linkml 1.7.7__py3-none-any.whl → 1.7.8__py3-none-any.whl

linkml/__init__.py

@@ -19,6 +19,13 @@ LOCAL_TYPES_YAML_FILE = linkml_files.LOCAL_PATH_FOR(Source.TYPES, Format.YAML)
 LOCAL_MAPPINGS_YAML_FILE = linkml_files.LOCAL_PATH_FOR(Source.MAPPINGS, Format.YAML)
 LOCAL_ANNOTATIONS_YAML_FILE = linkml_files.LOCAL_PATH_FOR(Source.ANNOTATIONS, Format.YAML)
 LOCAL_EXTENSIONS_YAML_FILE = linkml_files.LOCAL_PATH_FOR(Source.EXTENSIONS, Format.YAML)
+LOCAL_MODEL_YAML_FILES = (
+    LOCAL_METAMODEL_YAML_FILE,
+    LOCAL_TYPES_YAML_FILE,
+    LOCAL_MAPPINGS_YAML_FILE,
+    LOCAL_ANNOTATIONS_YAML_FILE,
+    LOCAL_EXTENSIONS_YAML_FILE,
+)
 
 # Local location of jsonld and context.jsonld files
 LOCAL_METAMODEL_LDCONTEXT_FILE = linkml_files.LOCAL_PATH_FOR(Source.META, Format.JSONLD)
@@ -55,6 +62,13 @@ METATYPE_NAMESPACE = METAMODEL_NAMESPACE
 METAMAPPING_NAMESPACE = METAMODEL_NAMESPACE
 METAANNOTATIONS_NAMESPACE = METAMODEL_NAMESPACE
 METAEXTENSIONS_NAMESPACE = METAMODEL_NAMESPACE
+NAMESPACES = (
+    METAMODEL_NAMESPACE,
+    METATYPE_NAMESPACE,
+    METAMAPPING_NAMESPACE,
+    METAANNOTATIONS_NAMESPACE,
+    METAEXTENSIONS_NAMESPACE,
+)
 
 # Metamodel Context URI
 METAMODEL_CONTEXT_URI = linkml_files.URL_FOR(Source.META, Format.JSONLD)

linkml/generators/docgen/subset.md.jinja2

@@ -43,20 +43,18 @@ URI: {{ gen.link(element) }}
 
 | Class | Description |
 | --- | --- |
-{% for c in gen.all_class_objects()|sort(attribute=sort_by) -%}
+{% for c in classes_in_subset -%}
 {%- if element.name in c.in_subset -%}
 | {{gen.link(c)}} | {{c.description|enshorten}} |
 {% endif -%}
 {% endfor %}
 
-{% for c in gen.all_class_objects()|sort(attribute=sort_by) -%}
+{% for c in classes_in_subset -%}
 {%- if element.name in c.in_subset -%}
-### {{ gen.name(c) }}
 
-{{c.description}}
+{% set induced_slots = gen.class_induced_slots(c.name)|sort(attribute=sort_by) %}
 
 {%- set filtered_slots = [] -%}
-
 {%- for s in induced_slots|sort(attribute=sort_by) -%}
     {%- if element.name in s.in_subset or element.name in schemaview.get_slot(s.name).in_subset -%}
         {% set _ = filtered_slots.append(s) %}
@@ -64,10 +62,12 @@ URI: {{ gen.link(element) }}
 {%- endfor %}
 
 {%- if filtered_slots|length > 0 -%}
-| Name | Cardinality and Range  | Description  |
+### Slots from {{ gen.link(c) }} also in _{{ element.name }}_
+
+| Name | Cardinality and Range | Description |
 | ---  | ---  | --- |
 {% for s in filtered_slots -%}
-| {{gen.link(s)}} | {{ gen.cardinality(s) }} <br/> {{gen.link(s.range)}}  | {{s.description|enshorten}} {% if s.identifier %}**identifier**{% endif %}  |
+| {{gen.link(s)}} | {{ gen.cardinality(s) }} <br/> {{gen.link(s.range)}} | {{s.description|enshorten}} {% if s.identifier %}**identifier**{% endif %} |
 {% endfor %}
 {%- endif %}
 

linkml/generators/jsonldgen.py

@@ -60,8 +60,8 @@ class JSONLDGenerator(Generator):
     """Path to a JSONLD context file"""
 
     def __post_init__(self) -> None:
-        super().__post_init__()
         self.original_schema = deepcopy(self.schema)
+        super().__post_init__()
 
     def _add_type(self, node: YAMLRoot) -> dict:
         if self.format == "jsonld":

linkml/generators/pydanticgen/array.py

@@ -30,7 +30,7 @@ else:
     from typing import Annotated
 
 from linkml.generators.pydanticgen.build import SlotResult
-from linkml.generators.pydanticgen.template import Import, Imports, ObjectImport
+from linkml.generators.pydanticgen.template import ConditionalImport, Import, Imports, ObjectImport
 
 
 class ArrayRepresentation(Enum):
@@ -54,7 +54,14 @@ if int(PYDANTIC_VERSION[0]) >= 2:
             item_schema = handler.generate_schema(item_type)
             if item_schema.get("type", "any") != "any":
                 item_schema["strict"] = True
-            array_ref = f"any-shape-array-{item_type.__name__}"
+
+            if item_type is Any:
+                # Before python 3.11, `Any` type was a special object without a __name__
+                item_name = "Any"
+            else:
+                item_name = item_type.__name__
+
+            array_ref = f"any-shape-array-{item_name}"
 
             schema = core_schema.definitions_schema(
                 core_schema.list_schema(core_schema.definition_reference_schema(array_ref)),
@@ -78,7 +85,6 @@ if int(PYDANTIC_VERSION[0]) >= 2:
         + Import(
             module="typing",
             objects=[
-                ObjectImport(name="Annotated"),
                 ObjectImport(name="Generic"),
                 ObjectImport(name="Iterable"),
                 ObjectImport(name="TypeVar"),
@@ -86,6 +92,12 @@ if int(PYDANTIC_VERSION[0]) >= 2:
                 ObjectImport(name="get_args"),
             ],
         )
+        + ConditionalImport(
+            condition="sys.version_info.minor > 8",
+            module="typing",
+            objects=[ObjectImport(name="Annotated")],
+            alternative=Import(module="typing_extensions", objects=[ObjectImport(name="Annotated")]),
+        )
         + Import(module="pydantic", objects=[ObjectImport(name="GetCoreSchemaHandler")])
         + Import(module="pydantic_core", objects=[ObjectImport(name="CoreSchema"), ObjectImport(name="core_schema")])
     )

linkml/generators/pydanticgen/pydanticgen.py

@@ -76,6 +76,7 @@ DEFAULT_IMPORTS = (
     + Import(module="decimal", objects=[ObjectImport(name="Decimal")])
     + Import(module="enum", objects=[ObjectImport(name="Enum")])
     + Import(module="re")
+    + Import(module="sys")
     + Import(
         module="typing",
         objects=[
@@ -644,10 +645,11 @@ class PydanticGenerator(OOCodeGenerator):
         for k, c in pyschema.classes.items():
             attrs = {}
             for attr_name, src_attr in c.attributes.items():
+                src_attr = src_attr._as_dict
                 new_fields = {
-                    k: src_attr._as_dict.get(k, None)
+                    k: src_attr.get(k, None)
                     for k in PydanticAttribute.model_fields.keys()
-                    if src_attr._as_dict.get(k, None) is not None
+                    if src_attr.get(k, None) is not None
                 }
                 predef_slot = predefined.get(k, {}).get(attr_name, None)
                 if predef_slot is not None:

linkml/generators/pydanticgen/template.py

@@ -1,3 +1,4 @@
+from copy import copy
 from importlib.util import find_spec
 from typing import Any, ClassVar, Dict, Generator, List, Literal, Optional, Union, overload
 
@@ -54,6 +55,10 @@ class TemplateModel(BaseModel):
     """
 
     template: ClassVar[str]
+    _environment: ClassVar[Environment] = Environment(
+        loader=PackageLoader("linkml.generators.pydanticgen", "templates"), trim_blocks=True, lstrip_blocks=True
+    )
+
     pydantic_ver: int = int(PYDANTIC_VERSION[0])
 
     def render(self, environment: Optional[Environment] = None, black: bool = False) -> str:
@@ -95,14 +100,11 @@ class TemplateModel(BaseModel):
     def environment(cls) -> Environment:
         """
         Default environment for Template models.
-
         uses a :class:`jinja2.PackageLoader` for the templates directory within this module
         with the ``trim_blocks`` and ``lstrip_blocks`` parameters set to ``True`` so that the
         default templates could be written in a more readable way.
         """
-        return Environment(
-            loader=PackageLoader("linkml.generators.pydanticgen", "templates"), trim_blocks=True, lstrip_blocks=True
-        )
+        return copy(cls._environment)
 
     if int(PYDANTIC_VERSION[0]) < 2:
         # simulate pydantic 2's model_fields behavior

linkml/generators/pythongen.py

@@ -4,6 +4,7 @@ import os
 import re
 from copy import copy
 from dataclasses import dataclass
+from pathlib import Path
 from types import ModuleType
 from typing import Callable, Dict, Iterator, List, Optional, Set, Tuple, Union
 
@@ -62,6 +63,8 @@ class PythonGenerator(Generator):
     emit_metadata: bool = True
 
     def __post_init__(self) -> None:
+        if isinstance(self.schema, Path):
+            self.schema = str(self.schema)
         self.sourcefile = self.schema
         self.schemaview = SchemaView(self.schema, base_dir=self.base_dir)
         super().__post_init__()

linkml/generators/rdfgen.py

@@ -7,10 +7,12 @@ Generate a JSON LD representation of the model
 
 import os
 import urllib.parse as urlparse
+from copy import deepcopy
 from dataclasses import dataclass
 from typing import List, Optional
 
 import click
+from linkml_runtime.linkml_model import SchemaDefinition
 from rdflib import Graph
 from rdflib.plugin import Parser as rdflib_Parser
 from rdflib.plugin import plugins as rdflib_plugins
@@ -35,13 +37,19 @@ class RDFGenerator(Generator):
     # ObjectVars
     emit_metadata: bool = False
     context: List[str] = None
+    original_schema: SchemaDefinition = None
+    """See https://github.com/linkml/linkml/issues/871"""
+
+    def __post_init__(self):
+        self.original_schema = deepcopy(self.schema)
+        super().__post_init__()
 
     def _data(self, g: Graph) -> str:
         return g.serialize(format="turtle" if self.format == "ttl" else self.format)
 
     def end_schema(self, output: Optional[str] = None, context: str = None, **_) -> None:
         gen = JSONLDGenerator(
-            self,
+            self.original_schema,
             format=JSONLDGenerator.valid_formats[0],
             metadata=self.emit_metadata,
             importmap=self.importmap,

linkml/generators/shaclgen.py

@@ -22,7 +22,8 @@ class ShaclGenerator(Generator):
     # ClassVars
     closed: bool = True
     """True means add 'sh:closed=true' to all shapes, except of mixin shapes and shapes, that have parents"""
-
+    suffix: str = None
+    """parameterized suffix to be appended. No suffix per default."""
     generatorname = os.path.basename(__file__)
     generatorversion = "0.0.1"
     valid_formats = ["ttl"]
@@ -59,9 +60,12 @@ class ShaclGenerator(Generator):
 
             def shape_pv(p, v):
                 if v is not None:
-                    g.add((class_uri, p, v))
+                    g.add((class_uri_with_suffix, p, v))
 
             class_uri = URIRef(sv.get_uri(c, expand=True))
+            class_uri_with_suffix = class_uri
+            if self.suffix is not None:
+                class_uri_with_suffix += self.suffix
             shape_pv(RDF.type, SH.NodeShape)
             shape_pv(SH.targetClass, class_uri)  # TODO
             if self.closed:
@@ -211,14 +215,21 @@ def add_simple_data_type(func: Callable, r: ElementName) -> None:
 
 
 @shared_arguments(ShaclGenerator)
+@click.command()
 @click.option(
     "--closed/--non-closed",
     default=True,
     show_default=True,
     help="Use '--closed' to generate closed SHACL shapes. Use '--non-closed' to generate open SHACL shapes.",
 )
+@click.option(
+    "-s",
+    "--suffix",
+    default=None,
+    show_default=True,
+    help="Use --suffix to append given string to SHACL class name (e. g. --suffix Shape: Person becomes PersonShape).",
+)
 @click.version_option(__version__, "-V", "--version")
-@click.command()
 def cli(yamlfile, **args):
     """Generate SHACL turtle from a LinkML model"""
     gen = ShaclGenerator(yamlfile, **args)

linkml/generators/sqlalchemygen.py

@@ -121,6 +121,7 @@ class SQLAlchemyGenerator(Generator):
             is_join_table=lambda c: any(tag for tag in c.annotations.keys() if tag == "linkml:derived_from"),
             classes=rel_schema_classes_ordered,
         )
+        logging.debug(f"# Generated code:\n{code}")
         return code
 
     def serialize(self, **kwargs) -> str:

linkml/generators/sqltablegen.py

@@ -211,7 +211,22 @@ class SQLTableGenerator(Generator):
                         col.comment = s.description
                     cols.append(col)
                 for uc_name, uc in c.unique_keys.items():
-                    sql_uc = UniqueConstraint(*[sql_name(sn) for sn in uc.unique_key_slots])
+
+                    def _sql_name(sn: str):
+                        if sn in c.attributes:
+                            return sql_name(sn)
+                        else:
+                            # for candidate in c.attributes.values():
+                            #    if "original_slot" in candidate.annotations:
+                            #        original = candidate.annotations["original_slot"]
+                            #        if original.value == sn:
+                            #            return sql_name(candidate.name)
+                            return None
+
+                    sql_names = [_sql_name(sn) for sn in uc.unique_key_slots]
+                    if any(sn is None for sn in sql_names):
+                        continue
+                    sql_uc = UniqueConstraint(*sql_names)
                     cols.append(sql_uc)
                 Table(sql_name(cn), schema_metadata, *cols, comment=str(c.description))
         schema_metadata.create_all(engine)

linkml/transformers/relmodel_transformer.py

@@ -226,6 +226,7 @@ class RelationalModelTransformer:
 
         # TODO: separate out the logic into separate testable methods
         target_sv.set_modified()
+        multivalued_slots_original = []
         # post-process target schema
         for cn, c in target_sv.all_classes().items():
             if self.foreign_key_policy == ForeignKeyPolicy.NO_FOREIGN_KEYS:
@@ -243,6 +244,7 @@ class RelationalModelTransformer:
                     slot.inlined or slot.inlined_as_list or "shared" in slot.annotations
                 )
                 if slot.multivalued:
+                    multivalued_slots_original.append(slot.name)
                     slot.multivalued = False
                     slot_name = slot.name
                     sn_singular = slot.singular_name if slot.singular_name else slot.name
@@ -332,6 +334,7 @@ class RelationalModelTransformer:
         # add PK and FK anns
         target_sv.set_modified()
         fk_policy = self.foreign_key_policy
+        forward_map = {}
         for c in target.classes.values():
             if self.foreign_key_policy == ForeignKeyPolicy.NO_FOREIGN_KEYS:
                 continue
@@ -356,14 +359,31 @@ class RelationalModelTransformer:
                         # if it is already an injected backref, no need to re-inject
                         if "backref" not in a.annotations:
                             del c.attributes[a.name]
+                            original_name = a.name
                             if "forwardref" not in a.annotations:
-                                add_annotation(a, "original_slot", a.name)
+                                add_annotation(a, "original_slot", original_name)
                             a.alias = f"{a.name}_{tc_pk_slot.name}"
                             a.name = a.alias
                             c.attributes[a.name] = a
+                            forward_map[original_name] = a.name
                     ann = Annotation("foreign_key", f"{tc.name}.{tc_pk_slot.name}")
                     a.annotations[ann.tag] = ann
                     target_sv.set_modified()
+            # Rewrite unique key constraints
+            # - if a slot has a range of object, it may be renamed, e.g. person => person_id
+            # - if a slot is multivalued then it is translated to backref and the UC must be dropped
+            removed_ucs = []
+            for uc_name, uc in c.unique_keys.items():
+                if any(sn in multivalued_slots_original for sn in uc.unique_key_slots):
+                    logging.warning(
+                        f"Cannot represent uniqueness constraint {uc_name}. "
+                        f"one of the slots {uc.unique_key_slots} is multivalued"
+                    )
+                    removed_ucs.append(uc_name)
+                new_slot_names = [forward_map.get(sn, sn) for sn in uc.unique_key_slots]
+                uc.unique_key_slots = new_slot_names
+            for uc_name in removed_ucs:
+                del c.unique_keys[uc_name]
 
         result = TransformationResult(target, mappings=mappings)
         return result

linkml/utils/generator.py

@@ -30,7 +30,6 @@ from typing import Callable, ClassVar, Dict, List, Mapping, Optional, Set, TextI
 import click
 from click import Argument, Command, Option
 from linkml_runtime import SchemaView
-from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.linkml_model.meta import (
     ClassDefinition,
     ClassDefinitionName,
@@ -83,7 +82,7 @@ class Generator(metaclass=abc.ABCMeta):
     For usage `Generator Docs <https://linkml.io/linkml/generators/>`_
     """
 
-    schema: Union[str, TextIO, SchemaDefinition, "Generator"]
+    schema: Union[str, TextIO, SchemaDefinition, "Generator", Path]
     """metamodel compliant schema.  Can be URI, file name, actual schema, another generator, an
         open file or a pre-parsed schema"""
 
@@ -130,7 +129,7 @@ class Generator(metaclass=abc.ABCMeta):
     useuris: Optional[bool] = None
     """True means declared class slot uri's are used.  False means use model uris"""
 
-    log_level: int = DEFAULT_LOG_LEVEL_INT
+    log_level: Optional[int] = DEFAULT_LOG_LEVEL_INT
     """Logging level, 0 is minimum"""
 
     mergeimports: Optional[bool] = True
@@ -180,6 +179,8 @@ class Generator(metaclass=abc.ABCMeta):
     def __post_init__(self) -> None:
         if not self.logger:
             self.logger = logging.getLogger()
+        if self.log_level is not None:
+            self.logger.setLevel(self.log_level)
         if self.format is None:
             self.format = self.valid_formats[0]
         if self.format not in self.valid_formats:
@@ -191,7 +192,11 @@ class Generator(metaclass=abc.ABCMeta):
             self.source_file_size = None
         if self.requires_metamodel:
             self.metamodel = _resolved_metamodel(self.mergeimports)
+
         schema = self.schema
+        if isinstance(schema, Path):
+            schema = str(schema)
+
         # TODO: remove aliasing
         self.emit_metadata = self.metadata
         if self.uses_schemaloader:
@@ -225,8 +230,7 @@ class Generator(metaclass=abc.ABCMeta):
                 # schemaloader based methods require schemas to have been created via SchemaLoader,
                 # which prepopulates some fields (e.g. definition_url). If the schema has not been processed through the
                 # loader, then roundtrip
-                if any(c for c in schema.classes.values() if not c.definition_uri):
-                    schema = yaml_dumper.dumps(schema)
+                schema = schema._as_dict
             loader = SchemaLoader(
                 schema,
                 self.base_dir,

linkml/utils/rawloader.py

@@ -1,5 +1,6 @@
 import copy
 from datetime import datetime
+from pathlib import Path
 from typing import Optional, TextIO, Union
 from urllib.parse import urlparse
 
@@ -29,7 +30,7 @@ SchemaDefinition.MissingRequiredField = mrf
 
 
 def load_raw_schema(
-    data: Union[str, dict, TextIO],
+    data: Union[str, dict, TextIO, Path],
     source_file: Optional[str] = None,
     source_file_date: Optional[str] = None,
     source_file_size: Optional[int] = None,
@@ -58,6 +59,9 @@ def load_raw_schema(
         assert source_file_date is None, "source_file_date parameter not allowed if data is a file or URL"
         assert source_file_size is None, "source_file_size parameter not allowed if data is a file or URL"
 
+    if isinstance(data, Path):
+        data = str(data)
+
     # Convert the input into a valid SchemaDefinition
     if isinstance(data, (str, dict, TextIO)):
         # TODO: Build a generic loader that detects type from suffix or content and invokes the appropriate loader

linkml/utils/schemaloader.py

@@ -2,6 +2,7 @@ import logging
 import os
 from collections import OrderedDict
 from copy import deepcopy
+from pathlib import Path
 from typing import Dict, Iterator, List, Mapping, Optional, Set, TextIO, Tuple, Union, cast
 from urllib.parse import urlparse
 
@@ -32,7 +33,7 @@ from linkml.utils.schemasynopsis import SchemaSynopsis
 class SchemaLoader:
     def __init__(
         self,
-        data: Union[str, TextIO, SchemaDefinition, dict],
+        data: Union[str, TextIO, SchemaDefinition, dict, Path],
         base_dir: Optional[str] = None,
         namespaces: Optional[Namespaces] = None,
         useuris: Optional[bool] = None,

linkml/utils/sqlutils.py

@@ -58,16 +58,22 @@ class SQLStore:
     - mapping your data/objects in any LinkML compliant data format (json. yaml, rdf) into ORM objects
     """
 
-    schema: Union[str, SchemaDefinition] = None
-    schemaview: SchemaView = None
-    engine: Engine = None
-    database_path: str = None
+    schema: Optional[Union[str, Path, SchemaDefinition]] = None
+    schemaview: Optional[SchemaView] = None
+    engine: Optional[Engine] = None
+    database_path: Union[str, Path] = None
     use_memory: bool = False
     """https://docs.sqlalchemy.org/en/20/dialects/sqlite.html#using-a-memory-database-in-multiple-threads"""
 
-    module: ModuleType = None
-    native_module: ModuleType = None
-    include_schema_in_database: bool = None
+    module: Optional[ModuleType] = None
+    native_module: Optional[ModuleType] = None
+    include_schema_in_database: bool = False
+
+    def __post_init__(self):
+        if self.database_path is None and not self.use_memory:
+            raise ValueError("Must have database path or use_memory must be True")
+        if self.schema is not None and self.schemaview is None:
+            self.schemaview = SchemaView(self.schema)
 
     def db_exists(self, create=True, force=False) -> Optional[str]:
         """
@@ -117,8 +123,6 @@ class SQLStore:
         """
         gen = SQLAlchemyGenerator(self.schema)
         self.module = gen.compile_sqla(template=TemplateEnum.DECLARATIVE)
-        if self.schemaview is None:
-            self.schemaview = SchemaView(self.schema)
         return self.module
 
     def compile_native(self) -> ModuleType:
@@ -223,7 +227,6 @@ class SQLStore:
             for n, nu_typ in inspect.getmembers(self.module):
                 # TODO: make more efficient
                 if n == typ.__name__:
-                    # print(f'Creating {nu_typ} from: {inst_args}')
                     nu_obj = nu_typ(**inst_args)
                     return nu_obj
             raise ValueError(f"Cannot find {typ.__name__} in {self.module}")
@@ -237,8 +240,6 @@ class SQLStore:
         :param obj: sqla object
         :return: native dataclass object
         """
-        if self.schemaview is None:
-            self.schemaview = SchemaView(self.schema)
         typ = type(obj)
         nm = self.schemaview.class_name_mappings()
         if typ.__name__ in nm:
@@ -262,9 +263,7 @@ class SQLStore:
             for n, nu_typ in inspect.getmembers(self.native_module):
                 # TODO: make more efficient
                 if n == typ.__name__:
-                    # print(f'CREATING {nu_typ} FROM {inst_args}')
                     nu_obj = nu_typ(**inst_args)
-                    # print(f'CREATED {nu_obj}')
                     return nu_obj
             raise ValueError(f"Cannot find {typ.__name__} in {self.native_module}")
         else:

linkml/validator/plugins/shacl_validation_plugin.py

@@ -34,21 +34,27 @@ class ShaclValidationPlugin(ValidationPlugin):
         self.closed = closed
         self.shacl_path = shacl_path
         self.raise_on_conversion_error = raise_on_conversion_error
+        self._loaded_graphs = {}
 
     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()
+            schema_hash = hash(str(context._schema))
+            if schema_hash in self._loaded_graphs:
+                g = self._loaded_graphs[schema_hash]
+            else:
+                gen = ShaclGenerator(context._schema)
+                g = gen.as_graph()
+                self._loaded_graphs[schema_hash] = g
         return g
 
     def process(self, instance: Any, context: ValidationContext) -> Iterator[ValidationResult]:
-        """Perform JSON Schema validation on the provided instance
+        """Perform SHACL Schema validation on the provided instance
 
         :param instance: The instance to validate
-        :param context: The validation context which provides a JSON Schema artifact
+        :param context: The validation context which provides a SHACL artifact
         :return: Iterator over validation results
         :rtype: Iterator[ValidationResult]
         """

{linkml-1.7.7.dist-info → linkml-1.7.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.7.7
+Version: 1.7.8
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -51,6 +51,7 @@ Requires-Dist: pyyaml
 Requires-Dist: rdflib (>=6.0.0)
 Requires-Dist: requests (>=2.22)
 Requires-Dist: sqlalchemy (>=1.4.31)
+Requires-Dist: typing-extensions (>=4.4.0) ; python_version < "3.9"
 Requires-Dist: watchdog (>=0.9.0)
 Project-URL: Documentation, https://linkml.io/linkml/
 Project-URL: Repository, https://github.com/linkml/linkml

{linkml-1.7.7.dist-info → linkml-1.7.8.dist-info}/RECORD

@@ -1,4 +1,4 @@
-linkml/__init__.py,sha256=jwtUdhwmquj-0fCR6VwPH5_RfSpuG94hLWdre_W_FD4,3327
+linkml/__init__.py,sha256=0REu65rXiOk3F1CYLzq60HiSZ2DfFySfGS6QFljZ01s,3663
 linkml/_version.py,sha256=udxv6OEqcE89DTVMYPtetXYg8IA8Sgc6yW26-6f8C3M,310
 linkml/generators/PythonGenNotes.md,sha256=wb9BPLLhF6378OKLbwSBAwmniLpwrcT5_bbfCHfLme8,51006
 linkml/generators/README.md,sha256=RMzT8EblC_GEdPy5WyfXHDBXlFI6k6mz3Cx2sdpcyWI,4438
@@ -14,7 +14,7 @@ linkml/generators/docgen/index.md.jinja2,sha256=wXUYTmayPLFltC0vbGE_Mf6m3GkkWav7
 linkml/generators/docgen/index.tex.jinja2,sha256=Go_EA-_N4JUpbOYbk3OY11mz5yV70VF2l2sMtgIPWw4,501
 linkml/generators/docgen/schema.md.jinja2,sha256=xlENfnzNRYgPT_0tdqNFxgklVM4Qf5BuzhFVvSMDuxs,70
 linkml/generators/docgen/slot.md.jinja2,sha256=ZGa-kaNvi5LknvFRIjKQyRpSynr1SlkLrpEmWDNPwDA,3226
-linkml/generators/docgen/subset.md.jinja2,sha256=fTNIpAkml5RKFbbtLore3IAzFN1cISVsyL1ru2-Z4oA,2665
+linkml/generators/docgen/subset.md.jinja2,sha256=EPln_fjlhlkmwEGEp2iPX-9Xm2vVodPZLlRBlYCB_sA,2705
 linkml/generators/docgen/type.md.jinja2,sha256=QmCMJZrFwP33eHkggBVtypbyrxTb-XZn9vHOYojVaYk,635
 linkml/generators/docgen.py,sha256=dz7OWxclX306EweVIgC765h3NKtJTRg0TPnqmltWygs,34347
 linkml/generators/dotgen.py,sha256=kzp1EYtF8bBqOuycJokDmsvHVDVkkW-J-6-MiUhwJH0,5013
@@ -27,7 +27,7 @@ linkml/generators/javagen/example_template.java.jinja2,sha256=ec4CVTv_0zS7V5Y-1E
 linkml/generators/javagen/java_record_template.jinja2,sha256=OQZffLSy_xR3FIhQMltvrYyVeut7l2Q-tzK7AOiVmWs,1729
 linkml/generators/javagen.py,sha256=KxwupMztyCRHcSsbtTnOovuj1WamsAny0mxbYWvTiDs,5324
 linkml/generators/jsonldcontextgen.py,sha256=N_XWCx_1eS5KcWlzlyl79C-dW0gfe32v886UskD1iTU,8644
-linkml/generators/jsonldgen.py,sha256=pk8Gmh2gSvXt_o7MTuJ71thNfIJuHUGkNl3yl3RIdsE,7728
+linkml/generators/jsonldgen.py,sha256=646aQc27CkuxxkDAJHSBcivCDwNAPl7OOT01OBR2AOI,7728
 linkml/generators/jsonschemagen.py,sha256=XOsYIrpA6BwtAcfh8GNGduIjpuPAsF2f_PQ1mghj_WU,27455
 linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/linkmlgen.py,sha256=1_Kt_7rD42WvCTjq0yaq1Of7jEDZR_uusyzAT-qWMHk,3471
@@ -40,11 +40,11 @@ linkml/generators/prefixmapgen.py,sha256=L9TccwKNHEguW0ox5qgf_GhIuqauYTI8d4jSjeq
 linkml/generators/projectgen.py,sha256=OuT_AneoZFNMCn50GllfZafadUHt50u61JcftM2eed4,9750
 linkml/generators/protogen.py,sha256=5UxThsFDVyDTzzTDh77Z0anx4-tLgz8kQQ-e7ywIqwI,2290
 linkml/generators/pydanticgen/__init__.py,sha256=uKGaaQSaeKqinHImXGFE448i-t8Oi0No8suIO76sep8,629
-linkml/generators/pydanticgen/array.py,sha256=imbHtwgQcz_uloFWDBDojIMydZw9eysQyQl6ppT5eL8,19045
+linkml/generators/pydanticgen/array.py,sha256=1QWWgz46yVmWkdNauI6Kjkbx3kexp-l210nOILoHJ18,19506
 linkml/generators/pydanticgen/black.py,sha256=c-Hgaao9hd4nPMU9w0Hmg2j4Wc81IcY0zAfppQPr1cM,721
 linkml/generators/pydanticgen/build.py,sha256=Ia8qy4C16b-KqO_fw4tGQW_Eo4grCVyX7RsuJ3uRTtk,2681
-linkml/generators/pydanticgen/pydanticgen.py,sha256=psEdNy_oJqHnTBZkQp4H8pNrFXv_y92j5oEoFcp_AEU,29809
-linkml/generators/pydanticgen/template.py,sha256=7I-qch_vr1elXwJ1kxRcZEl3j6-WTLYRh8_b2DjxjyE,19911
+linkml/generators/pydanticgen/pydanticgen.py,sha256=Gnii-UuKc7gyEpaN5XbRyzWp0v1F5eAUVVzMhFGX2rM,29863
+linkml/generators/pydanticgen/template.py,sha256=fAqRofLm7N94xUqXjkStdmugcxGQfiioGkxdIhLByik,19990
 linkml/generators/pydanticgen/templates/attribute.py.jinja,sha256=AlH_QFJJkONpzXQRGqnW4ufmjp9s9E7Q9W5r8ykNGeQ,443
 linkml/generators/pydanticgen/templates/base_model.py.jinja,sha256=48y64MnC9rjNSV-nKLMeDuHN4gm15UsInhnKxh65zoM,834
 linkml/generators/pydanticgen/templates/class.py.jinja,sha256=RIdkqdZS9rDILUuVqDIAWK_vATGkirLbPhdHSyHDAbY,565
@@ -54,19 +54,19 @@ linkml/generators/pydanticgen/templates/footer.py.jinja,sha256=WuWGJjkWDQcEPL2bG
 linkml/generators/pydanticgen/templates/imports.py.jinja,sha256=d1XFna2eOpkH8cgJML3vXwqGcocczvOcrbg6jjd4kP0,945
 linkml/generators/pydanticgen/templates/module.py.jinja,sha256=SkmtWtQS7D-xBiZI-sFiYC3WYPKi3VJCj_KtaMVxexM,438
 linkml/generators/pydanticgen/templates/validator.py.jinja,sha256=Yo4dubQal-HwEoJKztQkLYM5qCz1I8na2oaDlXuEpwU,532
-linkml/generators/pythongen.py,sha256=AvOQZJ-OT8lMYeaT2bdexHuRPRfTK7wpbmgAdfc2lW4,52805
-linkml/generators/rdfgen.py,sha256=L6F08iDUqVemXXrRbJmcOxvJTt14hR0oo8WLoqf4npw,2656
+linkml/generators/pythongen.py,sha256=4Tw4Zz5GPvvbvk10zrD1yJFdxY3cvXJYqmFKrms8aUs,52915
+linkml/generators/rdfgen.py,sha256=fPhTrMzUM6dkg3HllgD6biuRJl8afIfj7ZWu9e56MKo,2973
 linkml/generators/shacl/__init__.py,sha256=O-M-wndKw8rMW-U8X3QCNHal-ErXP6uXZqxiQSa77l4,108
 linkml/generators/shacl/ifabsent_processor.py,sha256=kV9BGA2ZPXLRfaFuW0o4jpkATvGggvrqpAo9c1UqWNE,2193
 linkml/generators/shacl/shacl_data_type.py,sha256=BT3C9tdFyBQnuucPN7YQiFAKEa9yuzy-Q26X6dmOXgo,1827
-linkml/generators/shaclgen.py,sha256=vCNAX15wg0h86ZplRjo721_58UHUSVHkQULTYV_1HZI,8324
+linkml/generators/shaclgen.py,sha256=P3Kf10a0_1MCk4-prai9rrgPRHnQqtgYoXof0VIVyws,8771
 linkml/generators/shexgen.py,sha256=KzhaL-A4R4peSdhY6nlDWmS-DPfnZMxMzrXhHGnA_Ag,9874
 linkml/generators/sparqlgen.py,sha256=c7x8GFChKWprBx4rToSnu9qN8OleWTCenVUdZ8XSTWM,6138
 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=TTc1oLLwG0c1BdvDXvSfGWAJCDlVvq7Y0r0yjXcdiW4,9268
-linkml/generators/sqltablegen.py,sha256=XorqF6lfZX6tHfi6O2aIjd2GU_JZx5BuERuC3P6utVE,11626
+linkml/generators/sqlalchemygen.py,sha256=5J9eQhTz7Ug-7WhZPv6zIaAbf7xlLi-0xMequ67pvgA,9320
+linkml/generators/sqltablegen.py,sha256=87057FJi9EUVPXOjRfHuSqY0lKmepXRNQsose2fGts4,12343
 linkml/generators/sssomgen.py,sha256=yur3q7so9uwIELWZaZRzkJwNbz_ppBL7IQki9XLIM3k,6879
 linkml/generators/string_template.md,sha256=kRcfic6entgIaJdpSg6GF3jcjC9wbKsCVM6wVT2qipc,1788
 linkml/generators/summarygen.py,sha256=crH_Hegd4Z7G7byUtgyXoP2XtG_4iblzZsu_pE4aQrk,2887
@@ -95,7 +95,7 @@ linkml/reporting/model.py,sha256=-10yNfk8wuRC48ZI-akrWvtlJ9a6RYWET2TzlZV3XXo,862
 linkml/transformers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/transformers/logical_model_transformer.py,sha256=Luc8cKWIGrRAXQ9DSLA03fgpIolLpsTT19OV9Coolvk,26522
 linkml/transformers/model_transformer.py,sha256=tK_MpRDI-q2qfe8KHT6qJHP8ZruKjYx1FcM-Fnjse-E,678
-linkml/transformers/relmodel_transformer.py,sha256=6tA-GkutJ0rgspjCF2NSCf2z-YdU2b4qPijabkroWfE,17704
+linkml/transformers/relmodel_transformer.py,sha256=aiSI2xaqRz4f0Z_0WFaBP5bknzX0pTnvxsR5mESFysg,18857
 linkml/transformers/schema_renamer.py,sha256=DYRbgL9j41M9FdbHYLY3u4YIdDM98laD3cv_lHcgWHQ,5275
 linkml/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/utils/cli_utils.py,sha256=MdVbox1qr6kDUHUCWAmFhV-D6ebs_nn8vVwB8KDQfew,742
@@ -103,17 +103,17 @@ linkml/utils/converter.py,sha256=snAF-pgZBSi4ANiaKXxqtZk5w3qonJjTfI4X5OVLmUE,628
 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=3q_PpZQxBTwpoN8lHHMkUhHm1gg0qXhiHgLWV9FIVLM,38363
+linkml/utils/generator.py,sha256=ytpcq3s7cJMYpLAcL2H_F-1FWbog3FlUXkylm1It25M,38394
 linkml/utils/helpers.py,sha256=yR8n4zFA5wPcYC7xzRuNF3wO16vG80v6j7DM3qTNmIc,447
 linkml/utils/ifabsent_functions.py,sha256=IkcBcmRYu8sllx7_mTCqu4aHfTxX2AnQoccZ1KOODds,5843
 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/rawloader.py,sha256=nUB8Gfn8yEVwyo6bx0TtB2mBGkilC-fybi0xvQ73Gks,4417
 linkml/utils/schema_builder.py,sha256=4qhrur8O0xRZnPm7H1h2BZmTkut5R4q-IE_1KKiHy_c,9937
 linkml/utils/schema_fixer.py,sha256=Uz8M3AOQ_BputJr1f6lbfk1iyvmANUNG80-0B3BQKJ8,16761
-linkml/utils/schemaloader.py,sha256=XkH3ARPVcJ3ggnk4qgHJBPepyII4UlSRHzBlTWZbpCo,46062
+linkml/utils/schemaloader.py,sha256=5fLM99v6RZ0OW4JHA0UAd_mtS_2HNubXAjlF5v8vHcw,46093
 linkml/utils/schemasynopsis.py,sha256=jKf5ZJxpNgSZ5x9oAcdGO3m1IwzcIU2Ni1ugm0SQq1g,18447
-linkml/utils/sqlutils.py,sha256=FsOC3Wut6qzzmsnIt9ROsiDt2wXOa1IZUUtJ_T4Nb6M,17071
+linkml/utils/sqlutils.py,sha256=Cwoaz44MLcvAGUEBshT4jtn0Z3w7jVOp85zGkd6FTHY,17071
 linkml/utils/typereferences.py,sha256=8Yfuz9-HAwOPoJLbIcO_sY9zf32hvPRzGeSOzECfMWA,2232
 linkml/utils/validation.py,sha256=eLw1-d8x3N1V14bSc6H_mJJXo59ryKvvUIBcOJ1dVMw,1438
 linkml/validator/__init__.py,sha256=djKc1IyxGKvVYaX5jSxsqjfcEYaw3rFgKbFJxI2wDNk,5002
@@ -128,7 +128,7 @@ 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/shacl_validation_plugin.py,sha256=X6h1O54m9P5USvqCvNqELD0YpzXkE6UrmxnV0ukU6E4,3888
 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=Pmccq-LQ9iEeLyZhamp3mKjjtwp4ji1hIe5TT05AUT4,2732
@@ -141,8 +141,8 @@ linkml/workspaces/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
 linkml/workspaces/datamodel/workspaces.py,sha256=4HdkqweGNfMPqnB1_Onc9DcTfkhoagTRcqruh08nRoI,14905
 linkml/workspaces/datamodel/workspaces.yaml,sha256=EjVrwPpeRZqJRjuGyyDRxxFzuv55SiLIXPBRUG6HStU,4233
 linkml/workspaces/example_runner.py,sha256=OmC_yZLIb4KXGQrstBVZL0UAQ9ZAaraguQF0RSf-snk,11611
-linkml-1.7.7.dist-info/entry_points.txt,sha256=7haDkIbyC7ZLhm5z-e3BhrLJpY2xoW1yuD8Y7QPNtVg,2093
-linkml-1.7.7.dist-info/METADATA,sha256=f74yR9Byjm8tw_y28edi2dJtVwthbMwMUocjhXiy0TQ,3656
-linkml-1.7.7.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-linkml-1.7.7.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
-linkml-1.7.7.dist-info/RECORD,,
+linkml-1.7.8.dist-info/METADATA,sha256=7Nrt0dXBtqeom1Q3W5wGtdrLzzEcIhoURNoTaZfRyiY,3724
+linkml-1.7.8.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
+linkml-1.7.8.dist-info/entry_points.txt,sha256=7haDkIbyC7ZLhm5z-e3BhrLJpY2xoW1yuD8Y7QPNtVg,2093
+linkml-1.7.8.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
+linkml-1.7.8.dist-info/RECORD,,