@jbrowse/core 1.7.10 → 1.7.11

package/assemblyManager/assembly.d.ts

@@ -1,7 +1,6 @@
 import { Instance, IAnyType } from 'mobx-state-tree';
-import { Feature } from '../util/simpleFeature';
 import PluginManager from '../PluginManager';
-import { Region } from '../util/types';
+import { Region, Feature } from '../util';
 declare type RefNameAliases = Record<string, string>;
 export interface BaseOptions {
     signal?: AbortSignal;
@@ -19,9 +18,8 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pluginMana
 }, {
     error: Error | undefined;
     regions: BasicRegion[] | undefined;
-    refNameAliases: {
-        [key: string]: string;
-    } | undefined;
+    refNameAliases: RefNameAliases | undefined;
+    lowerCaseRefNameAliases: RefNameAliases | undefined;
     cytobands: Feature[] | undefined;
 } & {
     readonly initialized: boolean;
@@ -39,14 +37,15 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pluginMana
     isValidRefName(refName: string): boolean;
 } & {
     setLoading(): void;
-    setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+    setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
         adapterRegionsWithAssembly: Region[];
         refNameAliases: RefNameAliases;
+        lowerCaseRefNameAliases: RefNameAliases;
         cytobands: Feature[];
     }): void;
     setError(e: Error): void;
     setRegions(regions: Region[]): void;
-    setRefNameAliases(refNameAliases: RefNameAliases): void;
+    setRefNameAliases(refNameAliases: RefNameAliases, lowerCaseRefNameAliases: RefNameAliases): void;
     setCytobands(cytobands: Feature[]): void;
     afterAttach(): void;
 } & {

package/assemblyManager/assembly.js

@@ -37,10 +37,11 @@ function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (O
 
 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; }
 
-// Based on the UCSC Genome Browser chromosome color palette:
+var refNameRegex = new RegExp('[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*'); // Based on the UCSC Genome Browser chromosome color palette:
 // https://github.com/ucscGenomeBrowser/kent/blob/a50ed53aff81d6fb3e34e6913ce18578292bc24e/src/hg/inc/chromColors.h
 // Some colors darkened to have at least a 3:1 contrast ratio on a white
 // background
+
 var refNameColors = ['rgb(153, 102, 0)', 'rgb(102, 102, 0)', 'rgb(153, 153, 30)', 'rgb(204, 0, 0)', 'rgb(255, 0, 0)', 'rgb(255, 0, 204)', 'rgb(165, 132, 132)', // originally 'rgb(255, 204, 204)'
 'rgb(204, 122, 0)', // originally rgb(255, 153, 0)'
 'rgb(178, 142, 0)', // originally 'rgb(255, 204, 0)'
@@ -64,7 +65,7 @@ function loadRefNameMap(_x, _x2, _x3, _x4) {
 
 
 function _loadRefNameMap() {
-  _loadRefNameMap = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(assembly, adapterConf, options, signal) {
+  _loadRefNameMap = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(assembly, adapterConfig, options, signal) {
     var sessionId, refNames, refNameAliases, refNameMap, reversed;
     return _regenerator.default.wrap(function _callee4$(_context4) {
       while (1) {
@@ -82,7 +83,7 @@ function _loadRefNameMap() {
           case 3:
             _context4.next = 5;
             return assembly.rpcManager.call(sessionId, 'CoreGetRefNames', _objectSpread({
-              adapterConfig: adapterConf,
+              adapterConfig: adapterConfig,
               signal: signal
             }, options), {
               timeout: 1000000
@@ -128,7 +129,7 @@ function _loadRefNameMap() {
 }
 
 function checkRefName(refName) {
-  if (!refName.match(/[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*/)) {
+  if (!refName.match(refNameRegex)) {
     throw new Error("Encountered invalid refName: \"".concat(refName, "\""));
   }
 }
@@ -170,6 +171,7 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       error: undefined,
       regions: undefined,
       refNameAliases: undefined,
+      lowerCaseRefNameAliases: undefined,
       cytobands: undefined
     };
   }).views(function (self) {
@@ -202,6 +204,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
         });
       },
 
+      // note: lowerCaseRefNameAliases not included here: this allows the list
+      // of refnames to be just the "normal casing", but things like
+      // getCanonicalRefName can resolve a lower-case name if needed
       get allRefNames() {
         return !self.refNameAliases ? undefined : Object.keys(self.refNameAliases);
       },
@@ -212,23 +217,18 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
 
       get refNameColors() {
         var colors = (0, _configuration.getConf)(self, 'refNameColors');
-
-        if (colors.length === 0) {
-          return refNameColors;
-        }
-
-        return colors;
+        return colors.length === 0 ? refNameColors : colors;
       }
 
     };
   }).views(function (self) {
     return {
       getCanonicalRefName: function getCanonicalRefName(refName) {
-        if (!self.refNameAliases) {
+        if (!self.refNameAliases || !self.lowerCaseRefNameAliases) {
           throw new Error('aliases not loaded, we expect them to be loaded before getCanonicalRefName can be called');
         }
 
-        return self.refNameAliases[refName];
+        return self.refNameAliases[refName] || self.lowerCaseRefNameAliases[refName];
       },
       getRefNameColor: function getRefNameColor(refName) {
         var _self$refNames;
@@ -257,9 +257,10 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       setLoaded: function setLoaded(_ref) {
         var adapterRegionsWithAssembly = _ref.adapterRegionsWithAssembly,
             refNameAliases = _ref.refNameAliases,
+            lowerCaseRefNameAliases = _ref.lowerCaseRefNameAliases,
             cytobands = _ref.cytobands;
         this.setRegions(adapterRegionsWithAssembly);
-        this.setRefNameAliases(refNameAliases);
+        this.setRefNameAliases(refNameAliases, lowerCaseRefNameAliases);
         this.setCytobands(cytobands);
       },
       setError: function setError(e) {
@@ -269,8 +270,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       setRegions: function setRegions(regions) {
         self.regions = regions;
       },
-      setRefNameAliases: function setRefNameAliases(refNameAliases) {
+      setRefNameAliases: function setRefNameAliases(refNameAliases, lowerCaseRefNameAliases) {
         self.refNameAliases = refNameAliases;
+        self.lowerCaseRefNameAliases = lowerCaseRefNameAliases;
       },
       setCytobands: function setCytobands(cytobands) {
         self.cytobands = cytobands;
@@ -404,7 +406,7 @@ function loadAssemblyReaction(_x5, _x6) {
 
 function _loadAssemblyReaction() {
   _loadAssemblyReaction = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(props, signal) {
-    var sequenceAdapterConfig, assemblyName, refNameAliasesAdapterConfig, cytobandAdapterConfig, pluginManager, adapterRegions, adapterRegionsWithAssembly, refNameAliases, aliases, cytobands;
+    var sequenceAdapterConfig, assemblyName, refNameAliasesAdapterConfig, cytobandAdapterConfig, pluginManager, adapterRegions, adapterRegionsWithAssembly, refNameAliases, aliases, cytobands, lowerCaseRefNameAliases;
     return _regenerator.default.wrap(function _callee5$(_context5) {
       while (1) {
         switch (_context5.prev = _context5.next) {
@@ -452,13 +454,21 @@ function _loadAssemblyReaction() {
             adapterRegionsWithAssembly.forEach(function (region) {
               refNameAliases[region.refName] = region.refName;
             });
+            lowerCaseRefNameAliases = Object.fromEntries(Object.entries(refNameAliases).map(function (_ref5) {
+              var _ref6 = (0, _slicedToArray2.default)(_ref5, 2),
+                  key = _ref6[0],
+                  val = _ref6[1];
+
+              return [key.toLowerCase(), val];
+            }));
             return _context5.abrupt("return", {
               adapterRegionsWithAssembly: adapterRegionsWithAssembly,
               refNameAliases: refNameAliases,
+              lowerCaseRefNameAliases: lowerCaseRefNameAliases,
               cytobands: cytobands
             });
 
-          case 17:
+          case 18:
           case "end":
             return _context5.stop();
         }

package/assemblyManager/assemblyManager.d.ts

@@ -7,7 +7,10 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [key: string]: string;
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -26,17 +29,22 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            lowerCaseRefNameAliases: {
+                [x: string]: string;
+            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
+        }, lowerCaseRefNameAliases: {
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
@@ -63,7 +71,10 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [key: string]: string;
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -82,17 +93,22 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            lowerCaseRefNameAliases: {
+                [x: string]: string;
+            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
+        }, lowerCaseRefNameAliases: {
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
@@ -117,7 +133,10 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [key: string]: string;
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -136,17 +155,22 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            lowerCaseRefNameAliases: {
+                [x: string]: string;
+            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
+        }, lowerCaseRefNameAliases: {
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
@@ -182,7 +206,10 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [key: string]: string;
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -201,17 +228,22 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            lowerCaseRefNameAliases: {
+                [x: string]: string;
+            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
+        }, lowerCaseRefNameAliases: {
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
@@ -236,7 +268,10 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [key: string]: string;
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -255,17 +290,22 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            lowerCaseRefNameAliases: {
+                [x: string]: string;
+            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
+        }, lowerCaseRefNameAliases: {
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
@@ -305,7 +345,10 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [key: string]: string;
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -324,17 +367,22 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            lowerCaseRefNameAliases: {
+                [x: string]: string;
+            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
+        }, lowerCaseRefNameAliases: {
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
@@ -359,7 +407,10 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [key: string]: string;
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -378,17 +429,22 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            lowerCaseRefNameAliases: {
+                [x: string]: string;
+            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
+        }, lowerCaseRefNameAliases: {
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;

package/assemblyManager/assemblyManager.js

@@ -115,29 +115,29 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
                 case 2:
                   assembly = self.get(assemblyName);
 
-                  if (!assembly) {
-                    _context.next = 9;
+                  if (assembly) {
+                    _context.next = 5;
                     break;
                   }
 
-                  _context.next = 6;
+                  return _context.abrupt("return", undefined);
+
+                case 5:
+                  _context.next = 7;
                   return (0, _util.when)(function () {
                     return Boolean(assembly.regions && assembly.refNameAliases) || !!assembly.error;
                   });
 
-                case 6:
+                case 7:
                   if (!assembly.error) {
-                    _context.next = 8;
+                    _context.next = 9;
                     break;
                   }
 
                   throw assembly.error;
 
-                case 8:
-                  return _context.abrupt("return", assembly);
-
                 case 9:
-                  return _context.abrupt("return", undefined);
+                  return _context.abrupt("return", assembly);
 
                 case 10:
                 case "end":

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.7.10",
+  "version": "1.7.11",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -32,7 +32,6 @@
     "@babel/runtime": "^7.17.9",
     "@material-ui/icons": "^4.0.1",
     "abortable-promise-cache": "^1.5.0",
-    "canvas": "^2.8.0",
     "canvas-sequencer": "^3.1.0",
     "canvas2svg": "^1.0.16",
     "clone": "^2.1.2",
@@ -76,5 +75,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "02d8c1e88e5603ea5855faed4ccb814e28071b32"
+  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
 }