@jbrowse/plugin-rdf 2.6.1

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Files changed (38) hide show
  1. package/LICENSE +201 -0
  2. package/dist/SPARQLAdapter/SPARQLAdapter.d.ts +23 -0
  3. package/dist/SPARQLAdapter/SPARQLAdapter.js +178 -0
  4. package/dist/SPARQLAdapter/SPARQLAdapter.js.map +1 -0
  5. package/dist/SPARQLAdapter/configSchema.d.ts +31 -0
  6. package/dist/SPARQLAdapter/configSchema.js +34 -0
  7. package/dist/SPARQLAdapter/configSchema.js.map +1 -0
  8. package/dist/SPARQLAdapter/index.d.ts +2 -0
  9. package/dist/SPARQLAdapter/index.js +11 -0
  10. package/dist/SPARQLAdapter/index.js.map +1 -0
  11. package/dist/index.d.ts +6 -0
  12. package/dist/index.js +39 -0
  13. package/dist/index.js.map +1 -0
  14. package/esm/SPARQLAdapter/SPARQLAdapter.d.ts +23 -0
  15. package/esm/SPARQLAdapter/SPARQLAdapter.js +172 -0
  16. package/esm/SPARQLAdapter/SPARQLAdapter.js.map +1 -0
  17. package/esm/SPARQLAdapter/configSchema.d.ts +31 -0
  18. package/esm/SPARQLAdapter/configSchema.js +32 -0
  19. package/esm/SPARQLAdapter/configSchema.js.map +1 -0
  20. package/esm/SPARQLAdapter/index.d.ts +2 -0
  21. package/esm/SPARQLAdapter/index.js +3 -0
  22. package/esm/SPARQLAdapter/index.js.map +1 -0
  23. package/esm/index.d.ts +6 -0
  24. package/esm/index.js +33 -0
  25. package/esm/index.js.map +1 -0
  26. package/package.json +56 -0
  27. package/src/SPARQLAdapter/README.md +115 -0
  28. package/src/SPARQLAdapter/SPARQLAdapter.test.ts +84 -0
  29. package/src/SPARQLAdapter/SPARQLAdapter.ts +257 -0
  30. package/src/SPARQLAdapter/__snapshots__/SPARQLAdapter.test.ts.snap +449 -0
  31. package/src/SPARQLAdapter/configSchema.ts +40 -0
  32. package/src/SPARQLAdapter/index.ts +2 -0
  33. package/src/SPARQLAdapter/test_data/emptyQueryResponse.json +30 -0
  34. package/src/SPARQLAdapter/test_data/queryResponse.json +3834 -0
  35. package/src/SPARQLAdapter/test_data/refNamesResponse.json +114 -0
  36. package/src/__snapshots__/index.test.ts.snap +3 -0
  37. package/src/index.test.ts +18 -0
  38. package/src/index.ts +46 -0
package/src/SPARQLAdapter/__snapshots__/SPARQLAdapter.test.ts.snap ADDED
@@ -0,0 +1,449 @@
1
+ // Jest Snapshot v1, https://goo.gl/fbAQLP
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+
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+ exports[`adapter can fetch variants from volvox.vcf.gz 1`] = `
4
+ [
5
+ {
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+ "description": "solute carrier family 45 member 1; Derived by automated computational analysis using gene prediction method: BestRefSeq,Gnomon.",
7
+ "end": 8344167,
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+ "faldo_type": "http://biohackathon.org/resource/faldo#ForwardStrandPosition",
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+ "name": "SLC45A1",
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+ "refName": "chr1",
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+ "start": 8318085,
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+ "strand": 1,
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+ "subfeatures": [
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+ {
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+ "class": "http://purl.obolibrary.org/obo/SO_0000316",
16
+ "description": "proton-associated sugar transporter A isoform X1",
17
+ "end": 8344013,
18
+ "name": "SLC45A1",
19
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318085-8344167:1:gene.266",
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+ "refName": "chr1",
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+ "start": 8318109,
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+ "strand": 1,
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+ "subfeatures": [
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+ {
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+ "end": 8318186,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ "refName": "chr1",
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+ "start": 8318109,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8318186:1:exon-urn:uuid:5f183854-6d7d-4481-a380-2f7589d95350",
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+ },
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+ {
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+ "end": 8324726,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ "refName": "chr1",
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+ "start": 8324306,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8324306-8324726:1:exon-urn:uuid:7c2b06d1-c04d-495f-ae34-4a7d6514b0de",
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+ },
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+ {
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+ "end": 8325390,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ "refName": "chr1",
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+ "start": 8325298,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8325298-8325390:1:exon-urn:uuid:db09fb23-4a13-45e2-8efe-046836811046",
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+ },
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+ {
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+ "end": 8326042,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ "refName": "chr1",
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+ "start": 8325818,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8325818-8326042:1:exon-urn:uuid:fa0bfc05-f7b9-4780-99e3-fbdd9309d7ff",
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+ },
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+ {
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+ "end": 8330936,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ "refName": "chr1",
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+ "start": 8330209,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8330209-8330936:1:exon-urn:uuid:39c5e70a-3f63-4fb2-beb3-391e69ac568f",
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+ },
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+ {
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+ "end": 8335614,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ "refName": "chr1",
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+ "start": 8335437,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8335437-8335614:1:exon-urn:uuid:41f103d9-ed77-41de-b99c-4198bd33bf24",
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+ },
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+ {
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+ "end": 8337992,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ "refName": "chr1",
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+ "start": 8337816,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8337816-8337992:1:exon-urn:uuid:63e3e11d-33a0-4000-97d6-fe7ad0aef31c",
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+ },
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+ {
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+ "end": 8339698,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ "refName": "chr1",
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+ "start": 8339493,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8339493-8339698:1:exon-urn:uuid:013977d3-aa64-4369-a10b-00c4c96a364b",
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+ },
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+ {
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+ "end": 8344013,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ "refName": "chr1",
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+ "start": 8343747,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8343747-8344013:1:exon-urn:uuid:8d04079b-e892-4a7d-bea0-d32f9f111a3a",
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+ },
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+ ],
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+ "type": "mRNA",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.703",
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+ },
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+ {
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+ "class": "http://purl.obolibrary.org/obo/SO_0000316",
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+ "description": "proton-associated sugar transporter A",
112
+ "end": 8344013,
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+ "name": "SLC45A1",
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318085-8344167:1:gene.266",
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+ "refName": "chr1",
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+ "start": 8318109,
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+ "strand": 1,
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+ "subfeatures": [
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+ {
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+ "end": 8318186,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ "refName": "chr1",
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+ "start": 8318109,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8318186:1:exon-urn:uuid:ac0240bc-d0bd-42c5-80b1-ce74ced7d0d3",
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+ },
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+ {
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+ "end": 8324726,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ "refName": "chr1",
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+ "start": 8324306,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8324306-8324726:1:exon-urn:uuid:e319de85-763c-41b9-886b-825c5802003b",
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+ },
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+ {
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+ "end": 8325390,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ "refName": "chr1",
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+ "start": 8325298,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8325298-8325390:1:exon-urn:uuid:8bc73805-a57b-4f97-989b-ec23381a3eef",
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+ },
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+ {
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+ "end": 8326042,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ "refName": "chr1",
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+ "start": 8325818,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8325818-8326042:1:exon-urn:uuid:ffd39d23-26ae-48a8-8a87-8a35b1659ded",
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+ },
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+ {
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+ "end": 8330936,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ "refName": "chr1",
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+ "start": 8330209,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8330209-8330936:1:exon-urn:uuid:66ee77ce-d711-4dcb-ab0c-78f236f787c8",
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+ },
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+ {
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+ "end": 8335590,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ "refName": "chr1",
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+ "start": 8335437,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8335437-8335590:1:exon-urn:uuid:7d3cd756-748b-48da-9684-b705b86fb523",
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+ },
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+ {
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+ "end": 8337992,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ "refName": "chr1",
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+ "start": 8337816,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8337816-8337992:1:exon-urn:uuid:baad05a5-dfb9-47d8-a2aa-e1a42a12770c",
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+ },
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+ {
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+ "end": 8339698,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ "refName": "chr1",
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+ "start": 8339493,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8339493-8339698:1:exon-urn:uuid:fb70eb86-e029-4900-9e99-75147688b037",
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+ },
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+ {
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+ "end": 8344013,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ "refName": "chr1",
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+ "start": 8343747,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8343747-8344013:1:exon-urn:uuid:cf8be8e0-cea6-45a6-8d73-fe3603e53980",
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+ },
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+ ],
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+ "type": "mRNA",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.704",
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+ },
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+ {
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+ "class": "http://purl.obolibrary.org/obo/SO_0000316",
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+ "description": "proton-associated sugar transporter A isoform X2",
207
+ "end": 8344013,
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+ "name": "SLC45A1",
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318085-8344167:1:gene.266",
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+ "refName": "chr1",
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+ "start": 8318109,
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+ "strand": 1,
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+ "subfeatures": [
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+ {
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+ "end": 8318186,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.705",
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+ "refName": "chr1",
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+ "start": 8318109,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8318186:1:exon-urn:uuid:8bf75796-5115-46fd-a7b7-bd12daea442b",
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+ },
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+ {
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+ "end": 8324726,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.705",
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+ "refName": "chr1",
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+ "start": 8324306,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8324306-8324726:1:exon-urn:uuid:39fb38ac-4d54-40d8-890f-fd758e04a354",
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+ },
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+ {
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.705",
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+ "refName": "chr1",
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+ },
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+ "refName": "chr1",
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+ "start": 8330209,
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+ },
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+ {
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.705",
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+ "refName": "chr1",
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+ "start": 8335437,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8335437-8335614:1:exon-urn:uuid:201f46b2-7520-4142-b38f-22af9a5ef78e",
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+ },
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+ {
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.705",
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+ "refName": "chr1",
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+ "start": 8337816,
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+ "strand": 1,
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+ {
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+ "refName": "chr1",
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+ "start": 8339493,
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+ "strand": 1,
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+ "type": "CDS",
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+ },
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+ {
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+ "end": 8344013,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.705",
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+ "refName": "chr1",
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+ "start": 8343747,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8343747-8344013:1:exon-urn:uuid:13868dc4-2041-4444-81ac-e8e1bbbca898",
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+ },
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+ ],
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+ "type": "mRNA",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.705",
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+ },
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+ {
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+ "class": "http://purl.obolibrary.org/obo/SO_0000316",
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+ "description": "proton-associated sugar transporter A isoform X3",
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+ "end": 8344013,
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+ "name": "SLC45A1",
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318085-8344167:1:gene.266",
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+ "refName": "chr1",
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+ "start": 8318109,
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+ "strand": 1,
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+ "subfeatures": [
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+ {
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+ "end": 8318186,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.706",
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+ "refName": "chr1",
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+ "start": 8318109,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8318186:1:exon-urn:uuid:0aa03467-9a14-4076-a4cd-a419d3bb212e",
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+ },
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+ {
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+ "end": 8324726,
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.706",
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+ "refName": "chr1",
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+ "start": 8324306,
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+ "strand": 1,
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+ "type": "CDS",
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+ },
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+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.706",
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+ "refName": "chr1",
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+ "start": 8325818,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8325818-8326042:1:exon-urn:uuid:aca48294-72a7-4d72-bea9-cc6d6bb49d7b",
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+ "refName": "chr1",
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+ "start": 8330209,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8330209-8330936:1:exon-urn:uuid:279e0669-870b-4fe5-86a6-b838bb3ebaa1",
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+ },
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+ {
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+ "end": 8335590,
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+ "refName": "chr1",
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+ "start": 8335437,
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+ "strand": 1,
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+ "type": "CDS",
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+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8335437-8335590:1:exon-urn:uuid:912a99dc-da26-4706-90ce-ca96eeb21c27",
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+ "refName": "chr1",
349
+ "start": 8337816,
350
+ "strand": 1,
351
+ "type": "CDS",
352
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8337816-8337992:1:exon-urn:uuid:3f7db5ba-57ef-4e05-a661-a93e1f434230",
353
+ },
354
+ {
355
+ "end": 8339698,
356
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.706",
357
+ "refName": "chr1",
358
+ "start": 8339493,
359
+ "strand": 1,
360
+ "type": "CDS",
361
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8339493-8339698:1:exon-urn:uuid:a03af8c7-31f3-42d9-8101-d72d1b13d114",
362
+ },
363
+ {
364
+ "end": 8344013,
365
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.706",
366
+ "refName": "chr1",
367
+ "start": 8343747,
368
+ "strand": 1,
369
+ "type": "CDS",
370
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8343747-8344013:1:exon-urn:uuid:b34637d9-77ed-4c06-a08b-03acb99a5ae4",
371
+ },
372
+ ],
373
+ "type": "mRNA",
374
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8318109-8344013:1:CDS.706",
375
+ },
376
+ {
377
+ "class": "http://purl.obolibrary.org/obo/SO_0000316",
378
+ "description": "proton-associated sugar transporter A isoform X4",
379
+ "end": 8344013,
380
+ "name": "SLC45A1",
381
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8318085-8344167:1:gene.266",
382
+ "refName": "chr1",
383
+ "start": 8325934,
384
+ "strand": 1,
385
+ "subfeatures": [
386
+ {
387
+ "end": 8326042,
388
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8325934-8344013:1:CDS.707",
389
+ "refName": "chr1",
390
+ "start": 8325934,
391
+ "strand": 1,
392
+ "type": "CDS",
393
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8325934-8326042:1:exon-urn:uuid:7626ebaf-dd9d-4f7b-8ca6-7e8bfcc7c5cf",
394
+ },
395
+ {
396
+ "end": 8330936,
397
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8325934-8344013:1:CDS.707",
398
+ "refName": "chr1",
399
+ "start": 8330209,
400
+ "strand": 1,
401
+ "type": "CDS",
402
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8330209-8330936:1:exon-urn:uuid:50112b56-90e8-432b-8075-e47920945781",
403
+ },
404
+ {
405
+ "end": 8335614,
406
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8325934-8344013:1:CDS.707",
407
+ "refName": "chr1",
408
+ "start": 8335437,
409
+ "strand": 1,
410
+ "type": "CDS",
411
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8335437-8335614:1:exon-urn:uuid:ca019537-cdb1-42f4-ad71-79d089b0af0c",
412
+ },
413
+ {
414
+ "end": 8337992,
415
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8325934-8344013:1:CDS.707",
416
+ "refName": "chr1",
417
+ "start": 8337816,
418
+ "strand": 1,
419
+ "type": "CDS",
420
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8337816-8337992:1:exon-urn:uuid:ca3a384c-0b5f-4e69-b89c-d34e179feba3",
421
+ },
422
+ {
423
+ "end": 8339698,
424
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8325934-8344013:1:CDS.707",
425
+ "refName": "chr1",
426
+ "start": 8339493,
427
+ "strand": 1,
428
+ "type": "CDS",
429
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8339493-8339698:1:exon-urn:uuid:81b25241-d953-41c7-a1c0-5303d8dc9618",
430
+ },
431
+ {
432
+ "end": 8344013,
433
+ "parentId": "http://identifiers.org/refseq/NC_000001.11#feature:8325934-8344013:1:CDS.707",
434
+ "refName": "chr1",
435
+ "start": 8343747,
436
+ "strand": 1,
437
+ "type": "CDS",
438
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8343747-8344013:1:exon-urn:uuid:429b344f-c6bd-4a6f-8a35-8b5164bdf252",
439
+ },
440
+ ],
441
+ "type": "mRNA",
442
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8325934-8344013:1:CDS.707",
443
+ },
444
+ ],
445
+ "type": "gene",
446
+ "uniqueId": "http://identifiers.org/refseq/NC_000001.11#feature:8318085-8344167:1:gene.266",
447
+ },
448
+ ]
449
+ `;
package/src/SPARQLAdapter/configSchema.ts ADDED
@@ -0,0 +1,40 @@
1
+ import { ConfigurationSchema } from '@jbrowse/core/configuration'
2
+
3
+ export default ConfigurationSchema(
4
+ 'SPARQLAdapter',
5
+ {
6
+ endpoint: {
7
+ type: 'fileLocation',
8
+ defaultValue: {
9
+ uri: 'https://somesite.com/sparql',
10
+ locationType: 'UriLocation',
11
+ },
12
+ description: 'URL of the SPARQL endpoint',
13
+ },
14
+ queryTemplate: {
15
+ type: 'text',
16
+ defaultValue: '',
17
+ description:
18
+ 'SPARQL query where {start} {end} and {refName} will get replaced for each call',
19
+ },
20
+ refNamesQueryTemplate: {
21
+ type: 'text',
22
+ defaultValue: '',
23
+ description:
24
+ 'SPARQL query that returns the possible refNames in a ?refName column',
25
+ },
26
+ refNames: {
27
+ type: 'stringArray',
28
+ defaultValue: [],
29
+ description:
30
+ 'Possible refNames used by the SPARQL endpoint (ignored if "refNamesQueryTemplate" is provided)',
31
+ },
32
+ additionalQueryParams: {
33
+ type: 'stringArray',
34
+ defaultValue: [],
35
+ description:
36
+ 'Additional parameters to add to the query, e.g. "format=JSON"',
37
+ },
38
+ },
39
+ { explicitlyTyped: true },
40
+ )
package/src/SPARQLAdapter/index.ts ADDED
@@ -0,0 +1,2 @@
1
+ export { default as AdapterClass } from './SPARQLAdapter'
2
+ export { default as configSchema } from './configSchema'
package/src/SPARQLAdapter/test_data/emptyQueryResponse.json ADDED
@@ -0,0 +1,30 @@
1
+ {
2
+ "head": {
3
+ "vars": [
4
+ "uniqueId",
5
+ "type",
6
+ "start",
7
+ "end",
8
+ "sub_uniqueId",
9
+ "sub_type",
10
+ "sub_start",
11
+ "sub_end",
12
+ "sub_sub_uniqueId",
13
+ "sub_sub_type",
14
+ "sub_sub_start",
15
+ "sub_sub_end",
16
+ "faldo_type",
17
+ "strand",
18
+ "sub_strand",
19
+ "sub_sub_strand",
20
+ "name",
21
+ "description",
22
+ "sub_name",
23
+ "sub_description",
24
+ "sub_class"
25
+ ]
26
+ },
27
+ "results": {
28
+ "bindings": []
29
+ }
30
+ }