Stephan Heunis
b1114a6d47
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102 lines
5 KiB
Diff
102 lines
5 KiB
Diff
This patches shaclgen.py to allow improved handling of slot annotations, sh:order, and
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prefixes. Firstly, it introduces the --exclude-order flag that allows to completely
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disable the automatic assignment of the sh:order field to exported property shapes. See:
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https://github.com/psychoinformatics-de/shacl-vue/issues/107#issuecomment-2866073117
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Secondly, if the --exclude-order flag is not used, the patch prevents creation of faulty
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sh:order lists by prioritizing sh:order provided via annotation, since sh:order should
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just be a single numerical value. See for context:
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https://github.com/linkml/linkml/pull/2111#issuecomment-2116208229
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Then, for a similar reason as before, it only sets sh:path automatically if the value
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has not already been set via annotation.
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Lastly, it introduces the --include-stripped-prefixes flag which allows inclusion of
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prefixes that are unused and hence stripped during rdflib serialization. This makes it
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possible to specify namespaces in the prefixes section of a schema that should propagate
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to the exported SHACL for downstream use.
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--- shaclgen.py
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+++ shaclgen.py
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@@ -30,6 +30,10 @@ class ShaclGenerator(Generator):
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"""parameterized suffix to be appended. No suffix per default."""
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include_annotations: bool = False
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"""True means include all class / slot / type annotations in generated Node or Property shapes"""
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+ exclude_order: bool = False
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+ """True means exclude the automatic addition of sh:order to Property shapes"""
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+ include_stripped_prefixes: bool = False
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+ """True means include the unused prefixes that are typically stripped during rdflib graph serialization"""
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exclude_imports: bool = False
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"""If True, elements from imported ontologies won't be included in the generator's output"""
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generatorname = os.path.basename(__file__)
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@@ -53,6 +57,8 @@ class ShaclGenerator(Generator):
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def serialize(self, **args) -> str:
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g = self.as_graph()
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data = g.serialize(format="turtle" if self.format in ["owl", "ttl"] else self.format)
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+ if self.include_stripped_prefixes:
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+ data = self._add_stripped_prefixes(data)
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return data
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def as_graph(self) -> Graph:
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@@ -114,8 +120,6 @@ class ShaclGenerator(Generator):
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g.add((pnode, p, Literal(v)))
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prop_pv(SH.path, slot_uri)
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- prop_pv_literal(SH.order, order)
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- order += 1
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prop_pv_literal(SH.name, s.title)
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prop_pv_literal(SH.description, s.description)
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# minCount
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@@ -223,6 +227,18 @@ class ShaclGenerator(Generator):
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default_value = ifabsent_processor.process_slot(s, c)
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if default_value:
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prop_pv(SH.defaultValue, default_value)
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+
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+ # Add the order automatically unless the --exclude-order flag was supplied
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+ if not self.exclude_order:
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+ # sh:order may already have been added to the graph via annotations
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+ if not (pnode, SH.order, None) in g:
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+ prop_pv_literal(SH.order, order)
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+ order += 1
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+
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+ # sh:path may already have been added to the graph via annotations
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+ if not (pnode, SH.path, None) in g:
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+ prop_pv(SH.path, slot_uri)
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+
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return g
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@@ -337,6 +353,17 @@ class ShaclGenerator(Generator):
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Collection(g, list_node, list(ignored_properties))
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return list_node
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+
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+ def _add_stripped_prefixes(self, data):
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+ # First remove all prefix lines from data string
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+ lines = [ln for ln in data.splitlines() if not ln.strip().startswith("@prefix")]
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+ # Now generate alphabetized lines from all prefixes:
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+ prefix_lines = [
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+ f"@prefix {str(pfx.prefix_prefix)}: <{pfx.prefix_reference}> ."
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+ for pfx in sorted(self.schema.prefixes.values(), key=lambda p: str(p.prefix_prefix).lower())
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+ ]
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+ # return the new prefix lines joined with prefix-stripped data
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+ return "\n".join(prefix_lines + [""] + lines)
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def add_simple_data_type(func: Callable, r: ElementName) -> None:
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@@ -366,6 +393,19 @@ def add_simple_data_type(func: Callable, r: ElementName) -> None:
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show_default=True,
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help="Use --include-annotations to include annotations of slots, types, and classes in the generated SHACL shapes.",
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)
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+@click.option(
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+ "--exclude-order/--include-order",
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+ default=False,
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+ show_default=True,
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+ help="Use --exclude-order to exclude sh:order from being added automatically to generated SHACL property shapes. "
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+ "Default behavior adds order. This flag has no influence on sh:order being added via annotations.",
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+)
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+@click.option(
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+ "--include-stripped-prefixes/--exclude-stripped-prefixes",
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+ default=False,
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+ show_default=True,
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+ help="Use --include-stripped-prefixes to include prefixes that are unused and hence stripped during rdflib serialization.",
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+)
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@click.option(
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"--exclude-imports/--include-imports",
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default=False,
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