fix(rdf): fix canonicalizer defects in base IRIs, fallback and JSON-LD

[jdsika]

Replaces linkml#3987, as requested there. It fixes the canonicalizer defects that the diffable-rdf comparison (linkml#3986, linkml#3987) recorded, in linkml_runtime.utils.rdf_canonicalize itself rather than by delegating to the library. There is no new dependency, and the diff_stable path is unchanged.

Fixes

Defect on main	Fix	Reference
A base IRI ending in # makes rdflib read relative references back as different IRIs (http://ex.org/d##a)	Declare the base without its fragment. On the rdflib fallback, keep the base only if the output reads back with the same absolute IRIs, because rdflib relativizes by string prefix	RFC 3986 §5.1, §5.2.2
N-Triples or N-Quads written for a relative IRI or a literal predicate, which no parser reads	ValueError. The fallback is taken because pyoxigraph's N-Triples parser refused exactly this text	N-Triples 1.1 §2.2
U+2028 in a literal breaks the fallback's line sort	The line sort is gone, because the fallback no longer writes line formats	—
Fallback Turtle and RDF/XML vary with the hash seed (statement order, ns1/ns2 names)	rdflib gets its statements, and names unbound namespaces, in sorted order	—
JSON-LD is not canonicalized	Serialized through pyoxigraph and indented. On the fallback, the node array is sorted	JSON-LD 1.1 §4.3 (non-normative: arrays convey no order by default)
The trailing newline differs by format	Exactly one	—
A Dataset is silently flattened	TypeError for context-aware graphs	—
JSON-LD with a base: rdflib relativizes @ids without declaring @base, so they resolve against the reader's location	pyoxigraph writes absolute IRIs. On the fallback, the base check drops the base	—
TriG on the fallback is written inside a graph named after a random blank node	Written as Turtle, which is TriG with every triple in the default graph, as on the pyoxigraph path	TriG §2.1
A shared rdf:List tail is written twice on the fallback	Fixed in rdflib (RDFLib/rdflib#3504, merged, not yet released). The test is a strict xfail for rdflib < 7.7	—

Behaviour changes

• nt and nquads raise ValueError for graphs pyoxigraph rejects, instead of returning text that no N-Triples parser accepts.
• A Dataset or ConjunctiveGraph raises TypeError. All generators and dumpers pass a plain Graph.
• JSON-LD output has canonical blank-node labels and writes rdf:type as a property rather than as @type. The RDF is the same.

Output

Run	Result
gen-owl, gen-shacl, gen-rdf and gen-shex --format rdf on the metamodel and personinfo	Turtle byte-identical to main
gen-shacl --include-annotations on the metamodel, the only generator run that reaches the fallback	One trailing blank line removed
gen-owl -f json-ld	Isomorphic to main's output (5,318 and 1,134 triples), and now identical across processes

Tests

New tests in test_rdf_canonicalize.py, each of which fails on main:

• An IRI written against a base reads back unchanged, for Turtle, N3, TriG, RDF/XML and JSON-LD, on both paths, with a base ending in # and one ending in /. 12 of these 20 cases fail on main.
• Cross-process determinism with four hash seeds: Turtle, N3, TriG, RDF/XML and JSON-LD on the fallback, and JSON-LD on the normal path.
• The line-format refusal, the newline, the Dataset refusal, and the shared list (strict xfail). fix(rdf): delegate canonicalization to the diffable-rdf library linkml/linkml#3987's defect file also passes against this module, except the shared list case, as expected with rdflib 7.6.

Two existing tests change:

• The unsupported-format test uses pretty-xml, because json-ld is now supported.
• The cross-process fallback test drops nt, which is now refused, and covers the formats above.

The PR also folds in the fixture cleanup from the linkml#3985 review: test_template_noblack uses mock_missing_import("black"), and mock_black_import is removed.

Local results: runtime suite 1,865 passed; compiler suite 12,393 passed; pre-commit clean.

Upstream and limitations

• rdflib changes that would let parts of the fallback handling go once released: fix: Turtle/longturtle collection syntax can silently corrupt shared RDF lists RDFLib/rdflib#3504 (shared list, merged), fix: resolve relative IRIs against a base without its fragment RDFLib/rdflib#3574 (base fragment in the Turtle parser), Relative IRI resolution and relativization deviate from RFC 3986 RDFLib/rdflib#3575 (relativization by string prefix), N-Triples serializer writes relative IRIs, producing output its own parser rejects RDFLib/rdflib#3544 and RDF/XML serializer output is not stable between processes; no canon equivalent RDFLib/rdflib#3545.
• gen-shacl --include-annotations writes an annotation tag without : as a literal predicate, which is not RDF. That is a separate generator defect.