SPARQLAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the rdf plugin. View source.

Example usage#

{refName}, {start} and {end} are substituted per request, so the endpoint is queried for the visible window rather than the whole genome. The result columns become feature fields, so the query has to select at least ?start, ?end and a ?uniqueID:

{
  type: 'FeatureTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'SPARQLAdapter',
    endpoint: { uri: 'https://example.com/sparql' },
    queryTemplate: `SELECT ?uniqueID ?start ?end ?strand ?name WHERE {
      ?f a :Feature ; :ref "{refName}" ; :start ?start ; :end ?end .
      FILTER(?start < {end} && ?end > {start})
    }`,
    refNamesQueryTemplate: 'SELECT DISTINCT ?refName WHERE { ?f :ref ?refName }',
  },
}

See the Config slots section below for all available configuration fields.

fetches features from a SPARQL endpoint, substituting the queried region into a query template

Related links#

• Track: FeatureTrack
• Display: LinearArcDisplay
• Display: LinearBasicDisplay
• Display: LinearMultiRowFeatureDisplay
• Display: LinearScoreDisplay

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "SPARQLAdapter", ... }. This adapter has no uri shorthand — give it the location slots below. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

{ uri: 'https://somesite.com/sparql', locationType: 'UriLocation' }