@jbrowse/plugin-config 2.5.0 → 2.6.2

package/src/ConfigurationEditorWidget/index.tsx

@@ -1,25 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import { isStateTreeNode, getType } from 'mobx-state-tree'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-export { default as stateModelFactory } from './model'
-export const configSchema = ConfigurationSchema('ConfigurationEditorWidget', {})
-export const HeadingComponent = observer(
-  ({ model }: { model?: { target: { type: string } } }) => {
-    if (model?.target) {
-      if (model.target.type) {
-        return <>{`${model.target.type} settings`}</>
-      }
-      if (isStateTreeNode(model.target)) {
-        const type = getType(model.target)
-        if (type?.name) {
-          return (
-            <>{`${type.name.replace('ConfigurationSchema', '')} settings`}</>
-          )
-        }
-      }
-    }
-    return <>Settings</>
-  },
-)

package/src/ConfigurationEditorWidget/model.ts

@@ -1,21 +0,0 @@
-import { types } from 'mobx-state-tree'
-import { ElementId } from '@jbrowse/core/util/types/mst'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-export default (pluginManager: PluginManager) =>
-  types
-    .model('ConfigurationEditorWidget', {
-      id: ElementId,
-      type: types.literal('ConfigurationEditorWidget'),
-      // If you add different types of targets, don't forget to account for that
-      // in the key of ./components/ConfigurationEditor.js
-      target: types.safeReference(
-        pluginManager.pluggableConfigSchemaType('track'),
-      ),
-    })
-    .actions(self => ({
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      setTarget(newTarget: any) {
-        self.target = newTarget
-      },
-    }))

package/src/FromConfigAdapter/FromConfigAdapter.test.ts

@@ -1,56 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './FromConfigAdapter'
-import configSchema from './configSchema'
-
-test('adapter can fetch features', async () => {
-  const features = [
-    { uniqueId: 'one', refName: 'ctgA', start: 20, end: 40 },
-    { uniqueId: 'two', refName: 'ctgB', start: 50, end: 60 },
-  ]
-  const adapter = new Adapter(configSchema.create({ features }))
-  const result = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-  })
-
-  const featuresArray = await firstValueFrom(result.pipe(toArray()))
-  expect(featuresArray.length).toBe(1)
-  expect(featuresArray[0].toJSON()).toEqual(features[0])
-})
-
-test('adapter can fetch features with subfeatures', async () => {
-  const features = [
-    {
-      refName: 'ctgA',
-      uniqueId: 'feat1',
-      start: 200,
-      end: 750,
-      name: 'Feature1',
-      subfeatures: [
-        {
-          uniqueId: 'feat2',
-          start: 225,
-          end: 300,
-          name: 'Feature2',
-        },
-        {
-          uniqueId: 'feat3',
-          start: 400,
-          end: 600,
-          name: 'Feature3',
-        },
-      ],
-    },
-  ]
-  const adapter = new Adapter(configSchema.create({ features }))
-  const result = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-  })
-
-  const featuresArray = await firstValueFrom(result.pipe(toArray()))
-  expect(featuresArray.length).toBe(1)
-})

package/src/FromConfigAdapter/FromConfigAdapter.ts

@@ -1,90 +0,0 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import SimpleFeature, {
-  Feature,
-  SimpleFeatureSerialized,
-} from '@jbrowse/core/util/simpleFeature'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-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 default class FromConfigAdapter extends BaseFeatureDataAdapter {
-  protected features: Map<string, Feature[]>
-
-  constructor(
-    conf: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    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 (let i = 0; i < fdata.length; i += 1) {
-      if (fdata[i]) {
-        const f = this.makeFeature(fdata[i])
-        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)
-  }
-
-  async getRefNames() {
-    return [...this.features.keys()]
-  }
-
-  async getRefNameAliases() {
-    return [...this.features.values()].map(featureArray => ({
-      refName: featureArray[0].get('refName'),
-      aliases: featureArray[0].get('aliases'),
-    }))
-  }
-
-  getFeatures(region: NoAssemblyRegion) {
-    const { refName, start, end } = region
-
-    return ObservableCreate<Feature>(async observer => {
-      const features = this.features.get(refName) || []
-      for (let i = 0; i < features.length; i++) {
-        const f = features[i]
-
-        if (f.get('end') > start && f.get('start') < end) {
-          observer.next(f)
-        }
-      }
-      observer.complete()
-    })
-  }
-
-  freeResources(/* { region } */): void {}
-}

package/src/FromConfigAdapter/configSchema.ts

@@ -1,22 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config FromConfigAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configSchema = ConfigurationSchema(
-  'FromConfigAdapter',
-  {
-    /**
-     * #slot
-     */
-    features: {
-      type: 'frozen',
-      defaultValue: [],
-    },
-  },
-  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
-)
-
-export default configSchema

package/src/FromConfigAdapter/index.ts

@@ -1,18 +0,0 @@
-import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'FromConfigAdapter',
-        configSchema,
-        getAdapterClass: () =>
-          import('./FromConfigAdapter').then(r => r.default),
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-      }),
-  )
-}

package/src/FromConfigRegionsAdapter/FromConfigRegionsAdapter.test.ts

@@ -1,58 +0,0 @@
-import Adapter from './FromConfigRegionsAdapter'
-import regionsConfigSchema from './configSchema'
-
-test('adapter can fetch regions 1', async () => {
-  const features = [
-    { uniqueId: 'one', refName: 'ctgA', start: 250, end: 400 },
-    { uniqueId: 'two', refName: 'ctgA', start: 150, end: 300 },
-    { uniqueId: 'three', refName: 'ctgB', start: 50, end: 60 },
-  ]
-  const adapter = new Adapter(regionsConfigSchema.create({ features }))
-  const result = await adapter.getRegions()
-  expect(result).toEqual([
-    { refName: 'ctgA', start: 150, end: 400 },
-    { refName: 'ctgB', start: 50, end: 60 },
-  ])
-})
-
-test('adapter can fetch regions 2', async () => {
-  const features = [
-    { uniqueId: 'three', refName: 'ctgB', start: 50, end: 60 },
-    { uniqueId: 'two', refName: 'ctgA', start: 150, end: 300 },
-    { uniqueId: 'one', refName: 'ctgA', start: 250, end: 400 },
-  ]
-  const adapter = new Adapter(regionsConfigSchema.create({ features }))
-  const result = await adapter.getRegions()
-  expect(result).toEqual([
-    { refName: 'ctgA', start: 150, end: 400 },
-    { refName: 'ctgB', start: 50, end: 60 },
-  ])
-})
-
-test('adapter can fetch regions 3', async () => {
-  const features = [
-    { uniqueId: 'two', refName: 'ctgA', start: 150, end: 300 },
-    { uniqueId: 'one', refName: 'ctgA', start: 250, end: 400 },
-    { uniqueId: 'three', refName: 'ctgB', start: 50, end: 60 },
-  ]
-  const adapter = new Adapter(regionsConfigSchema.create({ features }))
-  const result = await adapter.getRegions()
-  expect(result).toEqual([
-    { refName: 'ctgA', start: 150, end: 400 },
-    { refName: 'ctgB', start: 50, end: 60 },
-  ])
-})
-
-test('adapter can fetch regions 4', async () => {
-  const features = [
-    { uniqueId: 'two', refName: 'ctgA', start: 150, end: 300 },
-    { uniqueId: 'onePrime', refName: 'ctgA', start: 300, end: 400 },
-    { uniqueId: 'three', refName: 'ctgB', start: 50, end: 60 },
-  ]
-  const adapter = new Adapter(regionsConfigSchema.create({ features }))
-  const result = await adapter.getRegions()
-  expect(result).toEqual([
-    { refName: 'ctgA', start: 150, end: 400 },
-    { refName: 'ctgB', start: 50, end: 60 },
-  ])
-})

package/src/FromConfigRegionsAdapter/FromConfigRegionsAdapter.ts

@@ -1,81 +0,0 @@
-import {
-  BaseAdapter,
-  RegionsAdapter,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import {
-  Feature,
-  SimpleFeatureSerialized,
-} from '@jbrowse/core/util/simpleFeature'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-
-import FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter'
-
-/**
- * Adapter that just returns the features defined in its `features` configuration
- * key, like:
- *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
- */
-export default class FromConfigRegionsAdapter
-  extends BaseAdapter
-  implements RegionsAdapter
-{
-  private features: Map<string, Feature[]>
-
-  constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    const features = readConfObject(
-      config,
-      'features',
-    ) as SimpleFeatureSerialized[]
-    this.features = FromConfigAdapter.makeFeatures(features || [])
-  }
-
-  /**
-   * Get refName, start, and end for all features after collapsing any overlaps
-   */
-  async getRegions() {
-    const regions = []
-
-    // recall: features are stored in this object sorted by start coordinate
-    for (const [refName, features] of this.features) {
-      let currentRegion
-      for (const feature of features) {
-        if (
-          currentRegion &&
-          currentRegion.end >= feature.get('start') &&
-          currentRegion.start <= feature.get('end')
-        ) {
-          currentRegion.end = feature.get('end')
-        } else {
-          if (currentRegion) {
-            regions.push(currentRegion)
-          }
-          currentRegion = {
-            refName,
-            start: feature.get('start'),
-            end: feature.get('end'),
-          }
-        }
-      }
-      if (currentRegion) {
-        regions.push(currentRegion)
-      }
-    }
-
-    // sort the regions by refName
-    regions.sort((a, b) => a.refName.localeCompare(b.refName))
-
-    return regions
-  }
-
-  freeResources(/* { region } */): void {}
-}

package/src/FromConfigRegionsAdapter/configSchema.ts

@@ -1,24 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-/**
- * #config FromConfigRegionsAdapter
- * used for specifying refNames+sizes of an assembly
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const regionsConfigSchema = ConfigurationSchema(
-  'FromConfigRegionsAdapter',
-  {
-    /**
-     * #slot
-     */
-    features: {
-      type: 'frozen',
-      defaultValue: [],
-    },
-  },
-  {
-    explicitlyTyped: true,
-    implicitIdentifier: 'adapterId',
-  },
-)
-export default regionsConfigSchema

package/src/FromConfigRegionsAdapter/index.ts

@@ -1,18 +0,0 @@
-import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'FromConfigRegionsAdapter',
-        configSchema,
-        getAdapterClass: () =>
-          import('./FromConfigRegionsAdapter').then(r => r.default),
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-      }),
-  )
-}

package/src/FromConfigSequenceAdapter/FromConfigSequenceAdapter.test.ts

@@ -1,64 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './FromConfigSequenceAdapter'
-import sequenceConfigSchema from './configSchema'
-
-test('adapter can fetch sequences when there is just one feature representing whole refseq', async () => {
-  const features = [
-    {
-      uniqueId: 'one',
-      refName: 'ctgA',
-      start: 0,
-      end: 150,
-      seq: 'ccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctc',
-    },
-  ]
-  const adapter = new Adapter(sequenceConfigSchema.create({ features }))
-  const result = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 50,
-  })
-  const featuresArray = await firstValueFrom(result.pipe(toArray()))
-  expect(featuresArray.length).toBe(1)
-  expect(featuresArray[0].get('seq')).toBe(features[0].seq.slice(0, 50))
-
-  const result2 = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 100,
-    end: 150,
-  })
-  const featuresArray2 = await firstValueFrom(result2.pipe(toArray()))
-  expect(featuresArray2.length).toBe(1)
-  expect(featuresArray2[0].get('seq')).toBe(features[0].seq.slice(100, 150))
-})
-
-test("adapter can fetch sequences when the config's sequence doesn't start at 0", async () => {
-  const features = [
-    {
-      uniqueId: 'one',
-      refName: 'ctgA',
-      start: 5000,
-      end: 5150,
-      seq: 'ccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctc',
-    },
-  ]
-  const adapter = new Adapter(sequenceConfigSchema.create({ features }))
-  const result = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 4950,
-    end: 5050,
-  })
-  const featuresArray = await firstValueFrom(result.pipe(toArray()))
-  expect(featuresArray.length).toBe(1)
-  expect(featuresArray[0].get('seq')).toBe(features[0].seq.slice(0, 50))
-
-  const result2 = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 5050,
-    end: 5150,
-  })
-  const featuresArray2 = await firstValueFrom(result2.pipe(toArray()))
-  expect(featuresArray2.length).toBe(1)
-  expect(featuresArray2[0].get('seq')).toBe(features[0].seq.slice(50, 150))
-})

package/src/FromConfigSequenceAdapter/FromConfigSequenceAdapter.ts

@@ -1,86 +0,0 @@
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
-import { toArray } from 'rxjs/operators'
-import { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-
-// locals
-import FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter'
-import { firstValueFrom } from 'rxjs'
-
-export default class FromConfigSequenceAdapter
-  extends FromConfigAdapter
-  implements RegionsAdapter
-{
-  /**
-   * Fetch features for a certain region
-   * @param region - Region
-   * @returns Observable of Feature objects in the region
-   */
-  getFeatures(region: NoAssemblyRegion) {
-    return ObservableCreate<Feature>(async observer => {
-      const feats = await firstValueFrom(
-        super.getFeatures(region).pipe(toArray()),
-      )
-      const feat = feats[0]
-      observer.next(
-        new SimpleFeature({
-          ...feat.toJSON(),
-          uniqueId: `${feat.id()}:${region.start}-${region.end}`,
-          end: region.end,
-          start: region.start,
-          seq: feat
-            .get('seq')
-            .slice(
-              Math.max(region.start - feat.get('start'), 0),
-              Math.max(region.end - feat.get('start'), 0),
-            ),
-        }),
-      )
-
-      observer.complete()
-    })
-  }
-
-  /**
-   * Get refName, start, and end for all features after collapsing any overlaps
-   */
-  async getRegions() {
-    const regions = []
-
-    // recall: features are stored in this object sorted by start coordinate
-    for (const [refName, features] of this.features) {
-      let currentRegion
-      for (const feature of features) {
-        if (
-          currentRegion &&
-          currentRegion.end >= feature.get('start') &&
-          currentRegion.start <= feature.get('end')
-        ) {
-          currentRegion.end = feature.get('end')
-        } else {
-          if (currentRegion) {
-            regions.push(currentRegion)
-          }
-          currentRegion = {
-            refName,
-            start: feature.get('start'),
-            end: feature.get('end'),
-          }
-        }
-      }
-      if (currentRegion) {
-        regions.push(currentRegion)
-      }
-    }
-
-    return regions
-  }
-
-  /**
-   * 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(/* { region } */): void {}
-}

package/src/FromConfigSequenceAdapter/configSchema.ts

@@ -1,21 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-/**
- * #config FromConfigSequenceAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const sequenceConfigSchema = ConfigurationSchema(
-  'FromConfigSequenceAdapter',
-  {
-    /**
-     * #slot
-     */
-    features: {
-      type: 'frozen',
-      defaultValue: [],
-    },
-  },
-  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
-)
-
-export default sequenceConfigSchema

package/src/FromConfigSequenceAdapter/index.ts

@@ -1,19 +0,0 @@
-import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'FromConfigSequenceAdapter',
-        configSchema,
-        getAdapterClass: () =>
-          import('./FromConfigSequenceAdapter').then(r => r.default),
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-      }),
-  )
-}

package/src/RefNameAliasAdapter/RefNameAliasAdapter.test.ts

@@ -1,18 +0,0 @@
-import Adapter from './RefNameAliasAdapter'
-import configSchema from './configSchema'
-
-test('adapter can fetch a simple alias file', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      location: {
-        localPath: require.resolve('./test_data/simple_alias.txt'),
-        locationType: 'LocalPathLocation',
-      },
-    }),
-  )
-  const result = await adapter.getRefNameAliases()
-  expect(result[0].refName).toBe('chr1')
-  expect(result[0].aliases).toEqual(['1', 'NC_000001.10'])
-  expect(result[1].refName).toBe('chr2')
-  expect(result[1].aliases).toEqual(['2', 'NC_000002.11'])
-})

package/src/RefNameAliasAdapter/RefNameAliasAdapter.ts

@@ -1,30 +0,0 @@
-import {
-  BaseRefNameAliasAdapter,
-  BaseAdapter,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { openLocation } from '@jbrowse/core/util/io'
-
-export default class RefNameAliasAdapter
-  extends BaseAdapter
-  implements BaseRefNameAliasAdapter
-{
-  async getRefNameAliases() {
-    const loc = this.getConf('location')
-    if (loc.uri === '' || loc.uri === '/path/to/my/aliases.txt') {
-      return []
-    }
-    const results = await openLocation(loc, this.pluginManager).readFile('utf8')
-    const refColumn = this.getConf('refNameColumn')
-    return results
-      .trim()
-      .split(/\n|\r\n|\r/)
-      .filter(f => !!f && !f.startsWith('#'))
-      .map(row => {
-        const aliases = row.split('\t')
-        const [refName] = aliases.splice(refColumn, 1)
-        return { refName, aliases: aliases.filter(f => !!f.trim()) }
-      })
-  }
-
-  async freeResources() {}
-}