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

linkml/generators/common/template.py

@@ -0,0 +1,89 @@
+"""
+Base classes for jinja template handling classes.
+
+See :mod:`.linkml.generators.pydanticgen.template` for example implementation
+"""
+
+from copy import copy
+from typing import Any, ClassVar, Dict, List, Optional, Union
+
+from jinja2 import Environment
+from pydantic import BaseModel
+
+
+class TemplateModel(BaseModel):
+    """
+    Metaclass to render model results with jinja templates.
+
+    Each subclass needs to declare a :class:`typing.ClassVar` for a
+    jinja template within the `templates` directory.
+
+    Templates are written expecting each of the other TemplateModels
+    to already be rendered to strings - ie. rather than the ``class.py.jinja``
+    template receiving a full :class:`.PydanticAttribute` object or dictionary,
+    it receives it having already been rendered to a string. See the :meth:`.render` method.
+    """
+
+    template: ClassVar[str]
+    _environment: ClassVar[Environment]
+
+    meta_exclude: ClassVar[List[str]] = None
+
+    def render(self, environment: Optional[Environment] = None, **kwargs) -> str:
+        """
+        Recursively render a template model to a string.
+
+        For each field in the model, recurse through, rendering each :class:`.TemplateModel`
+        using the template set in :attr:`.TemplateModel.template` , but preserving the structure
+        of lists and dictionaries. Regular :class:`.BaseModel` s are rendered to dictionaries.
+        Any other value is passed through unchanged.
+
+        Args:
+            environment (:class:`jinja2.Environment`): Template environment - see :meth:`.environment`
+        """
+        if environment is None:
+            environment = TemplateModel.environment()
+
+        fields = {**self.model_fields, **self.model_computed_fields}
+
+        data = {k: _render(getattr(self, k, None), environment) for k in fields}
+        template = environment.get_template(self.template)
+        rendered = template.render(**data)
+        return rendered
+
+    @classmethod
+    def environment(cls) -> Environment:
+        """
+        Default environment for Template models.
+        uses a :class:`jinja2.PackageLoader` for the templates directory within this module
+        with the ``trim_blocks`` and ``lstrip_blocks`` parameters set to ``True`` so that the
+        default templates could be written in a more readable way.
+        """
+        return copy(cls._environment)
+
+    @classmethod
+    def exclude_from_meta(cls: "TemplateModel") -> List[str]:
+        """
+        Attributes in the source definition to exclude from linkml_meta
+        """
+        ret = [*cls.model_fields.keys()]
+        if cls.meta_exclude is not None:
+            ret = ret + cls.meta_exclude
+        return ret
+
+
+def _render(
+    item: Union[TemplateModel, Any, List[Union[Any, TemplateModel]], Dict[str, Union[Any, TemplateModel]]],
+    environment: Environment,
+) -> Union[str, List[str], Dict[str, str]]:
+    if isinstance(item, TemplateModel):
+        return item.render(environment)
+    elif isinstance(item, list):
+        return [_render(i, environment) for i in item]
+    elif isinstance(item, dict):
+        return {k: _render(v, environment) for k, v in item.items()}
+    elif isinstance(item, BaseModel):
+        fields = item.model_fields
+        return {k: _render(getattr(item, k, None), environment) for k in fields.keys()}
+    else:
+        return item

linkml/generators/csvgen.py

@@ -95,7 +95,7 @@ class CsvGenerator(Generator):
 
 
 @shared_arguments(CsvGenerator)
-@click.command()
+@click.command(name="csv")
 @click.version_option(__version__, "-V", "--version")
 @click.option("--root", "-r", multiple=True, help="Class(es) to transform")
 def cli(yamlfile, root=None, **args):

linkml/generators/docgen/slot.md.jinja2

@@ -34,6 +34,10 @@ _{{ element_description_line }}_
 {% endfor %}
 {% endif %}
 
+{% if element.abstract %}
+* __NOTE__: this is an abstract slot and should not be populated directly
+{% endif %}
+
 URI: {{ gen.uri_link(element) }}
 
 

linkml/generators/docgen.py

@@ -978,7 +978,7 @@ YAML, and including it when necessary but not by default (e.g. in documentation
 """,
 )
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="doc")
 def cli(
     yamlfile,
     directory,

linkml/generators/dotgen.py

@@ -136,7 +136,7 @@ class DotGenerator(Generator):
 
 
 @shared_arguments(DotGenerator)
-@click.command()
+@click.command(name="graphviz")
 @click.option(
     "--directory",
     "-d",

linkml/generators/erdiagramgen.py

@@ -312,7 +312,7 @@ class ERDiagramGenerator(Generator):
 @click.option("--classes", "-c", multiple=True, help="List of classes to serialize")
 @click.option("--include-upstream", is_flag=True, help="Include upstream classes")
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="erdiagram")
 def cli(
     yamlfile,
     classes: List[str],

linkml/generators/excelgen.py

@@ -167,7 +167,7 @@ class ExcelGenerator(Generator):
 
 
 @shared_arguments(ExcelGenerator)
-@click.command()
+@click.command(name="excel")
 @click.option(
     "--split-workbook-by-class",
     is_flag=True,

linkml/generators/golanggen.py

@@ -189,7 +189,7 @@ class GolangGenerator(Generator):
 
 @shared_arguments(GolangGenerator)
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="golang")
 def cli(yamlfile, **args):
     """Generate Golang types
 

linkml/generators/golrgen.py

@@ -101,7 +101,7 @@ class GolrSchemaGenerator(Generator):
 
 
 @shared_arguments(GolrSchemaGenerator)
-@click.command()
+@click.command(name="golr-views")
 @click.option("--dir", "-d", default="golr-views", show_default=True, help="Output directory")
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, dir=None, **args):

linkml/generators/graphqlgen.py

@@ -52,7 +52,7 @@ class GraphqlGenerator(Generator):
 
 
 @shared_arguments(GraphqlGenerator)
-@click.command()
+@click.command(name="graphql")
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **args):
     """Generate graphql representation of a LinkML model"""

linkml/generators/javagen.py

@@ -146,7 +146,7 @@ class JavaGenerator(OOCodeGenerator):
     help="Optional Java 17 record implementation",
 )
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="java")
 def cli(
     yamlfile,
     output_directory=None,

linkml/generators/jsonldcontextgen.py

@@ -18,11 +18,9 @@ from rdflib import SKOS, XSD, Namespace
 from linkml._version import __version__
 from linkml.utils.generator import Generator, shared_arguments
 
-URI_RANGES = (XSD.anyURI, SHEX.nonliteral, SHEX.bnode, SHEX.iri)
-
+URI_RANGES = (SHEX.nonliteral, SHEX.bnode, SHEX.iri)
 
 ENUM_CONTEXT = {
-    "@vocab": "@null",
     "text": "skos:notation",
     "description": "skos:prefLabel",
     "meaning": "@id",
@@ -99,7 +97,7 @@ class ContextGenerator(Generator):
             comments.generation_date = self.schema.generation_date
             comments.source = self.schema.source_file
             context.comments = comments
-        context_content = {}
+        context_content = {"xsd": "http://www.w3.org/2001/XMLSchema#"}
         if base:
             base = str(base)
             if "://" not in base:
@@ -193,6 +191,7 @@ class ContextGenerator(Generator):
         elif not uri_prefix or is_default_namespace:
             definition["@id"] = uri_suffix
         else:
+
             definition["@id"] = (uri_prefix + ":" + uri_suffix) if uri_prefix else uri
 
         if uri_prefix and not is_default_namespace:
@@ -203,7 +202,7 @@ class ContextGenerator(Generator):
 
 
 @shared_arguments(ContextGenerator)
-@click.command()
+@click.command(name="jsonld-context")
 @click.option("--base", help="Base URI for model")
 @click.option(
     "--prefixes/--no-prefixes",

linkml/generators/jsonldgen.py

@@ -192,7 +192,7 @@ class JSONLDGenerator(Generator):
 
 
 @shared_arguments(JSONLDGenerator)
-@click.command()
+@click.command(name="jsonld")
 @click.option(
     "--context",
     multiple=True,

linkml/generators/jsonschemagen.py

@@ -126,7 +126,13 @@ class JsonSchema(dict):
 
     @property
     def is_array(self):
-        return self.get("type") == "array"
+        typ = self.get("type", False)
+        if isinstance(typ, str):
+            return typ == "array"
+        elif isinstance(typ, list):
+            return "array" in typ
+        else:
+            return False
 
     @property
     def is_object(self):
@@ -136,7 +142,7 @@ class JsonSchema(dict):
         return json.dumps(self, **kwargs)
 
     @classmethod
-    def ref_for(cls, class_name: Union[str, List[str]], identifier_optional: bool = False):
+    def ref_for(cls, class_name: Union[str, List[str]], identifier_optional: bool = False, required: bool = True):
         def _ref(class_name):
             def_name = camelcase(class_name)
             def_suffix = cls.OPTIONAL_IDENTIFIER_SUFFIX if identifier_optional else ""
@@ -144,15 +150,27 @@ class JsonSchema(dict):
 
         if isinstance(class_name, list):
             if len(class_name) == 1:
-                return _ref(class_name[0])
+                ref = _ref(class_name[0])
             else:
-                return JsonSchema({"anyOf": [_ref(name) for name in class_name]})
+                ref = JsonSchema({"anyOf": [_ref(name) for name in class_name]})
         else:
-            return _ref(class_name)
+            ref = _ref(class_name)
+
+        if not required:
+            if "anyOf" in ref:
+                ref["anyOf"].append({"type": "null"})
+            else:
+                ref = JsonSchema({"anyOf": [ref, {"type": "null"}]})
+        return ref
 
     @classmethod
-    def array_of(cls, subschema: "JsonSchema") -> "JsonSchema":
-        schema = {"type": "array", "items": subschema}
+    def array_of(cls, subschema: "JsonSchema", required: bool = True) -> "JsonSchema":
+        if required:
+            typ = "array"
+        else:
+            typ = ["array", "null"]
+
+        schema = {"type": typ, "items": subschema}
 
         return JsonSchema(schema)
 
@@ -199,6 +217,9 @@ class JsonSchemaGenerator(Generator):
 
     top_level_schema: JsonSchema = None
 
+    include_null: bool = True
+    """Whether to include a "null" type in optional slots"""
+
     def __post_init__(self):
         if self.topClass:
             logging.warning("topClass is deprecated - use top_class")
@@ -315,7 +336,7 @@ class JsonSchemaGenerator(Generator):
 
         subschema = JsonSchema()
         for slot in cls.slot_conditions.values():
-            prop = self.get_subschema_for_slot(slot, omit_type=True)
+            prop = self.get_subschema_for_slot(slot, omit_type=True, include_null=False)
             value_required = False
             value_disallowed = False
             if slot.value_presence:
@@ -433,11 +454,17 @@ 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.equals_string_in:
+            constraints.add_keyword("enum", slot.equals_string_in)
         return constraints
 
     def get_subschema_for_slot(
-        self, slot: Union[SlotDefinition, AnonymousSlotExpression], omit_type: bool = False
+        self, slot: Union[SlotDefinition, AnonymousSlotExpression], omit_type: bool = False, include_null: bool = True
     ) -> JsonSchema:
+        """
+        Args:
+            include_null: Include ``type: null`` when generating ranges that are not required
+        """
         prop = JsonSchema()
         if isinstance(slot, SlotDefinition) and slot.array:
             # TODO: this is currently too lax, in that it will validate ANY array.
@@ -448,9 +475,10 @@ class JsonSchemaGenerator(Generator):
                     "additionalProperties": True,
                 }
             )
-            return JsonSchema.array_of(prop)
+            return JsonSchema.array_of(prop, required=slot.required)
         slot_is_multivalued = "multivalued" in slot and slot.multivalued
         slot_is_inlined = self.schemaview.is_inlined(slot)
+        slot_is_boolean = any([slot.any_of, slot.all_of, slot.exactly_one_of, slot.none_of])
         if not omit_type:
             typ, fmt, reference = self.get_type_info_for_slot_subschema(slot)
             if slot_is_inlined:
@@ -471,7 +499,9 @@ class JsonSchemaGenerator(Generator):
                         # If the range can be collected as a simple dict, then we can also accept the value
                         # of that simple dict directly.
                         if range_simple_dict_value_slot is not None:
-                            additionalProps.append(self.get_subschema_for_slot(range_simple_dict_value_slot))
+                            additionalProps.append(
+                                self.get_subschema_for_slot(range_simple_dict_value_slot, include_null=False)
+                            )
 
                         # If the range has no required slots, then null is acceptable
                         if len(range_required_slots) == 0:
@@ -483,12 +513,17 @@ class JsonSchemaGenerator(Generator):
                             additionalProps = additionalProps[0]
                         else:
                             additionalProps = JsonSchema({"anyOf": additionalProps})
-                        prop = JsonSchema({"type": "object", "additionalProperties": additionalProps})
+                        if slot.required or not include_null:
+                            typ = "object"
+                        else:
+                            typ = ["object", "null"]
+                        prop = JsonSchema({"type": typ, "additionalProperties": additionalProps})
                         self.top_level_schema.add_lax_def(reference, self.aliased_slot_name(range_id_slot))
                     else:
-                        prop = JsonSchema.array_of(JsonSchema.ref_for(reference))
+                        prop = JsonSchema.array_of(JsonSchema.ref_for(reference), required=slot.required)
                 else:
-                    prop = JsonSchema.ref_for(reference)
+                    prop = JsonSchema.ref_for(reference, required=slot.required or not include_null)
+
             else:
                 if reference is not None:
                     prop = JsonSchema.ref_for(reference)
@@ -498,7 +533,12 @@ class JsonSchemaGenerator(Generator):
                     prop = JsonSchema({"type": typ, "format": fmt})
 
                 if slot_is_multivalued:
-                    prop = JsonSchema.array_of(prop)
+                    prop = JsonSchema.array_of(prop, required=slot.required)
+                else:
+                    # handle optionals - bools like any_of, etc. below as they call this method recursively
+                    if not slot.required and not slot_is_boolean and include_null:
+                        if "type" in prop:
+                            prop["type"] = [prop["type"], "null"]
 
         prop.add_keyword("description", slot.description)
         if self.title_from == "title" and slot.title:
@@ -524,22 +564,29 @@ class JsonSchemaGenerator(Generator):
 
         bool_subschema = JsonSchema()
         if slot.any_of is not None and len(slot.any_of) > 0:
-            bool_subschema["anyOf"] = [self.get_subschema_for_slot(s) for s in slot.any_of]
+            bool_subschema["anyOf"] = [self.get_subschema_for_slot(s, include_null=False) for s in slot.any_of]
+            if not slot.required and not prop.is_array and include_null:
+                bool_subschema["anyOf"].append({"type": "null"})
 
         if slot.all_of is not None and len(slot.all_of) > 0:
-            bool_subschema["allOf"] = [self.get_subschema_for_slot(s) for s in slot.all_of]
+            bool_subschema["allOf"] = [self.get_subschema_for_slot(s, include_null=False) for s in slot.all_of]
 
         if slot.exactly_one_of is not None and len(slot.exactly_one_of) > 0:
-            bool_subschema["oneOf"] = [self.get_subschema_for_slot(s) for s in slot.exactly_one_of]
+            bool_subschema["oneOf"] = [self.get_subschema_for_slot(s, include_null=False) for s in slot.exactly_one_of]
 
         if slot.none_of is not None and len(slot.none_of) > 0:
-            bool_subschema["not"] = {"anyOf": [self.get_subschema_for_slot(s) for s in slot.none_of]}
+            bool_subschema["not"] = {
+                "anyOf": [self.get_subschema_for_slot(s, include_null=False) for s in slot.none_of]
+            }
 
         if bool_subschema:
             if prop.is_array:
                 if "items" not in prop:
                     prop["items"] = {}
-                prop["type"] = "array"
+                if slot.required or not include_null:
+                    prop["type"] = "array"
+                else:
+                    prop["type"] = ["array", "null"]
                 prop["items"].update(bool_subschema)
             else:
                 prop.update(bool_subschema)
@@ -554,7 +601,7 @@ class JsonSchemaGenerator(Generator):
         value_disallowed = slot.value_presence == PresenceEnum(PresenceEnum.ABSENT)
 
         aliased_slot_name = self.aliased_slot_name(slot)
-        prop = self.get_subschema_for_slot(slot)
+        prop = self.get_subschema_for_slot(slot, include_null=self.include_null)
         subschema.add_property(
             aliased_slot_name, prop, value_required=value_required, value_disallowed=value_disallowed
         )
@@ -625,7 +672,7 @@ class JsonSchemaGenerator(Generator):
 
 
 @shared_arguments(JsonSchemaGenerator)
-@click.command()
+@click.command(name="json-schema")
 @click.option(
     "-i",
     "--inline",

linkml/generators/linkmlgen.py

@@ -97,7 +97,7 @@ class LinkmlGenerator(Generator):
     help="Name of JSON or YAML file to be created",
 )
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="linkml")
 def cli(
     yamlfile,
     materialize_attributes: bool,

linkml/generators/markdowngen.py

@@ -789,7 +789,7 @@ def pad_heading(text: str) -> str:
 
 
 @shared_arguments(MarkdownGenerator)
-@click.command()
+@click.command(name="markdown")
 @click.option("--dir", "-d", required=True, help="Output directory")
 @click.option("--classes", "-c", multiple=True, help="Class(es) to emit")
 @click.option("--map-fields", "-M", multiple=True, help="Map metamodel fields, e.g. slot=field")

linkml/generators/namespacegen.py

@@ -195,7 +195,7 @@ def curie(identifier) -> str:
 
 @shared_arguments(NamespaceGenerator)
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="namespaces")
 def cli(yamlfile, **args):
     """Generate a namespace manager for all of the prefixes represented in a LinkML model"""
     print(NamespaceGenerator(yamlfile, **args).serialize(**args))

linkml/generators/oocodegen.py

@@ -76,6 +76,7 @@ class OOCodeGenerator(Generator):
     visit_all_class_slots = False
     uses_schemaloader = False
     requires_metamodel = False
+    schemaview: SchemaView = None
 
     template_file: str = None
     """Path to template"""
@@ -84,7 +85,7 @@ class OOCodeGenerator(Generator):
 
     def __post_init__(self):
         # TODO: consider moving up a level
-        self.schemaview = SchemaView(self.schema)
+        self.schemaview: SchemaView = SchemaView(self.schema)
         super().__post_init__()
 
     @abc.abstractmethod

linkml/generators/owlgen.py

@@ -1271,7 +1271,7 @@ class OwlSchemaGenerator(Generator):
 
 
 @shared_arguments(OwlSchemaGenerator)
-@click.command()
+@click.command(name="owl")
 @click.option("-o", "--output", help="Output file name")
 @click.option(
     "--metadata-profile",

linkml/generators/plantumlgen.py

@@ -339,7 +339,7 @@ class PlantumlGenerator(Generator):
 
 
 @shared_arguments(PlantumlGenerator)
-@click.command()
+@click.command(name="plantuml")
 @click.option("--classes", "-c", multiple=True, help="Class(es) to emit")
 @click.option(
     "--directory",

linkml/generators/prefixmapgen.py

@@ -112,7 +112,7 @@ class PrefixGenerator(Generator):
 
 
 @shared_arguments(PrefixGenerator)
-@click.command()
+@click.command(name="prefix-map")
 @click.option("--base", help="Base URI for model")
 @click.option("--output", "-o", help="Output file path")
 @click.version_option(__version__, "-V", "--version")

linkml/generators/projectgen.py

@@ -159,7 +159,7 @@ class ProjectGenerator:
                     gen.serialize(**serialize_args)
 
 
-@click.command()
+@click.command(name="project")
 @click.option(
     "--dir",
     "-d",

linkml/generators/protogen.py

@@ -69,7 +69,7 @@ class ProtoGenerator(Generator):
 
 @shared_arguments(ProtoGenerator)
 @click.version_option(__version__, "-V", "--version")
-@click.command()
+@click.command(name="proto")
 def cli(yamlfile, **args):
     """Generate proto representation of LinkML model"""
     print(ProtoGenerator(yamlfile, **args).serialize(**args))

linkml/generators/pydanticgen/__init__.py

@@ -1,4 +1,9 @@
-from linkml.generators.pydanticgen.pydanticgen import DEFAULT_IMPORTS, MetadataMode, PydanticGenerator, cli
+from linkml.generators.pydanticgen.pydanticgen import (
+    DEFAULT_IMPORTS,
+    MetadataMode,
+    PydanticGenerator,
+    cli,
+)
 from linkml.generators.pydanticgen.template import (
     ConditionalImport,
     Import,
@@ -8,8 +13,8 @@ from linkml.generators.pydanticgen.template import (
     PydanticClass,
     PydanticEnum,
     PydanticModule,
+    PydanticTemplateModel,
     PydanticValidator,
-    TemplateModel,
 )
 
 __all__ = [
@@ -26,5 +31,5 @@ __all__ = [
     "PydanticGenerator",
     "PydanticModule",
     "PydanticValidator",
-    "TemplateModel",
+    "PydanticTemplateModel",
 ]