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Rank name/level values in DB vs reported ranks #10

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dingosky opened this issue Feb 19, 2025 · 1 comment
Open

Rank name/level values in DB vs reported ranks #10

dingosky opened this issue Feb 19, 2025 · 1 comment

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@dingosky
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There look to be discrepancies between Concept rank level:name pairs in the DB with those deemed permissible via /v1/concept/ranks. I happened to hit this issue using the Concept below and have no idea if this is one-off or not.

To reproduce, use Concept Heterokonta:

GET /v1/concept/Heterokonta:

{
  "name": "Heterokonta",
  "alternateNames": [],
  "media": [],
  "linkRealizations": [],
  "rank": "infrakingdom",
  "rankName": "kingdom",
  "rankLevel": "infra",
  "author": "Cavalier-Smith, 1995",
  "aphiaId": null,
  "references": [],
  "id": 4924
}

The following entry is not in the return for /v1/concept/ranks:

{
    "rankLevel": "infra",
    "rankName": "kingdom"
}

I plead layman's ignorance as to who is right.

CAVEATS:

  • I am using the latest DB that is included with the m3-quickstart. It may be this is not a real production issue.
  • I actually hit this with a different Concept a few days ago, but discovered that was due to my using a DB I had done interim development against, and the issue then was a previous allowance of creating invalid rank level:name pairs (this was before the ranks call was implemented). I reloaded all of m3-quickstart at that time to "clear" the issue, but alas, hit it again, this time without any front-end shenanigans.
hohonuuli added a commit to mbari-org/oni that referenced this issue Feb 19, 2025
@hohonuuli
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hohonuuli commented Feb 19, 2025

It's hard to find the definitive list of taxa ranks :-(. But it looks like infra kingdom is actually a thing: https://www.marinespecies.org/aphia.php?p=taxdetails&id=368898

I've updated the taxa ranks, hopefully we've got them all covered now. docker pull mbari/oni. You should be at v0.4.11

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