INCATools / INCATools/ontology-access-kit

Move ontology-term-usage into OAK

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

Description

https://github.com/INCATools/ontology-term-usage

Steps for implementation:

0. make sure you understand the OAK interface vs adapter/implementation interface
1. define a new interface TermUsageInterface
2. this will have a single method, get_term_usage
3. make a new data model, a simple one that has a TermUsage structure
4. spread the original OTU code across existing adapters, creating new ones where appropriate. We now have ubergraph too
5. Add a simple command `term-usage`. Note like all commands this will work on a single adapter
6. Write a wrapper command outside the main `runoak` CLI, this won't follow the runoak conventions of having a single backend, it will broadcast to all endpoints, choosing remote ones as default

This seems a lot but each step is small and this will ensure extensibility

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the OAK interface versus adapter/implementation interface, then inspect the original ontology-term-usage repository. Done means defining TermUsageInterface and its data model, distributing the functionality across adapters, adding the term-usage command, and providing the broadcast wrapper across endpoints.

Written by the indexing model from the issue text.

Assessment

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

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