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/term/labels fails to produce label for (some?) post-composed terms #199

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hlapp opened this issue Feb 19, 2020 · 2 comments
Open

/term/labels fails to produce label for (some?) post-composed terms #199

hlapp opened this issue Feb 19, 2020 · 2 comments
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@hlapp
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hlapp commented Feb 19, 2020

I thought in general /term/labels can now produce labels for pregenerated post-composed terms too? The following one (http://purl.org/phenoscape/expression?value=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000050%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0010709%3E) fails:

curl -X GET "https://kb.phenoscape.org/api/term/labels?iris=%5B%22http%3A%2F%2Fpurl.org%2Fphenoscape%2Fexpression%3Fvalue%3D%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000050%253E%2Bsome%2B%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0010709%253E%22%5D" -H "accept: application/json"

Same result with /term/label.

However, the /term/classification endpoint does produce a label:

curl -X GET "https://kb.phenoscape.org/api/term/classification?iri=http%3A%2F%2Fpurl.org%2Fphenoscape%2Fexpression%3Fvalue%3D%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000050%253E%2Bsome%2B%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0010709%253E" -H "accept: application/json"
{
  "label": "part of some pelvic complex",
  "subClassOf": [],
  "equivalentTo": [],
  "superClassOf": [
    {
      "@id": "http://purl.obolibrary.org/obo/UBERON_0010742",
      "label": "bone of pelvic complex"
    },
    {
      "@id": "http://purl.obolibrary.org/obo/UBERON_0001464",
      "label": "hip"
    },
    {
      "@id": "http://purl.obolibrary.org/obo/UBERON_0005609",
      "label": "iliac artery"
    },
    {
      "@id": "http://purl.obolibrary.org/obo/UBERON_0014792",
      "label": "musculature of pelvic complex"
    },
    {
      "@id": "http://purl.obolibrary.org/obo/UBERON_0004709",
      "label": "pelvic appendage"
    },
    {
      "@id": "http://purl.obolibrary.org/obo/UBERON_0001271",
      "label": "pelvic girdle region"
    },
    {
      "@id": "http://purl.obolibrary.org/obo/UBERON_0012476",
      "label": "skeleton of pelvic complex"
    }
  ],
  "@id": "http://purl.org/phenoscape/expression?value=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000050%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0010709%3E"
}
@hlapp hlapp added the bug label Feb 19, 2020
@hlapp
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hlapp commented Feb 23, 2020

This issue is true for the pre-generated phenotype post-compositions as well (and for which /term/classification also does produce a label).

hlapp added a commit to phenoscape/rphenoscape that referenced this issue Feb 23, 2020
Due to an issue in the KB API (phenoscape/phenoscape-kb-services#199)
the /term/labels endpoint fails for most (all?) post-compositions.
This works around this bug for now by trying /term/classification for
those IDs for which /term/labels fails.

Includes tests.
hlapp added a commit to phenoscape/rphenoscape that referenced this issue Feb 23, 2020
Due to an issue in the KB API (phenoscape/phenoscape-kb-services#199)
the /term/labels endpoint fails for most (all?) post-compositions.
This works around this bug for now by trying /term/classification for
those IDs for which /term/labels fails.

Includes tests.
@Shalsh23
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Shalsh23 commented May 18, 2020

Refer #196 for relevant discussion.

johnbradley pushed a commit to phenoscape/rphenoscape that referenced this issue Jan 28, 2021
Due to an issue in the KB API (phenoscape/phenoscape-kb-services#199)
the /term/labels endpoint fails for most (all?) post-compositions.
This works around this bug for now by trying /term/classification for
those IDs for which /term/labels fails.

Includes tests.
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