INCATools / INCATools/ontology-access-kit

Search behavior on obo files not as expected

Open
#88 1 comment 0 reactions 0 assignees View on GitHub
bug
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

Open the contributing 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

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