfig = props.cytobandAdapterConfig, pluginManager = props.pluginManager;
+            _context5.next = 5;
+            return getAssemblyRegions(sequenceAdapterConfig, pluginManager, signal);
 
-            _context5.next = 9;
-            return getAdapterClass === null || getAdapterClass === void 0 ? void 0 : getAdapterClass();
-
-          case 9:
-            _context5.t0 = _context5.sent;
-
-          case 10:
-            CLASS = _context5.t0;
-
-            if (CLASS) {
-              _context5.next = 13;
-              break;
-            }
-
-            throw new Error('Failed to get adapter class');
-
-          case 13:
-            adapter = new CLASS(sequenceAdapterConfig);
-            _context5.next = 16;
-            return adapter.getRegions({
-              signal: signal
-            });
-
-          case 16:
+          case 5:
             adapterRegions = _context5.sent;
             adapterRegionsWithAssembly = adapterRegions.map(function (adapterRegion) {
-              var refName = adapterRegion.refName;
-              checkRefName(refName);
+              checkRefName(adapterRegion.refName);
               return _objectSpread(_objectSpread({}, adapterRegion), {}, {
                 assemblyName: assemblyName
               });
             });
             refNameAliases = {};
+            _context5.next = 10;
+            return getRefNameAliases(refNameAliasesAdapterConfig, pluginManager, signal);
 
-            if (!refNameAliasesAdapterConfig) {
-              _context5.next = 35;
-              break;
-            }
-
-            refAliasAdapterType = pluginManager.getAdapterType(refNameAliasesAdapterConfig.type);
-            RefAdapterClass = refAliasAdapterType.AdapterClass, getRefAdapterClass = refAliasAdapterType.getAdapterClass;
-            _context5.t1 = RefAdapterClass;
-
-            if (_context5.t1) {
-              _context5.next = 27;
-              break;
-            }
-
-            _context5.next = 26;
-            return getRefAdapterClass === null || getRefAdapterClass === void 0 ? void 0 : getRefAdapterClass();
-
-          case 26:
-            _context5.t1 = _context5.sent;
-
-          case 27:
-            REFCLASS = _context5.t1;
-
-            if (REFCLASS) {
-              _context5.next = 30;
-              break;
-            }
-
-            throw new Error('Failed to get REFCLASS');
-
-          case 30:
-            refNameAliasAdapter = new REFCLASS(refNameAliasesAdapterConfig);
-            _context5.next = 33;
-            return refNameAliasAdapter.getRefNameAliases({
-              signal: signal
-            });
+          case 10:
+            aliases = _context5.sent;
+            _context5.next = 13;
+            return getCytobands(cytobandAdapterConfig, pluginManager);
 
-          case 33:
-            refNameAliasesList = _context5.sent;
-            refNameAliasesList.forEach(function (_ref2) {
-              var refName = _ref2.refName,
-                  aliases = _ref2.aliases;
+          case 13:
+            cytobands = _context5.sent;
+            aliases.forEach(function (_ref4) {
+              var refName = _ref4.refName,
+                  aliases = _ref4.aliases;
               aliases.forEach(function (alias) {
                 checkRefName(alias);
                 refNameAliases[alias] = refName;
               });
-            });
+            }); // add identity to the refNameAliases list
 
-          case 35:
-            // add identity to the refNameAliases list
             adapterRegionsWithAssembly.forEach(function (region) {
               refNameAliases[region.refName] = region.refName;
             });
             return _context5.abrupt("return", {
               adapterRegionsWithAssembly: adapterRegionsWithAssembly,
-              refNameAliases: refNameAliases
+              refNameAliases: refNameAliases,
+              cytobands: cytobands
             });
 
-          case 37:
+          case 17:
           case "end":
             return _context5.stop();
         }
@@ -520,4 +466,101 @@ function _loadAssemblyReaction() {
     }, _callee5);
   }));
   return _loadAssemblyReaction.apply(this, arguments);
+}
+
+function getRefNameAliases(_x7, _x8, _x9) {
+  return _getRefNameAliases.apply(this, arguments);
+}
+
+function _getRefNameAliases() {
+  _getRefNameAliases = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(config, pluginManager, signal) {
+    var _type$getAdapterClass;
+
+    var type, CLASS, adapter;
+    return _regenerator.default.wrap(function _callee6$(_context6) {
+      while (1) {
+        switch (_context6.prev = _context6.next) {
+          case 0:
+            type = pluginManager.getAdapterType(config.type);
+            _context6.next = 3;
+            return (_type$getAdapterClass = type.getAdapterClass) === null || _type$getAdapterClass === void 0 ? void 0 : _type$getAdapterClass.call(type);
+
+          case 3:
+            CLASS = _context6.sent;
+            adapter = new CLASS(config, undefined, pluginManager);
+            return _context6.abrupt("return", adapter.getRefNameAliases({
+              signal: signal
+            }));
+
+          case 6:
+          case "end":
+            return _context6.stop();
+        }
+      }
+    }, _callee6);
+  }));
+  return _getRefNameAliases.apply(this, arguments);
+}
+
+function getCytobands(_x10, _x11) {
+  return _getCytobands.apply(this, arguments);
+}
+
+function _getCytobands() {
+  _getCytobands = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(config, pluginManager) {
+    var type, CLASS, adapter;
+    return _regenerator.default.wrap(function _callee7$(_context7) {
+      while (1) {
+        switch (_context7.prev = _context7.next) {
+          case 0:
+            type = pluginManager.getAdapterType(config.type);
+            _context7.next = 3;
+            return type.getAdapterClass();
+
+          case 3:
+            CLASS = _context7.sent;
+            adapter = new CLASS(config, undefined, pluginManager); // @ts-ignore
+
+            return _context7.abrupt("return", adapter.getData());
+
+          case 6:
+          case "end":
+            return _context7.stop();
+        }
+      }
+    }, _callee7);
+  }));
+  return _getCytobands.apply(this, arguments);
+}
+
+function getAssemblyRegions(_x12, _x13, _x14) {
+  return _getAssemblyRegions.apply(this, arguments);
+}
+
+function _getAssemblyRegions() {
+  _getAssemblyRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(config, pluginManager, signal) {
+    var type, CLASS, adapter;
+    return _regenerator.default.wrap(function _callee8$(_context8) {
+      while (1) {
+        switch (_context8.prev = _context8.next) {
+          case 0:
+            type = pluginManager.getAdapterType(config.type);
+            _context8.next = 3;
+            return type.getAdapterClass();
+
+          case 3:
+            CLASS = _context8.sent;
+            adapter = new CLASS(config, undefined, pluginManager);
+            return _context8.abrupt("return", adapter.getRegions({
+              signal: signal
+            }));
+
+          case 6:
+          case "end":
+            return _context8.stop();
+        }
+      }
+    }, _callee8);
+  }));
+  return _getAssemblyRegions.apply(this, arguments);
 }

package/assemblyManager/assemblyConfigSchema.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '../PluginManager';
+declare const _default: (pluginManager: PluginManager) => import("../configuration/configurationSchema").AnyConfigurationSchemaType;
+export default _default;

package/assemblyManager/{assemblyConfigSchemas.js → assemblyConfigSchema.js}

@@ -8,7 +8,7 @@ exports.default = void 0;
 var _configuration = require("../configuration");
 
 var _default = function _default(pluginManager) {
-  var BaseAssemblyConfigSchema = (0, _configuration.ConfigurationSchema)('BaseAssembly', {
+  return (0, _configuration.ConfigurationSchema)('BaseAssembly', {
     aliases: {
       type: 'stringArray',
       defaultValue: [],
@@ -20,6 +20,40 @@ var _default = function _default(pluginManager) {
       defaultValue: [],
       description: 'Define custom colors for each reference sequence. Will cycle through this list if there are not enough colors for every sequence.'
     },
+    refNameAliases: (0, _configuration.ConfigurationSchema)('RefNameAliases', {
+      adapter: pluginManager.pluggableConfigSchemaType('adapter')
+    }, {
+      preProcessSnapshot: function preProcessSnapshot(snap) {
+        // allow refNameAliases to be unspecified
+        // @ts-ignore
+        if (!snap.adapter) {
+          return {
+            adapter: {
+              type: 'RefNameAliasAdapter'
+            }
+          };
+        }
+
+        return snap;
+      }
+    }),
+    cytobands: (0, _configuration.ConfigurationSchema)('Cytoband', {
+      adapter: pluginManager.pluggableConfigSchemaType('adapter')
+    }, {
+      preProcessSnapshot: function preProcessSnapshot(snap) {
+        // allow cytoBand to be unspecified
+        // @ts-ignore
+        if (!snap.adapter) {
+          return {
+            adapter: {
+              type: 'CytobandAdapter'
+            }
+          };
+        }
+
+        return snap;
+      }
+    }),
     displayName: {
       type: 'string',
       defaultValue: '',
@@ -28,32 +62,6 @@ var _default = function _default(pluginManager) {
   }, {
     explicitIdentifier: 'name'
   });
-  var AssemblyConfigSchema = (0, _configuration.ConfigurationSchema)('Assembly', {
-    refNameAliases: (0, _configuration.ConfigurationSchema)('RefNameAliases', {
-      adapter: pluginManager.pluggableConfigSchemaType('adapter')
-    })
-  }, {
-    baseConfiguration: BaseAssemblyConfigSchema
-  });
-
-  function dispatcher(snapshot) {
-    if (!snapshot) {
-      return BaseAssemblyConfigSchema;
-    }
-
-    var refNameAliases = snapshot.refNameAliases;
-
-    if (refNameAliases) {
-      return AssemblyConfigSchema;
-    }
-
-    return BaseAssemblyConfigSchema;
-  }
-
-  return {
-    assemblyConfigSchemas: [AssemblyConfigSchema, BaseAssemblyConfigSchema],
-    dispatcher: dispatcher
-  };
 };
 
 exports.default = _default;