linkml 1.7.5__tar.gz → 1.7.7__tar.gz

{linkml-1.7.5 → linkml-1.7.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.7.5
+Version: 1.7.7
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -19,10 +19,15 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Provides-Extra: black
+Provides-Extra: shacl
+Provides-Extra: tests
 Requires-Dist: antlr4-python3-runtime (>=4.9.0,<4.10)
+Requires-Dist: black (>=24.0.0) ; extra == "black" or extra == "tests"
 Requires-Dist: click (>=7.0)
 Requires-Dist: graphviz (>=0.10.1)
 Requires-Dist: hbreader
@@ -31,13 +36,14 @@ Requires-Dist: jinja2 (>=3.1.0)
 Requires-Dist: jsonasobj2 (>=1.0.3,<2.0.0)
 Requires-Dist: jsonschema[format] (>=4.0.0)
 Requires-Dist: linkml-dataops
-Requires-Dist: linkml-runtime (>=1.7.0)
+Requires-Dist: linkml-runtime (>=1.7.4)
 Requires-Dist: openpyxl
 Requires-Dist: parse
 Requires-Dist: prefixcommons (>=0.1.7)
-Requires-Dist: prefixmaps (>=0.1.3)
+Requires-Dist: prefixmaps (>=0.2.2)
 Requires-Dist: pydantic (>=1.0.0,<3.0.0)
 Requires-Dist: pyjsg (>=0.11.6)
+Requires-Dist: pyshacl (>=0.25.0,<0.26.0) ; extra == "shacl" or extra == "tests"
 Requires-Dist: pyshex (>=0.7.20)
 Requires-Dist: pyshexc (>=0.8.3)
 Requires-Dist: python-dateutil
@@ -45,7 +51,6 @@ Requires-Dist: pyyaml
 Requires-Dist: rdflib (>=6.0.0)
 Requires-Dist: requests (>=2.22)
 Requires-Dist: sqlalchemy (>=1.4.31)
-Requires-Dist: typing-extensions (>=4.5.0,<5.0.0) ; python_version == "3.7"
 Requires-Dist: watchdog (>=0.9.0)
 Project-URL: Documentation, https://linkml.io/linkml/
 Project-URL: Repository, https://github.com/linkml/linkml

{linkml-1.7.5 → linkml-1.7.7}/linkml/generators/__init__.py

@@ -5,6 +5,7 @@ representation such as JsonSchema
 
 from linkml.generators.javagen import JavaGenerator
 from linkml.generators.jsonldcontextgen import ContextGenerator
+from linkml.generators.jsonldgen import JSONLDGenerator
 from linkml.generators.jsonschemagen import JsonSchemaGenerator
 from linkml.generators.owlgen import OwlSchemaGenerator
 from linkml.generators.pydanticgen import PydanticGenerator
@@ -43,6 +44,7 @@ __all__ = [
     "PythonGenerator",
     "JavaGenerator",
     "ContextGenerator",
+    "JSONLDGenerator",
     "JsonSchemaGenerator",
     "ShaclGenerator",
     "ShExGenerator",

{linkml-1.7.5 → linkml-1.7.7}/linkml/generators/docgen/class.md.jinja2

@@ -8,6 +8,19 @@
     {%- endif -%}
 {%- endif -%}
 
+{% macro compute_range(slot) -%}
+    {%- if slot.any_of or slot.exactly_one_of -%}
+        {%- for subslot_range in schemaview.slot_range_as_union(slot) -%}
+            {{ gen.link(subslot_range) }}
+            {%- if not loop.last -%}
+                &nbsp;or&nbsp;<br />
+            {%- endif -%}
+        {%- endfor -%}
+    {%- else -%}
+        {{ gen.link(slot.range) }}
+    {%- endif -%}
+{% endmacro %}
+
 # Class: {{ title }}
 
 {%- if header -%}
@@ -55,12 +68,12 @@ URI: {{ gen.uri_link(element) }}
 | ---  | --- | --- | --- |
 {% if gen.get_direct_slots(element)|length > 0 %}
 {%- for slot in gen.get_direct_slots(element) -%}
-| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} | direct |
+| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ compute_range(slot) }} | {{ slot.description|enshorten }} | direct |
 {% endfor -%}
 {% endif -%}
 {% if gen.get_indirect_slots(element)|length > 0 %}
 {%- for slot in gen.get_indirect_slots(element) -%}
-| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} | {{ gen.links(gen.get_slot_inherited_from(element.name, slot.name))|join(', ') }} |
+| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ compute_range(slot) }} | {{ slot.description|enshorten }} | {{ gen.links(gen.get_slot_inherited_from(element.name, slot.name))|join(', ') }} |
 {% endfor -%}
 {% endif %}
 

{linkml-1.7.5 → linkml-1.7.7}/linkml/generators/docgen/slot.md.jinja2

@@ -8,6 +8,19 @@
     {%- endif -%}
 {%- endif -%}
 
+{% macro compute_range(slot) -%}
+    {%- if slot.any_of or slot.exactly_one_of -%}
+        {%- for subslot_range in schemaview.slot_range_as_union(slot) -%}
+            {{ gen.link(subslot_range) }}
+            {%- if not loop.last -%}
+                &nbsp;or&nbsp;<br />
+            {%- endif -%}
+        {%- endfor -%}
+    {%- else -%}
+        {{ gen.link(slot.range) }}
+    {%- endif -%}
+{% endmacro %}
+
 # Slot: {{ title }}
 
 {%- if header -%}
@@ -33,14 +46,15 @@ URI: {{ gen.uri_link(element) }}
 <!-- no inheritance hierarchy -->
 {% endif %}
 
-{% if schemaview.get_classes_by_slot(element, include_induced=True) %}
+{% set classes_by_slot = schemaview.get_classes_by_slot(element, include_induced=True) %}
+{% if classes_by_slot %}
 
 ## Applicable Classes
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
-{% for c in schemaview.get_classes_by_slot(element, include_induced=True) -%}
-{{ gen.link(c) }} | {{ schemaview.get_class(c).description|enshorten }} | {% if c in schemaview.get_classes_modifying_slot(element) %} yes {% else %} no {% endif %} |
+{% for c in classes_by_slot -%}
+| {{ gen.link(c) }} | {{ schemaview.get_class(c).description|enshorten }} | {% if c in schemaview.get_classes_modifying_slot(element) %} yes {% else %} no {% endif %} |
 {% endfor %}
 
 {% endif %}
@@ -58,7 +72,7 @@ URI: {{ gen.uri_link(element) }}
 
 ## Properties
 
-* Range: {{gen.link(element.range)}}
+* Range: {{ compute_range(element) }}
 {% if element.multivalued %}
 * Multivalued: {{ element.multivalued }}
 {% endif -%}

{linkml-1.7.5 → linkml-1.7.7}/linkml/generators/docgen.py

@@ -192,52 +192,65 @@ class DocGenerator(Generator):
             "diagram_type": self.diagram_type.value if self.diagram_type else None,
             "include_top_level_diagram": self.include_top_level_diagram,
         }
+        self.logger.debug("Processing Index")
         template = self._get_template("index")
         out_str = template.render(gen=self, schema=sv.schema, schemaview=sv, **template_vars)
         self._write(out_str, directory, self.index_name)
         if self._is_single_file_format(self.format):
-            logging.info(f"{self.format} is a single-page format, skipping non-index elements")
+            self.logger.info(f"{self.format} is a single-page format, skipping non-index elements")
             return
+        self.logger.debug("Processing Schemas...")
         template = self._get_template("schema")
         for schema_name in sv.imports_closure():
+            self.logger.debug(f"  Generating doc for {schema_name}")
             imported_schema = sv.schema_map.get(schema_name)
             out_str = template.render(gen=self, schema=imported_schema, schemaview=sv, **template_vars)
             self._write(out_str, directory, imported_schema.name)
+        self.logger.debug("Processing Classes...")
         template = self._get_template("class")
         for cn, c in sv.all_classes().items():
             if self._is_external(c):
                 continue
             n = self.name(c)
+            self.logger.debug(f"  Generating doc for {n}")
             out_str = template.render(gen=self, element=c, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
+        self.logger.debug("Processing Slots...")
         template = self._get_template("slot")
         for sn, s in sv.all_slots().items():
             if self._is_external(s):
                 continue
             n = self.name(s)
+            self.logger.debug(f"  Generating doc for {n}")
             s = sv.induced_slot(sn)
             out_str = template.render(gen=self, element=s, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
+        self.logger.debug("Processing Enums...")
         template = self._get_template("enum")
         for en, e in sv.all_enums().items():
             if self._is_external(e):
                 continue
             n = self.name(e)
+            self.logger.debug(f"  Generating doc for {n}")
             out_str = template.render(gen=self, element=e, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
+        self.logger.debug("Processing Types...")
         template = self._get_template("type")
         for tn, t in sv.all_types().items():
             if self._exclude_type(t):
                 continue
             n = self.name(t)
+            self.logger.debug(f"  Generating doc for {n}")
             t = sv.induced_type(tn)
             out_str = template.render(gen=self, element=t, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
+        self.logger.debug("Processing Subsets...")
         template = self._get_template("subset")
         for _, s in sv.all_subsets().items():
             if self._is_external(c):
                 continue
             n = self.name(s)
+            self.logger.debug(f"  Generating doc for {n}")
             out_str = template.render(gen=self, element=s, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
 
@@ -253,6 +266,7 @@ class DocGenerator(Generator):
         path = Path(directory)
         path.mkdir(parents=True, exist_ok=True)
         file_name = f"{name}.{self._file_suffix()}"
+        self.logger.debug(f"  Writing file: {file_name}")
         with open(path / file_name, "w", encoding="UTF-8") as stream:
             stream.write(out_str)
 
@@ -294,7 +308,7 @@ class DocGenerator(Generator):
                 if p.is_file():
                     folder = self.template_directory
                 else:
-                    logging.info(
+                    self.logger.info(
                         f"Could not find {base_file_name} in {self.template_directory} - falling back to default"
                     )
             if not folder:
@@ -325,7 +339,7 @@ class DocGenerator(Generator):
 
         :param element: SchemaView element definition
         :return: slot name or numeric portion of CURIE prefixed
-        slot_uri
+            slot_uri
         """
         if type(element).class_name == "slot_definition":
             if self.use_slot_uris:

{linkml-1.7.5 → linkml-1.7.7}/linkml/generators/jsonldcontextgen.py

@@ -6,14 +6,14 @@ Generate JSON-LD contexts
 import os
 import re
 from dataclasses import dataclass, field
-from typing import Dict, Optional, Set
+from typing import Any, Dict, Optional, Set, Union
 
 import click
 from jsonasobj2 import JsonObj, as_json
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
 from linkml_runtime.linkml_model.types import SHEX
 from linkml_runtime.utils.formatutils import camelcase, underscore
-from rdflib import SKOS, XSD
+from rdflib import SKOS, XSD, Namespace
 
 from linkml._version import __version__
 from linkml.utils.generator import Generator, shared_arguments
@@ -47,7 +47,7 @@ class ContextGenerator(Generator):
     slot_class_maps: Dict = field(default_factory=lambda: dict())
     emit_metadata: bool = False
     model: Optional[bool] = True
-    base: Optional[str] = None
+    base: Optional[Union[str, Namespace]] = None
     output: Optional[str] = None
     prefixes: Optional[bool] = True
     flatprefixes: Optional[bool] = False
@@ -57,7 +57,7 @@ class ContextGenerator(Generator):
         if self.namespaces is None:
             raise TypeError("Schema text must be supplied to context generator.  Preparsed schema will not work")
 
-    def visit_schema(self, base: Optional[str] = None, output: Optional[str] = None, **_):
+    def visit_schema(self, base: Optional[Union[str, Namespace]] = None, output: Optional[str] = None, **_):
         # Add any explicitly declared prefixes
         for prefix in self.schema.prefixes.values():
             self.emit_prefixes.add(prefix.prefix_prefix)
@@ -80,11 +80,10 @@ class ContextGenerator(Generator):
                     self.namespaces[self.schema.name] = default_uri
                     self.emit_prefixes.add(self.schema.name)
             self.context_body["@vocab"] = default_uri
-            # self.context_body['@base'] = self.base_dir
 
     def end_schema(
         self,
-        base: Optional[str] = None,
+        base: Optional[Union[str, Namespace]] = None,
         output: Optional[str] = None,
         prefixes: Optional[bool] = True,
         flatprefixes: Optional[bool] = False,
@@ -102,6 +101,7 @@ class ContextGenerator(Generator):
             context.comments = comments
         context_content = {}
         if base:
+            base = str(base)
             if "://" not in base:
                 self.context_body["@base"] = os.path.relpath(base, os.path.dirname(self.schema.source_file))
             else:
@@ -133,16 +133,13 @@ class ContextGenerator(Generator):
         class_def = {}
         cn = camelcase(cls.name)
         self.add_mappings(cls)
-        cls_uri_prefix, cls_uri_suffix = self.namespaces.prefix_suffix(cls.class_uri)
-        if not self.default_ns or not cls_uri_prefix or cls_uri_prefix != self.default_ns:
-            class_def["@id"] = (cls_uri_prefix + ":" + cls_uri_suffix) if cls_uri_prefix else cls.class_uri
-            if cls_uri_prefix:
-                self.add_prefix(cls_uri_prefix)
+
+        self._build_element_id(class_def, cls.class_uri)
         if class_def:
             self.slot_class_maps[cn] = class_def
 
         # We don't bother to visit class slots - just all slots
-        return False
+        return True
 
     def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None:
         if slot.identifier:
@@ -169,15 +166,41 @@ class ContextGenerator(Generator):
                         slot_def["@type"] = "@id"
                     else:
                         slot_def["@type"] = range_type.uri
-                slot_prefix = self.namespaces.prefix_for(slot.slot_uri)
-                if not self.default_ns or not slot_prefix or slot_prefix != self.default_ns:
-                    slot_def["@id"] = slot.slot_uri
-                    if slot_prefix:
-                        self.add_prefix(slot_prefix)
+
+                self._build_element_id(slot_def, slot.slot_uri)
                 self.add_mappings(slot)
         if slot_def:
             self.context_body[underscore(aliased_slot_name)] = slot_def
 
+    def _build_element_id(self, definition: Any, uri: str) -> None:
+        """
+        Defines the elements @id attribute according to the default namespace prefix of the schema.
+
+        The @id namespace prefix is added only if it doesn't correspond to the default schema namespace prefix
+        whether it is in URI format or as an alias.
+
+        @param definition: the element (class or slot) definition
+        @param uri: the uri of the element (class or slot)
+        @return: None
+        """
+        uri_prefix, uri_suffix = self.namespaces.prefix_suffix(uri)
+        is_default_namespace = uri_prefix == self.context_body["@vocab"] or uri_prefix == self.namespaces.prefix_for(
+            self.context_body["@vocab"]
+        )
+
+        if not uri_prefix and not uri_suffix:
+            definition["@id"] = uri
+        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:
+            self.add_prefix(uri_prefix)
+
+    def serialize(self, base: Optional[Union[str, Namespace]] = None, **kwargs) -> str:
+        return super().serialize(base=base, **kwargs)
+
 
 @shared_arguments(ContextGenerator)
 @click.command()

{linkml-1.7.5 → linkml-1.7.7}/linkml/generators/jsonldgen.py

@@ -37,7 +37,8 @@ class JSONLDGenerator(Generator):
 
     Status: incompletely implemented
 
-    Note: this is distinct from :ref:`ContextGenerator`, which generates a JSON-LD context
+    Note: this is distinct from
+    :class:`~linkml.generators.jsonldcontextgen.ContextGenerator`, which generates a JSON-LD context
     """
 
     # ClassVars
@@ -49,6 +50,7 @@ class JSONLDGenerator(Generator):
     ]  # jsonld includes @type and @context.  json is pure JSON
     uses_schemaloader = True
     requires_metamodel = True
+    file_extension = "jsonld"
 
     # ObjectVars
     original_schema: SchemaDefinition = None

{linkml-1.7.5 → linkml-1.7.7}/linkml/generators/owlgen.py

@@ -22,6 +22,7 @@ from linkml_runtime.linkml_model.meta import (
     EnumDefinition,
     EnumDefinitionName,
     PermissibleValue,
+    SchemaDefinitionName,
     SlotDefinition,
     SlotDefinitionName,
     TypeDefinition,
@@ -199,6 +200,12 @@ class OwlSchemaGenerator(Generator):
         for enm in sv.all_enums(imports=mergeimports).values():
             self.add_enum(enm)
 
+        if not mergeimports:
+            for imp in schema.imports:
+                if imp == "linkml:types":
+                    continue
+                graph.add((base, OWL.imports, self._schema_uri(imp)))
+
         # Add metadata as annotation properties
         self.add_metadata(schema, base)
         return graph
@@ -267,6 +274,8 @@ class OwlSchemaGenerator(Generator):
                 self.graph.add((uri, metaslot_uri, obj))
 
         for k, v in e.annotations.items():
+            if isinstance(v, dict) or isinstance(v, list):
+                continue
             if ":" not in k:
                 default_prefix = this_sv.schema.default_prefix
                 if default_prefix in this_sv.schema.prefixes:
@@ -1129,6 +1138,13 @@ class OwlSchemaGenerator(Generator):
             default_prefix = self.schemaview.schema.default_prefix or ""
             return URIRef(self.schemaview.expand_curie(f"{default_prefix}:{underscore(p.name)}"))
 
+    def _schema_uri(self, scn: Union[str, SchemaDefinitionName]) -> URIRef:
+        if ":" in scn:
+            return URIRef(self.schemaview.expand_curie(scn))
+        else:
+            default_prefix = self.schemaview.schema.default_prefix or ""
+            return URIRef(self.schemaview.expand_curie(f"{default_prefix}:{scn}"))
+
     def _type_uri(self, tn: TypeDefinitionName, native: bool = None) -> URIRef:
         if native is None:
             # never use native unless type shadowing with objects is enabled

{linkml-1.7.5 → linkml-1.7.7}/linkml/generators/prefixmapgen.py

@@ -6,14 +6,14 @@ Generate JSON-LD contexts
 import csv
 import os
 from dataclasses import dataclass, field
-from typing import Dict, Optional, Set
+from typing import Dict, Optional, Set, Union
 
 import click
 from jsonasobj2 import JsonObj, as_json
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
 from linkml_runtime.linkml_model.types import SHEX
 from linkml_runtime.utils.formatutils import camelcase
-from rdflib import XSD
+from rdflib import XSD, Namespace
 
 from linkml._version import __version__
 from linkml.utils.generator import Generator, shared_arguments
@@ -35,7 +35,7 @@ class PrefixGenerator(Generator):
     default_ns: str = None
     context_body: Dict = field(default_factory=lambda: dict())
     slot_class_maps: Dict = field(default_factory=lambda: dict())
-    base: str = None
+    base: Optional[Union[str, Namespace]] = None
 
     def __post_init__(self):
         super().__post_init__()
@@ -59,9 +59,10 @@ class PrefixGenerator(Generator):
             if self.default_ns:
                 self.emit_prefixes.add(self.default_ns)
 
-    def end_schema(self, base: Optional[str] = None, output: Optional[str] = None, **_) -> None:
+    def end_schema(self, base: Optional[Union[str, Namespace]] = None, output: Optional[str] = None, **_) -> None:
         context = JsonObj()
         if base:
+            base = str(base)
             if "://" not in base:
                 self.context_body["@base"] = os.path.relpath(base, os.path.dirname(self.schema.source_file))
             else:

{linkml-1.7.5 → linkml-1.7.7}/linkml/generators/projectgen.py

@@ -198,26 +198,38 @@ def cli(
 
     Generate all downstream artefacts using default configuration:
 
-       gen-project -d . personinfo.yaml
+    .. code-block: bash
+
+        gen-project -d . personinfo.yaml
 
     Exclusion lists: all except ShEx:
 
-       gen-project --exclude shex -d . personinfo.yaml
+    .. code-block: bash
+
+        gen-project --exclude shex -d . personinfo.yaml
 
     Inclusion lists: only jsonschema and python:
 
+    .. code-block: bash
+
        gen-project -I python -I jsonschema -d . personinfo.yaml
 
     Configuration, on command line:
 
+    .. code-block: bash
+
         gen-project -A 'jsonschema: {top_class: Container}' -d . personinfo.yaml
 
     Configuration, via yaml file:
 
+    .. code-block: bash
+
         gen-project --config config.yaml personinfo.yaml
 
     config.yaml:
 
+    .. code-block: yaml
+
         directory: .
         generator_args:
           json_schema:

linkml-1.7.7/linkml/generators/pydanticgen/__init__.py

@@ -0,0 +1,29 @@
+from linkml.generators.pydanticgen.pydanticgen import DEFAULT_IMPORTS, PydanticGenerator, cli
+from linkml.generators.pydanticgen.template import (
+    ConditionalImport,
+    Import,
+    Imports,
+    PydanticAttribute,
+    PydanticBaseModel,
+    PydanticClass,
+    PydanticEnum,
+    PydanticModule,
+    PydanticValidator,
+    TemplateModel,
+)
+
+__all__ = [
+    "cli",
+    "ConditionalImport",
+    "DEFAULT_IMPORTS",
+    "Import",
+    "Imports",
+    "PydanticAttribute",
+    "PydanticBaseModel",
+    "PydanticClass",
+    "PydanticEnum",
+    "PydanticGenerator",
+    "PydanticModule",
+    "PydanticValidator",
+    "TemplateModel",
+]