@jbrowse/plugin-linear-genome-view 1.7.4 → 1.7.7

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -171,7 +171,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         headers?: Record<string, string>;
         signal?: AbortSignal;
         filters?: string[];
-    }): Promise<Stats>;
+    }): Promise<{}>;
     setRegionStatsP(p?: Promise<Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: Stats | undefined): void;
     clearRegionStats(): void;

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -291,6 +291,13 @@ var BaseLinearDisplay = _mobxStateTree.types.compose('BaseLinearDisplay', _model
           rpcManager = _getSession2.rpcManager;
 
       var adapterConfig = self.adapterConfig;
+
+      if (!adapterConfig) {
+        // A track extending the base track might not have an adapter config
+        // e.g. Apollo tracks don't use adapters
+        return Promise.resolve({});
+      }
+
       var sessionId = (0, _tracks.getRpcSessionId)(self);
 
       var params = _objectSpread({
@@ -464,15 +471,16 @@ var BaseLinearDisplay = _mobxStateTree.types.compose('BaseLinearDisplay', _model
                 return _context.abrupt("return");
 
               case 16:
-                _context.next = 21;
+                _context.next = 22;
                 break;
 
               case 18:
                 _context.prev = 18;
                 _context.t0 = _context["catch"](5);
+                console.error(_context.t0);
                 self.setError(_context.t0);
 
-              case 21:
+              case 22:
               case "end":
                 return _context.stop();
             }

package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts

@@ -82,6 +82,7 @@ export declare function renderBlockData(self: Instance<BlockStateModel>, optDisp
         adapterConfig: any;
         rendererType: any;
         sessionId: string;
+        layoutId: string;
         blockKey: string;
         reloadFlag: number;
         timeout: number;

package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js

@@ -219,6 +219,7 @@ function renderBlockData(self, optDisplay) {
 
     (0, _configuration.readConfObject)(config);
     var sessionId = (0, _tracks.getRpcSessionId)(display);
+    var layoutId = (0, _util.getContainingView)(display).id;
     var cannotBeRenderedReason = display.regionCannotBeRendered(self.region);
     return {
       rendererType: rendererType,
@@ -237,6 +238,7 @@ function renderBlockData(self, optDisplay) {
         adapterConfig: adapterConfig,
         rendererType: rendererType.name,
         sessionId: sessionId,
+        layoutId: layoutId,
         blockKey: self.key,
         reloadFlag: self.reloadFlag,
         timeout: 1000000 // 10000,

package/dist/LinearBareDisplay/model.d.ts

@@ -143,7 +143,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         headers?: Record<string, string> | undefined;
         signal?: AbortSignal | undefined;
         filters?: string[] | undefined;
-    }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    }): Promise<{}>;
     setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     clearRegionStats(): void;

package/dist/LinearBasicDisplay/model.d.ts

@@ -149,7 +149,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
         headers?: Record<string, string> | undefined;
         signal?: AbortSignal | undefined;
         filters?: string[] | undefined;
-    }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    }): Promise<{}>;
     setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     clearRegionStats(): void;

package/dist/LinearGenomeView/components/ScaleBar.d.ts

@@ -130,7 +130,7 @@ declare const _default: React.ForwardRefExoticComponent<{
         moveTrack(movingTrackId: string, targetTrackId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): void;
-        setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+        setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
         toggleCenterLine(): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -327,7 +327,7 @@ declare const _default: React.ForwardRefExoticComponent<{
         moveTrack(movingTrackId: string, targetTrackId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): void;
-        setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+        setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
         toggleCenterLine(): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;

package/dist/LinearGenomeView/components/SequenceDialog.js

@@ -71,7 +71,7 @@ function fetchSequence(_x, _x2, _x3) {
 
 function _fetchSequence() {
   _fetchSequence = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(model, regions, signal) {
-    var session, leftOffset, rightOffset, rpcManager, assemblyManager, assemblyName, assembly, adapterConfig, sessionId, chunks;
+    var session, leftOffset, rightOffset, rpcManager, assemblyManager, assemblyName, assembly, adapterConfig, sessionId;
     return _regenerator.default.wrap(function _callee2$(_context2) {
       while (1) {
         switch (_context2.prev = _context2.next) {
@@ -109,23 +109,14 @@ function _fetchSequence() {
           case 11:
             adapterConfig = (0, _configuration.getConf)(assembly, ['sequence', 'adapter']);
             sessionId = 'getSequence';
-            _context2.next = 15;
-            return Promise.all(regions.map(function (region) {
-              return rpcManager.call(sessionId, 'CoreGetFeatures', {
-                adapterConfig: adapterConfig,
-                region: region,
-                sessionId: sessionId,
-                signal: signal
-              });
+            return _context2.abrupt("return", rpcManager.call(sessionId, 'CoreGetFeatures', {
+              adapterConfig: adapterConfig,
+              regions: regions,
+              sessionId: sessionId,
+              signal: signal
             }));
 
-          case 15:
-            chunks = _context2.sent;
-            return _context2.abrupt("return", chunks.map(function (chunk) {
-              return chunk[0];
-            }));
-
-          case 17:
+          case 14:
           case "end":
             return _context2.stop();
         }

package/dist/LinearGenomeView/components/TrackLabel.js

@@ -105,12 +105,10 @@ var TrackLabel = /*#__PURE__*/_react.default.forwardRef(function (props, ref) {
   var trackName = (0, _configuration.getConf)(track, 'name');
 
   if ((0, _configuration.getConf)(track, 'type') === 'ReferenceSequenceTrack') {
-    trackName = 'Reference Sequence';
-    session.assemblies.forEach(function (assembly) {
-      if (assembly.sequence === trackConf) {
-        trackName = "Reference Sequence (".concat((0, _configuration.readConfObject)(assembly, 'name'), ")");
-      }
+    var r = session.assemblies.find(function (a) {
+      return a.sequence === trackConf;
     });
+    trackName = (0, _configuration.readConfObject)(trackConf, 'name') || (r ? "Reference Sequence (".concat((0, _configuration.readConfObject)(r, 'name'), ")") : 'Reference Sequence');
   }
 
   function handleMenuItemClick(_, callback) {

package/dist/index.d.ts

@@ -149,7 +149,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     headers?: Record<string, string> | undefined;
                     signal?: AbortSignal | undefined;
                     filters?: string[] | undefined;
-                }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+                }): Promise<{}>;
                 setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
                 setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
                 clearRegionStats(): void;
@@ -325,7 +325,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     headers?: Record<string, string> | undefined;
                     signal?: AbortSignal | undefined;
                     filters?: string[] | undefined;
-                }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+                }): Promise<{}>;
                 setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
                 setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
                 clearRegionStats(): void;
@@ -511,7 +511,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 headers?: Record<string, string> | undefined;
                 signal?: AbortSignal | undefined;
                 filters?: string[] | undefined;
-            }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+            }): Promise<{}>;
             setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
             setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
             clearRegionStats(): void;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "1.7.4",
+  "version": "1.7.7",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -57,5 +57,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "0a3e0c58055bbab8e3ab0270c139291b96eff403"
+  "gitHead": "2c26e04ae942c380bf2f5b79ef7a49cc32b7bfed"
 }

package/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx

@@ -247,6 +247,11 @@ export const BaseLinearDisplay = types
 
       const { rpcManager } = getSession(self)
       const { adapterConfig } = self
+      if (!adapterConfig) {
+        // A track extending the base track might not have an adapter config
+        // e.g. Apollo tracks don't use adapters
+        return Promise.resolve({})
+      }
       const sessionId = getRpcSessionId(self)
 
       const params = {
@@ -409,6 +414,7 @@ export const BaseLinearDisplay = types
             return
           }
         } catch (e) {
+          console.error(e)
           self.setError(e)
         }
       },

package/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts

@@ -6,6 +6,7 @@ import {
   assembleLocString,
   getSession,
   getContainingDisplay,
+  getContainingView,
   getViewParams,
   makeAbortableReaction,
   Feature,
@@ -221,6 +222,7 @@ export function renderBlockData(
     readConfObject(config)
 
     const sessionId = getRpcSessionId(display)
+    const layoutId = getContainingView(display).id
     const cannotBeRenderedReason = display.regionCannotBeRendered(self.region)
 
     return {
@@ -240,6 +242,7 @@ export function renderBlockData(
         adapterConfig,
         rendererType: rendererType.name,
         sessionId,
+        layoutId,
         blockKey: self.key,
         reloadFlag: self.reloadFlag,
         timeout: 1000000, // 10000,

package/src/LinearGenomeView/components/SequenceDialog.tsx

@@ -78,19 +78,12 @@ async function fetchSequence(
   const adapterConfig = getConf(assembly, ['sequence', 'adapter'])
 
   const sessionId = 'getSequence'
-  const chunks = (await Promise.all(
-    regions.map(region =>
-      rpcManager.call(sessionId, 'CoreGetFeatures', {
-        adapterConfig,
-        region,
-        sessionId,
-        signal,
-      }),
-    ),
-  )) as Feature[][]
-
-  // assumes that we get whole sequence in a single getFeatures call
-  return chunks.map(chunk => chunk[0])
+  return rpcManager.call(sessionId, 'CoreGetFeatures', {
+    adapterConfig,
+    regions,
+    sessionId,
+    signal,
+  }) as Promise<Feature[]>
 }
 
 function SequenceDialog({

package/src/LinearGenomeView/components/TrackLabel.tsx

@@ -89,12 +89,12 @@ const TrackLabel = React.forwardRef(
 
     let trackName = getConf(track, 'name')
     if (getConf(track, 'type') === 'ReferenceSequenceTrack') {
-      trackName = 'Reference Sequence'
-      session.assemblies.forEach(assembly => {
-        if (assembly.sequence === trackConf) {
-          trackName = `Reference Sequence (${readConfObject(assembly, 'name')})`
-        }
-      })
+      const r = session.assemblies.find(a => a.sequence === trackConf)
+      trackName =
+        readConfObject(trackConf, 'name') ||
+        (r
+          ? `Reference Sequence (${readConfObject(r, 'name')})`
+          : 'Reference Sequence')
     }
 
     function handleMenuItemClick(_: unknown, callback: Function) {