@jbrowse/plugin-legacy-jbrowse 2.6.1 → 2.6.2

package/src/NCListAdapter/NCListAdapter.ts

@@ -1,92 +0,0 @@
-import NCListStore from '@gmod/nclist'
-import { Region } from '@jbrowse/core/util/types'
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { checkAbortSignal } from '@jbrowse/core/util'
-import { RemoteFile } from 'generic-filehandle'
-import NCListFeature from './NCListFeature'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-
-export default class NCListAdapter extends BaseFeatureDataAdapter {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  private nclist: any
-
-  private configRefNames?: string[]
-
-  constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    const refNames = this.getConf('refNames')
-    const rootUrlTemplate = this.getConf('rootUrlTemplate')
-    this.configRefNames = refNames
-
-    this.nclist = new NCListStore({
-      baseUrl: '',
-      urlTemplate: rootUrlTemplate.uri,
-      readFile: (url: string) =>
-        new RemoteFile(
-          String(
-            rootUrlTemplate.baseUri
-              ? new URL(url, rootUrlTemplate.baseUri).toString()
-              : url,
-          ),
-        ).readFile(),
-    })
-  }
-
-  /**
-   * Fetch features for a certain region. Use getFeaturesInRegion() if you also
-   * want to verify that the store has features for the given reference sequence
-   * before fetching.
-   * @param region -
-   * @param opts - [signal] optional signalling object for aborting the fetch
-   * @returns Observable of Feature objects in the region
-   */
-  getFeatures(region: Region, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const { signal } = opts
-      for await (const feature of this.nclist.getFeatures(region, opts)) {
-        checkAbortSignal(signal)
-        observer.next(this.wrapFeature(feature))
-      }
-      observer.complete()
-    })
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  wrapFeature(ncFeature: any): NCListFeature {
-    return new NCListFeature(
-      ncFeature,
-      undefined,
-      `${this.id}-${ncFeature.id()}`,
-    )
-  }
-
-  async hasDataForRefName(refName: string) {
-    const root = await this.nclist.getDataRoot(refName)
-    return !!(root && root.stats && root.stats.featureCount)
-  }
-
-  /**
-   * NCList is unable to get list of ref names so returns empty
-   */
-  async getRefNames() {
-    return this.configRefNames || []
-  }
-
-  /**
-   * 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
-   */
-  freeResources() {}
-}

package/src/NCListAdapter/NCListFeature.ts

@@ -1,94 +0,0 @@
-import {
-  Feature,
-  SimpleFeatureSerialized,
-} from '@jbrowse/core/util/simpleFeature'
-
-const jb2ToJb1 = { refName: 'seq_id' }
-
-const jb1ToJb2 = { seq_id: 'refName' }
-
-/**
- * wrapper to adapt nclist features to act like jbrowse 2 features
- */
-export default class NCListFeature implements Feature {
-  private parentHandle?: Feature
-
-  private uniqueId: string
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  constructor(private ncFeature: any, parent?: Feature, id?: string) {
-    this.uniqueId = id || ncFeature.id()
-    this.parentHandle = parent
-  }
-
-  set(): void {
-    throw new Error('not implemented')
-  }
-
-  jb2TagToJb1Tag(tag: string): string {
-    // @ts-expect-error
-    const mapped = jb2ToJb1[tag] || tag
-    return mapped.toLowerCase()
-  }
-
-  jb1TagToJb2Tag(tag: string): string {
-    const t = tag.toLowerCase()
-    // @ts-expect-error
-    return jb1ToJb2[t] || t
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  get(attrName: string): any {
-    const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName))
-    if (attr && attrName === 'subfeatures') {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      return attr.map((subfeature: any) => new NCListFeature(subfeature, this))
-    }
-    return attr
-  }
-
-  /**
-   * Get an array listing which data keys are present in this feature.
-   */
-  tags(): string[] {
-    return this.ncFeature.tags().map((t: string) => this.jb1TagToJb2Tag(t))
-  }
-
-  /**
-   * Get the unique ID of this feature.
-   */
-  id(): string {
-    return this.uniqueId
-  }
-
-  /**
-   * Get this feature's parent feature, or undefined if none.
-   */
-  parent(): Feature | undefined {
-    return this.parentHandle
-  }
-
-  /**
-   * Get an array of child features, or undefined if none.
-   */
-  children(): Feature[] | undefined {
-    return this.get('subfeatures')
-  }
-
-  toJSON(): SimpleFeatureSerialized {
-    const data: SimpleFeatureSerialized = { uniqueId: this.id() }
-    this.ncFeature.tags().forEach((tag: string) => {
-      const mappedTag = this.jb1TagToJb2Tag(tag)
-      const value = this.ncFeature.get(tag)
-      if (mappedTag === 'subfeatures') {
-        data.subfeatures = (value || []).map((f: Feature) => {
-          // note: was new NCListFeature(f, `${this.id()}-${i}`, this).toJSON()
-          return new NCListFeature(f, this).toJSON()
-        })
-      } else {
-        data[mappedTag] = value
-      }
-    })
-    return data
-  }
-}