@apollo-annotation/jbrowse-plugin-apollo 0.1.0

package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts

@@ -0,0 +1,186 @@
+import { readConfObject } from '@jbrowse/core/configuration'
+import {
+  BaseOptions,
+  BaseSequenceAdapter,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
+import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types'
+import { nanoid } from 'nanoid'
+
+import { BackendDriver } from '../BackendDrivers'
+import { ApolloSessionModel } from '../session'
+
+// declare global {
+//   var rpcServer: import('librpc-web-mod').RpcServer
+// }
+
+export interface RefSeq {
+  _id: string
+  name: string
+  description: string
+  length: number
+}
+
+interface ApolloMessageData {
+  apollo: true
+  messageId: string
+  sequence: string
+  regions: Region[]
+}
+
+function isApolloMessageData(data?: unknown): data is ApolloMessageData {
+  return (
+    typeof data === 'object' &&
+    data !== null &&
+    'apollo' in data &&
+    data.apollo === true
+  )
+}
+
+const isInWebWorker = typeof sessionStorage === 'undefined'
+
+export class ApolloSequenceAdapter extends BaseSequenceAdapter {
+  private regions: NoAssemblyRegion[] | undefined
+
+  public async getRefNames(opts?: BaseOptions) {
+    const regions = await this.getRegions(opts)
+    return regions.map((regions) => regions.refName)
+  }
+
+  public async getRegions(opts?: BaseOptions): Promise<NoAssemblyRegion[]> {
+    if (this.regions) {
+      return this.regions
+    }
+    const assemblyId = readConfObject(this.config, 'assemblyId')
+    if (!isInWebWorker) {
+      const dataStore = (
+        this.pluginManager?.rootModel?.session as ApolloSessionModel | undefined
+      )?.apolloDataStore
+      if (!dataStore) {
+        throw new Error('No Apollo data store found')
+      }
+      const backendDriver = dataStore.getBackendDriver(
+        assemblyId,
+      ) as BackendDriver
+      const regions = await backendDriver.getRegions(assemblyId)
+      this.regions = regions
+      return regions
+    }
+    const regions = await new Promise(
+      (
+        resolve: (sequence: Region[]) => void,
+        reject: (reason: string) => void,
+      ) => {
+        const timeoutId = setTimeout(() => {
+          reject('timeout')
+        }, 20_000)
+        const messageId = nanoid()
+        const messageListener = (event: MessageEvent) => {
+          const { data } = event
+          if (!isApolloMessageData(data)) {
+            return
+          }
+          if (data.messageId !== messageId) {
+            return
+          }
+          clearTimeout(timeoutId)
+          removeEventListener('message', messageListener)
+          resolve(data.regions)
+        }
+        addEventListener('message', messageListener, opts)
+        // @ts-expect-error waiting for types to be published
+        globalThis.rpcServer.emit('apollo', {
+          apollo: true,
+          method: 'getRegions',
+          assembly: assemblyId,
+          messageId,
+        })
+      },
+    )
+    this.regions = regions
+    return regions
+  }
+
+  /**
+   * Fetch features for a certain region
+   * @param param -
+   * @returns Observable of Feature objects in the region
+   */
+  public getFeatures(region: Region, opts?: BaseOptions) {
+    const { end, refName, start } = region
+    const assemblyId = readConfObject(this.config, 'assemblyId')
+    const regionWithAssemblyName = { ...region, assemblyName: assemblyId }
+    return ObservableCreate<Feature>(async (observer) => {
+      if (!isInWebWorker) {
+        const dataStore = (
+          this.pluginManager?.rootModel?.session as
+            | ApolloSessionModel
+            | undefined
+        )?.apolloDataStore
+        if (!dataStore) {
+          observer.error('No Apollo data store found')
+          return
+        }
+        const backendDriver = dataStore.getBackendDriver(
+          assemblyId,
+        ) as BackendDriver
+        const { seq } = await backendDriver.getSequence(regionWithAssemblyName)
+        observer.next(
+          new SimpleFeature({
+            id: `${refName} ${start}-${end}`,
+            data: { refName, start, end, seq },
+          }),
+        )
+        observer.complete()
+        return
+      }
+      const seq = await new Promise(
+        (
+          resolve: (sequence: string) => void,
+          reject: (reason: string) => void,
+        ) => {
+          const timeoutId = setTimeout(() => {
+            reject('timeout')
+          }, 20_000)
+          const messageId = nanoid()
+          const messageListener = (event: MessageEvent) => {
+            const { data } = event
+            if (!isApolloMessageData(data)) {
+              return
+            }
+            if (data.messageId !== messageId) {
+              return
+            }
+            clearTimeout(timeoutId)
+            removeEventListener('message', messageListener)
+            resolve(data.sequence)
+          }
+          addEventListener('message', messageListener, opts)
+          // @ts-expect-error waiting for types to be published
+          globalThis.rpcServer.emit('apollo', {
+            apollo: true,
+            method: 'getSequence',
+            region: regionWithAssemblyName,
+            messageId,
+          })
+        },
+      )
+      observer.next(
+        new SimpleFeature({
+          id: `${refName} ${start}-${end}`,
+          data: { refName, start, end, seq },
+        }),
+      )
+      observer.complete()
+    })
+  }
+
+  /**
+   * called to provide a hint that data tied to a certain region
+   * will not be needed for the foreseeable future and can be purged
+   * from caches, etc
+   */
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
+  public freeResources(/* { region } */): void {}
+}

package/src/ApolloSequenceAdapter/configSchema.ts

@@ -0,0 +1,12 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+export default ConfigurationSchema(
+  'ApolloSequenceAdapter',
+  {
+    assemblyId: {
+      type: 'string',
+      defaultValue: '',
+    },
+  },
+  { explicitlyTyped: true },
+)

package/src/ApolloSequenceAdapter/index.ts

@@ -0,0 +1,21 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+import { ApolloSequenceAdapter } from './ApolloSequenceAdapter'
+import configSchema from './configSchema'
+
+export function installApolloSequenceAdapter(pluginManager: PluginManager) {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'ApolloSequenceAdapter',
+        configSchema,
+        adapterMetadata: {
+          category: undefined,
+          hiddenFromGUI: true,
+          description: undefined,
+        },
+        AdapterClass: ApolloSequenceAdapter,
+      }),
+  )
+}

package/src/ApolloSixFrameRenderer/ApolloSixFrameRenderer.tsx

@@ -0,0 +1,12 @@
+import { RenderProps, RendererType } from '@jbrowse/core/pluggableElementTypes'
+import RpcManager from '@jbrowse/core/rpc/RpcManager'
+
+export default class ApolloSixFrameRenderer extends RendererType {
+  async renderInClient(_rpcManager: RpcManager, args: RenderProps) {
+    return this.render(args)
+  }
+
+  async freeResourcesInClient(_rpcManager: RpcManager, _args: RenderProps) {
+    return 0
+  }
+}