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The RDF canonicalizer in linkml_runtime was extracted into diffable-rdf, and the two copies diverged. Calling the library fixes nine defects of the in-tree copy, each asserted against both entry points in test_rdf_canonicalize_defects.py: - a base IRI ending in # no longer rewrites every IRI sharing its prefix - a shared rdf:List tail is no longer duplicated - N-Triples refuses a relative IRI instead of writing a file its own parser rejects; N-Triples allows only absolute IRIs - literals containing U+2028 and other line separators survive sorting - degraded RDF/XML, degraded Turtle and JSON-LD are byte-identical across processes - every format ends with exactly one newline - a Dataset is refused instead of silently flattened diffable-rdf becomes a required dependency of linkml-runtime. It needs only rdflib and pyoxigraph, which the runtime already requires. The diff-stable extras remain as aliases. Turtle output of the four RDF generators is unchanged. The library logs degraded output; the runtime re-emits those records as RDFCanonicalizationWarning so they stay visible without logging configuration. Signed-off-by: jdsika <carlo.van-driesten@vdl.digital>
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Mirror of linkml#3987, same head. Review there; this PR tracks the fork stack.
Stacked on #24. #25 is folded into this PR.
Summary
linkml_runtime.utils.rdf_canonicalizewas extracted into diffable-rdf at the maintainers' request (linkml#3295), and the two copies diverged. This PR deletes the in-tree copy and calls the library. That fixes nine defects in the RDF output of every generator and RDF dumper onmain:main@baseending in#rdf:ListtailValueError, as N-Triples §2.2 says: "IRIs may be written only as absolute IRIs".gen-owl -f json-ldon personinfo with two hash seeds.rdflib.DatasetEach defect is a test in
test_rdf_canonicalize_defects.py, run against bothlinkml_runtime's function and the library's.Dependency
diffable-rdfbecomes a required dependency oflinkml-runtime, because the default path needs it. Facts for that decision:rdflib>=6.3.2andpyoxigraph>=0.5.4.linkml-runtimealready requiresrdflib>=7.6.0andpyoxigraph>=0.5.11. The license is Apache-2.0.--diff-stablestays opt-in, as discussed on feat(rdf): add opt-in diff-stable blank-node labels linkml/linkml#3985. Thediff-stableextras remain as aliases.The library logs degraded output, and
linkml_runtimere-emits it asRDFCanonicalizationWarning, so the warning stays visible without any logging configuration.Output
For the metamodel and personinfo, the Turtle output of
gen-owl,gen-shacl,gen-rdfandgen-shex --format rdfis byte-identical before and after this PR. JSON-LD output is now deterministic, and its graph is unchanged (isomorphic, 1,134 triples).Testing
test_rdf_canonicalize_defects.pycovers the nine properties above. Before delegation, each of them failed for linkml and passed for the library.Fork stack: #24 → #26; #27 (docs) is based on #24.