Add CoreGetRegions

packages/core/assemblyManager/assemblyConfigSchema.ts

@@ -2,10 +2,11 @@ import { ConfigurationSchema } from '../configuration'
 import PluginManager from '../PluginManager'
 
 /**
- * #config BaseAssembly
- * This corresponds to the assemblies section of the config
+ * #config Assembly
+ * This corresponds to the assemblies section of the config, generally accessed
+ * through the assemblyManager
  */
-function assemblyConfigSchema(pluginManager: PluginManager) {
+export default function assemblyConfigSchema(pluginManager: PluginManager) {
   return ConfigurationSchema(
     'BaseAssembly',
     {
@@ -21,8 +22,8 @@ function assemblyConfigSchema(pluginManager: PluginManager) {
 
       /**
        * #slot
-       * sequence refers to a reference sequence track that has an adapter containing,
-       * importantly, a sequence adapter such as IndexedFastaAdapter
+       * sequence refers to a reference sequence track that has an adapter
+       * containing, importantly, a sequence adapter such as IndexedFastaAdapter
        */
       sequence: pluginManager.getTrackType('ReferenceSequenceTrack')
         .configSchema,
@@ -42,9 +43,9 @@ function assemblyConfigSchema(pluginManager: PluginManager) {
         {
           /**
            * #slot refNameAliases.adapter
-           * refNameAliases help resolve e.g. chr1 and 1 as the same entity
-           * the data for refNameAliases are fetched from an adapter, that is
-           * commonly a tsv like chromAliases.txt from UCSC or similar
+           * refNameAliases help resolve e.g. chr1 and 1 as the same entity the
+           * data for refNameAliases are fetched from an adapter, that is commonly a tsv
+           * like chromAliases.txt from UCSC or similar
            */
           adapter: pluginManager.pluggableConfigSchemaType('adapter'),
         },
@@ -64,8 +65,8 @@ function assemblyConfigSchema(pluginManager: PluginManager) {
         {
           /**
            * #slot cytobands.adapter
-           * cytoband data is fetched from an adapter, and can be displayed by a
-           * view type as ideograms
+           * cytoband data is fetched from an adapter, and can be displayed by
+           * a view type as ideograms
            */
           adapter: pluginManager.pluggableConfigSchemaType('adapter'),
         },
@@ -94,13 +95,11 @@ function assemblyConfigSchema(pluginManager: PluginManager) {
     {
       /**
        * #identifier name
-       * the name acts as a unique identifier in the config, so it cannot be duplicated.
-       * it usually a short human readable "id" like hg38, but you can also optionally
-       * customize the assembly "displayName" config slot
+       * the name acts as a unique identifier in the config, so it cannot be
+       * duplicated. it usually a short human readable "id" like hg38, but you can
+       * also optionally customize the assembly "displayName" config slot
        */
       explicitIdentifier: 'name',
     },
   )
 }
-
-export default assemblyConfigSchema

packages/core/assemblyManager/assemblyManager.ts

@@ -6,13 +6,17 @@ import {
   Instance,
   IAnyType,
 } from 'mobx-state-tree'
-import { when } from '../util'
 import { reaction } from 'mobx'
+// locals
+import { when } from '../util'
 import { readConfObject, AnyConfigurationModel } from '../configuration'
 import assemblyFactory, { Assembly } from './assembly'
 import PluginManager from '../PluginManager'
 
-function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
+export default function assemblyManagerFactory(
+  conf: IAnyType,
+  pm: PluginManager,
+) {
   type Conf = Instance<typeof conf> | string
   return types
     .model({
@@ -116,21 +120,20 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
         addDisposer(
           self,
           reaction(
-            // have to slice it to be properly reacted to
             () => self.assemblyList,
-            assemblyConfigs => {
+            confs => {
               self.assemblies.forEach(asm => {
                 if (!asm.configuration) {
                   this.removeAssembly(asm)
                 }
               })
-              assemblyConfigs.forEach(assemblyConfig => {
-                const existingAssemblyIdx = self.assemblies.findIndex(
-                  assembly =>
-                    assembly.name === readConfObject(assemblyConfig, 'name'),
-                )
-                if (existingAssemblyIdx === -1) {
-                  this.addAssembly(assemblyConfig)
+              confs.forEach(conf => {
+                if (
+                  !self.assemblies.some(
+                    a => a.name === readConfObject(conf, 'name'),
+                  )
+                ) {
+                  this.addAssembly(conf)
                 }
               })
             },
@@ -154,5 +157,3 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
       },
     }))
 }
-
-export default assemblyManagerFactory

packages/core/assemblyManager/loadRefNameMap.ts

@@ -0,0 +1,65 @@
+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,
+  }
+}

packages/core/assemblyManager/util.ts

@@ -0,0 +1,69 @@
+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(
+  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)
+}

packages/core/pluggableElementTypes/models/BaseTrackModel.ts

@@ -221,7 +221,6 @@ export function createBaseTrackModel(
             onClick: () => {
               getSession(self).queueDialog(handleClose => [
                 SaveTrackDataDlg,
-                // @ts-ignore
                 { model: self, handleClose },
               ])
             },

packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx

@@ -11,6 +11,7 @@ import {
   TextField,
   Typography,
 } from '@mui/material'
+import { IAnyStateTreeNode } from 'mobx-state-tree'
 import { makeStyles } from 'tss-react/mui'
 import { saveAs } from 'file-saver'
 import { observer } from 'mobx-react'
@@ -22,7 +23,6 @@ import {
   Region,
 } from '@jbrowse/core/util'
 import { getConf } from '@jbrowse/core/configuration'
-import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes'
 
 // icons
 import GetAppIcon from '@mui/icons-material/GetApp'
@@ -41,7 +41,7 @@ const useStyles = makeStyles()({
 })
 
 async function fetchFeatures(
-  track: BaseTrackModel,
+  track: IAnyStateTreeNode,
   regions: Region[],
   signal?: AbortSignal,
 ) {
@@ -60,7 +60,7 @@ export default observer(function SaveTrackDataDlg({
   model,
   handleClose,
 }: {
-  model: BaseTrackModel
+  model: IAnyStateTreeNode
   handleClose: () => void
 }) {
   const { classes } = useStyles()
@@ -77,11 +77,9 @@ export default observer(function SaveTrackDataDlg({
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
-        const view = getContainingView(model)
+        const view = getContainingView(model) as { visibleRegions?: Region[] }
         setError(undefined)
-        setFeatures(
-          await fetchFeatures(model, view.dynamicBlocks.contentBlocks),
-        )
+        setFeatures(await fetchFeatures(model, view.visibleRegions || []))
       } catch (e) {
         console.error(e)
         setError(e)
@@ -92,20 +90,24 @@ export default observer(function SaveTrackDataDlg({
   useEffect(() => {
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
-      const view = getContainingView(model)
-      const session = getSession(model)
-      if (!features) {
-        return
-      }
-      const str = await (type === 'gff3'
-        ? stringifyGFF3(features)
-        : stringifyGenbank({
-            features,
-            session,
-            assemblyName: view.dynamicBlocks.contentBlocks[0].assemblyName,
-          }))
+      try {
+        const view = getContainingView(model)
+        const session = getSession(model)
+        if (!features) {
+          return
+        }
+        const str = await (type === 'gff3'
+          ? stringifyGFF3(features)
+          : stringifyGenbank({
+              features,
+              session,
+              assemblyName: view.dynamicBlocks.contentBlocks[0].assemblyName,
+            }))
 
-      setStr(str)
+        setStr(str)
+      } catch (e) {
+        setError(e)
+      }
     })()
   }, [type, features, model])
 
@@ -121,10 +123,7 @@ export default observer(function SaveTrackDataDlg({
 
         <FormControl>
           <FormLabel>File type</FormLabel>
-          <RadioGroup
-            value={type}
-            onChange={event => setType(event.target.value)}
-          >
+          <RadioGroup value={type} onChange={e => setType(e.target.value)}>
             {Object.entries(options).map(([key, val]) => (
               <FormControlLabel
                 key={key}
@@ -153,16 +152,10 @@ export default observer(function SaveTrackDataDlg({
       <DialogActions>
         <Button
           onClick={() => {
-            saveAs(
-              new Blob([str || ''], {
-                type: 'text/plain;charset=utf-8',
-              }),
-              `jbrowse_track_data.${
-                options[type as keyof typeof options].extension
-              }`,
-            )
+            const ext = options[type as keyof typeof options].extension
+            const blob = new Blob([str], { type: 'text/plain;charset=utf-8' })
+            saveAs(blob, `jbrowse_track_data.${ext}`)
           }}
-          disabled={!str || !!error}
           startIcon={<GetAppIcon />}
         >
           Download

packages/core/rpc/coreRpcMethods.ts

@@ -5,5 +5,6 @@ export { default as CoreGetFileInfo } from './methods/CoreGetFileInfo'
 export { default as CoreGetFeatures } from './methods/CoreGetFeatures'
 export { default as CoreRender } from './methods/CoreRender'
 export { default as CoreFreeResources } from './methods/CoreFreeResources'
-export { type RenderArgs } from './methods/util'
 export { default as CoreEstimateRegionStats } from './methods/CoreEstimateRegionStats'
+export { default as CoreGetRegions } from './methods/CoreGetRegions'
+export { type RenderArgs } from './methods/util'