linkml 1.8.1__py3-none-any.whl → 1.8.3__py3-none-any.whl

linkml/generators/python/python_ifabsent_processor.py

@@ -0,0 +1,92 @@
+from linkml_runtime.linkml_model import (
+    ClassDefinition,
+    EnumDefinitionName,
+    SlotDefinition,
+)
+
+from linkml.generators.common.ifabsent_processor import IfAbsentProcessor
+
+
+class PythonIfAbsentProcessor(IfAbsentProcessor):
+    UNIMPLEMENTED_DEFAULT_VALUES = ["class_curie", "class_uri", "slot_uri", "slot_curie", "default_range", "default_ns"]
+
+    def map_custom_default_values(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition) -> (bool, str):
+        if default_value in self.UNIMPLEMENTED_DEFAULT_VALUES:
+            return True, None
+
+        if default_value == "bnode":
+            return True, "bnode()"
+
+        return False, None
+
+    def map_string_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return self._strval(default_value)
+
+    def map_boolean_true_default_value(self, slot: SlotDefinition, cls: ClassDefinition):
+        return "True"
+
+    def map_boolean_false_default_value(self, slot: SlotDefinition, cls: ClassDefinition):
+        return "False"
+
+    def map_integer_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return default_value
+
+    def map_float_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return default_value
+
+    def map_double_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return default_value
+
+    def map_decimal_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return default_value
+
+    def map_time_default_value(self, hour: str, minutes: str, seconds: str, slot: SlotDefinition, cls: ClassDefinition):
+        return f"time({int(hour)}, {int(minutes)}, {int(seconds)})"
+
+    def map_date_default_value(self, year: str, month: str, day: str, slot: SlotDefinition, cls: ClassDefinition):
+        return f"date({int(year)}, {int(month)}, {int(day)})"
+
+    def map_datetime_default_value(
+        self,
+        year: str,
+        month: str,
+        day: str,
+        hour: str,
+        minutes: str,
+        seconds: str,
+        slot: SlotDefinition,
+        cls: ClassDefinition,
+    ):
+        return f"datetime({int(year)}, {int(month)}, {int(day)}, " f"{int(hour)}, {int(minutes)}, {int(seconds)})"
+
+    def map_uri_or_curie_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return self._uri_for(default_value)
+
+    def map_curie_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return self._uri_for(default_value)
+
+    def map_uri_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return self._uri_for(default_value)
+
+    def map_enum_default_value(
+        self, enum_name: EnumDefinitionName, permissible_value_name: str, slot: SlotDefinition, cls: ClassDefinition
+    ):
+        return f"{enum_name}.{permissible_value_name}"
+
+    def map_nc_name_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_object_identifier_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_node_identifier_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_json_pointer_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_json_path_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_sparql_path_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()

linkml/generators/pythongen.py

@@ -29,8 +29,8 @@ from rdflib import URIRef
 
 import linkml
 from linkml._version import __version__
+from linkml.generators.python.python_ifabsent_processor import PythonIfAbsentProcessor
 from linkml.utils.generator import Generator, shared_arguments
-from linkml.utils.ifabsent_functions import ifabsent_postinit_declaration, ifabsent_value_declaration
 
 
 @dataclass
@@ -54,12 +54,23 @@ class PythonGenerator(Generator):
     gen_slots: bool = True
     genmeta: bool = False
     emit_metadata: bool = True
+    dataclass_repr: bool = False
+    """
+    Whether generated dataclasses should also generate a default __repr__ method.
+    
+    Default ``False`` so that the parent :class:`linkml_runtime.utils.yamlutils.YAMLRoot` 's
+    ``__repr__`` method is inherited for model pretty printing.
+    
+    References:
+        - https://docs.python.org/3/library/dataclasses.html#dataclasses.dataclass
+    """
 
     def __post_init__(self) -> None:
         if isinstance(self.schema, Path):
             self.schema = str(self.schema)
         self.sourcefile = self.schema
         self.schemaview = SchemaView(self.schema, base_dir=self.base_dir)
+        self.ifabsent_processor = PythonIfAbsentProcessor(self.schemaview)
         super().__post_init__()
         if self.format is None:
             self.format = self.valid_formats[0]
@@ -143,7 +154,7 @@ import re
 from jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
-from datetime import date, datetime
+from datetime import date, datetime, time
 {enumimports}
 from linkml_runtime.utils.slot import Slot
 from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode
@@ -388,7 +399,7 @@ dataclasses._init_fn = dataclasses_init_fn_with_kwargs
             return f"\n{self.class_or_type_name(cls.name)} = Any"
 
         cd_str = (
-            ("\n@dataclass" if slotdefs else "")
+            (f"\n@dataclass(repr={self.dataclass_repr})" if slotdefs else "")
             + f"\nclass {self.class_or_type_name(cls.name)}{parentref}:{wrapped_description}"
             + f"{self.gen_inherited_slots(cls)}"
             + f"{self.gen_class_meta(cls)}"
@@ -505,7 +516,7 @@ dataclasses._init_fn = dataclasses_init_fn_with_kwargs
 
         return "\n\t".join(initializers)
 
-    def gen_class_variable(self, cls: ClassDefinition, slot: SlotDefinition, can_be_positional: bool) -> str:
+    def gen_class_variable(self, cls: ClassDefinition, slot: SlotDefinition, can_be_positional: bool = False) -> str:
         """
         Generate a class variable declaration for the supplied slot.  Note: the can_be_positional attribute works,
         but it makes tag/value lists unduly complex, as you can't load them with tag=..., value=... -- you HAVE
@@ -517,12 +528,9 @@ dataclasses._init_fn = dataclasses_init_fn_with_kwargs
         :param can_be_positional: True means that positional parameters are allowed.
         :return: Initializer string
         """
-        can_be_positional = False  # Force everything to be tag values
         slotname = self.slot_name(slot.name)
         slot_range, default_val = self.range_cardinality(slot, cls, can_be_positional)
-        ifabsent_text = (
-            ifabsent_value_declaration(slot.ifabsent, self, cls, slot) if slot.ifabsent is not None else None
-        )
+        ifabsent_text = self.ifabsent_processor.process_slot(slot, cls) if slot.ifabsent is not None else None
         if ifabsent_text is not None:
             default = f"= {ifabsent_text}"
         else:
@@ -627,15 +635,6 @@ dataclasses._init_fn = dataclasses_init_fn_with_kwargs
 
     def gen_postinits(self, cls: ClassDefinition) -> str:
         """Generate all the typing and existence checks post initialize"""
-        post_inits_pre_super = []
-        for slot in self.domain_slots(cls):
-            if slot.ifabsent:
-                dflt = ifabsent_postinit_declaration(slot.ifabsent, self, cls, slot)
-
-                if dflt and dflt != "None":
-                    post_inits_pre_super.append(f"if self.{self.slot_name(slot.name)} is None:")
-                    post_inits_pre_super.append(f"\tself.{self.slot_name(slot.name)} = {dflt}")
-
         post_inits = []
         if not (cls.mixin or cls.abstract):
             pkeys = self.primary_keys_for(cls)
@@ -666,20 +665,17 @@ dataclasses._init_fn = dataclasses_init_fn_with_kwargs
             if slot.name not in domain_slot_names and slot.designates_type:
                 post_inits_designators.append(self.gen_postinit(cls, slot))
 
-        post_inits_pre_super_line = "\n\t\t".join([p for p in post_inits_pre_super if p]) + (
-            "\n\t\t" if post_inits_pre_super else ""
-        )
         post_inits_post_super_line = "\n\t\t".join(post_inits_designators)
         post_inits_line = "\n\t\t".join([p for p in post_inits if p])
         return (
             (
                 f"""
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
-        {post_inits_pre_super_line}{post_inits_line}
+        {post_inits_line}
         super().__post_init__(**kwargs)
         {post_inits_post_super_line}"""
             )
-            if post_inits_line or post_inits_pre_super_line or post_inits_post_super_line
+            if post_inits_line or post_inits_post_super_line
             else ""
         )
 
@@ -1171,7 +1167,7 @@ class {enum_name}(EnumDefinitionImpl):
 
 
 @shared_arguments(PythonGenerator)
-@click.command()
+@click.command(name="python")
 @click.option("--head/--no-head", default=True, show_default=True, help="Emit metadata heading")
 @click.option(
     "--genmeta/--no-genmeta",

linkml/generators/rdfgen.py

@@ -76,7 +76,7 @@ class RDFGenerator(Generator):
 
 
 @shared_arguments(RDFGenerator)
-@click.command()
+@click.command(name="rdf")
 @click.option("-o", "--output", help="Output file name")
 @click.option(
     "--context",

linkml/generators/shacl/__init__.py

@@ -1,3 +1 @@
-from linkml.generators.shacl import ifabsent_processor
-
-__all__ = ["shacl_data_type", "ifabsent_processor"]
+__all__ = ["shacl_data_type", "shacl_ifabsent_processor"]

linkml/generators/shacl/shacl_data_type.py

@@ -20,7 +20,7 @@ class ShaclDataType(DataType, Enum):
     FLOAT = ("float", URIRef("http://www.w3.org/2001/XMLSchema#float"))
     DOUBLE = ("double", URIRef("http://www.w3.org/2001/XMLSchema#double"))
     URI = ("uri", URIRef("http://www.w3.org/2001/XMLSchema#anyURI"))
-    CURI = ("curi", URIRef("http://www.w3.org/2001/XMLSchema#string"))
+    CURIE = ("curi", URIRef("http://www.w3.org/2001/XMLSchema#string"))
     NCNAME = ("ncname", URIRef("http://www.w3.org/2001/XMLSchema#string"))
     OBJECT_IDENTIFIER = ("objectidentifier", URIRef("http://www.w3.org/ns/shex#iri"))
     NODE_IDENTIFIER = ("nodeidentifier", URIRef("http://www.w3.org/ns/shex#nonLiteral"))

linkml/generators/shacl/shacl_ifabsent_processor.py

@@ -0,0 +1,89 @@
+from linkml_runtime.linkml_model import ClassDefinition, EnumDefinitionName, SlotDefinition
+from rdflib import Literal, URIRef
+
+from linkml.generators.common.ifabsent_processor import IfAbsentProcessor
+from linkml.generators.shacl.shacl_data_type import ShaclDataType
+
+
+class ShaclIfAbsentProcessor(IfAbsentProcessor):
+
+    def map_custom_default_values(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition) -> (bool, str):
+        if default_value == "class_curie":
+            class_uri = self.schema_view.get_uri(cls, expand=True)
+            if class_uri:
+                return True, URIRef(class_uri)
+            return True, ""
+
+        return False, None
+
+    def map_enum_default_value(
+        self, enum_name: EnumDefinitionName, permissible_value_name: str, slot: SlotDefinition, cls: ClassDefinition
+    ):
+        return Literal(permissible_value_name)
+
+    def map_string_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(default_value, datatype=ShaclDataType.STRING.uri_ref)
+
+    def map_integer_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(default_value, datatype=ShaclDataType.INTEGER.uri_ref)
+
+    def map_boolean_true_default_value(self, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(True, datatype=ShaclDataType.BOOLEAN.uri_ref)
+
+    def map_boolean_false_default_value(self, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(False, datatype=ShaclDataType.BOOLEAN.uri_ref)
+
+    def map_float_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(default_value, datatype=ShaclDataType.FLOAT.uri_ref)
+
+    def map_double_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(default_value, datatype=ShaclDataType.DOUBLE.uri_ref)
+
+    def map_decimal_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(default_value, datatype=ShaclDataType.DECIMAL.uri_ref)
+
+    def map_time_default_value(self, hour: str, minutes: str, seconds: str, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(f"{hour}:{minutes}:{seconds}", datatype=ShaclDataType.TIME.uri_ref)
+
+    def map_date_default_value(self, year: str, month: str, day: str, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(f"{year}-{month}-{day}", datatype=ShaclDataType.DATE.uri_ref)
+
+    def map_datetime_default_value(
+        self,
+        year: str,
+        month: str,
+        day: str,
+        hour: str,
+        minutes: str,
+        seconds: str,
+        slot: SlotDefinition,
+        cls: ClassDefinition,
+    ):
+        return Literal(f"{year}-{month}-{day}T{hour}:{minutes}:{seconds}", datatype=ShaclDataType.DATETIME.uri_ref)
+
+    def map_uri_or_curie_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_curie_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(default_value, datatype=ShaclDataType.CURIE.uri_ref)
+
+    def map_uri_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        return Literal(default_value, datatype=ShaclDataType.URI.uri_ref)
+
+    def map_nc_name_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_object_identifier_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_node_identifier_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_json_pointer_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_json_path_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()
+
+    def map_sparql_path_default_value(self, default_value: str, slot: SlotDefinition, cls: ClassDefinition):
+        raise NotImplementedError()

linkml/generators/shaclgen.py

@@ -11,11 +11,11 @@ from linkml_runtime.utils.schemaview import SchemaView
 from linkml_runtime.utils.yamlutils import TypedNode, extended_float, extended_int, extended_str
 from rdflib import BNode, Graph, Literal, URIRef
 from rdflib.collection import Collection
-from rdflib.namespace import RDF, SH, XSD
+from rdflib.namespace import RDF, RDFS, SH, XSD
 
 from linkml._version import __version__
-from linkml.generators.shacl.ifabsent_processor import IfAbsentProcessor
 from linkml.generators.shacl.shacl_data_type import ShaclDataType
+from linkml.generators.shacl.shacl_ifabsent_processor import ShaclIfAbsentProcessor
 from linkml.utils.generator import Generator, shared_arguments
 
 
@@ -56,7 +56,7 @@ class ShaclGenerator(Generator):
         g = Graph()
         g.bind("sh", SH)
 
-        ifabsent_processor = IfAbsentProcessor(sv)
+        ifabsent_processor = ShaclIfAbsentProcessor(sv)
 
         for pfx in self.schema.prefixes.values():
             g.bind(str(pfx.prefix_prefix), pfx.prefix_reference)
@@ -73,6 +73,10 @@ class ShaclGenerator(Generator):
                 class_uri_with_suffix += self.suffix
             shape_pv(RDF.type, SH.NodeShape)
             shape_pv(SH.targetClass, class_uri)  # TODO
+
+            if c.is_a:
+                shape_pv(RDFS.subClassOf, URIRef(sv.get_uri(c.is_a, expand=True)))
+
             if self.closed:
                 if c.mixin or c.abstract:
                     shape_pv(SH.closed, Literal(False))
@@ -204,7 +208,9 @@ class ShaclGenerator(Generator):
                         # Map equal_string and equal_string_in to sh:in
                         self._and_equals_string(g, prop_pv, s.equals_string_in)
 
-                ifabsent_processor.process_slot(prop_pv, s, class_uri)
+                default_value = ifabsent_processor.process_slot(s, c)
+                if default_value:
+                    prop_pv(SH.defaultValue, default_value)
 
         return g
 
@@ -303,7 +309,7 @@ def add_simple_data_type(func: Callable, r: ElementName) -> None:
 
 
 @shared_arguments(ShaclGenerator)
-@click.command()
+@click.command(name="shacl")
 @click.option(
     "--closed/--non-closed",
     default=True,

linkml/generators/shexgen.py

@@ -223,7 +223,7 @@ class ShExGenerator(Generator):
 
 
 @shared_arguments(ShExGenerator)
-@click.command()
+@click.command(name="shex")
 @click.option("-o", "--output", help="Output file name")
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **args):

linkml/generators/sparqlgen.py

@@ -188,7 +188,7 @@ class SparqlGenerator(Generator):
 
 
 @shared_arguments(SparqlGenerator)
-@click.command()
+@click.command(name="sparql")
 @click.option("--dir", "-d", help="Directory in which queries will be deposited")
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, dir, **kwargs):

linkml/generators/sqlalchemygen.py

@@ -216,7 +216,7 @@ class SQLAlchemyGenerator(Generator):
     help="Emit FK declarations",
 )
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="sqla")
 def cli(yamlfile, declarative, generate_classes, pydantic, use_foreign_keys=True, **args):
     """Generate SQL DDL representation"""
     if pydantic:

linkml/generators/sqltablegen.py

@@ -290,7 +290,7 @@ class SQLTableGenerator(Generator):
 
 
 @shared_arguments(SQLTableGenerator)
-@click.command()
+@click.command(name="sqltables")
 @click.option(
     "--dialect",
     default="sqlite",

linkml/generators/sssomgen.py

@@ -180,7 +180,7 @@ class SSSOMGenerator(Generator):
 
 
 @shared_arguments(SSSOMGenerator)
-@click.command()
+@click.command(name="sssom")
 @click.option("-o", "--output", help="Output file name")
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **kwargs):

linkml/generators/summarygen.py

@@ -88,7 +88,7 @@ class SummaryGenerator(Generator):
 
 @shared_arguments(SummaryGenerator)
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="summary")
 def cli(yamlfile, **args):
     """Generate TSV summary files for viewing in Excel and the like"""
     print(SummaryGenerator(yamlfile, **args).serialize(**args))

linkml/generators/terminusdbgen.py

@@ -1,5 +1,6 @@
 import json
 import os
+import warnings
 from dataclasses import dataclass
 from typing import List
 
@@ -10,9 +11,7 @@ from linkml_runtime.utils.formatutils import be, camelcase, underscore
 try:
     from terminusdb_client.woqlquery import WOQLQuery as WQ
 except ImportError:
-    import warnings
-
-    warnings.warn("terminusdb_client is not a requirement of this package, please install it separately")
+    WQ = None
 
 from linkml._version import __version__
 from linkml.utils.generator import Generator, shared_arguments
@@ -67,6 +66,10 @@ class TerminusdbGenerator(Generator):
     raw_additions: List = None
     clswq: str = None
 
+    def __post_init__(self):
+        if WQ is None:
+            warnings.warn("terminusdb_client is not a requirement of this package, please install it separately")
+
     def visit_schema(self, inline: bool = False, **kwargs) -> None:
         self.classes = []
         self.raw_additions = []
@@ -134,7 +137,7 @@ class TerminusdbGenerator(Generator):
 
 @shared_arguments(TerminusdbGenerator)
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="terminusdb")
 def cli(yamlfile, **args):
     """Generate graphql representation of a LinkML model"""
     print(TerminusdbGenerator(yamlfile, **args).serialize(**args))

linkml/generators/typescriptgen.py

@@ -264,7 +264,7 @@ class TypescriptGenerator(OOCodeGenerator):
 @click.version_option(__version__, "-V", "--version")
 @click.option("--gen-type-utils/", "-u", help="Generate Type checking utils", is_flag=True)
 @click.option("--include-induced-slots/", help="Generate slots induced through inheritance", is_flag=True)
-@click.command()
+@click.command(name="typescript")
 def cli(yamlfile, gen_type_utils=False, include_induced_slots=False, **args):
     """Generate typescript interfaces and types
 

linkml/generators/yamlgen.py

@@ -36,7 +36,7 @@ class YAMLGenerator(Generator):
 
 
 @shared_arguments(YAMLGenerator)
-@click.command()
+@click.command(name="yaml")
 @click.option(
     "--raw/--no-raw",
     default=False,

linkml/generators/yumlgen.py

@@ -262,7 +262,7 @@ class YumlGenerator(Generator):
 
 
 @shared_arguments(YumlGenerator)
-@click.command()
+@click.command(name="yuml")
 @click.option("--classes", "-c", multiple=True, help="Class(es) to emit")
 @click.option(
     "--directory",

linkml/linter/cli.py

@@ -33,7 +33,7 @@ def get_yaml_files(root: Path, accept_dot_files: bool) -> Iterable[str]:
                     yield str(path)
 
 
-@click.command()
+@click.command(name="lint")
 @click.argument(
     "schema",
     type=click.Path(exists=True, dir_okay=True, file_okay=True, resolve_path=True, path_type=Path),