Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Remove baseIRI from n-Quads generation #231

Open
gaurav opened this issue Jan 25, 2022 · 3 comments
Open

Remove baseIRI from n-Quads generation #231

gaurav opened this issue Jan 25, 2022 · 3 comments

Comments

@gaurav
Copy link
Member

gaurav commented Jan 25, 2022

Because of phyloref/phyx.js#113, we need to include a baseIRI when generating n-Quads:

wrapped.toRDF('https://example.org/phyx#').then((content) => {

This issue a reminder to remove this once we fix this in phyx.js.

@gaurav gaurav added this to the Klados v1.0 milestone Jan 25, 2022
gaurav added a commit that referenced this issue Feb 15, 2022
This PR upgrades @phyloref/phyx.js to the latest version, allowing us to use reference-based (model 2.0) expectations (#65) and to export the ontology in n-Quads (#222). A few phyx.js methods have been renamed or replaced since this code was written; this PR updates them so that phyloref resolution works again.

See #231 and #232 for some follow-up changes that will be needed after this PR.

Closes #65, closes #204, closes #222.
@gaurav
Copy link
Member Author

gaurav commented Aug 24, 2022

Need to review.

@gaurav
Copy link
Member Author

gaurav commented May 24, 2023

Both the "Export as ontology" button and the "Export as JSON-LD" button use this baseIRI, and I don't think there's an obvious way to work around this (see phyloref/phyx.js#113 for our efforts in phyx.js). I propose we make this configurable in the "Advanced" modal -- if a user wants to set this to blank and export a JSON-LD or n-triples file containing only relative references (e.g. #phylogeny0 instead of https://example.org/phyx#phylogeny0), they should be able to do that, but Protege insists on only reading files that contain full IRIs, which is why a base IRI is required.

@hlapp
Copy link
Member

hlapp commented May 24, 2023

Protege insists on only reading files that contain full IRIs, which is why a base IRI is required.

Should we document this somewhere so that in the future we and others can remember why this is there?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

2 participants