linkml 1.7.2__py3-none-any.whl → 1.7.4__py3-none-any.whl

linkml/__init__.py

@@ -71,3 +71,10 @@ BIOLINK_MODEL_URI = "https://w3id.org/biolink/biolink-model"
 BIOLINK_MODEL_PYTHON_LOC = "biolink.model"
 
 TurtleSerializer.roundtrip_prefixes = [""]
+
+REQUESTS_TIMEOUT = 10
+"""
+Time (in seconds) to wait before failing a network request
+
+See: https://docs.python-requests.org/en/latest/user/advanced/#timeouts
+"""

linkml/generators/docgen.py

@@ -126,7 +126,7 @@ class DocGenerator(Generator):
     # ObjectVars
     dialect: Optional[Union[DIALECT, str]] = None
     """markdown dialect (e.g MyST, Python)"""
-    sort_by: str = field(default_factory=lambda: "name")
+    sort_by: str = "name"
     visit_all_class_slots = False
     template_mappings: Dict[str, str] = None
     directory: str = None
@@ -141,19 +141,19 @@ class DocGenerator(Generator):
     diagram_type: Optional[Union[DiagramType, str]] = None
     """style of diagram (ER, UML)"""
 
-    include_top_level_diagram: bool = field(default_factory=lambda: False)
+    include_top_level_diagram: bool = False
     """Whether the index page should include a schema diagram"""
 
     example_directory: Optional[str] = None
     example_runner: ExampleRunner = field(default_factory=lambda: ExampleRunner())
 
-    genmeta: bool = field(default_factory=lambda: False)
-    gen_classvars: bool = field(default_factory=lambda: True)
-    gen_slots: bool = field(default_factory=lambda: True)
-    no_types_dir: bool = field(default_factory=lambda: False)
-    use_slot_uris: bool = field(default_factory=lambda: False)
-    use_class_uris: bool = field(default_factory=lambda: False)
-    hierarchical_class_view: bool = field(default_factory=lambda: False)
+    genmeta: bool = False
+    gen_classvars: bool = True
+    gen_slots: bool = True
+    no_types_dir: bool = False
+    use_slot_uris: bool = False
+    use_class_uris: bool = False
+    hierarchical_class_view: bool = False
 
     def __post_init__(self):
         dialect = self.dialect

linkml/generators/erdiagramgen.py

@@ -1,5 +1,5 @@
 import os
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from enum import Enum
 from typing import List, Optional, Union
 
@@ -129,11 +129,11 @@ class ERDiagramGenerator(Generator):
     exclude_attributes: bool = False
     """If True, do not include attributes in entities"""
 
-    genmeta: bool = field(default_factory=lambda: False)
-    gen_classvars: bool = field(default_factory=lambda: True)
-    gen_slots: bool = field(default_factory=lambda: True)
-    no_types_dir: bool = field(default_factory=lambda: False)
-    use_slot_uris: bool = field(default_factory=lambda: False)
+    genmeta: bool = False
+    gen_classvars: bool = True
+    gen_slots: bool = True
+    no_types_dir: bool = False
+    use_slot_uris: bool = False
 
     def __post_init__(self):
         self.schemaview = SchemaView(self.schema)

linkml/generators/excelgen.py

@@ -1,5 +1,5 @@
 import logging
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from pathlib import Path
 from typing import List
 
@@ -22,8 +22,8 @@ class ExcelGenerator(Generator):
     uses_schemaloader = False
     requires_metamodel = False
 
-    split_workbook_by_class: bool = field(default_factory=lambda: False)
-    include_mixins: bool = field(default_factory=lambda: False)
+    split_workbook_by_class: bool = False
+    include_mixins: bool = False
 
     def __post_init__(self) -> None:
         super().__post_init__()

linkml/generators/golanggen.py

@@ -160,7 +160,7 @@ class GolangGenerator(Generator):
             rc_name = self.name(rc)
             id_slot = self.get_identifier_or_key_slot(r)
             if slot.multivalued:
-                if not id_slot or slot.inlined:
+                if not id_slot or slot.inlined or slot.inlined_as_list:
                     if slot.inlined_as_list or not id_slot:
                         return f"[]{rc_name}"
                     else:

linkml/generators/javagen.py

@@ -1,6 +1,6 @@
 import importlib.util
 import os
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import Optional
 
 import click
@@ -78,10 +78,10 @@ class JavaGenerator(OOCodeGenerator):
 
     template_file: Optional[str] = None
 
-    gen_classvars: bool = field(default_factory=lambda: True)
-    gen_slots: bool = field(default_factory=lambda: True)
-    genmeta: bool = field(default_factory=lambda: False)
-    emit_metadata: bool = field(default_factory=lambda: True)
+    gen_classvars: bool = True
+    gen_slots: bool = True
+    genmeta: bool = False
+    emit_metadata: bool = True
 
     def default_value_for_type(self, typ: str) -> str:
         return TYPE_DEFAULTS.get(typ, "null")

linkml/generators/jsonldcontextgen.py

@@ -45,12 +45,12 @@ class ContextGenerator(Generator):
     default_ns: str = None
     context_body: Dict = field(default_factory=lambda: dict())
     slot_class_maps: Dict = field(default_factory=lambda: dict())
-    emit_metadata: bool = field(default_factory=lambda: False)
-    model: Optional[bool] = field(default_factory=lambda: True)
+    emit_metadata: bool = False
+    model: Optional[bool] = True
     base: Optional[str] = None
     output: Optional[str] = None
-    prefixes: Optional[bool] = field(default_factory=lambda: True)
-    flatprefixes: Optional[bool] = field(default_factory=lambda: False)
+    prefixes: Optional[bool] = True
+    flatprefixes: Optional[bool] = False
 
     def __post_init__(self) -> None:
         super().__post_init__()
@@ -150,7 +150,8 @@ class ContextGenerator(Generator):
         else:
             slot_def = {}
             if not slot.usage_slot_name:
-                if slot.range in self.schema.classes:
+                any_of_ranges = [any_of_el.range for any_of_el in slot.any_of]
+                if slot.range in self.schema.classes or any(rng in self.schema.classes for rng in any_of_ranges):
                     slot_def["@type"] = "@id"
                 elif slot.range in self.schema.enums:
                     slot_def["@context"] = ENUM_CONTEXT

linkml/generators/jsonschemagen.py

@@ -2,7 +2,7 @@ import json
 import logging
 import os
 from copy import deepcopy
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import Any, Dict, List, Optional, Tuple, Union
 
 import click
@@ -179,7 +179,7 @@ class JsonSchemaGenerator(Generator):
     # @deprecated("Use top_class")
     topClass: Optional[str] = None
 
-    not_closed: Optional[bool] = field(default_factory=lambda: True)
+    not_closed: Optional[bool] = True
     """If not closed, then an open-ended set of attributes can be instantiated for any object"""
 
     indent: int = 4
@@ -188,7 +188,7 @@ class JsonSchemaGenerator(Generator):
     top_class: Optional[Union[ClassDefinitionName, str]] = None  # JSON object is one instance of this
     """Class instantiated by the root node of the document tree"""
 
-    include_range_class_descendants: bool = field(default_factory=lambda: False)
+    include_range_class_descendants: bool = False
     """If set, use an open world assumption and allow the range of a slot to be any descendant of the declared range.
     Note that if the range of a slot has a type designator, descendants will always be included.
     """

linkml/generators/linkmlgen.py

@@ -1,6 +1,6 @@
 import logging
 import os
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import Union
 
 import click
@@ -30,8 +30,8 @@ class LinkmlGenerator(Generator):
     uses_schemaloader = False
     requires_metamodel = False
 
-    materialize_attributes: bool = field(default_factory=lambda: False)
-    materialize_patterns: bool = field(default_factory=lambda: False)
+    materialize_attributes: bool = False
+    materialize_patterns: bool = False
 
     def __post_init__(self):
         # TODO: consider moving up a level

linkml/generators/markdowngen.py

@@ -1,6 +1,6 @@
 import os
 from contextlib import redirect_stdout
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from io import StringIO
 from typing import Any, Callable, Dict, List, Optional, Set, Union
 
@@ -47,7 +47,7 @@ class MarkdownGenerator(Generator):
     image_directory: Optional[str] = None
     classes: Set[ClassDefinitionName] = None
     image_dir: bool = False
-    index_file: str = field(default_factory=lambda: "index.md")
+    index_file: str = "index.md"
     noimages: bool = False
     noyuml: bool = False
     no_types_dir: bool = False

linkml/generators/oocodegen.py

@@ -141,7 +141,10 @@ class OOCodeGenerator(Generator):
                 enum["description"] = enum_original.description
 
             for pv in enum_original.permissible_values.values():
-                label = self.generate_enum_label(pv.text)
+                if pv.title:
+                    label = self.generate_enum_label(pv.title)
+                else:
+                    label = self.generate_enum_label(pv.text)
                 val = {"label": label, "value": pv.text.replace('"', '\\"')}
                 if hasattr(pv, "description"):
                     val["description"] = pv.description

linkml/generators/owlgen.py

@@ -118,29 +118,29 @@ class OwlSchemaGenerator(Generator):
     """By default, use the linkml metadata profile,
     this allows for overrides."""
 
-    metaclasses: bool = field(default_factory=lambda: True)
+    metaclasses: bool = True
     """if True, include OWL representations of ClassDefinition, SlotDefinition, etc. Introduces punning"""
 
-    add_root_classes: bool = field(default_factory=lambda: False)
+    add_root_classes: bool = False
 
-    add_ols_annotations: bool = field(default_factory=lambda: True)
+    add_ols_annotations: bool = True
     graph: Optional[Graph] = None
     """Mutable graph that is being built up during OWL generation."""
 
     top_value_uri: Optional[URIRef] = None
     """If metaclasses=True, then this property is used to connect object shadows to literals"""
 
-    type_objects: bool = field(default_factory=lambda: True)
+    type_objects: bool = True
     """if True, represents types as classes (and thus all slots are object properties);
     typed object classes effectively shadow the main xsd literal types.
     The purpose of this is to allow a uniform ObjectProperty representation for all slots,
     without having to commit to being either Data or Object property (OWL-DL does not
     allow a property to be both."""
 
-    assert_equivalent_classes: bool = field(default_factory=lambda: False)
+    assert_equivalent_classes: bool = False
     """If True, assert equivalence between definition_uris and class_uris"""
 
-    use_native_uris: bool = field(default_factory=lambda: True)
+    use_native_uris: bool = True
     """If True, use the definition_uris, otherwise use class_uris."""
 
     mixins_as_expressions: bool = None
@@ -152,10 +152,10 @@ class OwlSchemaGenerator(Generator):
     node_owltypes: Mapping[Union[BNode, URIRef], Set[OWL_TYPE]] = field(default_factory=lambda: defaultdict(set))
     """rdfs:Datatype, owl:Thing"""
 
-    simplify: bool = field(default_factory=lambda: True)
+    simplify: bool = True
     """Reduce complex expressions to simpler forms"""
 
-    use_swrl: bool = field(default_factory=lambda: False)
+    use_swrl: bool = False
     """Use of SWRL is experimental"""
 
     target_profile: OWLProfile = field(default_factory=lambda: OWLProfile.dl)
@@ -378,8 +378,12 @@ class OwlSchemaGenerator(Generator):
         # rules yield OWL GCI subClassOf axioms
         for rule in cls.rules:
             pre_node = condition_to_bnode(rule.preconditions)
+            if not pre_node:
+                continue
             pre_node = self._intersection_of([pre_node, subject_expr])
             post_node = condition_to_bnode(rule.postconditions)
+            if not post_node:
+                continue
             self.graph.add((pre_node, RDFS.subClassOf, post_node))
         # classification rules yield OWL GCI subClassOf axioms
         for expr in cls.classification_rules:
@@ -433,15 +437,10 @@ class OwlSchemaGenerator(Generator):
             if slot.name in slot_map:
                 for k, v in slot.__dict__.items():
                     curr = slot_map[slot.name].get(k, None)
-                    # print(f"MERGE={slot.name}.{k} = {v} // CURR={curr}")
                     if v and not curr:
                         slot_map[slot.name][k] = v
-                        # print(f"OVERRIDE={slot.name}, k={k}, v={v}")
             else:
                 slot_map[slot.name] = copy(slot.__dict__)
-                # print(f"INIT={slot.name}, vals={slot_map[slot.name]}")
-
-            # print(f"SN={slot.name}, vals={slot_map[slot.name]}")
         own_slots = [SlotDefinition(**v) for v in slot_map.values()]
         # sort by name
         own_slots.sort(key=lambda x: x.name)
@@ -462,6 +461,8 @@ class OwlSchemaGenerator(Generator):
         :param cls: LinkML class expression (anonymous if called recursively)
         :return: blank node representing the OWL expression
         """
+        if cls is None:
+            cls = AnonymousClassExpression()
         graph = self.graph
         sv = self.schemaview
         own_slots = self.get_own_slots(cls)
@@ -477,11 +478,13 @@ class OwlSchemaGenerator(Generator):
                 graph.add((cls_uri, OWL.disjointUnionOf, listnode))
             else:
                 sub_sub_exprs = []
-                for i, x in enumerate(sub_exprs):
-                    rest = sub_exprs[0:i] + sub_exprs[i + 1 :]
-                    neg_expr = self._complement_of_union_of(rest)
-                    sub_sub_exprs.append(self._intersection_of([x, neg_expr]))
-                sub_exprs.append(self._union_of(sub_sub_exprs))
+                for i, x in enumerate(cls.exactly_one_of):
+                    rest = cls.exactly_one_of[0:i] + cls.exactly_one_of[i + 1 :]
+                    neg_expr = self._complement_of_union_of([self.transform_class_expression(nx) for nx in rest])
+                    pos_expr = self._intersection_of([self.transform_class_expression(x), neg_expr])
+                    sub_sub_exprs.append(pos_expr)
+                owl_exprs.append(self._union_of(sub_sub_exprs))
+                # owl_exprs.extend(sub_exprs)
         if cls.all_of:
             owl_exprs.append(self._intersection_of([self.transform_class_expression(x) for x in cls.all_of]))
         if cls.none_of:
@@ -533,7 +536,8 @@ class OwlSchemaGenerator(Generator):
                 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))
+                if has_member_expr:
+                    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]:
@@ -558,7 +562,7 @@ class OwlSchemaGenerator(Generator):
         slot: Union[SlotDefinition, AnonymousSlotExpression],
         main_slot: SlotDefinition = None,
         owl_types: Set[OWL_TYPE] = None,
-    ) -> Union[BNode, URIRef]:
+    ) -> Optional[Union[BNode, URIRef]]:
         """
         Take a ClassExpression and SlotExpression combination and transform to a node.
 
@@ -597,11 +601,19 @@ class OwlSchemaGenerator(Generator):
                 )
             )
         if slot.exactly_one_of:
-            owl_exprs.append(
-                self._exactly_one_of(
-                    [self.transform_class_slot_expression(cls, x, main_slot, owl_types) for x in slot.exactly_one_of]
+            disj_exprs = []
+            for i, operand in enumerate(slot.exactly_one_of):
+                rest = slot.exactly_one_of[0:i] + slot.exactly_one_of[i + 1 :]
+                neg_expr = self._complement_of_union_of(
+                    [self.transform_class_slot_expression(cls, x, main_slot, owl_types) for x in rest],
+                    owl_types=owl_types,
                 )
-            )
+                pos_expr = self._intersection_of(
+                    [self.transform_class_slot_expression(cls, operand, main_slot, owl_types), neg_expr],
+                    owl_types=owl_types,
+                )
+                disj_exprs.append(pos_expr)
+            owl_exprs.append(self._union_of(disj_exprs, owl_types=owl_types))
         range = slot.range
         # if not range and not owl_exprs:
         #    range = sv.schema.default_range
@@ -929,6 +941,10 @@ class OwlSchemaGenerator(Generator):
                 triples.extend(graph.triples((obj, None, None)))
 
     def _some_values_from(self, property: URIRef, filler: Union[URIRef, BNode]) -> BNode:
+        if not property:
+            raise ValueError(f"Property is required, filler: {filler}")
+        if not filler:
+            raise ValueError(f"Filler is required, property: {property}")
         node = BNode()
         self.graph.add((node, RDF.type, OWL.Restriction))
         self.graph.add((node, OWL.onProperty, property))
@@ -970,11 +986,14 @@ class OwlSchemaGenerator(Generator):
     def _metaslot_uri(self, name: str) -> URIRef:
         return URIRef("https://w3id.org/linkml/" + name)
 
-    def _complement_of_union_of(self, exprs: List[Union[BNode, URIRef]], **kwargs) -> Optional[Union[BNode, URIRef]]:
+    def _complement_of_union_of(
+        self, exprs: List[Union[BNode, URIRef]], owl_types: Set[OWL_TYPE] = None, **kwargs
+    ) -> Optional[Union[BNode, URIRef]]:
         if not exprs:
             raise ValueError("Must pass at least one")
         neg_expr = BNode()
-        owl_types = self._get_owltypes(set(), exprs)
+        if not owl_types:
+            owl_types = self._get_owltypes(set(), exprs)
         complement_predicate = OWL.complementOf
         if len(owl_types) == 1:
             if RDFS.Literal in owl_types:

linkml/generators/plantumlgen.py

@@ -7,7 +7,7 @@ https://plantuml.com/
 import base64
 import os
 import zlib
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import Callable, List, Optional, Set, cast
 
 import click
@@ -19,6 +19,7 @@ from linkml_runtime.linkml_model.meta import (
 )
 from linkml_runtime.utils.formatutils import camelcase, underscore
 
+from linkml import REQUESTS_TIMEOUT
 from linkml._version import __version__
 from linkml.utils.generator import Generator, shared_arguments
 
@@ -48,7 +49,7 @@ class PlantumlGenerator(Generator):
     classes: Set[ClassDefinitionName] = None
     directory: Optional[str] = None
     kroki_server: Optional[str] = "https://kroki.io"
-    load_image: bool = field(default_factory=lambda: True)
+    load_image: bool = True
 
     def visit_schema(
         self,
@@ -101,7 +102,7 @@ class PlantumlGenerator(Generator):
                 camelcase(sorted(classes)[0] if classes else self.schema.name) + file_suffix,
             )
             if load_image:
-                resp = requests.get(plantuml_url, stream=True)
+                resp = requests.get(plantuml_url, stream=True, timeout=REQUESTS_TIMEOUT)
                 if resp.ok:
                     with open(self.output_file_name, "wb") as f:
                         for chunk in resp.iter_content(chunk_size=2048):

linkml/generators/protogen.py

@@ -1,5 +1,5 @@
 import os
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 
 import click
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
@@ -24,7 +24,7 @@ class ProtoGenerator(Generator):
     uses_schemaloader = True
 
     # ObjectVars
-    relative_slot_num: int = field(default_factory=lambda: 0)
+    relative_slot_num: int = 0
 
     def __post_init__(self):
         super().__post_init__()

linkml/generators/pydanticgen.py

@@ -1,10 +1,11 @@
+import inspect
 import logging
 import os
 from collections import defaultdict
 from copy import deepcopy
 from dataclasses import dataclass, field
 from types import ModuleType
-from typing import Dict, List, Optional, Set
+from typing import Dict, List, Optional, Set, Type, Union
 
 import click
 from jinja2 import Template
@@ -32,7 +33,9 @@ from linkml.utils.generator import shared_arguments
 from linkml.utils.ifabsent_functions import ifabsent_value_declaration
 
 
-def default_template(pydantic_ver: str = "1", extra_fields: str = "forbid") -> str:
+def default_template(
+    pydantic_ver: str = "1", extra_fields: str = "forbid", injected_classes: Optional[List[Union[Type, str]]] = None
+) -> str:
     """Constructs a default template for pydantic classes based on the version of pydantic"""
     ### HEADER ###
     template = """
@@ -46,6 +49,7 @@ from enum import Enum
 {% if uses_numpy -%}
 import numpy as np
 {%- endif %}
+from decimal import Decimal
 from typing import List, Dict, Optional, Any, Union"""
     if pydantic_ver == "1":
         template += """
@@ -61,7 +65,26 @@ if sys.version_info >= (3, 8):
 else:
     from typing_extensions import Literal
 
-
+{% if imports is not none %}
+{%- for import_module, import_classes in imports.items() -%}
+{% if import_classes is none -%}
+import {{ import_module }}
+{% elif import_classes is mapping -%}
+import {{ import_module }} as {{ import_classes['as'] }}
+{% else -%}
+from {{ import_module }} import (
+    {% for imported_class in import_classes %}
+    {%- if imported_class is string -%}
+    {{ imported_class }}
+    {%- else -%}
+    {{ imported_class['name'] }} as {{ imported_class['as'] }}
+    {%- endif -%}
+    {%- if not loop.last %},{{ '\n    ' }}{% else %}{{ '\n' }}{%- endif -%}
+    {% endfor -%}
+)
+{% endif -%}
+{% endfor -%}
+{% endif %}
 metamodel_version = "{{metamodel_version}}"
 version = "{{version if version else None}}"
 """
@@ -78,7 +101,6 @@ class ConfiguredBaseModel(WeakRefShimBaseModel,
                 extra = '{extra_fields}',
                 arbitrary_types_allowed = True,
                 use_enum_values = True):
-    pass
 """
     else:
         template += f"""
@@ -89,9 +111,27 @@ class ConfiguredBaseModel(BaseModel):
         extra = '{extra_fields}',
         arbitrary_types_allowed=True,
         use_enum_values = True)
-    pass
 """
 
+    ### Fields injected into base model
+    template += """{% if injected_fields is not none %}
+    {% for field in injected_fields -%}
+    {{ field }}
+    {% endfor %}
+{% else %}
+    pass
+{% endif %}
+        """
+
+    ### Extra classes
+    if injected_classes is not None and len(injected_classes) > 0:
+        template += """{{ '\n\n' }}"""
+        for cls in injected_classes:
+            if isinstance(cls, str):
+                template += cls + "\n\n"
+            else:
+                template += inspect.getsource(cls) + "\n\n"
+
     ### ENUMS ###
     template += """
 {% for e in enums.values() %}
@@ -270,14 +310,75 @@ class PydanticGenerator(OOCodeGenerator):
     # ObjectVars
     pydantic_version: str = field(default_factory=lambda: PYDANTIC_VERSION[0])
     template_file: str = None
-    extra_fields: str = field(default_factory=lambda: "forbid")
-    gen_mixin_inheritance: bool = field(default_factory=lambda: True)
+    extra_fields: str = "forbid"
+    gen_mixin_inheritance: bool = True
+    injected_classes: Optional[List[Union[Type, str]]] = None
+    """
+    A list/tuple of classes to inject into the generated module.
+    
+    Accepts either live classes or strings. Live classes will have their source code
+    extracted with inspect.get - so they need to be standard python classes declared in a
+    source file (ie. the module they are contained in needs a ``__file__`` attr, 
+    see: :func:`inspect.getsource` )
+    """
+    injected_fields: Optional[List[str]] = None
+    """
+    A list/tuple of field strings to inject into the base class.
+    
+    Examples:
+    
+    .. code-block:: python
+
+        injected_fields = (
+            'object_id: Optional[str] = Field(None, description="Unique UUID for each object")',
+        )
+    
+    """
+    imports: Optional[Dict[str, Union[None, Dict[str, str], List[Union[str, Dict[str, str]]]]]] = None
+    """
+    Additional imports to inject into generated module. 
+    
+    A dictionary mapping a module to a list of objects to import. 
+    If the value of an entry is ``None`` , import the whole module.
+    
+    Import Aliases:
+    If the value of a module import is a dictionary with a key "as",
+    or a class is specified as a dictionary with a "name" and "as",
+    then the import is renamed like "from module import class as renamedClass".
+    
+    Examples:
+        
+    .. code-block:: python
+    
+        imports = {
+            'typing': ['Dict', 'List', 'Union'],
+            'types': None,
+            'numpy': {'as': 'np'},
+            'collections': [{'name': 'OrderedDict', 'as': 'odict'}]
+        }
+        
+    becomes:
+    
+    .. code-block:: python
+    
+        from typing import (
+            Dict,
+            List,
+            Union
+        )
+        import types
+        import numpy as np
+        from collections import (
+            OrderedDict as odict
+        )
+    
+    """
 
     # ObjectVars (identical to pythongen)
-    gen_classvars: bool = field(default_factory=lambda: True)
-    gen_slots: bool = field(default_factory=lambda: True)
-    genmeta: bool = field(default_factory=lambda: False)
-    emit_metadata: bool = field(default_factory=lambda: True)
+    gen_classvars: bool = True
+    gen_slots: bool = True
+    genmeta: bool = False
+    emit_metadata: bool = True
 
     def compile_module(self, **kwargs) -> ModuleType:
         """
@@ -525,12 +626,48 @@ class PydanticGenerator(OOCodeGenerator):
             return list(collection_keys)[0]
         return None
 
+    def _inline_as_simple_dict_with_value(self, slot_def: SlotDefinition, sv: SchemaView) -> Optional[str]:
+        """
+        Determine if a slot should be inlined as a simple dict with a value.
+
+        For example, if we have a class such as Prefix, with two slots prefix and expansion,
+        then an inlined list of prefixes can be serialized as:
+
+        .. code-block:: yaml
+
+            prefixes:
+                prefix1: expansion1
+                prefix2: expansion2
+                ...
+
+        Provided that the prefix slot is the identifier slot for the Prefix class.
+
+        TODO: move this to SchemaView
+
+        :param slot_def: SlotDefinition
+        :param sv: SchemaView
+        :return: str
+        """
+        if slot_def.inlined and not slot_def.inlined_as_list:
+            if slot_def.range in sv.all_classes():
+                id_slot = sv.get_identifier_slot(slot_def.range, use_key=True)
+                if id_slot is not None:
+                    range_cls_slots = sv.class_induced_slots(slot_def.range)
+                    if len(range_cls_slots) == 2:
+                        non_id_slots = [slot for slot in range_cls_slots if slot.name != id_slot.name]
+                        if len(non_id_slots) == 1:
+                            value_slot = non_id_slots[0]
+                            value_slot_range_type = sv.get_type(value_slot.range)
+                            if value_slot_range_type is not None:
+                                return _get_pyrange(value_slot_range_type, sv)
+        return None
+
     def serialize(self) -> str:
         if self.template_file is not None:
             with open(self.template_file) as template_file:
                 template_obj = Template(template_file.read())
         else:
-            template_obj = Template(default_template(self.pydantic_version, self.extra_fields))
+            template_obj = Template(default_template(self.pydantic_version, self.extra_fields, self.injected_classes))
 
         sv: SchemaView
         sv = self.schemaview
@@ -610,7 +747,14 @@ class PydanticGenerator(OOCodeGenerator):
                     if s.inlined is False or collection_key is None or s.inlined_as_list is True:
                         pyrange = f"List[{pyrange}]"
                     else:
-                        pyrange = f"Dict[{collection_key}, {pyrange}]"
+                        simple_dict_value = None
+                        if len(slot_ranges) == 1:
+                            simple_dict_value = self._inline_as_simple_dict_with_value(s, sv)
+                        if simple_dict_value:
+                            # inlining as simple dict
+                            pyrange = f"Dict[str, {simple_dict_value}]"
+                        else:
+                            pyrange = f"Dict[{collection_key}, {pyrange}]"
                 if not (s.required or s.identifier or s.key) and not s.designates_type:
                     pyrange = f"Optional[{pyrange}]"
                 ann = Annotation("python_range", pyrange)
@@ -624,6 +768,8 @@ class PydanticGenerator(OOCodeGenerator):
             metamodel_version=self.schema.metamodel_version,
             version=self.schema.version,
             class_isa_plus_mixins=self.get_class_isa_plus_mixins(),
+            imports=self.imports,
+            injected_fields=self.injected_fields,
             uses_numpy=uses_numpy,
         )
         return code

linkml/generators/pythongen.py

@@ -3,7 +3,7 @@ import logging
 import os
 import re
 from copy import copy
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from types import ModuleType
 from typing import Callable, Dict, Iterator, List, Optional, Set, Tuple, Union
 
@@ -60,10 +60,10 @@ class PythonGenerator(Generator):
     uses_schemaloader = True
 
     # ObjectVars
-    gen_classvars: bool = field(default_factory=lambda: True)
-    gen_slots: bool = field(default_factory=lambda: True)
-    genmeta: bool = field(default_factory=lambda: False)
-    emit_metadata: bool = field(default_factory=lambda: True)
+    gen_classvars: bool = True
+    gen_slots: bool = True
+    genmeta: bool = False
+    emit_metadata: bool = True
 
     def __post_init__(self) -> None:
         self.sourcefile = self.schema

linkml/generators/rdfgen.py

@@ -7,7 +7,7 @@ Generate a JSON LD representation of the model
 
 import os
 import urllib.parse as urlparse
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import List, Optional
 
 import click
@@ -33,7 +33,7 @@ class RDFGenerator(Generator):
     uses_schemaloader = True
 
     # ObjectVars
-    emit_metadata: bool = field(default_factory=lambda: False)
+    emit_metadata: bool = False
     context: List[str] = None
 
     def _data(self, g: Graph) -> str:

linkml/generators/shaclgen.py

@@ -1,6 +1,6 @@
 import logging
 import os
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 
 import click
 from linkml_runtime.utils.formatutils import underscore
@@ -31,7 +31,7 @@ LINK_ML_TYPES_NODE_ID = URIRef("http://www.w3.org/ns/shex#nonLiteral")
 @dataclass
 class ShaclGenerator(Generator):
     # ClassVars
-    closed: bool = field(default_factory=lambda: True)
+    closed: bool = True
     """True means add 'sh:closed=true' to all shapes, except of mixin shapes and shapes, that have parents"""
 
     generatorname = os.path.basename(__file__)

linkml/generators/sqltablegen.py

@@ -1,6 +1,6 @@
 import logging
 import os
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import Optional
 
 import click
@@ -123,12 +123,12 @@ class SQLTableGenerator(Generator):
 
     # ObjectVars
     use_inherits: bool = False  # postgresql supports inheritance
-    dialect: str = field(default_factory=lambda: "sqlite")
-    inject_primary_keys: bool = field(default_factory=lambda: True)
-    use_foreign_keys: bool = field(default_factory=lambda: True)
-    rename_foreign_keys: bool = field(default_factory=lambda: False)
-    direct_mapping: bool = field(default_factory=lambda: False)
-    relative_slot_num: bool = field(default_factory=lambda: 0)
+    dialect: str = "sqlite"
+    inject_primary_keys: bool = True
+    use_foreign_keys: bool = True
+    rename_foreign_keys: bool = False
+    direct_mapping: bool = False
+    relative_slot_num: bool = False
 
     def serialize(self, **kwargs) -> str:
         return self.generate_ddl(**kwargs)
@@ -220,8 +220,12 @@ class SQLTableGenerator(Generator):
             schema = SchemaLoader(data=self.schema).resolve()
 
         if range in schema.classes:
-            # FKs treated as Text
-            return Text()
+            # FK type should be the same as the identifier of the foreign key
+            fk = SchemaView(schema).get_identifier_slot(range)
+            if fk:
+                return self.get_sql_range(fk, schema)
+            else:
+                return Text()
         if range in schema.enums:
             e = schema.enums[range]
             if e.permissible_values is not None:

linkml/generators/summarygen.py

@@ -5,7 +5,7 @@
 import os
 import sys
 from csv import DictWriter
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import Optional
 
 import click
@@ -26,7 +26,7 @@ class SummaryGenerator(Generator):
     dirname: str = None
     classtab: Optional[DictWriter] = None
     slottab: Optional[DictWriter] = None
-    dialect: str = field(default_factory=lambda: "excel-tab")
+    dialect: str = "excel-tab"
 
     def visit_schema(self, **_) -> None:
         self.classtab = DictWriter(

linkml/generators/yamlgen.py

@@ -3,7 +3,7 @@
 """
 
 import os
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 
 import click
 from linkml_runtime.utils.yamlutils import as_yaml
@@ -26,7 +26,7 @@ class YAMLGenerator(Generator):
     uses_schemaloader = True
 
     # ObjectVars
-    validateonly: bool = field(default_factory=lambda: False)
+    validateonly: bool = False
 
     def serialize(self, validateonly: bool = False, **kwargs) -> str:
         if validateonly:

linkml/generators/yumlgen.py

@@ -5,7 +5,7 @@ https://yuml.me/diagram/scruffy/class/samples
 """
 
 import os
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import Callable, List, Optional, Set, cast
 
 import click
@@ -14,6 +14,7 @@ from linkml_runtime.linkml_model.meta import ClassDefinition, ClassDefinitionNam
 from linkml_runtime.utils.formatutils import camelcase, underscore
 from rdflib import Namespace
 
+from linkml import REQUESTS_TIMEOUT
 from linkml.utils.generator import Generator, shared_arguments
 
 yuml_is_a = "^-"
@@ -49,7 +50,7 @@ class YumlGenerator(Generator):
     classes: Set[ClassDefinitionName] = None
     directory: Optional[str] = None
     diagram_name: Optional[str] = None
-    load_image: bool = field(default_factory=lambda: True)
+    load_image: bool = True
 
     def visit_schema(
         self,
@@ -95,10 +96,10 @@ class YumlGenerator(Generator):
                 payload = "dsl_text=" + (",".join(yumlclassdef))
                 payload = payload.replace("%3F", "?").replace("%2B", "+")
                 url = "https://yuml.me/diagram/plain/class/"
-                resp = requests.post(url, data=payload)
+                resp = requests.post(url, data=payload, timeout=REQUESTS_TIMEOUT)
                 if resp.ok:
                     filename = resp.text.strip().replace(".svg", file_suffix)
-                    resp = requests.get(f"https://yuml.me/{filename}", stream=True)
+                    resp = requests.get(f"https://yuml.me/{filename}", stream=True, timeout=REQUESTS_TIMEOUT)
                     with open(self.output_file_name, "wb") as f:
                         for chunk in resp.iter_content(chunk_size=2048):
                             f.write(chunk)

linkml/transformers/relmodel_transformer.py

@@ -140,11 +140,11 @@ class RelationalModelTransformer:
     """
 
     schemaview: SchemaView = None
-    # dialect: str = field(default_factory=lambda : 'sqlite')
-    skip_tree_root: bool = field(default_factory=lambda: False)
-    skip_abstract: bool = field(default_factory=lambda: True)
-    skip_mixins: bool = field(default_factory=lambda: True)
-    join_table_separator: str = field(default_factory=lambda: "_")
+    # dialect: str = 'sqlite'
+    skip_tree_root: bool = False
+    skip_abstract: bool = True
+    skip_mixins: bool = True
+    join_table_separator: str = "_"
     foreign_key_policy: ForeignKeyPolicy = field(default_factory=lambda: ForeignKeyPolicy.INJECT_FK_FOR_NESTED)
 
     def transform(self, tgt_schema_name: str = None, top_class: ClassDefinitionName = None) -> TransformationResult:

linkml/utils/converter.py

@@ -1,7 +1,6 @@
 import logging
 import os
 import sys
-from typing import List
 
 import click
 from linkml_runtime.linkml_model import Prefix
@@ -77,7 +76,7 @@ def cli(
     output=None,
     input_format=None,
     output_format=None,
-    prefix: List = [],
+    prefix=None,
     target_class_from_path=None,
     schema=None,
     validate=None,
@@ -98,6 +97,8 @@ def cli(
 
     For more information, see https://linkml.io/linkml/data/index.html
     """
+    if prefix is None:
+        prefix = []
     if module is None:
         if schema is None:
             raise Exception("must pass one of module OR schema")

linkml/utils/generator.py

@@ -124,7 +124,7 @@ class Generator(metaclass=abc.ABCMeta):
 
     file_extension: ClassVar[str] = None
 
-    metadata: bool = field(default_factory=lambda: True)
+    metadata: bool = True
     """True means include date, generator, etc. information in source header if appropriate"""
 
     useuris: Optional[bool] = None
@@ -133,7 +133,7 @@ class Generator(metaclass=abc.ABCMeta):
     log_level: int = DEFAULT_LOG_LEVEL_INT
     """Logging level, 0 is minimum"""
 
-    mergeimports: Optional[bool] = field(default_factory=lambda: True)
+    mergeimports: Optional[bool] = True
     """True means merge non-linkml sources into importing package.  False means separate packages"""
 
     source_file_date: Optional[str] = None
@@ -465,7 +465,7 @@ class Generator(metaclass=abc.ABCMeta):
         """Return an ordered list of ancestor names for the supplied slot or class
 
         @param element: Slot or class name or definition
-        @return: Ordered list of of ancestor names
+        @return: Ordered list of ancestor names
         """
         return [element.name] + ([] if element.is_a is None else self.ancestors(self.parent(element)))
 
@@ -620,7 +620,7 @@ class Generator(metaclass=abc.ABCMeta):
 
     def slot_range_path(self, slot_or_name: Union[str, SlotDefinition]) -> List[str]:
         """
-        Return a ordered list of slot ranges from distal to proximal
+        Return an ordered list of slot ranges from distal to proximal
 
         :param slot_or_name: slot whose range is being typed
         :return: ordered list of types from base type forward

linkml/utils/sqlutils.py

@@ -18,10 +18,11 @@ from linkml_runtime.utils.formatutils import underscore
 from linkml_runtime.utils.introspection import package_schemaview
 from linkml_runtime.utils.yamlutils import YAMLRoot
 from pydantic import BaseModel
-from sqlalchemy import StaticPool, create_engine
+from sqlalchemy import create_engine
 from sqlalchemy.engine import Engine
 from sqlalchemy.ext.associationproxy import _AssociationCollection
 from sqlalchemy.orm import sessionmaker
+from sqlalchemy.pool import StaticPool
 
 from linkml._version import __version__
 from linkml.generators.pythongen import PythonGenerator

{linkml-1.7.2.dist-info → linkml-1.7.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.7.2
+Version: 1.7.4
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -22,7 +22,6 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Provides-Extra: docs
 Requires-Dist: antlr4-python3-runtime (>=4.9.0,<4.10)
 Requires-Dist: click (>=7.0)
 Requires-Dist: graphviz (>=0.10.1)

{linkml-1.7.2.dist-info → linkml-1.7.4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-linkml/__init__.py,sha256=na-VVMb-hXm-6jDPgs-arvkOMx1LAryNDxnnfVwkKe0,3164
+linkml/__init__.py,sha256=jwtUdhwmquj-0fCR6VwPH5_RfSpuG94hLWdre_W_FD4,3327
 linkml/_version.py,sha256=udxv6OEqcE89DTVMYPtetXYg8IA8Sgc6yW26-6f8C3M,310
 linkml/generators/PythonGenNotes.md,sha256=wb9BPLLhF6378OKLbwSBAwmniLpwrcT5_bbfCHfLme8,51006
 linkml/generators/README.md,sha256=RMzT8EblC_GEdPy5WyfXHDBXlFI6k6mz3Cx2sdpcyWI,4438
@@ -16,33 +16,33 @@ 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=Kwg4ZIXL2e9G-q-_CUoj8Bgnpyyvvh5fKPnseDcTK04,33755
+linkml/generators/docgen.py,sha256=265bWbIkH4z5Cc7RLmyMTi2YR6hXAPBEdo5t1dqALYk,33476
 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/erdiagramgen.py,sha256=xCnxIldDYZ7xnQ-vLaXlH3FH8MH3cxu-E0j8it-lyJE,10153
+linkml/generators/excelgen.py,sha256=VsvdaGAOcNZ3qPLq-3lycGe_atG6B3hid3WMCV99XZI,7668
+linkml/generators/golanggen.py,sha256=lGP0wDU6QwLjfiUDpTLFvJsnaDGKxOyQLizlz2lGfPc,5775
 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=l3NUWCQMtJOTOIuao237hLYlILliLilVQXxdlJ5haIQ,5455
-linkml/generators/jsonldcontextgen.py,sha256=nLcASMmxoT57dRj1A9W5qqwg-5TDpsGblMb9gt940Zs,7871
+linkml/generators/javagen.py,sha256=KxwupMztyCRHcSsbtTnOovuj1WamsAny0mxbYWvTiDs,5324
+linkml/generators/jsonldcontextgen.py,sha256=RQFBgNjWMdnjf0j8S_k1lyMauI9Ia5Ao0ruuFjLwhdA,7886
 linkml/generators/jsonldgen.py,sha256=BtPXLYbnXTXorUcoe6y4DL0xa-TPjHOvtXdhv-ppW3I,7656
-linkml/generators/jsonschemagen.py,sha256=osol3CJBNB_YgZtvyryWywzpESXHfpDwn_5igvEMBF4,27524
+linkml/generators/jsonschemagen.py,sha256=XOsYIrpA6BwtAcfh8GNGduIjpuPAsF2f_PQ1mghj_WU,27455
 linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/generators/linkmlgen.py,sha256=QhIPA1v2g_g5fien3ZKN-L6TkDk3t7puVFrcoEnwkwY,3540
-linkml/generators/markdowngen.py,sha256=LU4Z8k9ag6aDURQKZAsEa_p9PEUGWsc_oMLJRx_pamI,32964
+linkml/generators/linkmlgen.py,sha256=1_Kt_7rD42WvCTjq0yaq1Of7jEDZR_uusyzAT-qWMHk,3471
+linkml/generators/markdowngen.py,sha256=dDMyusNXLvM2raIW-_vd2AQBhDHn0P_rMeDq3QFuacs,32926
 linkml/generators/namespacegen.py,sha256=vVcIyM0zlKd7XRvtdzwTwHjG4Pg49801gy4FUmjJlqQ,6450
-linkml/generators/oocodegen.py,sha256=l-5zck_NNAUxJiApJrnDPkqxCv3b6v5s4hC_smelszU,7620
-linkml/generators/owlgen.py,sha256=aF7dufP2WqaYmbG8W41_6Dx0j3u654NmuaXvHAY1aj4,52476
-linkml/generators/plantumlgen.py,sha256=jN40_1_0_YI6Dir8wbxdVm-Upy6rxIYLFSNW-V0WKFY,14871
+linkml/generators/oocodegen.py,sha256=cWjQSFJmhrnRRsHqOa9dOks0k-QogrP97m5lEkLRxdY,7738
+linkml/generators/owlgen.py,sha256=Oo3ACE5BXRbQU1p4XhyYhP4JQgAW4w2nmNZ591FWkVM,53142
+linkml/generators/plantumlgen.py,sha256=tk-_XJtBA5EqYJSUTc3bdMdCwqlC-rc9VYO9A2V_HpM,14895
 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=_SGYR_y-k67b91lWLtQcCU2vNRv19hrnRK9vQ_6_sZM,52560
-linkml/generators/rdfgen.py,sha256=94SRun1DDJwMiKVJU-BpU0jwhac2GW7gv4Gaug7iJ6o,2694
-linkml/generators/shaclgen.py,sha256=H63DCUjTGYdrKRG5j7Ep8sOgFTXqmaEkH8Rne8ANvFo,8724
+linkml/generators/protogen.py,sha256=5UxThsFDVyDTzzTDh77Z0anx4-tLgz8kQQ-e7ywIqwI,2290
+linkml/generators/pydanticgen.py,sha256=syiqMBBiGWwT_ZD5KLstGGMdh4d2fNQ3o2qZRfQLtqs,30539
+linkml/generators/pythongen.py,sha256=JCFuGishyoBx75sGFL2zWlHj-qsyBizyZIc_jqpzdTU,52429
+linkml/generators/rdfgen.py,sha256=L6F08iDUqVemXXrRbJmcOxvJTt14hR0oo8WLoqf4npw,2656
+linkml/generators/shaclgen.py,sha256=jxQjQ-iT2SYpLso3aIyBtqaVVPvZflrVzWaNA7nxQa0,8686
 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
@@ -50,14 +50,14 @@ linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py,sha256=X_Ws1NUBi
 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=ickgQovcWunsBRMpHBDTGxGlZKU9kfExb-XQPBS6qPs,18437
-linkml/generators/sqltablegen.py,sha256=h_zVuNC8huRzzTa9nSHNWBxq-4TuLq7nR5nZfpDnWiM,11481
+linkml/generators/sqltablegen.py,sha256=yaGdnl1kbovf9b4Qi6dx5VpRlBfy4PX1dtHsXtvg6qQ,11494
 linkml/generators/sssomgen.py,sha256=yur3q7so9uwIELWZaZRzkJwNbz_ppBL7IQki9XLIM3k,6879
 linkml/generators/string_template.md,sha256=kRcfic6entgIaJdpSg6GF3jcjC9wbKsCVM6wVT2qipc,1788
-linkml/generators/summarygen.py,sha256=67XKbzM_aCwJXEpgtsffWf7RGljeHJYE8dCIjMHXlH8,2925
+linkml/generators/summarygen.py,sha256=crH_Hegd4Z7G7byUtgyXoP2XtG_4iblzZsu_pE4aQrk,2887
 linkml/generators/terminusdbgen.py,sha256=_po9KnOz6Uoctb9Y4fJuU_voW4uA5pepvZTmHLQ2_DE,4470
 linkml/generators/typescriptgen.py,sha256=VDJ-97jk7zqYx6XlnIcxZmY8mCv885T7D2brKJHaihI,8565
-linkml/generators/yamlgen.py,sha256=0hYw2hW4A92As9x3k_7T7y05y25unfK2v3NPFfrtdbw,1652
-linkml/generators/yumlgen.py,sha256=nIwOYCCBWPnS8xk2y922qGlYSpoHNtMQcdB4L716iqo,12146
+linkml/generators/yamlgen.py,sha256=PKssrY5VHpdbOU54PVwLVLbsRqHwoOgOImlMb6DVcXM,1614
+linkml/generators/yumlgen.py,sha256=lnHcLY0VwlU_i8QporSmwR62CXSV4aOCXKxRDw5AxUk,12196
 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
@@ -79,15 +79,15 @@ linkml/reporting/model.py,sha256=-10yNfk8wuRC48ZI-akrWvtlJ9a6RYWET2TzlZV3XXo,862
 linkml/transformers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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/relmodel_transformer.py,sha256=STQ4ALoJpPKW5-soTVcErHof_1kEDJEEZ1EJrzneql4,17680
 linkml/transformers/schema_renamer.py,sha256=Cr18TyktX64b5iFh5V6R_ILPVzXjbDYVDDZQyqFiAv8,5271
 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/converter.py,sha256=snAF-pgZBSi4ANiaKXxqtZk5w3qonJjTfI4X5OVLmUE,6283
 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=fIoBa5zVXXOpW7ibIRCh0FADycdSXcrH98fMuzq6sng,38271
+linkml/utils/generator.py,sha256=YB2HXb9_aJx284xHnVq-glVgTtvWnBaE-yGCJXZ6nFM,38207
 linkml/utils/helpers.py,sha256=yR8n4zFA5wPcYC7xzRuNF3wO16vG80v6j7DM3qTNmIc,447
 linkml/utils/ifabsent_functions.py,sha256=C2mllfh7aIZgVqqJjN5nydurVUk0hV62Wy7uVMYfPDg,5801
 linkml/utils/logictools.py,sha256=GSmBiobC49TcQjE08RtXEE3JwJEOV7eEREio25uJiFs,21184
@@ -97,7 +97,7 @@ linkml/utils/schema_builder.py,sha256=WLSit3J4lTifaFLLWTwjqIRiTru1pqvTIUuC1TrxS6
 linkml/utils/schema_fixer.py,sha256=ajsxpwD4yMjDk1iDtoKJTsa34SIqGshWxlnSNXVZ52w,16745
 linkml/utils/schemaloader.py,sha256=bBSTqimMDTFH2FcKtRz99dKNJzV_myPsZSkIFp_6-A0,46421
 linkml/utils/schemasynopsis.py,sha256=jKf5ZJxpNgSZ5x9oAcdGO3m1IwzcIU2Ni1ugm0SQq1g,18447
-linkml/utils/sqlutils.py,sha256=86XeEbfY0Dk-EObw4q5-dxyzSeBtmIhjqqyDcR8ALS0,16591
+linkml/utils/sqlutils.py,sha256=FPUA6Smn3FogE97TZZZtGNhaMK9kpC-qJ5Ylo1mg9l8,16618
 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
@@ -125,8 +125,8 @@ 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-1.7.2.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-linkml-1.7.2.dist-info/entry_points.txt,sha256=za8r49Z5gcz3rAYTZLbxw5EPZr1rGuxSe1uiRUpf8R0,2143
-linkml-1.7.2.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
-linkml-1.7.2.dist-info/METADATA,sha256=2c6xc6B8gzMFAwrOe8soo7lLERpNDNYnCct9OK3-zcQ,3484
-linkml-1.7.2.dist-info/RECORD,,
+linkml-1.7.4.dist-info/METADATA,sha256=-EvbTFKzOQZ3HPP2-hd7LmWlELMPIF6ZUWqvGnPGoGs,3463
+linkml-1.7.4.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
+linkml-1.7.4.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
+linkml-1.7.4.dist-info/entry_points.txt,sha256=za8r49Z5gcz3rAYTZLbxw5EPZr1rGuxSe1uiRUpf8R0,2143
+linkml-1.7.4.dist-info/RECORD,,