INCATools / INCATools/ontology-access-kit

Resolve sqlite handling differences when using Semsimian and when on Windows

Open
#638 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
198
Forks
35
Avg merge
3d 4h
Merged PRs (30d)
1

Description

At present, OAK semsim operations using Semsimian pass a sqlite resource path to Semsimian, where the DB is actually loaded.
#631 covers some of this, but it's kind of messy - ideally, OAK will just pass the filepath to Semsimian and then it will be processed accordingly.
The current approach also breaks in Windows as the filepath isn't parsed in the way Semsimian expects.

@cmungall says:

> I’m a bit worried about the logic. It will work but it’s odd, as you either have one strategy or the other:
> 1. it’s the job of OAK to query sqlite and pass those to semsimian (caching results)
> 2. oak just passes the sqlite handle to rust and says “you handle it all”
> ...
> ideally it would be a prioritization scheme so it uses 2 if a sqlite is being wrapped, otherwise defers to 1

Contributor guide

Open the contributing guide

Research direction

Start by tracing OAK semsim operations that use Semsimian and the Semsimian sqlite resource-path handling described in the issue. Compare the current path behavior on Windows with other platforms and resolve whether OAK passes a filepath or delegates through a sqlite handle. Done means sqlite-backed Semsim operations use a consistent strategy without Windows path parsing failures.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, rust, sqlite
Domain
backend-api-design, databases
Issue type
Bug
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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