Use noAssemblyManager flag on config

GMOD · Feb 13, 2021 · 1883cc1 · 1883cc1
1 parent 520b3e3
commit 1883cc1
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Showing 5 changed files with 23 additions and 5 deletions.
diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts
@@ -760,14 +760,19 @@ export async function renameRegionsIfNeeded<
     ...args,
     regions: [...(args.regions || [])],
   }
-  if (assemblyName && adapterConfig.type !== 'FromConfigSequenceAdapter') {
+
+  // configs can choose to not be associated with the assemblyManager (as with
+  // the "read assembly" in the read vs ref comparisons) and in this case a
+  // special flag exists (currently set on the FromConfigSequenceAdapter)
+  // called noAssemblyManager
+  // @ts-ignore
+  if (assemblyName && !adapterConfig.noAssemblyManager) {
     const refNameMap = await assemblyManager.getRefNameMapForAdapter(
       adapterConfig,
       assemblyName,
       newArgs,
     )
 
-    // console.log(`${JSON.stringify(regions)} ${JSON.stringify(refNameMap)}`)
     if (refNameMap && regions && newArgs.regions) {
       for (let i = 0; i < regions.length; i += 1) {
         newArgs.regions[i] = renameRegionIfNeeded(refNameMap, regions[i])

diff --git a/plugins/config/src/FromConfigAdapter/FromConfigSequenceAdapter.ts b/plugins/config/src/FromConfigAdapter/FromConfigSequenceAdapter.ts
@@ -22,6 +22,7 @@ export default class FromSequenceConfigAdapter extends FromConfigAdapter {
         .toPromise()
       // return ObservableCreate<Feature>(async observer => {
       //   const feats = await super.getFeatures(region).pipe(toArray()).toPromise()
+
       feats.forEach(feat => {
         const featStart = feat.get('start')
         const seqStart = start - featStart
@@ -32,9 +33,10 @@ export default class FromSequenceConfigAdapter extends FromConfigAdapter {
         observer.next(
           new SimpleFeature({
             ...feat.toJSON(),
-            seq,
             end: region.end,
             start: region.start,
+            seq,
+            uniqueId: `${Math.random()}`,
           }),
         )
       })

diff --git a/plugins/config/src/FromConfigAdapter/configSchema.ts b/plugins/config/src/FromConfigAdapter/configSchema.ts
@@ -41,6 +41,14 @@ export const sequenceConfigSchema = ConfigurationSchema(
       type: 'string',
       defaultValue: 'SimpleFeature',
     },
+
+    // occasionally assemblies may not be associated with the assemblyManager
+    // e.g. in the case of the "read assembly" that is used in read vs ref
+    // visualizations
+    noAssemblyManager: {
+      type: 'boolean',
+      defaultValue: false,
+    },
   },
   { explicitlyTyped: true },
 )
diff --git a/plugins/linear-comparative-view/src/LinearComparativeView/model.ts b/plugins/linear-comparative-view/src/LinearComparativeView/model.ts
@@ -65,8 +65,10 @@ export default function stateModelFactory(pluginManager: PluginManager) {
           pluginManager.pluggableConfigSchemaType('track'),
         ),
 
-        // this represents assemblies in the specialized
-        // read vs ref dotplot view
+        // this represents assemblies in the specialized read vs ref dotplot
+        // view. note that this was a types.frozen but is turned into an actual
+        // assembly type because we need to be able to use resolveIdentifier to
+        // resolve the sequence track inside the assembly
         viewAssemblyConfigs: types.array(assemblyConfigSchemasType),
       }),
     )

diff --git a/plugins/linear-comparative-view/src/index.tsx b/plugins/linear-comparative-view/src/index.tsx
@@ -320,6 +320,7 @@ function WindowSizeDlg(props: {
               assemblyNames: [readAssembly],
               adapter: {
                 type: 'FromConfigSequenceAdapter',
+                noAssemblyManager: true,
                 features: [
                   {
                     start: 0,