SPARQLAdapter

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the rdf plugin. View source.

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

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 }',
  },
}

Related links#

• Track: FeatureTrack
• Display: LinearBasicDisplay
• Display: LinearManhattanDisplay
• Display: LinearMarkDisplay
• Display: LinearMultiRowFeatureDisplay
• Display: LinearScoreDisplay
• Display: LinearWiggleDisplay

Config slots#

Adapter slots go inside the track's adapter: "adapter": { "type": "SPARQLAdapter", ... }. SPARQLAdapter 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' }