@jbrowse/plugin-rdf 2.6.1 → 2.6.3

package/dist/SPARQLAdapter/SPARQLAdapter.js

@@ -175,4 +175,3 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources( /* { region } */) { }
 }
 exports.default = SPARQLAdapter;
-//# sourceMappingURL=SPARQLAdapter.js.map

package/dist/SPARQLAdapter/configSchema.js

@@ -31,4 +31,3 @@ exports.default = (0, configuration_1.ConfigurationSchema)('SPARQLAdapter', {
         description: 'Additional parameters to add to the query, e.g. "format=JSON"',
     },
 }, { explicitlyTyped: true });
-//# sourceMappingURL=configSchema.js.map

package/dist/SPARQLAdapter/index.js

@@ -8,4 +8,3 @@ var SPARQLAdapter_1 = require("./SPARQLAdapter");
 Object.defineProperty(exports, "AdapterClass", { enumerable: true, get: function () { return __importDefault(SPARQLAdapter_1).default; } });
 var configSchema_1 = require("./configSchema");
 Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
-//# sourceMappingURL=index.js.map

package/dist/index.js

@@ -36,4 +36,3 @@ class RdfPlugin extends Plugin_1.default {
     }
 }
 exports.default = RdfPlugin;
-//# sourceMappingURL=index.js.map

package/esm/SPARQLAdapter/SPARQLAdapter.js

@@ -169,4 +169,3 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-//# sourceMappingURL=SPARQLAdapter.js.map

package/esm/SPARQLAdapter/configSchema.js

@@ -29,4 +29,3 @@ export default ConfigurationSchema('SPARQLAdapter', {
         description: 'Additional parameters to add to the query, e.g. "format=JSON"',
     },
 }, { explicitlyTyped: true });
-//# sourceMappingURL=configSchema.js.map

package/esm/SPARQLAdapter/index.js

@@ -1,3 +1,2 @@
 export { default as AdapterClass } from './SPARQLAdapter';
 export { default as configSchema } from './configSchema';
-//# sourceMappingURL=index.js.map

package/esm/index.js

@@ -30,4 +30,3 @@ export default class RdfPlugin extends Plugin {
         });
     }
 }
-//# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-rdf",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "description": "JBrowse 2 RDF resources",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
@@ -52,5 +51,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }

package/dist/SPARQLAdapter/SPARQLAdapter.js.map

@@ -1 +0,0 @@
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package/dist/SPARQLAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/dist/SPARQLAdapter/index.js.map

@@ -1 +0,0 @@
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package/dist/index.js.map

@@ -1 +0,0 @@
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package/esm/SPARQLAdapter/SPARQLAdapter.js.map

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package/src/SPARQLAdapter/README.md

@@ -1,115 +0,0 @@
-# SPARQL Adapter
-
-JBrowse can display genomic information stored in RDF data stores by accessing
-them via a SPARQL endpoint. This is done by configuring a SPARQL adapter.
-
-## Query template
-
-The most basic configuration starts with a SPARQL query that returns features in
-a genomic range, i.e. on a particular chromosome/contig and between a start and
-end position. In such a query, replace the chromosome/contig name with
-`{refName}` and the start and end with `{start}` and `{end}`. For example
-
-```sparql
-PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX  rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX  faldo: <http://biohackathon.org/resource/faldo#>
-PREFIX  dc:   <http://purl.org/dc/elements/1.1/>
-
-SELECT DISTINCT  ?gene (?id AS ?uniqueId) (?label AS ?name) (?desc AS ?note) ?strand ?start ?end
-WHERE
-  { VALUES ?location_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }
-    ?location  faldo:begin     _:b0 .
-    _:b0      rdf:type         ?location_type ;
-              faldo:position   ?faldo_begin .
-    ?location  faldo:end       _:b1 .
-    _:b1      rdf:type         ?location_type ;
-              faldo:position   ?faldo_end .
-    ?location  faldo:reference  <http://rdf.ebi.ac.uk/resource/ensembl/97/homo_sapiens/GRCh38/{refName}> .
-    ?gene     rdf:type         ?type ;
-              rdfs:label       ?label ;
-              dc:description   ?desc ;
-              dc:identifier    ?id ;
-              faldo:location   ?location
-    BIND(if(( ?location_type = faldo:ForwardStrandPosition ), 1, if(( ?location_type = faldo:ReverseStrandPosition ), -1, 0)) AS ?strand)
-    BIND(if(( ?strand = -1 ), ?faldo_end, ?faldo_begin) AS ?start)
-    BIND(if(( ?strand = -1 ), ?faldo_begin, ?faldo_end) AS ?end)
-    FILTER ( ( ?start >= {start} ) && ( ?end <= {end} ) )
-  }
-```
-
-The SELECT in the the query must provide at least the variables `?start`,
-`?end`, and `?uniqueId`. Any other variables will be added to the feature data.
-
-## Adding a track
-
-From a JBrowse track selector, click the "+" icon and choose "Add track". When
-asked for the location of the data source, enter the SPARQL endpoint. If the
-endpoint ends with `/sparql`, JBrowse will automatically choose the SPARQL
-adapter. If not, choose "SPARQL adapter" in the resulting dialog. (You can use
-https://www.ebi.ac.uk/rdf/services/sparql as the endpoint to demonstrate the
-above example.)
-
-You will then be able to choose a track name and type as well as the assembly to
-which the track should be added. BasicTrack is suggested for most
-configurations, and using other track types is covered below. Click the "Add"
-button to add the track.
-
-Next, in the track selector click the settings icon next to the track which was
-just added. Paste the query template (see above) in the "queryTemplate" section.
-You can also configure other aspects of the track such as a description,
-category, etc.
-
-## Advanced configuration
-
-### Subfeatures
-
-There are two ways to provide subfeature information. The first is to include a
-`?parentUniqueId` variable with a feature. It will be created as a subfeature of
-the feature with a matching `?uniqueId`.
-
-The second way is useful if a single query response line contains information
-for more than one feature, e.g. gene, transcript, and exon information on a
-single line. For this type of data prefix all variables for the subfeature with
-`sub_`, which will allow you to define multiple features from the same line. It
-also works for deeper nested features, too, by using `sub_sub_`, etc. Parent
-features that are duplicated across lines will be resolved into a single
-feature. For example, take the following SPARQL query result lines:
-
-| uniqueId   | type | start    | end      | sub_uniqueId     | sub_type   | sub_start | sub_end  | sub_sub_uniqueId | sub_sub_type | sub_sub_start | sub_sub_end |
-| ---------- | ---- | -------- | -------- | ---------------- | ---------- | --------- | -------- | ---------------- | ------------ | ------------- | ----------- |
-| geneId0001 | gene | 10430102 | 10452003 | transcriptId0001 | transcript | 10430518  | 10442405 | exonId0001       | exon         | 10430518      | 10430568    |
-| geneId0001 | gene | 10430102 | 10452003 | transcriptId0001 | transcript | 10430518  | 10442405 | exonId0002       | exon         | 10432568      | 10433965    |
-
-These two lines will resolve into a singe feature "geneId0001" with one child
-feature "transcriptId0001", which will then itself have two child features
-"exonId0001" and "exonId0002".
-
-### Additional query parameters
-
-JBrowse will automatically send a header stating that it expects responses to be
-in the `application/json` or `application/sparql-results+json` format. Some
-SPARQL endpoints, however, require additional query parameters to be passed in
-order for the results be returned in JSON format, for example `format=json`.
-These can be added to the "additionalQueryParams" section and will be appended
-to each SPARQL request.
-
-### Reference sequence renaming
-
-In order for the track to take advantage of JBrowse's reference name aliasing,
-it must know what reference name the SPARQL store uses. These can be entered in
-one of two ways. The first is by entering a SPARQL query in the
-"refNamesQueryTemplate" config section. This query should return a line for each
-reference name in a `refName` column.
-
-The second option is to enumerate the reference names explicitly in the
-"refNames" config section. These will be ignored if a "refNamesQueryTemplate" is
-defined.
-
-### Other track types
-
-BasicTracks are flexible because they don't require any additional information,
-any any additional info provided in the query is just added to the feature. You
-can use other tracks as well, though, as long as you make sure the SPARQL query
-provides any info the track requires. For example, if you want to use a
-VariantTrack, the SPARQL query must provide REF, ALT, QUAL, etc.

package/src/SPARQLAdapter/SPARQLAdapter.test.ts

@@ -1,84 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import 'whatwg-fetch'
-import Adapter from './SPARQLAdapter'
-import emptyQueryResponse from './test_data/emptyQueryResponse.json'
-import queryResponse from './test_data/queryResponse.json'
-import refNamesResponse from './test_data/refNamesResponse.json'
-
-import configSchema from './configSchema'
-
-// window.fetch = jest.fn(url => new Promise(resolve => resolve()))
-
-test('adapter can fetch variants from volvox.vcf.gz', async () => {
-  function mockFetch(url: RequestInfo | URL) {
-    let response = {}
-    if (`${url}`.includes('chr1')) {
-      response = queryResponse
-    }
-    if (`${url}`.includes('chr80')) {
-      response = emptyQueryResponse
-    } else if (`${url}`.includes('fakeRefNamesQuery')) {
-      response = refNamesResponse
-    }
-
-    return Promise.resolve(new Response(JSON.stringify(response)))
-  }
-
-  const spy = jest.spyOn(global, 'fetch')
-  spy.mockImplementation(mockFetch)
-  const adapter = new Adapter(
-    configSchema.create({
-      endpoint: {
-        uri: 'http://somesite.com/sparql',
-        locationType: 'UriLocation',
-      },
-      queryTemplate: 'fakeSPARQLQuery-start{start}-end{end}-{refName}',
-      refNamesQueryTemplate: 'fakeRefNamesQuery',
-      additionalQueryParams: ['format=json'],
-      refNames: [],
-    }),
-  )
-
-  const refNames = await adapter.getRefNames()
-  expect(spy).toHaveBeenLastCalledWith(
-    'http://somesite.com/sparql?query=fakeRefNamesQuery&format=json',
-    {
-      headers: { accept: 'application/json,application/sparql-results+json' },
-      signal: undefined,
-    },
-  )
-  expect(refNames.length).toBe(17)
-  expect(refNames[0]).toBe('NC_004353.4')
-
-  const features = adapter.getFeatures({
-    refName: 'chr1',
-    start: 0,
-    end: 20000,
-  })
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray).toMatchSnapshot()
-  expect(spy).toHaveBeenLastCalledWith(
-    'http://somesite.com/sparql?query=fakeSPARQLQuery-start0-end20000-chr1&format=json',
-    {
-      headers: { accept: 'application/json,application/sparql-results+json' },
-      signal: undefined,
-    },
-  )
-
-  const featuresNonExist = adapter.getFeatures({
-    refName: 'chr80',
-    start: 0,
-    end: 20000,
-  })
-  const featuresArrayNonExist = await featuresNonExist
-    .pipe(toArray())
-    .toPromise()
-  expect(featuresArrayNonExist).toEqual([])
-  expect(spy).toHaveBeenLastCalledWith(
-    'http://somesite.com/sparql?query=fakeSPARQLQuery-start0-end20000-chr80&format=json',
-    {
-      headers: { accept: 'application/json,application/sparql-results+json' },
-      signal: undefined,
-    },
-  )
-})

package/src/SPARQLAdapter/SPARQLAdapter.ts

@@ -1,257 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import format from 'string-template'
-
-import { Instance } from 'mobx-state-tree'
-import { readConfObject } from '@jbrowse/core/configuration'
-import MyConfigSchema from './configSchema'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-
-interface SPARQLEntry {
-  type: string
-  value: string
-  dataTypes?: string
-}
-
-interface SPARQLBinding {
-  [key: string]: SPARQLEntry
-}
-
-interface SPARQLResponseHead {
-  vars: string[]
-}
-
-interface SPARQLResponseResults {
-  bindings: SPARQLBinding[]
-}
-
-interface SPARQLResponse {
-  head: SPARQLResponseHead
-  results: SPARQLResponseResults
-}
-
-interface SPARQLFeatureData {
-  start: number
-  end: number
-  strand: number
-  subfeatures?: SPARQLFeatureData[]
-  uniqueId: string
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  [propName: string]: any
-}
-
-interface SPARQLFeature {
-  data: SPARQLFeatureData
-}
-
-export default class SPARQLAdapter extends BaseFeatureDataAdapter {
-  private endpoint: string
-
-  private queryTemplate: string
-
-  private refNamesQueryTemplate: string
-
-  private additionalQueryParams: string[]
-
-  private configRefNames: string[]
-
-  private refNames: string[] | undefined
-
-  public constructor(
-    config: Instance<typeof MyConfigSchema>,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    this.endpoint = readConfObject(config, 'endpoint').uri
-    this.queryTemplate = readConfObject(config, 'queryTemplate')
-    this.additionalQueryParams = readConfObject(config, 'additionalQueryParams')
-    this.refNamesQueryTemplate = readConfObject(config, 'refNamesQueryTemplate')
-    this.configRefNames = readConfObject(config, 'refNames')
-  }
-
-  public async getRefNames(opts: BaseOptions = {}): Promise<string[]> {
-    if (this.refNames) {
-      return this.refNames
-    }
-    let refNames = [] as string[]
-    if (this.refNamesQueryTemplate) {
-      const queryTemplate = encodeURIComponent(this.refNamesQueryTemplate)
-      const results = await this.querySparql(queryTemplate, opts)
-      refNames = this.resultsToRefNames(results)
-    } else if (this.configRefNames) {
-      refNames = this.configRefNames
-    }
-    this.refNames = refNames
-    return refNames
-  }
-
-  public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const filledTemplate = encodeURIComponent(
-        format(this.queryTemplate, query),
-      )
-      const { refName } = query
-      const results = await this.querySparql(filledTemplate, opts)
-      this.resultsToFeatures(results, refName).forEach(feature => {
-        observer.next(feature)
-      })
-      observer.complete()
-    }, opts.signal)
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  private async querySparql(query: string, opts?: BaseOptions): Promise<any> {
-    let additionalQueryParams = ''
-    if (this.additionalQueryParams.length) {
-      additionalQueryParams = `&${this.additionalQueryParams.join('&')}`
-    }
-    const signal = opts && opts.signal
-    const response = await fetch(
-      `${this.endpoint}?query=${query}${additionalQueryParams}`,
-      {
-        headers: { accept: 'application/json,application/sparql-results+json' },
-        signal,
-      },
-    )
-    return response.json()
-  }
-
-  private resultsToRefNames(response: SPARQLResponse): string[] {
-    const rows = ((response || {}).results || {}).bindings || []
-    if (!rows.length) {
-      return []
-    }
-    const fields = response.head.vars
-    if (!fields.includes('refName')) {
-      throw new Error('"refName" not found in refNamesQueryTemplate response')
-    }
-    return rows.map(row => row.refName.value)
-  }
-
-  private resultsToFeatures(
-    results: SPARQLResponse,
-    refName: string,
-  ): SimpleFeature[] {
-    const rows = ((results || {}).results || {}).bindings || []
-    if (!rows.length) {
-      return []
-    }
-    const fields = results.head.vars
-    const requiredFields = ['start', 'end', 'uniqueId']
-    requiredFields.forEach(requiredField => {
-      if (!fields.includes(requiredField)) {
-        console.error(
-          `Required field ${requiredField} missing from feature data`,
-        )
-      }
-    })
-    const seenFeatures: Record<string, SPARQLFeature> = {}
-    rows.forEach(row => {
-      const rawData: Record<string, string>[] = [{}]
-      fields.forEach(field => {
-        if (field in row) {
-          const { value } = row[field]
-          let idx = 0
-          while (field.startsWith('sub_')) {
-            field = field.slice(4)
-            idx += 1
-          }
-          while (idx > rawData.length - 1) {
-            rawData.push({})
-          }
-          rawData[idx][field] = value
-        }
-      })
-
-      rawData.forEach((rd, idx) => {
-        const { uniqueId } = rd
-        if (idx < rawData.length - 1) {
-          rawData[idx + 1].parentUniqueId = uniqueId
-        }
-        seenFeatures[uniqueId] = {
-          data: {
-            ...rd,
-            uniqueId,
-            refName,
-            start: parseInt(rd.start, 10),
-            end: parseInt(rd.end, 10),
-            strand: parseInt(rd.strand, 10) || 0,
-          },
-        }
-      })
-    })
-
-    // resolve subfeatures, keeping only top-level features in seenFeatures
-    for (const [uniqueId, f] of Object.entries(seenFeatures)) {
-      const pid = f.data.parentUniqueId
-      delete f.data.parentUniqueId
-      if (pid) {
-        const p = seenFeatures[pid]
-        if (p) {
-          if (!p.data.subfeatures) {
-            p.data.subfeatures = []
-          }
-          p.data.subfeatures.push({
-            ...f.data,
-            uniqueId,
-          })
-          delete seenFeatures[uniqueId]
-        } else {
-          const subfeatures = Object.values(seenFeatures)
-            .map(sf => sf.data.subfeatures)
-            .filter(sf => !!sf)
-            .flat()
-          let found = false
-          for (const subfeature of subfeatures) {
-            if (subfeature && subfeature.uniqueId === pid) {
-              if (!subfeature.subfeatures) {
-                subfeature.subfeatures = []
-              }
-              subfeature.subfeatures.push({
-                ...f.data,
-                uniqueId,
-              })
-              delete seenFeatures[uniqueId]
-              found = true
-              break
-            } else if (subfeature && subfeature.subfeatures) {
-              subfeatures.push(...subfeature.subfeatures)
-            }
-          }
-          if (!found) {
-            console.error(`Could not find parentID ${pid}`)
-          }
-        }
-      }
-    }
-
-    return Object.keys(seenFeatures).map(
-      seenFeature =>
-        new SimpleFeature({
-          ...seenFeatures[seenFeature].data,
-          uniqueId: seenFeature,
-          subfeatures: seenFeatures[seenFeature].data.subfeatures,
-        }),
-    )
-  }
-
-  public async hasDataForRefName(
-    refName: string,
-    opts: BaseOptions = {},
-  ): Promise<boolean> {
-    const refNames = await this.getRefNames(opts)
-    if (refNames.length && !refNames.includes(refName)) {
-      return false
-    }
-    return true
-  }
-
-  public freeResources(/* { region } */): void {}
-}