From bf340734b42b52f53d8d6b9f9c3ea0c271262ae7 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Thu, 25 Jul 2024 11:47:31 -0400
Subject: [PATCH] Rm

---
 .../core/assemblyManager/loadRefNameMap.ts    | 65 -----------------
 packages/core/assemblyManager/util.ts         | 70 -------------------
 2 files changed, 135 deletions(-)
 delete mode 100644 packages/core/assemblyManager/loadRefNameMap.ts
 delete mode 100644 packages/core/assemblyManager/util.ts

diff --git a/packages/core/assemblyManager/loadRefNameMap.ts b/packages/core/assemblyManager/loadRefNameMap.ts
deleted file mode 100644
index 67928d2b7c..0000000000
--- a/packages/core/assemblyManager/loadRefNameMap.ts
+++ /dev/null
@@ -1,65 +0,0 @@
-import { BaseOptions, checkRefName, RefNameAliases } from './util'
-import RpcManager from '../rpc/RpcManager'
-import { when } from '../util'
-
-export interface BasicRegion {
-  start: number
-  end: number
-  refName: string
-  assemblyName: string
-}
-
-export async function loadRefNameMap(
-  assembly: {
-    name: string
-    regions: BasicRegion[] | undefined
-    refNameAliases: RefNameAliases | undefined
-    getCanonicalRefName: (arg: string) => string
-    rpcManager: RpcManager
-  },
-  adapterConfig: unknown,
-  options: BaseOptions,
-  signal?: AbortSignal,
-) {
-  const { sessionId } = options
-  await when(() => !!(assembly.regions && assembly.refNameAliases), {
-    signal,
-    name: 'when assembly ready',
-  })
-
-  const refNames = (await assembly.rpcManager.call(
-    sessionId,
-    'CoreGetRefNames',
-    {
-      adapterConfig,
-      signal,
-      ...options,
-    },
-    { timeout: 1000000 },
-  )) as string[]
-
-  const { refNameAliases } = assembly
-  if (!refNameAliases) {
-    throw new Error(`error loading assembly ${assembly.name}'s refNameAliases`)
-  }
-
-  const refNameMap = Object.fromEntries(
-    refNames.map(name => {
-      checkRefName(name)
-      return [assembly.getCanonicalRefName(name), name]
-    }),
-  )
-
-  // make the reversed map too
-  const reversed = Object.fromEntries(
-    Object.entries(refNameMap).map(([canonicalName, adapterName]) => [
-      adapterName,
-      canonicalName,
-    ]),
-  )
-
-  return {
-    forwardMap: refNameMap,
-    reverseMap: reversed,
-  }
-}
diff --git a/packages/core/assemblyManager/util.ts b/packages/core/assemblyManager/util.ts
deleted file mode 100644
index e779fec009..0000000000
--- a/packages/core/assemblyManager/util.ts
+++ /dev/null
@@ -1,70 +0,0 @@
-import { AnyConfigurationModel } from '../configuration'
-import jsonStableStringify from 'json-stable-stringify'
-import { BaseRefNameAliasAdapter } from '../data_adapters/BaseAdapter'
-import PluginManager from '../PluginManager'
-import { BasicRegion } from './loadRefNameMap'
-
-export type RefNameAliases = Record<string, string>
-
-export interface BaseOptions {
-  signal?: AbortSignal
-  sessionId: string
-  statusCallback?: Function
-}
-
-export async function getRefNameAliases(
-  config: AnyConfigurationModel,
-  pm: PluginManager,
-  signal?: AbortSignal,
-) {
-  const type = pm.getAdapterType(config.type)
-  const CLASS = await type.getAdapterClass()
-  const adapter = new CLASS(config, undefined, pm) as BaseRefNameAliasAdapter
-  return adapter.getRefNameAliases({ signal })
-}
-
-export async function getCytobands(
-  config: AnyConfigurationModel,
-  pm: PluginManager,
-) {
-  const type = pm.getAdapterType(config.type)
-  const CLASS = await type.getAdapterClass()
-  const adapter = new CLASS(config, undefined, pm)
-
-  // @ts-expect-error
-  return adapter.getData()
-}
-
-export async function getAssemblyRegions(
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  assembly: any,
-  adapterConfig: AnyConfigurationModel,
-  signal?: AbortSignal,
-): Promise<BasicRegion[]> {
-  const sessionId = 'loadRefNames'
-  return assembly.rpcManager.call(
-    sessionId,
-    'CoreGetRegions',
-    {
-      adapterConfig,
-      sessionId,
-      signal,
-    },
-    { timeout: 1000000 },
-  )
-}
-
-const refNameRegex = new RegExp(
-  '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*',
-)
-
-// Valid refName pattern from https://samtools.github.io/hts-specs/SAMv1.pdf
-export function checkRefName(refName: string) {
-  if (!refNameRegex.test(refName)) {
-    throw new Error(`Encountered invalid refName: "${refName}"`)
-  }
-}
-
-export function getAdapterId(adapterConf: unknown) {
-  return jsonStableStringify(adapterConf)
-}