INCATools / INCATools/ontology-access-kit

requesting a new `sqlite:obo:xyz` input only says "urllib.error.HTTPError: HTTP Error 404: Not Found" if an ontology with abbreviation xyz can't be found

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Dominant language
Python
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198
Forks
35
Avg merge
3d 4h
Merged PRs (30d)
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Description

For example, I couldn't retrieve the Experimental Factor Intology and had to figure it out for myself.

```shell
runoak --input sqlite:obo:efi info --output-type tsv .desc//p=i sequencer
```

> urllib.error.HTTPError: HTTP Error 404: Not Found

Contributor guide

Open the contributing guide

Research direction

Start by reproducing the `runoak --input sqlite:obo:efi` command and inspect the input handling behind the `sqlite:obo` scheme. Check how an unavailable ontology abbreviation such as `xyz` becomes an HTTP 404; done means the command reports which abbreviation or ontology could not be found instead of exposing only the raw urllib error.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, sqlite
Domain
cli
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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