Add subadapter + reflection pattern to ExtendedVariantAdapter in order to delete VCFTabixAdapter

Author: Sebastian Benjamin

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVariantAdapter.ts

@@ -1,14 +1,57 @@
 import QuickLRU from '@jbrowse/core/util/QuickLRU';
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseOptions, BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import ExtendedVcfFeature from './ExtendedVcfFeature';
 import { VcfFeature } from '@jbrowse/plugin-variants';
-import { default as VcfTabixAdapter } from './VcfTabixAdapter';
 
-export default class extends VcfTabixAdapter {
+export default class extends BaseFeatureDataAdapter {
     protected featureCache = new QuickLRU({ maxSize: 20 })
+    private subAdapterP?: Promise<any>
+
+    constructor(...args: any[]) {
+      super(...args)
+
+      // Return a Proxy that forwards any unknown member access to the sub-adapter.
+      // This avoids re-implementing methods like getHeader/getRefNames/getMetadata/etc.
+      const self = this
+      return new Proxy(this, {
+        get(target, prop, receiver) {
+          // If we have it already (e.g., getFeatures, getFeaturesAsArray, BaseFeatureDataAdapter-derived properties), use it directly
+          if (prop in target || typeof prop === 'symbol') {
+            return Reflect.get(target, prop, receiver)
+          }
+
+          // Otherwise, forward to the VcfTabixAdapter sub-adapter
+          return async (...callArgs: any[]) => {
+            const sub = await self.getVcfSubAdapter()
+            const value = (sub as any)[prop]
+
+            // If it’s a method, call it; otherwise return the property value
+            if (typeof value === 'function') {
+              return value.apply(sub, callArgs)
+            }
+            return value
+          }
+        },
+      })
+    }
+
+    private async getVcfSubAdapter(): Promise<any> {
+        if (!this.subAdapterP) {
+            const vcfGzLocation = this.getConf('vcfGzLocation')
+            const index = this.getConf(['index'])
+            const vcfAdapterConf = { type: 'VcfTabixAdapter', vcfGzLocation, index }
+            this.subAdapterP = this.getSubAdapter!(vcfAdapterConf)
+                .then(({ dataAdapter }) => dataAdapter)
+                .catch(e => {
+                    this.subAdapterP = undefined
+                    throw e
+                })
+            }
+            return this.subAdapterP
+    }
 
     public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
         return ObservableCreate<Feature>(async observer => {
@@ -50,4 +93,19 @@ export default class extends VcfTabixAdapter {
 
         return features
     }
+
+    // Typescript errors at compile time without these stubs
+    async configure(opts?: BaseOptions) {
+        const sub = await this.getVcfSubAdapter()
+        return sub.configure(opts)
+    }
+
+    async getRefNames(opts: BaseOptions = {}) {
+        const sub = await this.getVcfSubAdapter()
+        return sub.getRefNames(opts)
+    }
+
+    freeResources(): void {
+        void this.getVcfSubAdapter().then(sub => sub.freeResources?.())
+    }
 }