Speed up large FromConfigAdapter usages with alternative adapter id calculation

package.json

@@ -71,7 +71,6 @@
     "@types/jest-image-snapshot": "^6.1.0",
     "@types/jexl": "^2.3.0",
     "@types/json-parse-better-errors": "^1.0.0",
-    "@types/json-stable-stringify": "^1.0.32",
     "@types/lodash.merge": "^4.6.6",
     "@types/node": "^14.14.0",
     "@types/node-fetch": "^2.5.7",

packages/core/assemblyManager/assembly.ts

@@ -1,5 +1,4 @@
 import { getParent, types, Instance, IAnyType } from 'mobx-state-tree'
-import jsonStableStringify from 'json-stable-stringify'
 import AbortablePromiseCache from 'abortable-promise-cache'
 
 // locals
@@ -13,6 +12,9 @@ import PluginManager from '../PluginManager'
 import { when, Region, Feature } from '../util'
 import QuickLRU from '../util/QuickLRU'
 import RpcManager from '../rpc/RpcManager'
+import { adapterConfigCacheKey } from '../data_adapters/dataAdapterCache'
+
+type AdapterConf = Record<string, unknown>
 
 const refNameRegex = new RegExp(
   '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*',
@@ -107,10 +109,6 @@ function checkRefName(refName: string) {
   }
 }
 
-function getAdapterId(adapterConf: unknown) {
-  return jsonStableStringify(adapterConf)
-}
-
 type RefNameAliases = Record<string, string | undefined>
 
 interface CacheData {
@@ -430,14 +428,13 @@ export default function assemblyFactory(
       /**
        * #method
        */
-      getAdapterMapEntry(adapterConf: unknown, options: BaseOptions) {
+      getAdapterMapEntry(adapterConf: AdapterConf, options: BaseOptions) {
         const { signal, statusCallback, ...rest } = options
         if (!options.sessionId) {
           throw new Error('sessionId is required')
         }
-        const adapterId = getAdapterId(adapterConf)
         return adapterLoads.get(
-          adapterId,
+          adapterConfigCacheKey(adapterConf),
           {
             adapterConf,
             self: self as Assembly,
@@ -455,7 +452,10 @@ export default function assemblyFactory(
        * #method
        * get Map of `canonical-name -> adapter-specific-name`
        */
-      async getRefNameMapForAdapter(adapterConf: unknown, opts: BaseOptions) {
+      async getRefNameMapForAdapter(
+        adapterConf: AdapterConf,
+        opts: BaseOptions,
+      ) {
         if (!opts?.sessionId) {
           throw new Error('sessionId is required')
         }
@@ -468,7 +468,7 @@ export default function assemblyFactory(
        * get Map of `adapter-specific-name -> canonical-name`
        */
       async getReverseRefNameMapForAdapter(
-        adapterConf: unknown,
+        adapterConf: AdapterConf,
         opts: BaseOptions,
       ) {
         const map = await this.getAdapterMapEntry(adapterConf, opts)

packages/core/assemblyManager/assemblyManager.ts

@@ -13,6 +13,8 @@ import assemblyFactory, { Assembly } from './assembly'
 import PluginManager from '../PluginManager'
 import RpcManager from '../rpc/RpcManager'
 
+type AdapterConf = Record<string, unknown>
+
 /**
  * #stateModel AssemblyManager
  */
@@ -105,7 +107,7 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
         await assembly.load()
         await when(
           () =>
-            Boolean(assembly?.regions && assembly.refNameAliases) ||
+            !!(assembly?.regions && assembly.refNameAliases) ||
             !!assembly?.error,
         )
         if (assembly.error) {
@@ -118,7 +120,7 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
        * #method
        */
       async getRefNameMapForAdapter(
-        adapterConf: unknown,
+        adapterConf: AdapterConf,
         assemblyName: string | undefined,
         opts: { signal?: AbortSignal; sessionId: string },
       ) {
@@ -133,7 +135,7 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
        * #method
        */
       async getReverseRefNameMapForAdapter(
-        adapterConf: unknown,
+        adapterConf: AdapterConf,
         assemblyName: string | undefined,
         opts: { signal?: AbortSignal; sessionId: string },
       ) {

packages/core/data_adapters/dataAdapterCache.ts

@@ -6,8 +6,8 @@ import idMaker from '../util/idMaker'
 
 type ConfigSnap = SnapshotIn<AnyConfigurationSchemaType>
 
-function adapterConfigCacheKey(adapterConfig: ConfigSnap) {
-  return `${idMaker(adapterConfig)}`
+export function adapterConfigCacheKey(conf: Record<string, unknown> = {}) {
+  return `${idMaker(conf)}`
 }
 
 interface AdapterCacheEntry {

packages/core/package.json

@@ -47,7 +47,6 @@
     "http-range-fetcher": "^2.0.0",
     "is-object": "^1.0.1",
     "jexl": "^2.3.0",
-    "json-stable-stringify": "^1.0.1",
     "librpc-web-mod": "^1.1.5",
     "load-script": "^2.0.0",
     "material-ui-popup-state": "^5.0.0",

packages/core/util/index.ts

@@ -780,7 +780,7 @@ export async function renameRegionsIfNeeded<
     assemblyName?: string
     regions?: Region[]
     signal?: AbortSignal
-    adapterConfig: unknown
+    adapterConfig: Record<string, unknown>
     sessionId: string
     statusCallback?: (arg: string) => void
   },

plugins/config/src/FromConfigAdapter/FromConfigAdapter.ts

@@ -12,11 +12,29 @@ import {
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
-/**
- * Adapter that just returns the features defined in its `features` configuration
- * key, like:
- *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
- */
+export function makeFeatures(fdata: SimpleFeatureSerialized[]) {
+  const features = new Map<string, Feature[]>()
+  for (const entry of fdata) {
+    if (entry) {
+      const f = new SimpleFeature(entry)
+      const refName = f.get('refName') as string
+      let bucket = features.get(refName)
+      if (!bucket) {
+        bucket = []
+        features.set(refName, bucket)
+      }
+
+      bucket.push(f)
+    }
+  }
+
+  // sort the features on each reference sequence by start coordinate
+  for (const refFeatures of features.values()) {
+    refFeatures.sort((a, b) => a.get('start') - b.get('start'))
+  }
+
+  return features
+}
 
 export default class FromConfigAdapter extends BaseFeatureDataAdapter {
   protected features: Map<string, Feature[]>
@@ -28,35 +46,7 @@ export default class FromConfigAdapter extends BaseFeatureDataAdapter {
   ) {
     super(conf, getSubAdapter, pluginManager)
     const feats = readConfObject(conf, 'features') as SimpleFeatureSerialized[]
-    this.features = FromConfigAdapter.makeFeatures(feats || [])
-  }
-
-  static makeFeatures(fdata: SimpleFeatureSerialized[]) {
-    const features = new Map<string, Feature[]>()
-    for (const entry of fdata) {
-      if (entry) {
-        const f = this.makeFeature(entry)
-        const refName = f.get('refName') as string
-        let bucket = features.get(refName)
-        if (!bucket) {
-          bucket = []
-          features.set(refName, bucket)
-        }
-
-        bucket.push(f)
-      }
-    }
-
-    // sort the features on each reference sequence by start coordinate
-    for (const refFeatures of features.values()) {
-      refFeatures.sort((a, b) => a.get('start') - b.get('start'))
-    }
-
-    return features
-  }
-
-  static makeFeature(data: SimpleFeatureSerialized) {
-    return new SimpleFeature(data)
+    this.features = makeFeatures(feats || [])
   }
 
   async getRefNames() {

plugins/config/src/FromConfigRegionsAdapter/FromConfigRegionsAdapter.ts

@@ -12,8 +12,7 @@ import {
 } from '@jbrowse/core/configuration'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-
-import FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter'
+import { makeFeatures } from '../FromConfigAdapter/FromConfigAdapter'
 
 /**
  * Adapter that just returns the features defined in its `features` configuration
@@ -32,11 +31,8 @@ export default class FromConfigRegionsAdapter
     pluginManager?: PluginManager,
   ) {
     super(config, getSubAdapter, pluginManager)
-    const features = readConfObject(
-      config,
-      'features',
-    ) as SimpleFeatureSerialized[]
-    this.features = FromConfigAdapter.makeFeatures(features || [])
+    const f = readConfObject(config, 'features') as SimpleFeatureSerialized[]
+    this.features = makeFeatures(f || [])
   }
 
   /**

yarn.lock

@@ -4417,11 +4417,6 @@
   resolved "https://registry.yarnpkg.com/@types/json-schema/-/json-schema-7.0.15.tgz#596a1747233694d50f6ad8a7869fcb6f56cf5841"
   integrity sha512-5+fP8P8MFNC+AyZCDxrB2pkZFPGzqQWUzpSeuuVLvm8VMcorNYavBqoFcxK8bQz4Qsbn4oUEEem4wDLfcysGHA==
 
-"@types/json-stable-stringify@^1.0.32":
-  version "1.0.36"
-  resolved "https://registry.yarnpkg.com/@types/json-stable-stringify/-/json-stable-stringify-1.0.36.tgz#fe6c6001a69ff8160a772da08779448a333c7ddd"
-  integrity sha512-b7bq23s4fgBB76n34m2b3RBf6M369B0Z9uRR8aHTMd8kZISRkmDEpPD8hhpYvDFzr3bJCPES96cm3Q6qRNDbQw==
-
 "@types/keyv@^3.1.4":
   version "3.1.4"
   resolved "https://registry.yarnpkg.com/@types/keyv/-/keyv-3.1.4.tgz#3ccdb1c6751b0c7e52300bcdacd5bcbf8faa75b6"
@@ -11538,16 +11533,6 @@ json-stable-stringify-without-jsonify@^1.0.1:
   resolved "https://registry.yarnpkg.com/json-stable-stringify-without-jsonify/-/json-stable-stringify-without-jsonify-1.0.1.tgz#9db7b59496ad3f3cfef30a75142d2d930ad72651"
   integrity sha512-Bdboy+l7tA3OGW6FjyFHWkP5LuByj1Tk33Ljyq0axyzdk9//JSi2u3fP1QSmd1KNwq6VOKYGlAu87CisVir6Pw==
 
-json-stable-stringify@^1.0.1:
-  version "1.1.0"
-  resolved "https://registry.yarnpkg.com/json-stable-stringify/-/json-stable-stringify-1.1.0.tgz#43d39c7c8da34bfaf785a61a56808b0def9f747d"
-  integrity sha512-zfA+5SuwYN2VWqN1/5HZaDzQKLJHaBVMZIIM+wuYjdptkaQsqzDdqjqf+lZZJUuJq1aanHiY8LhH8LmH+qBYJA==
-  dependencies:
-    call-bind "^1.0.5"
-    isarray "^2.0.5"
-    jsonify "^0.0.1"
-    object-keys "^1.1.1"
-
 json-stringify-nice@^1.1.4:
   version "1.1.4"
   resolved "https://registry.yarnpkg.com/json-stringify-nice/-/json-stringify-nice-1.1.4.tgz#2c937962b80181d3f317dd39aa323e14f5a60a67"
@@ -11584,11 +11569,6 @@ jsonfile@^6.0.1:
   optionalDependencies:
     graceful-fs "^4.1.6"
 
-jsonify@^0.0.1:
-  version "0.0.1"
-  resolved "https://registry.yarnpkg.com/jsonify/-/jsonify-0.0.1.tgz#2aa3111dae3d34a0f151c63f3a45d995d9420978"
-  integrity sha512-2/Ki0GcmuqSrgFyelQq9M05y7PS0mEwuIzrf3f1fPqkVDVRvZrPZtVSMHxdgo8Aq0sxAOb/cr2aqqA3LeWHVPg==
-
 jsonparse@^1.2.0, jsonparse@^1.3.1:
   version "1.3.1"
   resolved "https://registry.yarnpkg.com/jsonparse/-/jsonparse-1.3.1.tgz#3f4dae4a91fac315f71062f8521cc239f1366280"