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
Open
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
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
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