fix(generators): add --normalize-prefixes flag for well-known prefix names

packages/linkml/src/linkml/generators/jsonldcontextgen.py

@@ -15,7 +15,7 @@
 
 from linkml._version import __version__
 from linkml.utils.deprecation import deprecated_fields
-from linkml.utils.generator import Generator, shared_arguments
+from linkml.utils.generator import Generator, shared_arguments, well_known_prefix_map
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
 from linkml_runtime.linkml_model.types import SHEX
 from linkml_runtime.utils.formatutils import camelcase, underscore
@@ -66,6 +66,9 @@ class ContextGenerator(Generator):
     frame_root: str | None = None
 
     def __post_init__(self) -> None:
+        # Must be set before super().__post_init__() because the parent triggers
+        # the visitor pattern (visit_schema), which accesses _prefix_remap.
+        self._prefix_remap: dict[str, str] = {}
         super().__post_init__()
         if self.namespaces is None:
             raise TypeError("Schema text must be supplied to context generator.  Preparsed schema will not work")
@@ -80,22 +83,92 @@ def __post_init__(self) -> None:
             self._local_classes = set(sv.all_classes(imports=False).keys())
             self._local_slots = set(sv.all_slots(imports=False).keys())
 
+    def add_prefix(self, ncname: str) -> None:
+        """Add a prefix, applying well-known prefix normalisation when enabled."""
+        super().add_prefix(self._prefix_remap.get(ncname, ncname))
+
     def visit_schema(self, base: str | Namespace | None = None, output: str | None = None, **_):
-        # Add any explicitly declared prefixes
+        # Add any explicitly declared prefixes.
+        # Direct .add() is safe here: the normalisation block below explicitly
+        # rewrites emit_prefixes entries for any renamed prefixes (Cases 1-3).
         for prefix in self.schema.prefixes.values():
             self.emit_prefixes.add(prefix.prefix_prefix)
 
         # Add any prefixes explicitly declared
         for pfx in self.schema.emit_prefixes:
             self.add_prefix(pfx)
 
+        # Normalise well-known prefix names when --normalize-prefixes is set.
+        # If the schema declares a non-standard alias for a namespace that has
+        # a well-known standard name (e.g. ``sdo`` for
+        # ``https://schema.org/``), replace the alias with the standard name
+        # so that generated JSON-LD contexts use the conventional prefix.
+        #
+        # Three cases are handled:
+        # 1. Standard prefix is not yet bound → just rebind from old to new.
+        # 2. Standard prefix is bound to a *different* URI:
+        #    a. User-declared (in schema.prefixes) → collision, skip with warning.
+        #    b. Runtime default (e.g. linkml-runtime's ``schema: http://…``)
+        #       → remove stale binding, then rebind.
+        # 3. Standard prefix is already bound to the *same* URI (duplicate)
+        #    → just drop the non-standard alias.
+        #
+        # A remap dict is stored for ``_build_element_id`` because
+        # ``prefix_suffix()`` splits CURIEs on ``:`` without looking up the
+        # namespace dict.
+        self._prefix_remap.clear()
+        if self.normalize_prefixes:
+            wk = well_known_prefix_map()
+            for old_pfx in list(self.namespaces):
+                url = str(self.namespaces[old_pfx])
+                std_pfx = wk.get(url)
+                if not std_pfx or std_pfx == old_pfx:
+                    continue
+                if std_pfx in self.namespaces:
+                    if str(self.namespaces[std_pfx]) != url:
+                        # Case 2: std_pfx is bound to a different URI.
+                        # If the user explicitly declared std_pfx in the schema,
+                        # it is intentional — skip to avoid data loss.
+                        if std_pfx in self.schema.prefixes:
+                            self.logger.warning(
+                                "Prefix collision: cannot rename '%s' to '%s' because '%s' is "
+                                "already declared for <%s>; skipping normalisation for <%s>",
+                                old_pfx,
+                                std_pfx,
+                                std_pfx,
+                                str(self.namespaces[std_pfx]),
+                                url,
+                            )
+                            continue
+                        # Not user-declared (e.g. linkml-runtime default) — safe to remove
+                        self.emit_prefixes.discard(std_pfx)
+                        del self.namespaces[std_pfx]
+                    else:
+                        # Case 3: standard prefix already bound to same URI
+                        # — just drop the non-standard alias
+                        del self.namespaces[old_pfx]
+                        if old_pfx in self.emit_prefixes:
+                            self.emit_prefixes.discard(old_pfx)
+                            self.emit_prefixes.add(std_pfx)
+                        self._prefix_remap[old_pfx] = std_pfx
+                        continue
+                # Case 1 (or Case 2 after stale removal): bind standard name
+                self.namespaces[std_pfx] = self.namespaces[old_pfx]
+                del self.namespaces[old_pfx]
+                if old_pfx in self.emit_prefixes:
+                    self.emit_prefixes.discard(old_pfx)
+                    self.emit_prefixes.add(std_pfx)
+                self._prefix_remap[old_pfx] = std_pfx
+
         # Add the default prefix
         if self.schema.default_prefix:
             dflt = self.namespaces.prefix_for(self.schema.default_prefix)
             if dflt:
                 self.default_ns = dflt
             if self.default_ns:
                 default_uri = self.namespaces[self.default_ns]
+                # Direct .add() is safe: default_ns is already resolved from
+                # the (possibly normalised) namespace bindings above.
                 self.emit_prefixes.add(self.default_ns)
             else:
                 default_uri = self.schema.default_prefix
@@ -310,6 +383,11 @@ def _build_element_id(self, definition: Any, uri: str) -> None:
         @return: None
         """
         uri_prefix, uri_suffix = self.namespaces.prefix_suffix(uri)
+        # Apply well-known prefix normalisation (e.g. sdo → schema).
+        # prefix_suffix() splits CURIEs on ':' without checking the
+        # namespace dict, so it may return a stale alias.
+        if uri_prefix and uri_prefix in self._prefix_remap:
+            uri_prefix = self._prefix_remap[uri_prefix]
         is_default_namespace = uri_prefix == self.context_body["@vocab"] or uri_prefix == self.namespaces.prefix_for(
             self.context_body["@vocab"]
         )

packages/linkml/src/linkml/generators/jsonldgen.py

@@ -178,6 +178,11 @@ def end_schema(self, context: str | Sequence[str] | None = None, context_kwargs:
             # TODO: The _visit function above alters the schema in situ
             # force some context_kwargs
             context_kwargs["metadata"] = False
+            # Forward generator flags so prefix normalisation and deterministic
+            # output propagate into the inline @context produced for JSON-LD.
+            for flag in ("normalize_prefixes", "deterministic"):
+                if hasattr(self, flag):
+                    context_kwargs.setdefault(flag, getattr(self, flag))
             add_prefixes = ContextGenerator(self.original_schema, **context_kwargs).serialize()
             add_prefixes_json = loads(add_prefixes)
             metamodel_ctx = self.metamodel_context or METAMODEL_CONTEXT_URI

packages/linkml/src/linkml/generators/owlgen.py

@@ -20,7 +20,7 @@
 from linkml import METAMODEL_NAMESPACE_NAME
 from linkml._version import __version__
 from linkml.utils.deprecation import deprecation_warning
-from linkml.utils.generator import Generator, shared_arguments
+from linkml.utils.generator import Generator, normalize_graph_prefixes, shared_arguments
 from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model.meta import (
     AnonymousClassExpression,
@@ -233,6 +233,10 @@ def as_graph(self) -> Graph:
             self.graph.bind(prefix, self.metamodel.namespaces[prefix])
         for pfx in schema.prefixes.values():
             self.graph.namespace_manager.bind(pfx.prefix_prefix, URIRef(pfx.prefix_reference))
+        if self.normalize_prefixes:
+            normalize_graph_prefixes(
+                graph, {str(v.prefix_prefix): str(v.prefix_reference) for v in schema.prefixes.values()}
+            )
         graph.add((base, RDF.type, OWL.Ontology))
 
         # Add main schema elements

packages/linkml/src/linkml/generators/shaclgen.py

@@ -13,7 +13,7 @@
 from linkml.generators.common.subproperty import get_subproperty_values, is_uri_range
 from linkml.generators.shacl.shacl_data_type import ShaclDataType
 from linkml.generators.shacl.shacl_ifabsent_processor import ShaclIfAbsentProcessor
-from linkml.utils.generator import Generator, shared_arguments
+from linkml.utils.generator import Generator, normalize_graph_prefixes, shared_arguments
 from linkml_runtime.linkml_model.meta import ClassDefinition, ElementName
 from linkml_runtime.utils.formatutils import underscore
 from linkml_runtime.utils.yamlutils import TypedNode, extended_float, extended_int, extended_str
@@ -105,6 +105,10 @@ def as_graph(self) -> Graph:
 
         for pfx in self.schema.prefixes.values():
             g.bind(str(pfx.prefix_prefix), pfx.prefix_reference)
+        if self.normalize_prefixes:
+            normalize_graph_prefixes(
+                g, {str(v.prefix_prefix): str(v.prefix_reference) for v in self.schema.prefixes.values()}
+            )
 
         for c in sv.all_classes(imports=not self.exclude_imports).values():
 

packages/linkml/src/linkml/utils/generator.py

@@ -20,11 +20,12 @@
 import os
 import re
 import sys
+import types
 from collections.abc import Callable, Mapping
 from dataclasses import dataclass, field
 from functools import lru_cache
 from pathlib import Path
-from typing import ClassVar, TextIO, Union, cast
+from typing import TYPE_CHECKING, ClassVar, TextIO, Union, cast
 
 import click
 from click import Argument, Command, Option
@@ -58,6 +59,9 @@
 from linkml_runtime.utils.formatutils import camelcase, underscore
 from linkml_runtime.utils.namespaces import Namespaces
 
+if TYPE_CHECKING:
+    from rdflib import Graph
+
 logger = logging.getLogger(__name__)
 
 
@@ -78,6 +82,138 @@ def _resolved_metamodel(mergeimports):
     return metamodel
 
 
+def well_known_prefix_map() -> dict[str, str]:
+    """Return a mapping from namespace URI to standard prefix name.
+
+    Uses a frozen, version-independent map derived from rdflib 7.x curated
+    defaults (which align with the `prefix.cc <https://prefix.cc>`_ community
+    consensus registry).  The map is **not** computed at runtime from
+    ``Graph().namespaces()`` because those defaults can change across rdflib
+    releases (they differ between 6.x and 7.x), which would silently alter
+    generator output.
+
+    This allows generators to normalise non-standard prefix aliases
+    (e.g. ``sdo`` for ``https://schema.org/``) to their conventional names.
+
+    Both ``http`` and ``https`` variants of schema.org are included because
+    the linkml-runtime historically binds ``schema: http://schema.org/``
+    while rdflib (and the W3C) prefer ``https://schema.org/``.
+    """
+    return dict(_WELL_KNOWN_PREFIX_MAP)
+
+
+# Frozen, version-independent map: namespace URI → canonical prefix name.
+# Source: rdflib 7.x defaults, cross-checked against https://prefix.cc
+_WELL_KNOWN_PREFIX_MAP: types.MappingProxyType[str, str] = types.MappingProxyType(
+    {
+        "https://brickschema.org/schema/Brick#": "brick",
+        "http://www.w3.org/ns/csvw#": "csvw",
+        "http://purl.org/dc/elements/1.1/": "dc",
+        "http://purl.org/dc/dcam/": "dcam",
+        "http://www.w3.org/ns/dcat#": "dcat",
+        "http://purl.org/dc/dcmitype/": "dcmitype",
+        "http://purl.org/dc/terms/": "dcterms",
+        "http://usefulinc.com/ns/doap#": "doap",
+        "http://xmlns.com/foaf/0.1/": "foaf",
+        "http://www.opengis.net/ont/geosparql#": "geo",
+        "http://www.w3.org/ns/odrl/2/": "odrl",
+        "http://www.w3.org/ns/org#": "org",
+        "http://www.w3.org/2002/07/owl#": "owl",
+        "http://www.w3.org/ns/dx/prof/": "prof",
+        "http://www.w3.org/ns/prov#": "prov",
+        "http://purl.org/linked-data/cube#": "qb",
+        "http://www.w3.org/1999/02/22-rdf-syntax-ns#": "rdf",
+        "http://www.w3.org/2000/01/rdf-schema#": "rdfs",
+        "https://schema.org/": "schema",
+        "http://schema.org/": "schema",  # HTTP variant (linkml-runtime uses this)
+        "http://www.w3.org/ns/shacl#": "sh",
+        "http://www.w3.org/2004/02/skos/core#": "skos",
+        "http://www.w3.org/ns/sosa/": "sosa",
+        "http://www.w3.org/ns/ssn/": "ssn",
+        "http://www.w3.org/2006/time#": "time",
+        "http://purl.org/vocab/vann/": "vann",
+        "http://rdfs.org/ns/void#": "void",
+        "https://www.w3.org/2003/01/geo/wgs84_pos#": "wgs",
+        "http://www.w3.org/2003/01/geo/wgs84_pos#": "wgs",  # HTTP variant (W3C canonical)
+        "http://www.w3.org/XML/1998/namespace": "xml",
+        "http://www.w3.org/2001/XMLSchema#": "xsd",
+    }
+)
+
+
+def normalize_graph_prefixes(graph: "Graph", schema_prefixes: dict[str, str]) -> None:
+    """Normalise non-standard prefix aliases in an rdflib Graph.
+
+    For each prefix bound in *schema_prefixes* (mapping prefix name →
+    namespace URI), check whether ``well_known_prefix_map()`` knows a
+    standard name for that URI.  If the standard name differs from the
+    schema-declared name, rebind the namespace to the standard name.
+
+    This is the **shared implementation** used by OWL, SHACL, and (via a
+    different code-path) JSON-LD context generators so that all serialisation
+    formats agree on prefix names when ``--normalize-prefixes`` is active.
+
+    :param graph: rdflib Graph whose namespace bindings should be adjusted.
+    :param schema_prefixes: mapping of prefix name → namespace URI string,
+        typically from ``schema.prefixes``.
+    """
+    from rdflib import Namespace
+
+    wk = well_known_prefix_map()
+
+    # Phase 1: normalise schema-declared prefixes.
+    for old_pfx, ns_uri in schema_prefixes.items():
+        ns_str = str(ns_uri)
+        std_pfx = wk.get(ns_str)
+        if not std_pfx or std_pfx == old_pfx:
+            continue
+        # Collision: the user explicitly declared std_pfx for a different
+        # namespace — do not clobber their binding.
+        if std_pfx in schema_prefixes and schema_prefixes[std_pfx] != ns_str:
+            logger.warning(
+                "Prefix collision: cannot rename '%s' to '%s' because '%s' is already "
+                "declared for <%s>; skipping normalisation for <%s>",
+                old_pfx,
+                std_pfx,
+                std_pfx,
+                schema_prefixes[std_pfx],
+                ns_str,
+            )
+            continue
+        # Rebind: remove old prefix, add standard prefix.
+        # ``replace=True`` forces the new prefix even if the prefix name
+        # is already bound to a different namespace.
+        graph.bind(std_pfx, Namespace(ns_str), override=True, replace=True)
+
+    # Phase 2: normalise runtime-injected bindings (e.g. metamodel defaults).
+    # The linkml-runtime / rdflib may inject well-known namespaces under
+    # non-standard prefix names.  After Phase 1 rebinds schema-declared
+    # prefixes, orphaned runtime bindings can appear as ``schema1``, ``dc0``,
+    # etc.  Scan the graph's current bindings and fix any that map to a
+    # well-known namespace under a non-standard name, provided the standard
+    # name isn't already claimed by the user for a different namespace.
+    #
+    # Guard: if Phase 1 already bound std_pfx to a different URI (e.g.
+    # ``schema`` → ``https://schema.org/``), do not clobber it with the
+    # HTTP variant (``http://schema.org/``).  Build a snapshot of the
+    # current bindings after Phase 1 to detect this.
+    current_bindings = {str(p): str(n) for p, n in graph.namespaces()}
+    for pfx, ns in list(graph.namespaces()):
+        pfx_str, ns_str = str(pfx), str(ns)
+        std_pfx = wk.get(ns_str)
+        if not std_pfx or std_pfx == pfx_str:
+            continue
+        # Same collision check as Phase 1: respect user-declared prefixes.
+        if std_pfx in schema_prefixes and schema_prefixes[std_pfx] != ns_str:
+            continue
+        # Guard: if std_pfx is already bound to a different (correct) URI
+        # by Phase 1, do not overwrite it.  This prevents the HTTP variant
+        # of schema.org from clobbering the HTTPS binding.
+        if std_pfx in current_bindings and current_bindings[std_pfx] != ns_str:
+            continue
+        graph.bind(std_pfx, Namespace(ns_str), override=True, replace=True)
+
+
 @dataclass
 class Generator(metaclass=abc.ABCMeta):
     """
@@ -180,6 +316,12 @@ class Generator(metaclass=abc.ABCMeta):
     stacktrace: bool = False
     """True means print stack trace, false just error message"""
 
+    normalize_prefixes: bool = False
+    """True means normalise non-standard prefix aliases to well-known names
+    from the static ``_WELL_KNOWN_PREFIX_MAP`` (derived from rdflib 7.x
+    defaults / prefix.cc consensus).  E.g. ``sdo`` → ``schema`` for
+    ``https://schema.org/``."""
+
     include: str | Path | SchemaDefinition | None = None
     """If set, include extra schema outside of the imports mechanism"""
 
@@ -986,6 +1128,16 @@ def decorator(f: Command) -> Command:
                 callback=stacktrace_callback,
             )
         )
+        f.params.append(
+            Option(
+                ("--normalize-prefixes/--no-normalize-prefixes",),
+                default=False,
+                show_default=True,
+                help="Normalise non-standard prefix aliases to rdflib's curated default names "
+                "(e.g. sdo → schema for https://schema.org/). "
+                "Supported by OWL, SHACL, and JSON-LD Context generators.",
+            )
+        )
 
         return f