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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.
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.
Because of phyloref/phyx.js#113, we need to include a baseIRI when generating n-Quads:
klados/src/components/sidebar/Sidebar.vue
Line 445 in 2e338c1
This issue a reminder to remove this once we fix this in phyx.js.
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