linkml 1.6.7__py3-none-any.whl → 1.6.9__py3-none-any.whl

linkml/generators/docgen/class.md.jinja2

@@ -33,6 +33,10 @@ URI: {{ gen.uri_link(element) }}
 ```{{ gen.mermaid_directive() }}
 {{ gen.mermaid_diagram([element.name]) }}
 ```
+{% elif diagram_type == "plantuml_class_diagram" %}
+```puml
+{{ gen.mermaid_diagram([element.name]) }}
+```
 {% else %}
 {% include "class_diagram.md.jinja2" %}
 {% endif %}

linkml/generators/docgen/class_diagram.md.jinja2

@@ -13,7 +13,7 @@
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} : {{gen.name(s)}}
         {% if s.range not in gen.all_type_object_names() %}
-          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+          {{ gen.name(element) }} --> {{ s.range }} : {{ gen.name(s) }}
         {% endif %}
       {% endfor %}
 ```
@@ -27,7 +27,7 @@
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} : {{gen.name(s)}}
         {% if s.range not in gen.all_type_object_names() %}
-          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+          {{ gen.name(element) }} --> {{ s.range }} : {{ gen.name(s) }}
         {% endif %}
       {% endfor %}
 ```
@@ -41,7 +41,7 @@
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} : {{gen.name(s)}}
         {% if s.range not in gen.all_type_object_names() %}
-          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+          {{ gen.name(element) }} --> {{ s.range }} : {{ gen.name(s) }}
         {% endif %}
       {% endfor %}
 ```
@@ -52,7 +52,7 @@
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} : {{gen.name(s)}}
         {% if s.range not in gen.all_type_object_names() %}
-          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+          {{ gen.name(element) }} --> {{ s.range }} : {{ gen.name(s) }}
         {% endif %}
       {% endfor %}
 ```

linkml/generators/docgen.py

@@ -28,6 +28,7 @@ from linkml_runtime.utils.schemaview import SchemaView
 
 from linkml._version import __version__
 from linkml.generators.erdiagramgen import ERDiagramGenerator
+from linkml.generators.plantumlgen import PlantumlGenerator
 from linkml.utils.generator import Generator, shared_arguments
 from linkml.workspaces.example_runner import ExampleRunner
 
@@ -38,7 +39,8 @@ class MarkdownDialect(Enum):
 
 
 class DiagramType(Enum):
-    uml_class_diagram = "uml_class_diagram"
+    mermaid_class_diagram = "mermaid_class_diagram"
+    plantuml_class_diagram = "plantuml_class_diagram"
     er_diagram = "er_diagram"
 
 
@@ -593,8 +595,13 @@ class DocGenerator(Generator):
                 return erdgen.serialize_classes(class_names, follow_references=True, max_hops=2)
             else:
                 return erdgen.serialize()
-        elif self.diagram_type.value == DiagramType.uml_class_diagram.value:
+        elif self.diagram_type.value == DiagramType.mermaid_class_diagram.value:
             self.logger.info("This is currently handled in the jinja templates")
+        elif self.diagram_type.value == DiagramType.plantuml_class_diagram.value:
+            plantumlgen = PlantumlGenerator(self.schema)
+            plantuml_diagram = plantumlgen.serialize(classes=class_names)
+            self.logger.debug(f"Created PlantUML diagram for class: {class_names}")
+            return plantuml_diagram
         else:
             raise NotImplementedError(f"Diagram type {self.diagram_type} not implemented")
 

linkml/generators/jsonschemagen.py

@@ -1,7 +1,6 @@
 import json
 import logging
 import os
-from collections import UserDict
 from copy import deepcopy
 from dataclasses import dataclass, field
 from typing import Any, Dict, List, Optional, Tuple, Union
@@ -43,7 +42,7 @@ json_schema_types: Dict[str, Tuple[str, Optional[str]]] = {
 }
 
 
-class JsonSchema(UserDict):
+class JsonSchema(dict):
     OPTIONAL_IDENTIFIER_SUFFIX = "__identifier_optional"
 
     def __init__(self, *args, **kwargs):
@@ -83,7 +82,9 @@ class JsonSchema(UserDict):
                 lax_cls["required"].remove(identifier_name)
                 self["$defs"][canonical_name + self.OPTIONAL_IDENTIFIER_SUFFIX] = lax_cls
 
-    def add_property(self, name: str, subschema: "JsonSchema", required: bool = False) -> None:
+    def add_property(
+        self, name: str, subschema: "JsonSchema", *, value_required: bool = False, value_disallowed: bool = False
+    ) -> None:
         canonical_name = underscore(name)
 
         if "properties" not in self:
@@ -91,12 +92,32 @@ class JsonSchema(UserDict):
 
         self["properties"][canonical_name] = subschema
 
-        if required:
+        if value_required:
             if "required" not in self:
                 self["required"] = []
 
             self["required"].append(canonical_name)
 
+        # JSON Schema does not have a very natural way to express that a property cannot be present.
+        # The apparent best way to do it is to use:
+        # {
+        #   properties: {
+        #     foo: ...
+        #   },
+        #   not: {
+        #     required: ['foo']
+        #   }
+        # }
+        # The {required: [foo]} subschema evaluates to true if the foo property is present with any
+        # value. Wrapping that in a `not` keyword inverts that condition.
+        if value_disallowed:
+            if "not" not in self:
+                self["not"] = {}
+            if "required" not in self["not"]:
+                self["not"]["required"] = []
+
+            self["not"]["required"].append(canonical_name)
+
     def add_keyword(self, keyword: str, value: Any):
         if value is None:
             return
@@ -112,7 +133,7 @@ class JsonSchema(UserDict):
         return self.get("type") == "object"
 
     def to_json(self, **kwargs) -> str:
-        return json.dumps(self.data, default=lambda d: d.data, **kwargs)
+        return json.dumps(self, **kwargs)
 
     @classmethod
     def ref_for(cls, class_name: Union[str, List[str]], identifier_optional: bool = False):
@@ -190,7 +211,7 @@ class JsonSchemaGenerator(Generator):
 
         self.top_level_schema = JsonSchema(
             {
-                "$schema": "http://json-schema.org/draft-07/schema#",
+                "$schema": "https://json-schema.org/draft/2019-09/schema",
                 "$id": self.schema.id,
                 "metamodel_version": metamodel_version,
                 "version": self.schema.version if self.schema.version else None,
@@ -204,13 +225,15 @@ class JsonSchemaGenerator(Generator):
         if cls.mixin or cls.abstract:
             return
 
+        subschema_type = "object"
         additional_properties = False
         if self.is_class_unconstrained(cls):
+            subschema_type = ["null", "boolean", "object", "number", "string"]
             additional_properties = True
 
         class_subschema = JsonSchema(
             {
-                "type": "object",
+                "type": subschema_type,
                 "additionalProperties": additional_properties,
                 "description": be(cls.description),
             }
@@ -220,42 +243,44 @@ class JsonSchemaGenerator(Generator):
             self.handle_class_slot(subschema=class_subschema, cls=cls, slot=slot_definition)
 
         rule_subschemas = []
-        for rule in cls.rules:
-            subschema = JsonSchema()
+        for ancestor_class_name in self.schemaview.class_ancestors(cls.name):
+            ancestor_class = self.schemaview.get_class(ancestor_class_name)
+            for rule in ancestor_class.rules:
+                subschema = JsonSchema()
 
-            open_world = rule.open_world
-            if open_world is None:
-                open_world = False
+                open_world = rule.open_world
+                if open_world is None:
+                    open_world = False
 
-            if_subschema = self.get_subschema_for_anonymous_class(rule.preconditions, properties_required=True)
-            if if_subschema:
-                subschema["if"] = if_subschema
+                if_subschema = self.get_subschema_for_anonymous_class(rule.preconditions, properties_required=True)
+                if if_subschema:
+                    subschema["if"] = if_subschema
 
-            then_subschema = self.get_subschema_for_anonymous_class(
-                rule.postconditions, properties_required=not open_world
-            )
-            if then_subschema:
-                subschema["then"] = then_subschema
+                then_subschema = self.get_subschema_for_anonymous_class(
+                    rule.postconditions, properties_required=not open_world
+                )
+                if then_subschema:
+                    subschema["then"] = then_subschema
 
-            # same as required requirements as postconditions?
-            else_subschema = self.get_subschema_for_anonymous_class(
-                rule.elseconditions, properties_required=not open_world
-            )
-            if else_subschema:
-                subschema["else"] = else_subschema
+                # same as required requirements as postconditions?
+                else_subschema = self.get_subschema_for_anonymous_class(
+                    rule.elseconditions, properties_required=not open_world
+                )
+                if else_subschema:
+                    subschema["else"] = else_subschema
 
-            rule_subschemas.append(subschema)
+                rule_subschemas.append(subschema)
 
-            if rule.bidirectional:
-                inverse_subschema = JsonSchema()
+                if rule.bidirectional:
+                    inverse_subschema = JsonSchema()
 
-                if then_subschema:
-                    inverse_subschema["if"] = then_subschema
+                    if then_subschema:
+                        inverse_subschema["if"] = then_subschema
 
-                if if_subschema:
-                    inverse_subschema["then"] = if_subschema
+                    if if_subschema:
+                        inverse_subschema["then"] = if_subschema
 
-                rule_subschemas.append(inverse_subschema)
+                    rule_subschemas.append(inverse_subschema)
 
         if len(rule_subschemas) == 1:
             class_subschema.update(rule_subschemas[0])
@@ -285,20 +310,20 @@ class JsonSchemaGenerator(Generator):
         subschema = JsonSchema()
         for slot in cls.slot_conditions.values():
             prop = self.get_subschema_for_slot(slot, omit_type=True)
+            value_required = False
+            value_disallowed = False
             if slot.value_presence:
                 if slot.value_presence == PresenceEnum(PresenceEnum.PRESENT):
-                    this_properties_required = True
+                    value_required = True
                 elif slot.value_presence == PresenceEnum(PresenceEnum.ABSENT):
-                    this_properties_required = False
-                    # make the slot unsatisfiable
-                    prop["enum"] = []
-                else:
-                    this_properties_required = False
+                    value_disallowed = True
             elif slot.required is not None:
-                this_properties_required = slot.required
+                value_required = slot.required
             else:
-                this_properties_required = properties_required
-            subschema.add_property(self.aliased_slot_name(slot), prop, this_properties_required)
+                value_required = properties_required
+            subschema.add_property(
+                self.aliased_slot_name(slot), prop, value_required=value_required, value_disallowed=value_disallowed
+            )
 
         if cls.any_of is not None and len(cls.any_of) > 0:
             subschema["anyOf"] = [self.get_subschema_for_anonymous_class(c, properties_required) for c in cls.any_of]
@@ -343,7 +368,9 @@ class JsonSchemaGenerator(Generator):
             enum_schema["enum"] = permissible_values_texts
         self.top_level_schema.add_def(enum.name, enum_schema)
 
-    def get_type_info_for_slot_subschema(self, slot: AnonymousSlotExpression) -> Tuple[str, str, Union[str, List[str]]]:
+    def get_type_info_for_slot_subschema(
+        self, slot: Union[SlotDefinition, AnonymousSlotExpression]
+    ) -> Tuple[str, str, Union[str, List[str]]]:
         # JSON Schema type (https://json-schema.org/understanding-json-schema/reference/type.html)
         typ = None
         # Reference to a JSON schema entity (https://json-schema.org/understanding-json-schema/structuring.html#ref)
@@ -379,7 +406,7 @@ class JsonSchemaGenerator(Generator):
 
         return (typ, fmt, reference)
 
-    def get_value_constraints_for_slot(self, slot: Union[AnonymousSlotExpression, None]) -> JsonSchema:
+    def get_value_constraints_for_slot(self, slot: Union[SlotDefinition, AnonymousSlotExpression, None]) -> JsonSchema:
         if slot is None:
             return JsonSchema()
 
@@ -397,11 +424,6 @@ class JsonSchemaGenerator(Generator):
         constraints.add_keyword("maximum", slot.maximum_value)
         constraints.add_keyword("const", slot.equals_string)
         constraints.add_keyword("const", slot.equals_number)
-        if slot.value_presence:
-            if slot.value_presence == PresenceEnum(PresenceEnum.PRESENT):
-                constraints.add_keyword("required", True)
-            elif slot.value_presence == PresenceEnum(PresenceEnum.ABSENT):
-                constraints.add_keyword("enum", [])
         return constraints
 
     def get_subschema_for_slot(self, slot: SlotDefinition, omit_type: bool = False) -> JsonSchema:
@@ -503,17 +525,22 @@ class JsonSchemaGenerator(Generator):
 
     def handle_class_slot(self, subschema: JsonSchema, cls: ClassDefinition, slot: SlotDefinition) -> None:
         class_id_slot = self.schemaview.get_identifier_slot(cls.name, use_key=True)
-        slot_is_required = slot.required or slot == class_id_slot
+        value_required = (
+            slot.required or slot == class_id_slot or slot.value_presence == PresenceEnum(PresenceEnum.PRESENT)
+        )
+        value_disallowed = slot.value_presence == PresenceEnum(PresenceEnum.ABSENT)
 
         aliased_slot_name = self.aliased_slot_name(slot)
         prop = self.get_subschema_for_slot(slot)
-        subschema.add_property(aliased_slot_name, prop, slot_is_required)
+        subschema.add_property(
+            aliased_slot_name, prop, value_required=value_required, value_disallowed=value_disallowed
+        )
 
         if slot.designates_type:
             type_value = get_type_designator_value(self.schemaview, slot, cls)
             prop["enum"] = [type_value]
 
-    def generate(self) -> dict:
+    def generate(self) -> JsonSchema:
         self.start_schema()
         for enum_definition in self.schemaview.all_enums().values():
             self.handle_enum(enum_definition)

linkml/generators/pydanticgen.py

@@ -43,6 +43,9 @@ def default_template(pydantic_ver: str = "1", extra_fields: str = "forbid") -> s
 from __future__ import annotations
 from datetime import datetime, date
 from enum import Enum
+{% if uses_numpy -%}
+import numpy as np
+{%- endif %}
 from typing import List, Dict, Optional, Any, Union"""
     if pydantic_ver == "1":
         template += """
@@ -86,7 +89,9 @@ class ConfiguredBaseModel(BaseModel):
         extra = '{extra_fields}',
         arbitrary_types_allowed=True,
         use_enum_values = True)
+    pass
 """
+
     ### ENUMS ###
     template += """
 {% for e in enums.values() %}
@@ -157,7 +162,7 @@ class {{ c.name }}
                 raise ValueError(f"Invalid {{attr.name}} format: {v}")
         return v
     {% endif -%}
-    {% endfor %}    
+    {% endfor %}
 {% endfor %}
 """
     elif pydantic_ver == "2":
@@ -209,7 +214,7 @@ class {{ c.name }}
                 raise ValueError(f"Invalid {{attr.name}} format: {v}")
         return v
     {% endif -%}
-    {% endfor %}    
+    {% endfor %}
 {% endfor %}
 """
 
@@ -344,6 +349,8 @@ class PydanticGenerator(OOCodeGenerator):
                 # Multivalued slots that are either not inlined (just an identifier) or are
                 # inlined as lists should get default_factory list, if they're inlined but
                 # not as a list, that means a dictionary
+                elif "linkml:elements" in slot.implements:
+                    slot_values[camelcase(class_def.name)][slot.name] = None
                 elif slot.multivalued:
                     has_identifier_slot = self.range_class_has_identifier_slot(slot)
 
@@ -535,6 +542,8 @@ class PydanticGenerator(OOCodeGenerator):
         )
         enums = self.generate_enums(sv.all_enums())
 
+        uses_numpy = False
+
         sorted_classes = self.sort_classes(list(sv.all_classes().values()))
         self.sorted_class_names = [camelcase(c.name) for c in sorted_classes]
 
@@ -587,7 +596,13 @@ class PydanticGenerator(OOCodeGenerator):
                 else:
                     raise Exception(f"Could not generate python range for {class_name}.{s.name}")
 
-                if s.multivalued:
+                if "linkml:elements" in s.implements:
+                    # TODO add support for xarray
+                    pyrange = "np.ndarray"
+                    if "linkml:ColumnOrderedArray" in class_def.implements:
+                        raise NotImplementedError("Cannot generate Pydantic code for ColumnOrderedArrays.")
+                    uses_numpy = True
+                elif s.multivalued:
                     if s.inlined or s.inlined_as_list:
                         collection_key = self.generate_collection_key(slot_ranges, s, class_def)
                     else:
@@ -609,6 +624,7 @@ class PydanticGenerator(OOCodeGenerator):
             metamodel_version=self.schema.metamodel_version,
             version=self.schema.version,
             class_isa_plus_mixins=self.get_class_isa_plus_mixins(),
+            uses_numpy=uses_numpy,
         )
         return code
 

linkml/generators/shexgen.py

@@ -2,6 +2,7 @@
 
 """
 import os
+import urllib.parse as urlparse
 from dataclasses import dataclass, field
 from typing import List, Optional, Union
 
@@ -139,7 +140,24 @@ class ShExGenerator(Generator):
             constraint.predicate = self.namespaces.uri_for(slot.slot_uri)
             constraint.min = int(bool(slot.required))
             constraint.max = 1 if not slot.multivalued else -1
-            constraint.valueExpr = self._class_or_type_uri(slot.range)
+            if slot.range in self.schema.enums:
+                # Handle permissible values from enums
+                enum = self.schema.enums[slot.range]
+                values = []
+                for value in enum.permissible_values.values():
+                    if value.meaning:
+                        values.append(self.namespaces.uri_for(value.meaning))
+                    else:
+                        value_uri = f"{self._class_or_type_uri(enum.name)}#{urlparse.quote(value.text)}"
+                        values.append(value_uri)
+                if values:
+                    node_constraint = NodeConstraint(
+                        # id=self._class_or_type_uri(slot.range),
+                        values=values,
+                    )
+                    constraint.valueExpr = node_constraint
+            else:
+                constraint.valueExpr = self._class_or_type_uri(slot.range)
 
     def end_schema(self, output: Optional[str] = None, **_) -> None:
         self.shex.shapes = self.shapes if self.shapes else [Shape()]

linkml/generators/typescriptgen.py

@@ -84,11 +84,11 @@ export function is{{gen.name(c)}}(o: object): o is {{gen.name(c)}} {
     {%- set rcs = gen.required_slots(c) %}
     {%- set comp = "&&" if rcs else "||" %}
     {%- set cs = rcs if rcs else view.class_slots(c.name, direct=False) %}
-    return {
+    return (
         {%- for sn in cs %}
         '{{sn}}' in o {%- if not loop.last %} {{comp}}{% endif -%}
         {%- endfor %}
-    }
+    )
 }
 
 export function to{{gen.name(c)}}(o: {{gen.name(c)}}): {{gen.name(c)}} {

linkml/linter/cli.py

@@ -16,7 +16,7 @@ YAML_SUFFIXES = [".yml", ".yaml"]
 DEFAULT_CONFIG_FILES = [".linkmllint.yaml", ".linkmllint.yml"]
 
 
-def get_yaml_files(root: Path) -> Iterable[str]:
+def get_yaml_files(root: Path, accept_dot_files: bool) -> Iterable[str]:
     if root.is_file():
         if root.suffix not in YAML_SUFFIXES:
             raise click.UsageError("SCHEMA must be a YAML file")
@@ -26,6 +26,8 @@ def get_yaml_files(root: Path) -> Iterable[str]:
             for file in files:
                 if file in DEFAULT_CONFIG_FILES:
                     continue
+                if file.startswith(".") and not accept_dot_files:
+                    continue
                 path = Path(dir, file)
                 if path.suffix in YAML_SUFFIXES:
                     yield str(path)
@@ -36,6 +38,7 @@ def get_yaml_files(root: Path) -> Iterable[str]:
     "schema",
     type=click.Path(exists=True, dir_okay=True, file_okay=True, resolve_path=True, path_type=Path),
 )
+@click.option("-a", "--all", is_flag=True, default=False, help="Process files that start with '.'.")
 @click.option(
     "-c",
     "--config",
@@ -82,6 +85,7 @@ def get_yaml_files(root: Path) -> Iterable[str]:
 def main(
     schema: Path,
     fix: bool,
+    all: bool,
     config: str,
     format: str,
     validate: bool,
@@ -124,7 +128,7 @@ def main(
     error_count = 0
     warning_count = 0
     formatter.start_report()
-    for path in get_yaml_files(schema):
+    for path in get_yaml_files(schema, all):
         formatter.start_schema(path)
         report = linter.lint(path, fix=fix, validate_schema=validate, validate_only=validate_only)
         for problem in report:

linkml/linter/linter.py

@@ -1,5 +1,4 @@
 import inspect
-import json
 from copy import deepcopy
 from dataclasses import dataclass
 from functools import lru_cache
@@ -38,8 +37,9 @@ def get_named_config(name: str) -> Dict[str, Any]:
 @lru_cache
 def get_metamodel_validator() -> jsonschema.Validator:
     meta_json_gen = JsonSchemaGenerator(LOCAL_METAMODEL_YAML_FILE, not_closed=False)
-    meta_json_schema = json.loads(meta_json_gen.serialize())
-    validator = jsonschema.Draft7Validator(meta_json_schema)
+    meta_json_schema = meta_json_gen.generate()
+    validator_cls = jsonschema.validators.validator_for(meta_json_schema, default=jsonschema.Draft7Validator)
+    validator = validator_cls(meta_json_schema, format_checker=validator_cls.FORMAT_CHECKER)
     return validator
 
 

linkml/utils/datautils.py

@@ -79,14 +79,14 @@ def infer_root_class(sv: SchemaView) -> Optional[ClassDefinitionName]:
         if c.tree_root:
             return c.name
     refs = defaultdict(int)
-    for cn in sv.all_class().keys():
+    for cn in sv.all_classes().keys():
         for sn in sv.class_slots(cn):
             slot = sv.induced_slot(sn, cn)
             r = slot.range
-            if r in sv.all_class():
+            if r in sv.all_classes():
                 for a in sv.class_ancestors(r):
                     refs[a] += 1
-    candidates = [cn for cn in sv.all_class().keys() if cn not in refs]
+    candidates = [cn for cn in sv.all_classes().keys() if cn not in refs]
 
     # throw Exception if unambiguous root cannot be inferred
     if len(candidates) > 1:
@@ -106,7 +106,7 @@ def infer_index_slot(sv: SchemaView, root_class: ClassDefinitionName) -> Optiona
     index_slots = []
     for sn in sv.class_slots(root_class):
         slot = sv.induced_slot(sn, root_class)
-        if slot.multivalued and slot.range in sv.all_class():
+        if slot.multivalued and slot.range in sv.all_classes():
             index_slots.append(sn)
     if len(index_slots) == 1:
         return index_slots[0]

linkml/validator/plugins/jsonschema_validation_plugin.py

@@ -1,7 +1,6 @@
 import os
 from typing import Any, Iterator, Optional
 
-import jsonschema
 from jsonschema.exceptions import best_match
 
 from linkml.validator.plugins.validation_plugin import ValidationPlugin
@@ -41,12 +40,11 @@ class JsonschemaValidationPlugin(ValidationPlugin):
         :return: Iterator over validation results
         :rtype: Iterator[ValidationResult]
         """
-        json_schema = context.json_schema(
+        validator = context.json_schema_validator(
             closed=self.closed,
             include_range_class_descendants=self.include_range_class_descendants,
             path_override=self.json_schema_path,
         )
-        validator = jsonschema.Draft7Validator(json_schema, format_checker=jsonschema.Draft7Validator.FORMAT_CHECKER)
         for error in validator.iter_errors(instance):
             best_error = best_match([error])
             yield ValidationResult(

linkml/validator/validation_context.py

@@ -3,6 +3,7 @@ import os
 from functools import lru_cache
 from typing import Optional
 
+import jsonschema
 from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model import SchemaDefinition
 
@@ -29,26 +30,29 @@ class ValidationContext:
         return self._target_class
 
     @lru_cache
-    def json_schema(
+    def json_schema_validator(
         self,
         *,
         closed: bool,
         include_range_class_descendants: bool,
         path_override: Optional[os.PathLike] = None,
-    ):
+    ) -> jsonschema.Validator:
         if path_override:
             with open(path_override) as json_schema_file:
-                return json.load(json_schema_file)
+                json_schema = json.load(json_schema_file)
+        else:
+            not_closed = not closed
+            jsonschema_gen = JsonSchemaGenerator(
+                schema=self._schema,
+                mergeimports=True,
+                top_class=self._target_class,
+                not_closed=not_closed,
+                include_range_class_descendants=include_range_class_descendants,
+            )
+            json_schema = jsonschema_gen.generate()
 
-        not_closed = not closed
-        jsonschema_gen = JsonSchemaGenerator(
-            schema=self._schema,
-            mergeimports=True,
-            top_class=self._target_class,
-            not_closed=not_closed,
-            include_range_class_descendants=include_range_class_descendants,
-        )
-        return jsonschema_gen.generate()
+        validator_cls = jsonschema.validators.validator_for(json_schema, default=jsonschema.Draft7Validator)
+        return validator_cls(json_schema, format_checker=validator_cls.FORMAT_CHECKER)
 
     def pydantic_model(self, *, closed: bool):
         module = self._pydantic_module(closed=closed)

linkml/validators/jsonschemavalidator.py

@@ -105,7 +105,8 @@ class JsonSchemaDataValidator(DataValidator):
         jsonschema_obj = _generate_jsonschema(
             self._hashable_schema, target_class_name, closed, self.include_range_class_descendants
         )
-        validator = jsonschema.Draft7Validator(jsonschema_obj, format_checker=jsonschema.Draft7Validator.FORMAT_CHECKER)
+        validator_cls = jsonschema.validators.validator_for(jsonschema_obj, default=jsonschema.Draft7Validator)
+        validator = validator_cls(jsonschema_obj, format_checker=validator_cls.FORMAT_CHECKER)
         for error in validator.iter_errors(data):
             best_error = best_match([error])
             # TODO: This should return some kind of standard validation result

{linkml-1.6.7.dist-info → linkml-1.6.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.6.7
+Version: 1.6.9
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -18,7 +18,6 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Topic :: Software Development :: Libraries :: Python Modules

{linkml-1.6.7.dist-info → linkml-1.6.9.dist-info}/RECORD

@@ -6,8 +6,8 @@ linkml/generators/__init__.py,sha256=qa22iTeBrcds6ndst_iTPVWLQtBF6NGyhVngBhbhIpc
 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/docgen/class.md.jinja2,sha256=05Kbl83ApOMzA7gZeRJjPU7jkZHCIsaKN1BYWNMRTfM,3275
-linkml/generators/docgen/class_diagram.md.jinja2,sha256=ShRhNnIae54Y_4zrfXuIF6BjX8oCHRZJnovE8G1fjOU,2542
+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
 linkml/generators/docgen/enum.md.jinja2,sha256=mXnUrRkleY2bOTEyAZ5c4pcUnqhs6BNa8a-4LVve-eo,1014
 linkml/generators/docgen/index.md.jinja2,sha256=wXUYTmayPLFltC0vbGE_Mf6m3GkkWav7FOEjCvEpHp4,1466
@@ -16,7 +16,7 @@ linkml/generators/docgen/schema.md.jinja2,sha256=xlENfnzNRYgPT_0tdqNFxgklVM4Qf5B
 linkml/generators/docgen/slot.md.jinja2,sha256=XVd0M4gKx9Q2fONcsUGBRj_bJivyN4P9jhj9IO496jQ,2817
 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=zsLzbXN2t9pafQubEnb7QshufMKBMqUWjdLE1OyFyq8,33296
+linkml/generators/docgen.py,sha256=Kwg4ZIXL2e9G-q-_CUoj8Bgnpyyvvh5fKPnseDcTK04,33755
 linkml/generators/dotgen.py,sha256=CnbVY6CO1OMuiYXYnvxgNN2IW1mtOQW-J-QnwZlXkUI,5012
 linkml/generators/erdiagramgen.py,sha256=Gu-_nhLuEPTsYYaoV6tNS1V6cZ2dNJdm6YwxC0VGl7g,10315
 linkml/generators/excelgen.py,sha256=OhVzuQaDESYpAGR8Zv13hiWlDDJA8ugtSZatBJH0hzA,7737
@@ -28,7 +28,7 @@ linkml/generators/javagen/java_record_template.jinja2,sha256=OQZffLSy_xR3FIhQMlt
 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=WxwjuoBweicb14X0kThRl06LGV8AEdGcRVMunpDQXEc,24231
+linkml/generators/jsonschemagen.py,sha256=8fzOoR5ZRgchg7r-QxZsbkxlnfD7ytrLw6qKjIRgmWo,25294
 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
@@ -39,11 +39,11 @@ linkml/generators/plantumlgen.py,sha256=Vs__5x9ioiT4IBTbvZUpgT8MsYJ0amfBL64MB_nm
 linkml/generators/prefixmapgen.py,sha256=JJ7hgzuqKVfFZrbDV76Dk8dR2NHsmpp-eNUAspXkfwA,4626
 linkml/generators/projectgen.py,sha256=g3JR2oXPM_QXhWUGukP9ts1P7tqxIeABaRdv130gbo4,9578
 linkml/generators/protogen.py,sha256=9YfxBZkQdBWwsUbstxEUR4xRWNuAKSfz9zXPhgIYePU,2328
-linkml/generators/pydanticgen.py,sha256=lwdIJ81fRoDUs0AyYw6eS5xZ06Br8Q8xXb39qRBbB0I,24904
+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=Awtn5SyjS-TUcVCwMdT0F7hNO4K8VcSCYBaFru45Mwg,8994
+linkml/generators/shexgen.py,sha256=E-R8jg5Z3JzzsVAIPu6Fs9FtFF7k-I5-5vMwG1jGW2U,9858
 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
@@ -55,11 +55,11 @@ linkml/generators/sssomgen.py,sha256=yur3q7so9uwIELWZaZRzkJwNbz_ppBL7IQki9XLIM3k
 linkml/generators/string_template.md,sha256=kRcfic6entgIaJdpSg6GF3jcjC9wbKsCVM6wVT2qipc,1788
 linkml/generators/summarygen.py,sha256=aeWAUeOaWhn1WHZKnJ3TcKVku_6psrw88ubMc-GQzEc,2924
 linkml/generators/terminusdbgen.py,sha256=_po9KnOz6Uoctb9Y4fJuU_voW4uA5pepvZTmHLQ2_DE,4470
-linkml/generators/typescriptgen.py,sha256=QYa8HGWFY3wL3bNZBax4LG_T62b2sXIAzDYsIp_ry3Y,8565
+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/linter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/linter/cli.py,sha256=RpZYyR_Re0E7yh1fifvQVJagi8KvLDaseF3Zgs2E3uw,4254
+linkml/linter/cli.py,sha256=BpQiETcRfQlZsI1-JALyU9wXPgPOm_KE_n11p0iJaC8,4494
 linkml/linter/config/datamodel/.linkmllint.yaml,sha256=40rNhcL35FXQSjlVBMWnyPgplwEUqFT_sJmeZqUzxMw,292
 linkml/linter/config/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/linter/config/datamodel/config.py,sha256=4HtqHF2ZiYx0Izm50eUQRvygsm1xSnkc49w0nd9zbGk,16837
@@ -72,7 +72,7 @@ linkml/linter/formatters/json_formatter.py,sha256=rrOELuETUCFTl1Ewnrus9Rx9hl2g4u
 linkml/linter/formatters/markdown_formatter.py,sha256=sumF2MNJYL5oipLwCftCr3AiaCmVhd9V6di9aYpJ29I,2605
 linkml/linter/formatters/terminal_formatter.py,sha256=xmNwlRieVCssRt3fpnNP5WWw_YXGmaBsbxFoMWufy5M,2085
 linkml/linter/formatters/tsv_formatter.py,sha256=1VW-1Tv16mwhIDpHdExYpJJR3z42K5_XK2C-4mmYYdE,871
-linkml/linter/linter.py,sha256=Bh153eN1Gb1EL7kM20w15CTPovbJYJoravXd5zxiVHQ,4984
+linkml/linter/linter.py,sha256=B4zPHkS_8qWV2WJY74HDiIroajsXRmfJLIlwYky-cyA,5101
 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
@@ -84,7 +84,7 @@ linkml/transformers/schema_renamer.py,sha256=Cr18TyktX64b5iFh5V6R_ILPVzXjbDYVDDZ
 linkml/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/utils/cli_utils.py,sha256=MdVbox1qr6kDUHUCWAmFhV-D6ebs_nn8vVwB8KDQfew,742
 linkml/utils/converter.py,sha256=rdhCI7Tsjddr3o1rVBfMq5gQubk_GE6fqlBBmyxI5_M,6270
-linkml/utils/datautils.py,sha256=2XWM9LBSVp8v3SwIZECrX3SjDUYzdnP-syjp6YdL89E,3734
+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
@@ -109,23 +109,23 @@ linkml/validator/loaders/loader.py,sha256=YKQXmSZhCymvvb2Dbr4lVCKVDt-lOIayzRD7CW
 linkml/validator/loaders/passthrough_loader.py,sha256=fQvBZqzGnpdwpZio4Mbehmsb6ePpzcacHPuR1QWuhFM,525
 linkml/validator/loaders/yaml_loader.py,sha256=ZsMz-oGDkX9oPEOVcKnFRGhU9q0fKoHcL6BLOkCeB4c,914
 linkml/validator/plugins/__init__.py,sha256=F7Un7bfdpSRXvk8LTb7Z4Q22rCtJJKjNkqUfIVLFtT8,702
-linkml/validator/plugins/jsonschema_validation_plugin.py,sha256=GII3zGI727rFJlqZ40Yf5L8aP3i1NiO3IRfoTyAbmlE,2656
+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/validation_plugin.py,sha256=9SMHF8b2bgG9-8351e8bY676e0A4aEBJSXvMjMF5kXg,1548
 linkml/validator/report.py,sha256=kkkuh-IZF9--cO-2wGjwP3PDLvOcjjvC8AOlxXUIOAM,870
-linkml/validator/validation_context.py,sha256=MmOwLk4cF_Cy7fPdFK61Eti3c3dgzKSIu6r_PmkkoZs,2388
+linkml/validator/validation_context.py,sha256=2BYbw0czAYepJUNoIINyTnmW6SrgK6et7SNvH5ejzgU,2700
 linkml/validator/validator.py,sha256=sdWbAOlnNYQWnZSEIuLpGQqH3W4cNq_8M_CdLtsNMH0,5648
 linkml/validators/__init__.py,sha256=43W3J5NPKhwa3ZFHLRYsJMocwQKWGYCF9Ki9r0ccGbc,202
-linkml/validators/jsonschemavalidator.py,sha256=_v0finzU2RGPC5xo0CylYge9XkY7oAigcly2SKLwFuI,7865
+linkml/validators/jsonschemavalidator.py,sha256=_ku7MQGqA6KplbHMiyzDRqgRwwXGloobhLptuXqLCp4,7951
 linkml/validators/sparqlvalidator.py,sha256=JowuZ5KxmWkldgWIXAb8DJi7YCPm8x3it0QkgM4lSi0,4612
 linkml/workspaces/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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-1.6.7.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-linkml-1.6.7.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
-linkml-1.6.7.dist-info/entry_points.txt,sha256=za8r49Z5gcz3rAYTZLbxw5EPZr1rGuxSe1uiRUpf8R0,2143
-linkml-1.6.7.dist-info/METADATA,sha256=O7e8VhzgYyaMkWRTvG4asdaG7nHdDYRdo4dnqAXghX0,3496
-linkml-1.6.7.dist-info/RECORD,,
+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,,