feat(generators): allow java/ts/owl gen via makefile

[noelmcloughlin]

This PR allows user to trigger java and typescript generators via config.env and make setup because user might want them but gen-project excludes. Additional user can re-trigger owl generator if linkml/linkml#1453 is an issue.

Changes are transparent to existing users.

Once owl bug is fixed and gen-project includes java/ts then most of this PR could be reverted.

[sierra-moxon]

Hi @noelmcloughlin - I'm confused at the difference between this PR and this one: https://github.com/linkml/linkml-project-cookiecutter/blob/main/%7B%7Bcookiecutter.project_name%7D%7D/config.yaml :) can you help me figure out why we need both config.env and config.yaml? (maybe its just ease of use for folks more comfortable with env file vs. yaml?)

[noelmcloughlin]

Ideally config.yaml is enough and make setup and make gendoc are exhaustive.

However there are 3 issues where expected behavior does not match actual.

• make setup does not generate typescript and java artifacts
• make gendoc ignores config.yaml (I think)
• there is a bug using with gen-owl + config.yaml (Parm 'owl: {metadata_profile: rdfs} in config.yaml error linkml#1453)

For long time I planned doing linkml demo to some colleagues, but working through few things first. So this project is good starting point - however, I would prefer not to maintain my own fork to address issues, so I proposed config.env as short term workaround.

I'm also willing to raise issues for above and link to this PR

[noelmcloughlin]

I corrupted my branch so closing - will have to redo