INCATools / INCATools/ontology-access-kit
Search behavior on obo files not as expected
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
I noticed this first when going through the tutorials and running search via the cli:
```sh
runoak --input obolibrary:fbbt.obo search 'wing vein'
```
What is expected in the tutorial is:
```sh
FBbt:00004751 ! wing vein
FBbt:00004754 ! axillary vein
FBbt:00004759 ! wing vein L1
FBbt:00004760 ! wing vein L2
```
But what is returned by OAK is:
```sh
FBbt:00004751 ! wing vein
```
This behavior is seen on:
- `main` (ref `9bd64d9`)
- v0.1.19
After a bit of tinkering I realized that this might be because the default search behavior might have changed from `SearchTermSyntax.REGULAR_EXPRESSION` to `SearchTermSyntax.STARTS_WITH`.
Contributor guide
Research direction
Start by running the documented `runoak --input obolibrary:fbbt.obo search 'wing vein'` command and inspect the default handling of `SearchTermSyntax.REGULAR_EXPRESSION` versus `SearchTermSyntax.STARTS_WITH`. Compare the result with the four expected tutorial matches; done means the CLI returns those matches on main and v0.1.19 behavior is understood or corrected.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, search
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100