linkml 1.8.7__py3-none-any.whl → 1.9.1rc2__py3-none-any.whl

linkml/generators/shaclgen.py

@@ -1,7 +1,7 @@
 import logging
 import os
 from dataclasses import dataclass
-from typing import Callable, List
+from typing import Callable
 
 import click
 from jsonasobj2 import JsonObj, as_dict
@@ -30,6 +30,8 @@ class ShaclGenerator(Generator):
     """parameterized suffix to be appended. No suffix per default."""
     include_annotations: bool = False
     """True means include all class / slot / type annotations in generated Node or Property shapes"""
+    exclude_imports: bool = False
+    """If True, elements from imported ontologies won't be included in the generator's output"""
     generatorname = os.path.basename(__file__)
     generatorversion = "0.0.1"
     valid_formats = ["ttl"]
@@ -63,7 +65,7 @@ class ShaclGenerator(Generator):
         for pfx in self.schema.prefixes.values():
             g.bind(str(pfx.prefix_prefix), pfx.prefix_reference)
 
-        for c in sv.all_classes().values():
+        for c in sv.all_classes(imports=not self.exclude_imports).values():
 
             def shape_pv(p, v):
                 if v is not None:
@@ -256,7 +258,7 @@ class ShaclGenerator(Generator):
         else:
             logger.error(f"No URI for type {rt.name}")
 
-    def _and_equals_string(self, g: Graph, func: Callable, values: List) -> None:
+    def _and_equals_string(self, g: Graph, func: Callable, values: list) -> None:
         pv_node = BNode()
         Collection(
             g,
@@ -271,7 +273,7 @@ class ShaclGenerator(Generator):
         annotations = item.annotations
         # item could be a class, slot or type
         # annotation type could be dict (on types) or JsonObj (on slots)
-        if type(annotations) == JsonObj:
+        if type(annotations) is JsonObj:
             annotations = as_dict(annotations)
         for a in annotations.values():
             # If ':' is in the tag, treat it as a CURIE, otherwise string Literal
@@ -281,7 +283,7 @@ class ShaclGenerator(Generator):
                 N_predicate = Literal(a["tag"], datatype=XSD.string)
             # If the value is a string and ':' is in the value, treat it as a CURIE,
             # otherwise treat as Literal with derived XSD datatype
-            if type(a["value"]) == extended_str and ":" in a["value"]:
+            if type(a["value"]) is extended_str and ":" in a["value"]:
                 N_object = URIRef(sv.expand_curie(a["value"]))
             else:
                 N_object = Literal(a["value"], datatype=self._getXSDtype(a["value"]))
@@ -290,19 +292,19 @@ class ShaclGenerator(Generator):
 
     def _getXSDtype(self, value):
         value_type = type(value)
-        if value_type == bool:
+        if value_type is bool:
             return XSD.boolean
-        elif value_type == extended_str:
+        elif value_type is extended_str:
             return XSD.string
-        elif value_type == extended_int:
+        elif value_type is extended_int:
             return XSD.integer
-        elif value_type == extended_float:
+        elif value_type is extended_float:
             # TODO: distinguish between xsd:decimal and xsd:double?
             return XSD.decimal
         else:
             return None
 
-    def _and_equals_string(self, g: Graph, func: Callable, values: List) -> None:
+    def _and_equals_string(self, g: Graph, func: Callable, values: list) -> None:
         pv_node = BNode()
         Collection(
             g,
@@ -364,6 +366,13 @@ def add_simple_data_type(func: Callable, r: ElementName) -> None:
     show_default=True,
     help="Use --include-annotations to include annotations of slots, types, and classes in the generated SHACL shapes.",
 )
+@click.option(
+    "--exclude-imports/--include-imports",
+    default=False,
+    show_default=True,
+    help="Use --exclude-imports to exclude imported elements from the generated SHACL shapes. This is useful when "
+    "extending a substantial ontology to avoid large output files.",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **args):
     """Generate SHACL turtle from a LinkML model"""

linkml/generators/shexgen.py

@@ -3,7 +3,7 @@
 import os
 import urllib.parse as urlparse
 from dataclasses import dataclass, field
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import click
 from jsonasobj import as_json as as_json_1
@@ -40,9 +40,9 @@ class ShExGenerator(Generator):
 
     # ObjectVars
     shex: Schema = field(default_factory=lambda: Schema())  # ShEx Schema being generated
-    shapes: List = field(default_factory=lambda: [])
+    shapes: list = field(default_factory=lambda: [])
     shape: Optional[Shape] = None  # Current shape being defined
-    list_shapes: List[IRIREF] = field(default_factory=lambda: [])  # Shapes that have been defined as lists
+    list_shapes: list[IRIREF] = field(default_factory=lambda: [])  # Shapes that have been defined as lists
 
     def __post_init__(self):
         super().__post_init__()

linkml/generators/sparqlgen.py

@@ -3,7 +3,7 @@ import os
 from collections import defaultdict
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Dict, List, Optional
+from typing import Optional
 
 import click
 from jinja2 import Template
@@ -137,7 +137,7 @@ class SparqlGenerator(Generator):
     uses_schemaloader = False
 
     # ObjectVars
-    named_graphs: Optional[List[str]] = None
+    named_graphs: Optional[list[str]] = None
     limit: Optional[int] = None
     sparql: Optional[str] = None
 
@@ -172,7 +172,7 @@ class SparqlGenerator(Generator):
         return self.sparql
 
     @staticmethod
-    def split_sparql(sparql: str) -> Dict[str, str]:
+    def split_sparql(sparql: str) -> dict[str, str]:
         lines = sparql.split("\n")
         prolog = ""
         queries = defaultdict(str)

linkml/generators/sqlalchemygen.py

@@ -3,7 +3,7 @@ import os
 from collections import defaultdict
 from dataclasses import dataclass
 from types import ModuleType
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import click
 from jinja2 import Template
@@ -180,7 +180,7 @@ class SQLAlchemyGenerator(Generator):
 
     # TODO: move this
     @staticmethod
-    def order_classes_by_hierarchy(sv: SchemaView) -> List[ClassDefinitionName]:
+    def order_classes_by_hierarchy(sv: SchemaView) -> list[ClassDefinitionName]:
         olist = sv.class_roots()
         unprocessed = [cn for cn in sv.all_classes() if cn not in olist]
         while len(unprocessed) > 0:

linkml/generators/terminusdbgen.py

@@ -2,7 +2,6 @@ import json
 import os
 import warnings
 from dataclasses import dataclass
-from typing import List
 
 import click
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
@@ -62,8 +61,8 @@ class TerminusdbGenerator(Generator):
     uses_schemaloader = True
 
     # ObjectVars
-    classes: List = None
-    raw_additions: List = None
+    classes: list = None
+    raw_additions: list = None
     clswq: str = None
 
     def __post_init__(self):

linkml/generators/typescriptgen.py

@@ -1,7 +1,7 @@
 import logging
 import os
 from dataclasses import dataclass
-from typing import List, Optional
+from typing import Optional
 
 import click
 from jinja2 import Template
@@ -252,7 +252,7 @@ class TypescriptGenerator(OOCodeGenerator):
             return "null"
 
     @staticmethod
-    def parents(cls: ClassDefinition) -> List[ClassDefinitionName]:
+    def parents(cls: ClassDefinition) -> list[ClassDefinitionName]:
         if cls.is_a:
             parents = [cls.is_a]
         else:
@@ -262,7 +262,7 @@ class TypescriptGenerator(OOCodeGenerator):
     def default_value_for_type(self, typ: str) -> str:
         pass
 
-    def required_slots(self, cls: ClassDefinition) -> List[SlotDefinitionName]:
+    def required_slots(self, cls: ClassDefinition) -> list[SlotDefinitionName]:
         return [s for s in self.schemaview.class_slots(cls.name) if self.schemaview.induced_slot(s, cls.name).required]
 
 

linkml/generators/yumlgen.py

@@ -6,7 +6,7 @@ https://yuml.me/diagram/scruffy/class/samples
 
 import os
 from dataclasses import dataclass
-from typing import Callable, List, Optional, Set, cast
+from typing import Callable, Optional, cast
 
 import click
 import requests
@@ -39,22 +39,22 @@ class YumlGenerator(Generator):
     valid_formats = ["yuml", "png", "pdf", "jpg", "json", "svg"]
     visit_all_class_slots = False
 
-    referenced: Optional[Set[ClassDefinitionName]] = None  # List of classes that have to be emitted
-    generated: Optional[Set[ClassDefinitionName]] = None  # List of classes that have been emitted
-    box_generated: Optional[Set[ClassDefinitionName]] = None  # Class boxes that have been emitted
-    associations_generated: Optional[Set[ClassDefinitionName]] = None  # Classes with associations generated
-    focus_classes: Optional[Set[ClassDefinitionName]] = None  # Classes to be completely filled
-    gen_classes: Optional[Set[ClassDefinitionName]] = None  # Classes to be generated
+    referenced: Optional[set[ClassDefinitionName]] = None  # List of classes that have to be emitted
+    generated: Optional[set[ClassDefinitionName]] = None  # List of classes that have been emitted
+    box_generated: Optional[set[ClassDefinitionName]] = None  # Class boxes that have been emitted
+    associations_generated: Optional[set[ClassDefinitionName]] = None  # Classes with associations generated
+    focus_classes: Optional[set[ClassDefinitionName]] = None  # Classes to be completely filled
+    gen_classes: Optional[set[ClassDefinitionName]] = None  # Classes to be generated
     output_file_name: Optional[str] = None  # Location of output file if directory used
 
-    classes: Set[ClassDefinitionName] = None
+    classes: set[ClassDefinitionName] = None
     directory: Optional[str] = None
     diagram_name: Optional[str] = None
     load_image: bool = True
 
     def visit_schema(
         self,
-        classes: Set[ClassDefinitionName] = None,
+        classes: set[ClassDefinitionName] = None,
         directory: Optional[str] = None,
         diagram_name: Optional[str] = None,
         load_image: bool = True,
@@ -75,7 +75,7 @@ class YumlGenerator(Generator):
             self.gen_classes = self.synopsis.roots.classrefs
         self.referenced = self.gen_classes
         self.generated = set()
-        yumlclassdef: List[str] = []
+        yumlclassdef: list[str] = []
         while self.referenced.difference(self.generated):
             cn = sorted(list(self.referenced.difference(self.generated)), reverse=True)[0]
             self.generated.add(cn)
@@ -115,7 +115,7 @@ class YumlGenerator(Generator):
         @param cn:
         @return:
         """
-        slot_defs: List[str] = []
+        slot_defs: list[str] = []
         if cn not in self.box_generated and (not self.focus_classes or cn in self.focus_classes):
             cls = self.schema.classes[cn]
             for slot in self.filtered_cls_slots(cn, all_slots=True, filtr=lambda s: s.range not in self.schema.classes):
@@ -142,7 +142,7 @@ class YumlGenerator(Generator):
 
         # NOTE: YUML diagrams draw in the opposite order in which they are created, so we work from bottom to top and
         # from right to left
-        assocs: List[str] = []
+        assocs: list[str] = []
         if cn not in self.associations_generated and (not self.focus_classes or cn in self.focus_classes):
             cls = self.schema.classes[cn]
 
@@ -222,7 +222,7 @@ class YumlGenerator(Generator):
         cn: ClassDefinitionName,
         all_slots: bool = True,
         filtr: Callable[[SlotDefinition], bool] = lambda: True,
-    ) -> List[SlotDefinition]:
+    ) -> list[SlotDefinition]:
         """Return the set of slots associated with the class that meet the filter criteria.  Slots will be returned
         in defining order, with class slots returned last
 

linkml/linter/cli.py

@@ -1,7 +1,7 @@
 import os
 import sys
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Iterable
 
 import click
 import yaml