linkml 1.6.9__py3-none-any.whl → 1.6.11__py3-none-any.whl

linkml/generators/__init__.py

@@ -4,6 +4,7 @@ representation such as JsonSchema
 """
 
 from linkml.generators.javagen import JavaGenerator
+from linkml.generators.jsonldcontextgen import ContextGenerator
 from linkml.generators.jsonschemagen import JsonSchemaGenerator
 from linkml.generators.owlgen import OwlSchemaGenerator
 from linkml.generators.pydanticgen import PydanticGenerator
@@ -41,6 +42,7 @@ __all__ = [
     "PydanticGenerator",
     "PythonGenerator",
     "JavaGenerator",
+    "ContextGenerator",
     "JsonSchemaGenerator",
     "ShaclGenerator",
     "ShExGenerator",

linkml/generators/csvgen.py

@@ -1,6 +1,7 @@
 """
 Generate CSVs
 """
+
 import os
 import sys
 from csv import DictWriter

linkml/generators/dotgen.py

@@ -1,6 +1,7 @@
 """
 Generate dotfiles
 """
+
 import os
 from dataclasses import dataclass
 from typing import List, Optional

linkml/generators/golrgen.py

@@ -6,6 +6,7 @@ These can be converted to solr schema-xml, and used in amigo-bbop tools
 See the golr-views directory in this repo for examples
 
 """
+
 import os
 from dataclasses import dataclass
 from typing import List, Optional

linkml/generators/javagen.py

@@ -70,6 +70,7 @@ class JavaGenerator(OOCodeGenerator):
     generatorname = os.path.basename(__file__)
     generatorversion = "0.0.1"
     valid_formats = ["java"]
+    file_extension = "java"
 
     # ObjectVars
     generate_records: bool = False

linkml/generators/jsonldcontextgen.py

@@ -2,6 +2,7 @@
 Generate JSON-LD contexts
 
 """
+
 import os
 import re
 from dataclasses import dataclass, field
@@ -37,6 +38,7 @@ class ContextGenerator(Generator):
     visit_all_class_slots = False
     uses_schemaloader = True
     requires_metamodel = True
+    file_extension = "context.jsonld"
 
     # ObjectVars
     emit_prefixes: Set[str] = field(default_factory=lambda: set())

linkml/generators/jsonldgen.py

@@ -1,6 +1,7 @@
 """ Generate JSONld
 
 """
+
 import os
 from copy import deepcopy
 from dataclasses import dataclass
@@ -99,13 +100,15 @@ class JSONLDGenerator(Generator):
             return (
                 ClassDefinitionName(camelcase(node))
                 if node in self.schema.classes
-                else SlotDefinitionName(underscore(node))
-                if node in self.schema.slots
-                else SubsetDefinitionName(camelcase(node))
-                if node in self.schema.subsets
-                else TypeDefinitionName(underscore(node))
-                if node in self.schema.types
-                else None
+                else (
+                    SlotDefinitionName(underscore(node))
+                    if node in self.schema.slots
+                    else (
+                        SubsetDefinitionName(camelcase(node))
+                        if node in self.schema.subsets
+                        else TypeDefinitionName(underscore(node)) if node in self.schema.types else None
+                    )
+                )
             )
         return None
 

linkml/generators/jsonschemagen.py

@@ -193,6 +193,9 @@ class JsonSchemaGenerator(Generator):
     Note that if the range of a slot has a type designator, descendants will always be included.
     """
 
+    title_from: str = "name"
+    """The slot from which to populate JSONSchema title annotation."""
+
     top_level_schema: JsonSchema = None
 
     def __post_init__(self):
@@ -215,7 +218,7 @@ class JsonSchemaGenerator(Generator):
                 "$id": self.schema.id,
                 "metamodel_version": metamodel_version,
                 "version": self.schema.version if self.schema.version else None,
-                "title": self.schema.name,
+                "title": self.schema.title if self.title_from == "title" and self.schema.title else self.schema.name,
                 "type": "object",
                 "additionalProperties": self.not_closed,
             }
@@ -238,6 +241,8 @@ class JsonSchemaGenerator(Generator):
                 "description": be(cls.description),
             }
         )
+        if self.title_from == "title" and cls.title:
+            class_subschema["title"] = cls.title
 
         for slot_definition in self.schemaview.class_induced_slots(cls.name):
             self.handle_class_slot(subschema=class_subschema, cls=cls, slot=slot_definition)
@@ -364,6 +369,9 @@ class JsonSchemaGenerator(Generator):
                 "description": be(enum.description),
             }
         )
+        if self.title_from == "title" and enum.title:
+            enum_schema["title"] = enum.title
+
         if permissible_values_texts:
             enum_schema["enum"] = permissible_values_texts
         self.top_level_schema.add_def(enum.name, enum_schema)
@@ -480,6 +488,8 @@ class JsonSchemaGenerator(Generator):
                     prop = JsonSchema.array_of(prop)
 
         prop.add_keyword("description", slot.description)
+        if self.title_from == "title" and slot.title:
+            prop.add_keyword("title", slot.title)
 
         own_constraints = self.get_value_constraints_for_slot(slot)
 
@@ -569,9 +579,34 @@ class JsonSchemaGenerator(Generator):
         ]
         non_id_required_slots = [s for s in non_id_slots if s.required]
 
+        # Some lists of objects can be serialized as SimpleDicts.
+        # A SimpleDict is serialized as simple key-value pairs where the value is atomic.
+        # The key must be declared as a key, and the value must satisfy one of the following conditions:
+        # 1. The value slot is the only other slot in the object other than the key
+        # 2. The value slot is explicitly annotated as a simple_dict_value
+        # 3. The value slot is the only non-key that is required
+        # See also: https://github.com/linkml/linkml/issues/1250
         range_simple_dict_value_slot = None
         if len(non_id_slots) == 1:
             range_simple_dict_value_slot = non_id_slots[0]
+        elif len(non_id_slots) > 1:
+            candidate_non_id_slots = []
+            for non_id_slot in non_id_slots:
+                if isinstance(non_id_slot.annotations, dict):
+                    is_simple_dict_value = non_id_slot.annotations.get("simple_dict_value", False)
+                else:
+                    is_simple_dict_value = getattr(non_id_slot.annotations, "simple_dict_value", False)
+                if is_simple_dict_value:
+                    candidate_non_id_slots.append(non_id_slot)
+            if len(candidate_non_id_slots) == 1:
+                range_simple_dict_value_slot = candidate_non_id_slots[0]
+            else:
+                candidate_non_id_slots = []
+                for non_id_slot in non_id_slots:
+                    if non_id_slot.required:
+                        candidate_non_id_slots.append(non_id_slot)
+                if len(candidate_non_id_slots) == 1:
+                    range_simple_dict_value_slot = candidate_non_id_slots[0]
 
         return range_class_id_slot, range_simple_dict_value_slot, non_id_required_slots
 
@@ -619,6 +654,14 @@ If this is a positive number the resulting JSON will be pretty-printed with that
 disable pretty-printing and return the most compact JSON representation
 """,
 )
+@click.option(
+    "--title-from",
+    type=click.Choice(["name", "title"], case_sensitive=False),
+    default="name",
+    help="""
+Specify from which slot are JSON Schema 'title' annotations generated.
+""",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **kwargs):
     """Generate JSON Schema representation of a LinkML model"""

linkml/generators/markdowngen.py

@@ -456,11 +456,11 @@ class MarkdownGenerator(Generator):
         filename = (
             self.formatted_element_name(obj)
             if isinstance(obj, ClassDefinition)
-            else underscore(obj.name)
-            if isinstance(obj, SlotDefinition)
-            else underscore(obj.name)
-            if isinstance(obj, EnumDefinition)
-            else camelcase(obj.name)
+            else (
+                underscore(obj.name)
+                if isinstance(obj, SlotDefinition)
+                else underscore(obj.name) if isinstance(obj, EnumDefinition) else camelcase(obj.name)
+            )
         )
         subdir = "/types" if isinstance(obj, TypeDefinition) and not self.no_types_dir else ""
         return f"{self.directory}{subdir}/{filename}.md"

linkml/generators/owlgen.py

@@ -1,4 +1,5 @@
 """Generate OWL ontology representation of a LinkML schema."""
+
 import logging
 import os
 from collections import defaultdict
@@ -499,7 +500,7 @@ class OwlSchemaGenerator(Generator):
                     elif range in sv.all_enums():
                         x = self._enum_uri(range)
                     elif range in sv.all_classes():
-                        x = self._enum_uri(range)
+                        x = self._class_uri(range)
                     else:
                         raise ValueError(f"Unknown range {range}")
                         # x = self._class_uri(range)
@@ -530,6 +531,9 @@ class OwlSchemaGenerator(Generator):
                 graph.add((max_card_expr, RDF.type, OWL.Restriction))
                 graph.add((max_card_expr, OWL.maxCardinality, Literal(1)))
                 graph.add((max_card_expr, OWL.onProperty, slot_uri))
+            if slot.has_member:
+                has_member_expr = self.transform_class_slot_expression(cls, slot.has_member, slot)
+                owl_exprs.append(self._some_values_from(slot_uri, has_member_expr))
         return self._intersection_of(owl_exprs)
 
     def slot_node_owltypes(self, slot: Union[SlotDefinition, AnonymousSlotExpression]) -> Set[URIRef]:
@@ -571,18 +575,8 @@ class OwlSchemaGenerator(Generator):
 
         owl_exprs = []
 
-        if slot.has_member:
-            owl_exprs.append(
-                self._union_of(
-                    [self.transform_class_slot_expression(cls, x, main_slot, owl_types) for x in slot.has_member]
-                )
-            )
         if slot.all_members:
-            owl_exprs.append(
-                self._union_of(
-                    [self.transform_class_slot_expression(cls, x, main_slot, owl_types) for x in slot.all_members]
-                )
-            )
+            owl_exprs.append(self.transform_class_slot_expression(cls, slot.all_members, main_slot, owl_types))
 
         if slot.any_of:
             owl_exprs.append(
@@ -1219,6 +1213,12 @@ class OwlSchemaGenerator(Generator):
     show_default=True,
     help="If true, then mixins are represented as existential expressions",
 )
+@click.option(
+    "--use-native-uris/--no-use-native-uris",
+    default=True,
+    show_default=True,
+    help="Use model URIs rather than class/slot URIs",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, metadata_profile: str, **kwargs):
     """Generate an OWL representation of a LinkML model
@@ -1238,7 +1238,8 @@ def cli(yamlfile, metadata_profile: str, **kwargs):
         metadata_profiles = [MetadataProfile(metadata_profile)]
     else:
         metadata_profiles = [MetadataProfile.linkml]
-    print(OwlSchemaGenerator(yamlfile, metadata_profiles=metadata_profiles, **kwargs).serialize(**kwargs))
+    gen = OwlSchemaGenerator(yamlfile, metadata_profiles=metadata_profiles, **kwargs)
+    print(gen.serialize(**kwargs))
 
 
 if __name__ == "__main__":

linkml/generators/plantumlgen.py

@@ -3,6 +3,7 @@
 https://plantuml.com/
 
 """
+
 import base64
 import os
 import zlib

linkml/generators/prefixmapgen.py

@@ -2,6 +2,7 @@
 Generate JSON-LD contexts
 
 """
+
 import csv
 import os
 from dataclasses import dataclass, field

linkml/generators/rdfgen.py

@@ -4,6 +4,7 @@ YAML Schema to RDF Generator
 Generate a JSON LD representation of the model
 
 """
+
 import os
 import urllib.parse as urlparse
 from dataclasses import dataclass, field

linkml/generators/shaclgen.py

@@ -116,6 +116,7 @@ class ShaclGenerator(Generator):
                     prop_pv_literal(SH.minCount, 1)
                 prop_pv_literal(SH.minInclusive, s.minimum_value)
                 prop_pv_literal(SH.maxInclusive, s.maximum_value)
+                prop_pv_literal(SH.hasValue, s.equals_number)
                 r = s.range
                 if r in sv.all_classes():
                     range_ref = sv.get_uri(r, expand=True)

linkml/generators/shexgen.py

@@ -1,6 +1,7 @@
 """Generate ShEx definition of a model
 
 """
+
 import os
 import urllib.parse as urlparse
 from dataclasses import dataclass, field

linkml/generators/sqlddlgen.py

@@ -1,4 +1,5 @@
 """DEPRECATED: Use SQLTableGenerator instead"""
+
 import logging
 import os
 from contextlib import redirect_stdout

linkml/generators/summarygen.py

@@ -1,6 +1,7 @@
 """Generate Summary Spreadsheets
 
 """
+
 import os
 import sys
 from csv import DictWriter

linkml/generators/yamlgen.py

@@ -1,6 +1,7 @@
 """Validate linkml input and optionally emit completely resolved biolink yaml output
 
 """
+
 import os
 from dataclasses import dataclass, field
 

linkml/generators/yumlgen.py

@@ -3,6 +3,7 @@
 https://yuml.me/diagram/scruffy/class/samples
 
 """
+
 import os
 from dataclasses import dataclass, field
 from typing import Callable, List, Optional, Set, cast

linkml/transformers/logical_model_transformer.py

@@ -12,6 +12,7 @@ of constraints in both classes hold.
 These logical constraints are then simplified by translating to disjunctive normal form,
 and applying simplification rules.
 """
+
 import logging
 from copy import deepcopy
 from dataclasses import dataclass

linkml/utils/generator.py

@@ -14,6 +14,7 @@ New generators should always using the latter approach
 See: https://github.com/linkml/linkml/issues/923
 
 """
+
 import abc
 import logging
 import os
@@ -453,9 +454,11 @@ class Generator(metaclass=abc.ABCMeta):
         return (
             None
             if element.is_a is None
-            else self.schema.classes[element.is_a]
-            if isinstance(element, ClassDefinition)
-            else self.schema.slots[element.is_a]
+            else (
+                self.schema.classes[element.is_a]
+                if isinstance(element, ClassDefinition)
+                else self.schema.slots[element.is_a]
+            )
         )
 
     def ancestors(self, element: Union[ClassDefinition, SlotDefinition]) -> List[ElementName]:
@@ -904,7 +907,7 @@ def shared_arguments(g: Type[Generator]) -> Callable[[Command], Command]:
                 ("--useuris/--metauris",),
                 default=True,
                 show_default=True,
-                help="Include metadata in output",
+                help="Use class and slot URIs over model uris",
             )
         )
         f.params.append(Option(("--importmap", "-im"), type=click.File(), help="Import mapping file"))

linkml/utils/ifabsent_functions.py

@@ -113,7 +113,13 @@ default_library: List[
 
 def isabsent_match(
     txt: Text,
-) -> Optional[Tuple[Match[str], bool, Callable[[Match[str], SchemaLoader, ClassDefinition, SlotDefinition], str],]]:
+) -> Optional[
+    Tuple[
+        Match[str],
+        bool,
+        Callable[[Match[str], SchemaLoader, ClassDefinition, SlotDefinition], str],
+    ]
+]:
     txt = str(txt)
     for pattern, postinit, f in default_library:
         m = re.match(pattern + "$", txt)

linkml/utils/schemasynopsis.py

@@ -120,13 +120,11 @@ class SchemaSynopsis:
         self.add_ref(
             SlotType,
             k,
-            ClassType
-            if v.range in self.schema.classes
-            else EnumType
-            if v.range in self.schema.enums
-            else TypeType
-            if v.range in self.schema.types
-            else None,
+            (
+                ClassType
+                if v.range in self.schema.classes
+                else EnumType if v.range in self.schema.enums else TypeType if v.range in self.schema.types else None
+            ),
             v.range,
         )
 

linkml/validator/__init__.py

@@ -3,6 +3,7 @@ The ``linkml.validator`` package contains a new LinkML validation framework that
 than the ``linkml.validators`` package. While that package still exists, it may become deprecated
 in the future.
 """
+
 import os
 from pathlib import Path
 from typing import Any, Optional, Union

linkml/validator/loaders/__init__.py

@@ -4,6 +4,7 @@ instance from a source. Instances of these classes are passed to
 :meth:`linkml.validator.Validator.validate_source` and
 :meth:`linkml.validator.Validator.iter_results_from_source`
 """
+
 import os
 from typing import Union
 

linkml/validator/plugins/shacl_validation_plugin.py

@@ -0,0 +1,93 @@
+import os
+from typing import Any, Iterator, Optional
+
+import rdflib
+from linkml_runtime.dumpers import rdflib_dumper
+
+from linkml.generators import PythonGenerator, ShaclGenerator
+from linkml.validator.plugins.validation_plugin import ValidationPlugin
+from linkml.validator.report import Severity, ValidationResult
+from linkml.validator.validation_context import ValidationContext
+
+SH = rdflib.Namespace("http://www.w3.org/ns/shacl#")
+
+
+class ShaclValidationPlugin(ValidationPlugin):
+    """A validation plugin which validates instances using SHACL.
+
+    :param shacl_path: If provided, SHACL will not be generated from the schema,
+        instead it will be read from this path.
+    :param closed: If ``True``, additional properties are not allowed on instances.
+        Defaults to ``False``.
+    :param raise_on_conversion_error: If ``True``, raise an exception if the instance
+        cannot be converted to a Python class. Otherwise, treat as a ValidationError.
+        Defaults to ``False``.
+    """
+
+    def __init__(
+        self,
+        *,
+        closed: bool = False,
+        shacl_path: Optional[os.PathLike] = None,
+        raise_on_conversion_error: bool = False,
+    ) -> None:
+        self.closed = closed
+        self.shacl_path = shacl_path
+        self.raise_on_conversion_error = raise_on_conversion_error
+
+    def _shacl_graph(self, context: ValidationContext) -> Optional[rdflib.Graph]:
+        g = rdflib.Graph()
+        if self.shacl_path:
+            g.parse(str(self.shacl_path))
+        else:
+            gen = ShaclGenerator(context._schema)
+            g = gen.as_graph()
+        return g
+
+    def process(self, instance: Any, context: ValidationContext) -> Iterator[ValidationResult]:
+        """Perform JSON Schema validation on the provided instance
+
+        :param instance: The instance to validate
+        :param context: The validation context which provides a JSON Schema artifact
+        :return: Iterator over validation results
+        :rtype: Iterator[ValidationResult]
+        """
+        import pyshacl
+
+        shacl_graph = self._shacl_graph(context)
+        if isinstance(instance, dict):
+            pygen = PythonGenerator(context._schema)
+            mod = pygen.compile_module()
+            py_cls = getattr(mod, context._target_class)
+            if self.raise_on_conversion_error:
+                instance = py_cls(**instance)
+            else:
+                try:
+                    instance = py_cls(**instance)
+                except (ValueError, TypeError):
+                    yield ValidationResult(
+                        type="shacl validation",
+                        severity=Severity.ERROR,
+                        instance=instance,
+                        instantiates=context.target_class,
+                        message="failed at class instantiation stage",
+                    )
+                    return
+        data_graph = rdflib_dumper.as_rdf_graph(instance, schemaview=context.schema_view)
+        validator = pyshacl.Validator(
+            shacl_graph=shacl_graph,
+            data_graph=data_graph,
+            inference="rdfs",
+        )
+        conforms, report_graph, report_text = validator.run()
+        for s, _, o in report_graph.triples((None, SH.result, None)):
+            msg = ""
+            for p, o2 in report_graph.predicate_objects(o):
+                msg += f"{p} {o2}\n"
+            yield ValidationResult(
+                type="shacl validation",
+                severity=Severity.ERROR,
+                instance=instance,
+                instantiates=context.target_class,
+                message=f"{msg}",
+            )

linkml/validator/validator.py

@@ -29,7 +29,7 @@ class Validator:
         schema: Union[str, dict, TextIO, Path, SchemaDefinition],
         validation_plugins: Optional[List[ValidationPlugin]] = None,
         *,
-        strict: bool = False
+        strict: bool = False,
     ) -> None:
         if isinstance(schema, Path):
             schema = str(schema)

linkml/workspaces/example_runner.py

@@ -1,6 +1,7 @@
 """Iterate through all examples in a folder testing them for validity.
 
 """
+
 import glob
 import json
 import logging

{linkml-1.6.9.dist-info → linkml-1.6.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.6.9
+Version: 1.6.11
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink

{linkml-1.6.9.dist-info → linkml-1.6.11.dist-info}/RECORD

@@ -2,10 +2,10 @@ linkml/__init__.py,sha256=Ofc1RAB9gfvvRqinXih4eExeeSi2hTGhwTHbIGr5gLE,3215
 linkml/_version.py,sha256=udxv6OEqcE89DTVMYPtetXYg8IA8Sgc6yW26-6f8C3M,310
 linkml/generators/PythonGenNotes.md,sha256=wb9BPLLhF6378OKLbwSBAwmniLpwrcT5_bbfCHfLme8,51006
 linkml/generators/README.md,sha256=RMzT8EblC_GEdPy5WyfXHDBXlFI6k6mz3Cx2sdpcyWI,4438
-linkml/generators/__init__.py,sha256=qa22iTeBrcds6ndst_iTPVWLQtBF6NGyhVngBhbhIpc,1350
+linkml/generators/__init__.py,sha256=0KxTxNpQBnq4JTsDtwXQ1RYsRdmxfkegVBJKupti4Jg,1438
 linkml/generators/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/common/type_designators.py,sha256=lgVcIRJJ-yCvVGeP9U_gQZpm77UmJBQo9Bh3lGJITno,1956
-linkml/generators/csvgen.py,sha256=h-Mj-uNrzuETx_G3dW6eFbk1jj0NHSwqbehqR5tA6PM,2955
+linkml/generators/csvgen.py,sha256=X0f4qKXahSDtkzM9Y47rwWqdseP1O6PTZ_WKiOqOrQI,2956
 linkml/generators/docgen/class.md.jinja2,sha256=_nQr8ge57ZkX3Hrh-cqPUm8Z7HCnJuuRCgYm0g21mS8,3381
 linkml/generators/docgen/class_diagram.md.jinja2,sha256=lLU_0sQZBttOX5Wiup2oZwrxHuiQtbU9ZgLi66aJvOo,2538
 linkml/generators/docgen/common_metadata.md.jinja2,sha256=zy8Ua3gDtAAq8VA3e3O3ft9W7eJopVZaq5efP8LU_hU,1321
@@ -17,47 +17,47 @@ linkml/generators/docgen/slot.md.jinja2,sha256=XVd0M4gKx9Q2fONcsUGBRj_bJivyN4P9j
 linkml/generators/docgen/subset.md.jinja2,sha256=fTNIpAkml5RKFbbtLore3IAzFN1cISVsyL1ru2-Z4oA,2665
 linkml/generators/docgen/type.md.jinja2,sha256=QmCMJZrFwP33eHkggBVtypbyrxTb-XZn9vHOYojVaYk,635
 linkml/generators/docgen.py,sha256=Kwg4ZIXL2e9G-q-_CUoj8Bgnpyyvvh5fKPnseDcTK04,33755
-linkml/generators/dotgen.py,sha256=CnbVY6CO1OMuiYXYnvxgNN2IW1mtOQW-J-QnwZlXkUI,5012
+linkml/generators/dotgen.py,sha256=kzp1EYtF8bBqOuycJokDmsvHVDVkkW-J-6-MiUhwJH0,5013
 linkml/generators/erdiagramgen.py,sha256=Gu-_nhLuEPTsYYaoV6tNS1V6cZ2dNJdm6YwxC0VGl7g,10315
 linkml/generators/excelgen.py,sha256=OhVzuQaDESYpAGR8Zv13hiWlDDJA8ugtSZatBJH0hzA,7737
 linkml/generators/golanggen.py,sha256=Dnl7dhmb1AIK3Is7KRaUbxPd3kBTjWuspFqardiBTJ8,5751
-linkml/generators/golrgen.py,sha256=tIsbsr4SM9HxeK7TCUwnq-GdSKZ_qW5f7fybg_aqCZE,3436
+linkml/generators/golrgen.py,sha256=OUBYRWicP7G7lrPu1VrxumbVpx3CBJal-o2imyeP05M,3437
 linkml/generators/graphqlgen.py,sha256=6qZpI0rwg3ypsv_KrLVzXgdsJfR8LNPqgMwaRwzwnDs,2151
 linkml/generators/javagen/example_template.java.jinja2,sha256=ec4CVTv_0zS7V5Y-1E6H4lRraya10gfX7BEMBlu38X4,444
 linkml/generators/javagen/java_record_template.jinja2,sha256=OQZffLSy_xR3FIhQMltvrYyVeut7l2Q-tzK7AOiVmWs,1729
-linkml/generators/javagen.py,sha256=oZfUowKnBQNdklRqOM-yKptO4Te4y4N5ItIc5jTuWKU,5427
-linkml/generators/jsonldcontextgen.py,sha256=2TUzEzFBX7wDOYJ51Kg0hp2CVXcOzJhgIbq0CrzL2oc,7832
-linkml/generators/jsonldgen.py,sha256=KQYurjqp3gI0bevjzmrw4WDEgz4Yf4o4TJfZsqK4_vs,7575
-linkml/generators/jsonschemagen.py,sha256=8fzOoR5ZRgchg7r-QxZsbkxlnfD7ytrLw6qKjIRgmWo,25294
+linkml/generators/javagen.py,sha256=l3NUWCQMtJOTOIuao237hLYlILliLilVQXxdlJ5haIQ,5455
+linkml/generators/jsonldcontextgen.py,sha256=nLcASMmxoT57dRj1A9W5qqwg-5TDpsGblMb9gt940Zs,7871
+linkml/generators/jsonldgen.py,sha256=BtPXLYbnXTXorUcoe6y4DL0xa-TPjHOvtXdhv-ppW3I,7656
+linkml/generators/jsonschemagen.py,sha256=osol3CJBNB_YgZtvyryWywzpESXHfpDwn_5igvEMBF4,27524
 linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/linkmlgen.py,sha256=QhIPA1v2g_g5fien3ZKN-L6TkDk3t7puVFrcoEnwkwY,3540
-linkml/generators/markdowngen.py,sha256=ZPLahEPjWsrAsKq4CHbVDXeVd0n1NO-2STs068-g0Ac,32948
+linkml/generators/markdowngen.py,sha256=LU4Z8k9ag6aDURQKZAsEa_p9PEUGWsc_oMLJRx_pamI,32964
 linkml/generators/namespacegen.py,sha256=vVcIyM0zlKd7XRvtdzwTwHjG4Pg49801gy4FUmjJlqQ,6450
 linkml/generators/oocodegen.py,sha256=l-5zck_NNAUxJiApJrnDPkqxCv3b6v5s4hC_smelszU,7620
-linkml/generators/owlgen.py,sha256=omOfL5oKHeQs-JARbGbTvydZ6DX4Bzyv5pukgW02kds,52419
-linkml/generators/plantumlgen.py,sha256=Vs__5x9ioiT4IBTbvZUpgT8MsYJ0amfBL64MB_nmQPc,14870
-linkml/generators/prefixmapgen.py,sha256=JJ7hgzuqKVfFZrbDV76Dk8dR2NHsmpp-eNUAspXkfwA,4626
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+linkml/generators/plantumlgen.py,sha256=jN40_1_0_YI6Dir8wbxdVm-Upy6rxIYLFSNW-V0WKFY,14871
+linkml/generators/prefixmapgen.py,sha256=-IGKre3rRxCdNs0BP3Oo7Wzv8edeUQXkjjwN7od3qjU,4627
 linkml/generators/projectgen.py,sha256=g3JR2oXPM_QXhWUGukP9ts1P7tqxIeABaRdv130gbo4,9578
 linkml/generators/protogen.py,sha256=9YfxBZkQdBWwsUbstxEUR4xRWNuAKSfz9zXPhgIYePU,2328
 linkml/generators/pydanticgen.py,sha256=Ak0bpRoQsirnnBd091NiJvMZ-2d0qaQbhxADHy5ocwY,25529
 linkml/generators/pythongen.py,sha256=yGYlRJ4rNm2QQLFDjyuUnqCyKlzz-b3eSOhkSu8aCwI,52491
-linkml/generators/rdfgen.py,sha256=LxzYBaFEkV7rlf54nWv_6H6AGcWMRXwkaeVXq9VYEc8,2693
-linkml/generators/shaclgen.py,sha256=KxNmDZW2ciCuSqUhJ65TxLTjF8jME1FmN5SaWJCuW9k,8662
-linkml/generators/shexgen.py,sha256=E-R8jg5Z3JzzsVAIPu6Fs9FtFF7k-I5-5vMwG1jGW2U,9858
+linkml/generators/rdfgen.py,sha256=94SRun1DDJwMiKVJU-BpU0jwhac2GW7gv4Gaug7iJ6o,2694
+linkml/generators/shaclgen.py,sha256=H63DCUjTGYdrKRG5j7Ep8sOgFTXqmaEkH8Rne8ANvFo,8724
+linkml/generators/shexgen.py,sha256=VVlSrGCighLf0YSStK_VeMnCK0imAL4BJNDRVTpUFkw,9859
 linkml/generators/sparqlgen.py,sha256=xIT4abjYTjPvAjczZ2mkqfap5z8-AImK_jaCvgZyRGs,6120
 linkml/generators/sqlalchemy/__init__.py,sha256=mb9AC1rIFkSiNZhhG0TAk45ol9PjS1XvsrvCjgfVUpQ,249
 linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py,sha256=X_Ws1NUBikMI5HuNgEhl_PIeWM-B-c2B0W9KUBH4QTg,2542
 linkml/generators/sqlalchemy/sqlalchemy_imperative_template.py,sha256=u4ZpponG1h6XROrOHGOf_0H2e6xL1_s8twAOA-gx94A,1622
 linkml/generators/sqlalchemygen.py,sha256=XjvyCYr9h0EsFaKy4y-lMXunYw4dnk9vSpwlPjZK8gU,9186
-linkml/generators/sqlddlgen.py,sha256=t7U0-ZOWnulA7CMrlaih73H7fQdaGNRhdVLmvWGxFT4,18436
+linkml/generators/sqlddlgen.py,sha256=ickgQovcWunsBRMpHBDTGxGlZKU9kfExb-XQPBS6qPs,18437
 linkml/generators/sqltablegen.py,sha256=h_zVuNC8huRzzTa9nSHNWBxq-4TuLq7nR5nZfpDnWiM,11481
 linkml/generators/sssomgen.py,sha256=yur3q7so9uwIELWZaZRzkJwNbz_ppBL7IQki9XLIM3k,6879
 linkml/generators/string_template.md,sha256=kRcfic6entgIaJdpSg6GF3jcjC9wbKsCVM6wVT2qipc,1788
-linkml/generators/summarygen.py,sha256=aeWAUeOaWhn1WHZKnJ3TcKVku_6psrw88ubMc-GQzEc,2924
+linkml/generators/summarygen.py,sha256=67XKbzM_aCwJXEpgtsffWf7RGljeHJYE8dCIjMHXlH8,2925
 linkml/generators/terminusdbgen.py,sha256=_po9KnOz6Uoctb9Y4fJuU_voW4uA5pepvZTmHLQ2_DE,4470
 linkml/generators/typescriptgen.py,sha256=VDJ-97jk7zqYx6XlnIcxZmY8mCv885T7D2brKJHaihI,8565
-linkml/generators/yamlgen.py,sha256=bI4ebWe8vebR3xGVgto5TH0ZDej-RlZPTYqJ26BxKpg,1651
-linkml/generators/yumlgen.py,sha256=547atFkqJd9WtL_LdR-tUME9g7lWaFa3yHFvpnX6J1E,12145
+linkml/generators/yamlgen.py,sha256=0hYw2hW4A92As9x3k_7T7y05y25unfK2v3NPFfrtdbw,1652
+linkml/generators/yumlgen.py,sha256=nIwOYCCBWPnS8xk2y922qGlYSpoHNtMQcdB4L716iqo,12146
 linkml/linter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/linter/cli.py,sha256=BpQiETcRfQlZsI1-JALyU9wXPgPOm_KE_n11p0iJaC8,4494
 linkml/linter/config/datamodel/.linkmllint.yaml,sha256=40rNhcL35FXQSjlVBMWnyPgplwEUqFT_sJmeZqUzxMw,292
@@ -77,7 +77,7 @@ linkml/linter/rules.py,sha256=Bk87FMKgdF_aSBqeLe1uQartcTxV3-ZwUu-QRp2iK4s,11164
 linkml/reporting/__init__.py,sha256=Jo0V_nyEcnWhMukMW-bqW9dlbgCfaRlWm3CO-XzgU84,92
 linkml/reporting/model.py,sha256=-10yNfk8wuRC48ZI-akrWvtlJ9a6RYWET2TzlZV3XXo,8622
 linkml/transformers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/transformers/logical_model_transformer.py,sha256=fD9cFwnOf_Zur6-8wvPcXgagf8n4-ApV83HwaHn5Jvc,26509
+linkml/transformers/logical_model_transformer.py,sha256=1ZSB-HBoI0E2X2NV9TSgbTghp2GO4HQA27JaK0XiPBE,26510
 linkml/transformers/model_transformer.py,sha256=tK_MpRDI-q2qfe8KHT6qJHP8ZruKjYx1FcM-Fnjse-E,678
 linkml/transformers/relmodel_transformer.py,sha256=hRUVtH4gylDssOXoWvVxTetF9ESbITrAZOFu53b_Eg0,17836
 linkml/transformers/schema_renamer.py,sha256=Cr18TyktX64b5iFh5V6R_ILPVzXjbDYVDDZQyqFiAv8,5271
@@ -87,22 +87,22 @@ linkml/utils/converter.py,sha256=rdhCI7Tsjddr3o1rVBfMq5gQubk_GE6fqlBBmyxI5_M,627
 linkml/utils/datautils.py,sha256=QlbzwXykh5Fphfe5KxPo6_ekXfniLbHiEGJtLWjUrvY,3742
 linkml/utils/datavalidator.py,sha256=kBdWaVi8IZT1bOwEJgJYx-wZAb_PTBObB9nHpYORfKA,472
 linkml/utils/execute_tutorial.py,sha256=T4kHTSyz3ItJGEUZxVjR-3yLVKnOr5Ix4NMGE47-IuE,6912
-linkml/utils/generator.py,sha256=WAlP_gfZfAZYNklsh8l4GtiWZ338kjLg7xpQAANgUNg,38217
+linkml/utils/generator.py,sha256=fIoBa5zVXXOpW7ibIRCh0FADycdSXcrH98fMuzq6sng,38271
 linkml/utils/helpers.py,sha256=yR8n4zFA5wPcYC7xzRuNF3wO16vG80v6j7DM3qTNmIc,447
-linkml/utils/ifabsent_functions.py,sha256=FZwceqwlq81lMPDsdNfSHhtzDXSf8F4cbbhRdnDzjss,5765
+linkml/utils/ifabsent_functions.py,sha256=C2mllfh7aIZgVqqJjN5nydurVUk0hV62Wy7uVMYfPDg,5801
 linkml/utils/logictools.py,sha256=GSmBiobC49TcQjE08RtXEE3JwJEOV7eEREio25uJiFs,21184
 linkml/utils/mergeutils.py,sha256=QVm2iQB4v_L2rSvPBsPe9C865R03BgV3TzlPoTTTwWQ,9044
 linkml/utils/rawloader.py,sha256=QB7Rdvy4o4ZJEWBWa2_2xzz2TOh_6Oe4slvUn8IBVIc,4329
 linkml/utils/schema_builder.py,sha256=WLSit3J4lTifaFLLWTwjqIRiTru1pqvTIUuC1TrxS6Y,9902
 linkml/utils/schema_fixer.py,sha256=ajsxpwD4yMjDk1iDtoKJTsa34SIqGshWxlnSNXVZ52w,16745
 linkml/utils/schemaloader.py,sha256=bBSTqimMDTFH2FcKtRz99dKNJzV_myPsZSkIFp_6-A0,46421
-linkml/utils/schemasynopsis.py,sha256=6NKa89bkZfZQE9QM0St-6xQcrsHPkYmBgnnWnlgAcQ4,18455
+linkml/utils/schemasynopsis.py,sha256=jKf5ZJxpNgSZ5x9oAcdGO3m1IwzcIU2Ni1ugm0SQq1g,18447
 linkml/utils/sqlutils.py,sha256=86XeEbfY0Dk-EObw4q5-dxyzSeBtmIhjqqyDcR8ALS0,16591
 linkml/utils/typereferences.py,sha256=8Yfuz9-HAwOPoJLbIcO_sY9zf32hvPRzGeSOzECfMWA,2232
 linkml/utils/validation.py,sha256=eLw1-d8x3N1V14bSc6H_mJJXo59ryKvvUIBcOJ1dVMw,1438
-linkml/validator/__init__.py,sha256=59EBUp0G0MckoMFjhBEczXbQq7SweUINjD5Mya-Youk,5001
+linkml/validator/__init__.py,sha256=djKc1IyxGKvVYaX5jSxsqjfcEYaw3rFgKbFJxI2wDNk,5002
 linkml/validator/cli.py,sha256=VwYWDvR2fN37tOyz9L2k_TlE_NpUQx-MYeJ9p1O0qaI,7261
-linkml/validator/loaders/__init__.py,sha256=jmnzKaSxhacVPFDQTvfFr3bp1jtyGAD7_vgd1-26RhA,1164
+linkml/validator/loaders/__init__.py,sha256=FjUqEfBHeT5PEMBEZ9XwpclyQOysr4OCI1M0w_MYPVc,1165
 linkml/validator/loaders/delimited_file_loader.py,sha256=fdh61ZMPTfH29_DM93f5dY0jLP7KQPNh_QAHZppsdNw,2616
 linkml/validator/loaders/json_loader.py,sha256=Qy42naS2clb0fNXbUushckRu5AIX32b3UFUL6KMhxDE,809
 linkml/validator/loaders/loader.py,sha256=YKQXmSZhCymvvb2Dbr4lVCKVDt-lOIayzRD7CWrdsJI,559
@@ -112,10 +112,11 @@ linkml/validator/plugins/__init__.py,sha256=F7Un7bfdpSRXvk8LTb7Z4Q22rCtJJKjNkqUf
 linkml/validator/plugins/jsonschema_validation_plugin.py,sha256=hMPlCyAdMg_N_OHiHMaxcG0fsOA50V4oBNqorNz_oqE,2528
 linkml/validator/plugins/pydantic_validation_plugin.py,sha256=C-Vp74bz5oqp5V-iuhXW8p0PPDoFY8NCU5x36Ur5Og4,1985
 linkml/validator/plugins/recommended_slots_plugin.py,sha256=kOdoYQyye47nLA7BjorVmydS84nGpiVy3MoCbPq1Ymo,2308
+linkml/validator/plugins/shacl_validation_plugin.py,sha256=A6x3tiX-p03_i_VmR2xnw28j0dpiUw6WIAG-gllwJ8Q,3624
 linkml/validator/plugins/validation_plugin.py,sha256=9SMHF8b2bgG9-8351e8bY676e0A4aEBJSXvMjMF5kXg,1548
 linkml/validator/report.py,sha256=kkkuh-IZF9--cO-2wGjwP3PDLvOcjjvC8AOlxXUIOAM,870
 linkml/validator/validation_context.py,sha256=2BYbw0czAYepJUNoIINyTnmW6SrgK6et7SNvH5ejzgU,2700
-linkml/validator/validator.py,sha256=sdWbAOlnNYQWnZSEIuLpGQqH3W4cNq_8M_CdLtsNMH0,5648
+linkml/validator/validator.py,sha256=BFgfKdu9Nad2dc9XTpmz9daQTj_FTcvo6mBq3e8fhJs,5649
 linkml/validators/__init__.py,sha256=43W3J5NPKhwa3ZFHLRYsJMocwQKWGYCF9Ki9r0ccGbc,202
 linkml/validators/jsonschemavalidator.py,sha256=_ku7MQGqA6KplbHMiyzDRqgRwwXGloobhLptuXqLCp4,7951
 linkml/validators/sparqlvalidator.py,sha256=JowuZ5KxmWkldgWIXAb8DJi7YCPm8x3it0QkgM4lSi0,4612
@@ -123,9 +124,9 @@ linkml/workspaces/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU
 linkml/workspaces/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/workspaces/datamodel/workspaces.py,sha256=4HdkqweGNfMPqnB1_Onc9DcTfkhoagTRcqruh08nRoI,14905
 linkml/workspaces/datamodel/workspaces.yaml,sha256=EjVrwPpeRZqJRjuGyyDRxxFzuv55SiLIXPBRUG6HStU,4233
-linkml/workspaces/example_runner.py,sha256=uumXyPZ7xUJSZyRtjDP4TCCxgKSSOfebpufXc0_l0jY,11610
-linkml-1.6.9.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-linkml-1.6.9.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
-linkml-1.6.9.dist-info/entry_points.txt,sha256=za8r49Z5gcz3rAYTZLbxw5EPZr1rGuxSe1uiRUpf8R0,2143
-linkml-1.6.9.dist-info/METADATA,sha256=KsqVPfLcVUKxAlb-hz4AFdd6Pk5VGUjtmGx3wj5x7U8,3446
-linkml-1.6.9.dist-info/RECORD,,
+linkml/workspaces/example_runner.py,sha256=OmC_yZLIb4KXGQrstBVZL0UAQ9ZAaraguQF0RSf-snk,11611
+linkml-1.6.11.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
+linkml-1.6.11.dist-info/METADATA,sha256=0RyiHg0LnaAnrM3mRymCMT9pwefYYwa965a4HAzJCTQ,3447
+linkml-1.6.11.dist-info/entry_points.txt,sha256=za8r49Z5gcz3rAYTZLbxw5EPZr1rGuxSe1uiRUpf8R0,2143
+linkml-1.6.11.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
+linkml-1.6.11.dist-info/RECORD,,