linkml 1.8.0__py3-none-any.whl → 1.8.1__py3-none-any.whl

linkml/generators/jsonschemagen.py

@@ -435,8 +435,20 @@ class JsonSchemaGenerator(Generator):
         constraints.add_keyword("const", slot.equals_number)
         return constraints
 
-    def get_subschema_for_slot(self, slot: SlotDefinition, omit_type: bool = False) -> JsonSchema:
+    def get_subschema_for_slot(
+        self, slot: Union[SlotDefinition, AnonymousSlotExpression], omit_type: bool = False
+    ) -> JsonSchema:
         prop = JsonSchema()
+        if isinstance(slot, SlotDefinition) and slot.array:
+            # TODO: this is currently too lax, in that it will validate ANY array.
+            # see https://github.com/linkml/linkml/issues/2188
+            prop = JsonSchema(
+                {
+                    "type": ["null", "boolean", "object", "number", "string", "array"],
+                    "additionalProperties": True,
+                }
+            )
+            return JsonSchema.array_of(prop)
         slot_is_multivalued = "multivalued" in slot and slot.multivalued
         slot_is_inlined = self.schemaview.is_inlined(slot)
         if not omit_type:

linkml/generators/plantumlgen.py

@@ -12,7 +12,11 @@ from typing import Callable, List, Optional, Set, cast
 
 import click
 import requests
-from linkml_runtime.linkml_model.meta import ClassDefinition, ClassDefinitionName, SlotDefinition
+from linkml_runtime.linkml_model.meta import (
+    ClassDefinition,
+    ClassDefinitionName,
+    SlotDefinition,
+)
 from linkml_runtime.utils.formatutils import camelcase, underscore
 
 from linkml import REQUESTS_TIMEOUT
@@ -46,6 +50,7 @@ class PlantumlGenerator(Generator):
     directory: Optional[str] = None
     kroki_server: Optional[str] = "https://kroki.io"
     load_image: bool = True
+    tooltips_flag: bool = False
 
     def visit_schema(
         self,
@@ -132,18 +137,28 @@ class PlantumlGenerator(Generator):
                         "    {field} "
                         + underscore(self.aliased_slot_name(slot))
                         + mod
-                        + ": "
+                        + " : "
                         + underscore(slot.range)
+                        + " "
                         + self.cardinality(slot)
                     )
             self.class_generated.add(cn)
         self.referenced.add(cn)
         cls = self.schema.classes[cn]
+
+        tooltip_contents = str(cls.description)
+        first_newline_index = tooltip_contents.find("\n")
+        tooltip_contents = tooltip_contents if first_newline_index < 0 else tooltip_contents[0:first_newline_index]
+
+        if self.format == "svg" and len(tooltip_contents) > 200:
+            tooltip_contents = tooltip_contents[0:197] + " ... "
+
+        tooltip = " [[{" + tooltip_contents + "}]] "
         if cls.abstract:
             class_type = "abstract"
         else:
             class_type = "class"
-        return class_type + ' "' + cn + ('" {\n' + "\n".join(slot_defs) + "\n}" if slot_defs else '"')
+        return class_type + ' "' + cn + '"' + tooltip + ("{\n" + "\n".join(slot_defs) + "\n}")
 
     def class_associations(self, cn: ClassDefinitionName, must_render: bool = False) -> str:
         """Emit all associations for a focus class.  If none are specified, all classes are generated
@@ -217,7 +232,7 @@ class PlantumlGenerator(Generator):
                     classes.append(self.add_class(cn))
                 if mixin not in self.class_generated:
                     classes.append(self.add_class(mixin))
-                assocs.append(cn + plantuml_uses[0] + mixin + plantuml_uses[1])
+                assocs.append('"' + cn + '" ' + plantuml_uses[0] + ' "' + mixin + '" ' + plantuml_uses[1])
 
             # Classes that use the class as a mixin
             if cls.name in self.synopsis.mixinrefs:
@@ -226,7 +241,9 @@ class PlantumlGenerator(Generator):
                         classes.append(self.add_class(ClassDefinitionName(mixin)))
                     if cn not in self.class_generated:
                         classes.append(self.add_class(cn))
-                    assocs.append(ClassDefinitionName(mixin) + plantuml_uses[0] + cn + plantuml_uses[1])
+                    assocs.append(
+                        '"' + ClassDefinitionName(mixin) + '" ' + plantuml_uses[0] + ' "' + cn + '" ' + plantuml_uses[1]
+                    )
 
             # Classes that inject information
             if cn in self.synopsis.applytos.classrefs:
@@ -265,7 +282,7 @@ class PlantumlGenerator(Generator):
             if slot.multivalued:
                 return " [1..*]" if slot.required else " [0..*]"
             else:
-                return " [req]" if slot.required else " [opt]"
+                return " "
         else:
             if slot.multivalued:
                 return '"1..*" ' if slot.required else '"0..*" '

linkml/generators/pydanticgen/__init__.py

@@ -1,4 +1,4 @@
-from linkml.generators.pydanticgen.pydanticgen import DEFAULT_IMPORTS, PydanticGenerator, cli
+from linkml.generators.pydanticgen.pydanticgen import DEFAULT_IMPORTS, MetadataMode, PydanticGenerator, cli
 from linkml.generators.pydanticgen.template import (
     ConditionalImport,
     Import,
@@ -18,6 +18,7 @@ __all__ = [
     "DEFAULT_IMPORTS",
     "Import",
     "Imports",
+    "MetadataMode",
     "PydanticAttribute",
     "PydanticBaseModel",
     "PydanticClass",

linkml/generators/pydanticgen/includes.py

@@ -19,6 +19,9 @@ class LinkMLMeta(BaseModel):
     
     def __setitem__(self, key:str, value):
         self.__root__[key] = value
+        
+    def __contains__(self, key:str) -> bool:
+        return key in self.__root__
    
     class Config:
         allow_mutation = False
@@ -37,6 +40,9 @@ class LinkMLMeta(RootModel):
     
     def __setitem__(self, key:str, value):
         self.root[key] = value
+        
+    def __contains__(self, key:str) -> bool:
+        return key in self.root
     
 """
 

linkml/generators/pydanticgen/pydanticgen.py

@@ -582,17 +582,22 @@ class PydanticGenerator(OOCodeGenerator):
         elif self.metadata_mode in (MetadataMode.EXCEPT_CHILDREN, MetadataMode.EXCEPT_CHILDREN.value):
             meta = {}
             for k, v in remove_empty_items(source).items():
+                if k in ("slots", "classes") and isinstance(model, PydanticModule):
+                    # FIXME: Special-case removal of slots until we generate class-level slots
+                    continue
+
                 if not hasattr(model, k):
                     meta[k] = v
-                elif isinstance(getattr(model, k), list) and not any(
-                    [isinstance(item, TemplateModel) for item in getattr(model, k)]
-                ):
+                    continue
+
+                model_attr = getattr(model, k)
+                if isinstance(model_attr, list) and not any([isinstance(item, TemplateModel) for item in model_attr]):
                     meta[k] = v
-                elif isinstance(getattr(model, k), dict) and not any(
-                    [isinstance(item, TemplateModel) for item in getattr(model, k).values()]
+                elif isinstance(model_attr, dict) and not any(
+                    [isinstance(item, TemplateModel) for item in model_attr.values()]
                 ):
                     meta[k] = v
-                elif not isinstance(getattr(model, k), TemplateModel):
+                elif not isinstance(model_attr, (list, dict, TemplateModel)):
                     meta[k] = v
 
         elif self.metadata_mode in (MetadataMode.FULL, MetadataMode.FULL.value):
@@ -600,7 +605,7 @@ class PydanticGenerator(OOCodeGenerator):
         else:
             raise ValueError(
                 f"Unknown metadata mode '{self.metadata_mode}', needs to be one of "
-                f"{[mode.value for mode in MetadataMode]}"
+                f"{[mode for mode in MetadataMode]}"
             )
 
         model.meta = meta
@@ -753,22 +758,17 @@ class PydanticGenerator(OOCodeGenerator):
                 new_class.bases = bases[k]
             classes[k] = new_class
 
-        schema_meta = {
-            k: v for k, v in remove_empty_items(schema).items() if k not in PydanticModule.exclude_from_meta()
-        }
-
         module = PydanticModule(
             pydantic_ver=self.pydantic_version,
             metamodel_version=self.schema.metamodel_version,
             version=self.schema.version,
-            imports=imports.imports,
+            python_imports=imports.imports,
             base_model=base_model,
             injected_classes=injected_classes,
             enums=enums,
             classes=classes,
-            meta=schema_meta,
         )
-        module = self.include_metadata(module, pyschema)
+        module = self.include_metadata(module, schema)
         return module
 
     def serialize(self) -> str:
@@ -830,6 +830,14 @@ Available templates to override:
     default=False,
     help="Format generated models with black (must be present in the environment)",
 )
+@click.option(
+    "--meta",
+    type=click.Choice([k for k in MetadataMode]),
+    default="auto",
+    help="How to include linkml schema metadata in generated pydantic classes. "
+    "See docs for MetadataMode for full description of choices. "
+    "Default (auto) is to include all metadata that can't be otherwise represented",
+)
 @click.version_option(__version__, "-V", "--version")
 @click.command()
 def cli(
@@ -844,6 +852,7 @@ def cli(
     pydantic_version=int(PYDANTIC_VERSION[0]),
     extra_fields: Literal["allow", "forbid", "ignore"] = "forbid",
     black: bool = False,
+    meta: MetadataMode = "auto",
     **args,
 ):
     """Generate pydantic classes to represent a LinkML model"""
@@ -870,6 +879,7 @@ def cli(
         gen_slots=slots,
         template_dir=template_dir,
         black=black,
+        metadata_mode=meta,
         **args,
     )
     print(gen.serialize())

linkml/generators/pydanticgen/template.py

@@ -322,6 +322,11 @@ class PydanticClass(TemplateModel):
         def validators(self) -> Optional[Dict[str, PydanticValidator]]:
             return self._validators()
 
+        @computed_field
+        def slots(self) -> Optional[Dict[str, PydanticAttribute]]:
+            """alias of attributes"""
+            return self.attributes
+
     else:
         validators: Optional[Dict[str, PydanticValidator]]
 
@@ -575,7 +580,7 @@ class PydanticModule(TemplateModel):
     version: Optional[str] = None
     base_model: PydanticBaseModel = PydanticBaseModel()
     injected_classes: Optional[List[str]] = None
-    imports: List[Union[Import, ConditionalImport]] = Field(default_factory=list)
+    python_imports: List[Union[Import, ConditionalImport]] = Field(default_factory=list)
     enums: Dict[str, PydanticEnum] = Field(default_factory=dict)
     classes: Dict[str, PydanticClass] = Field(default_factory=dict)
     meta: Optional[Dict[str, Any]] = None

linkml/generators/pydanticgen/templates/module.py.jinja

@@ -1,4 +1,4 @@
-{% for import in imports %}
+{% for import in python_imports %}
 {{ import }}
 {%- endfor -%}
 

{linkml-1.8.0.dist-info → linkml-1.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.8.0
+Version: 1.8.1
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink

{linkml-1.8.0.dist-info → linkml-1.8.1.dist-info}/RECORD

@@ -28,24 +28,24 @@ linkml/generators/javagen/java_record_template.jinja2,sha256=OQZffLSy_xR3FIhQMlt
 linkml/generators/javagen.py,sha256=KxwupMztyCRHcSsbtTnOovuj1WamsAny0mxbYWvTiDs,5324
 linkml/generators/jsonldcontextgen.py,sha256=y_AE1JF0QS75VDfOAquToClrWGAWb_ltsGN5r-Q20F8,8638
 linkml/generators/jsonldgen.py,sha256=FamA0pbbc9U3kEslsjvgJoJXjQ80VzoPbHmClVGPvKE,7757
-linkml/generators/jsonschemagen.py,sha256=Oi55uJJmKiSLoZWn_snN5rx51q0DEGqzHv6VgCLfodY,27747
+linkml/generators/jsonschemagen.py,sha256=sQXlaT_UOiJfbRoxH-hFY4nM0ELdjRlCFnS8HqVzqb8,28263
 linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/linkmlgen.py,sha256=1_Kt_7rD42WvCTjq0yaq1Of7jEDZR_uusyzAT-qWMHk,3471
 linkml/generators/markdowngen.py,sha256=mwydWkrF-WzsTiKwJqqe9NUya5VaTj7ywKqodP85A44,34449
 linkml/generators/namespacegen.py,sha256=vVcIyM0zlKd7XRvtdzwTwHjG4Pg49801gy4FUmjJlqQ,6450
 linkml/generators/oocodegen.py,sha256=r73QI08ajbTZTobc9OIG6BMWZft3zdu76vKVR33pyYg,7774
 linkml/generators/owlgen.py,sha256=NHIcL1d79WoeqfiZRj6kRk5aTXcQ6JDNXV_VAtH6Vt0,57554
-linkml/generators/plantumlgen.py,sha256=2e4ejw0B72Sl_-mipgpKz743LVMs0kRZc8E0MK7gxFY,14919
+linkml/generators/plantumlgen.py,sha256=JgAox2o_HQgXR4ZxdHwdRUzcHSbpsAdv15Qsq1vnEZs,15463
 linkml/generators/prefixmapgen.py,sha256=w8gMCFOI0DmZsNvo9IkbhOqVWqqWYEN6SXnAP3BgFSk,4240
 linkml/generators/projectgen.py,sha256=OuT_AneoZFNMCn50GllfZafadUHt50u61JcftM2eed4,9750
 linkml/generators/protogen.py,sha256=i4sEhNdAiFFP12fwfRdype1MX8yU-E5fF7XzkcpBCd0,2512
-linkml/generators/pydanticgen/__init__.py,sha256=uKGaaQSaeKqinHImXGFE448i-t8Oi0No8suIO76sep8,629
+linkml/generators/pydanticgen/__init__.py,sha256=-972x-uV0atgveW_n5qvG1WelKANvsk9ZseZOIH_tNI,663
 linkml/generators/pydanticgen/array.py,sha256=EYqAkT2_wE82kZ-niUWAC5U3V8EvjjyfSH7tz5GYKWo,19461
 linkml/generators/pydanticgen/black.py,sha256=BaJ7b-kMUbIN_cKRT3yCaMEbFwxzj1_U7w4fKQnkL44,723
 linkml/generators/pydanticgen/build.py,sha256=Ia8qy4C16b-KqO_fw4tGQW_Eo4grCVyX7RsuJ3uRTtk,2681
-linkml/generators/pydanticgen/includes.py,sha256=PIVbACrtqQS6LFrXqQsJC6dQUcGBM3uY4E4qLQWJrnk,998
-linkml/generators/pydanticgen/pydanticgen.py,sha256=WZxFfLvXhHXVtDQpLjMf63eoBMUxcW0oEMS14jbDOWo,34458
-linkml/generators/pydanticgen/template.py,sha256=HESLY1Rd7N_e92dqrh_fif_yp3oDl0n1UAghklMyphA,20982
+linkml/generators/pydanticgen/includes.py,sha256=0CZi8vs6Z2eVvMOWhbTphCYoI3X8E9-8LgSaCBeiuCY,1174
+linkml/generators/pydanticgen/pydanticgen.py,sha256=kaUBENnVEGpFs3gGK8kQbR2ZoZ1eg9Jiz0yNtXajbEw,34900
+linkml/generators/pydanticgen/template.py,sha256=gffWyzJNmjw2Kf1UszRp97qGrnkAGd4UnLimU2nEsEA,21154
 linkml/generators/pydanticgen/templates/attribute.py.jinja,sha256=S_T-M7n_eeM3LW5gQUuTPH1-Oc1CEtL7Bve7qAFouYQ,688
 linkml/generators/pydanticgen/templates/base_model.py.jinja,sha256=48y64MnC9rjNSV-nKLMeDuHN4gm15UsInhnKxh65zoM,834
 linkml/generators/pydanticgen/templates/class.py.jinja,sha256=V_lyvFcZ9QhlKZi2bL5iff8RjHir2SQTTypOzQMOfmk,744
@@ -53,7 +53,7 @@ linkml/generators/pydanticgen/templates/conditional_import.py.jinja,sha256=Yhekn
 linkml/generators/pydanticgen/templates/enum.py.jinja,sha256=572XFQyEMZfL-G_Cj68T-NI_mUnDoFOAVJOGIKu2Hb8,338
 linkml/generators/pydanticgen/templates/footer.py.jinja,sha256=WuWGJjkWDQcEPL2bGk5fdGuhO0gQRUJzpo4CQHHxQNQ,385
 linkml/generators/pydanticgen/templates/imports.py.jinja,sha256=d1XFna2eOpkH8cgJML3vXwqGcocczvOcrbg6jjd4kP0,945
-linkml/generators/pydanticgen/templates/module.py.jinja,sha256=nymjtSX4jqV9deSsXrsh1HWR90ygECHE4CV9MCyNrTY,615
+linkml/generators/pydanticgen/templates/module.py.jinja,sha256=gYauXrq8ML3ieaN_DFGB9yj9VfZV2yHG5LRQUzWy4VA,622
 linkml/generators/pydanticgen/templates/validator.py.jinja,sha256=Yo4dubQal-HwEoJKztQkLYM5qCz1I8na2oaDlXuEpwU,532
 linkml/generators/pythongen.py,sha256=CiLmc964siGeJWZC_bOffsqrSnJ5qzn7Eu961C47xgo,52850
 linkml/generators/rdfgen.py,sha256=eQi3XXjWk6xliTLncQ4G0VYzGCJwCU_FFG-O7tA8DSA,2959
@@ -143,8 +143,8 @@ 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=hDk2RGxRE5-WYNriWknugtbm3Mhn8bFcAcXGMlkYxVk,11705
-linkml-1.8.0.dist-info/entry_points.txt,sha256=7haDkIbyC7ZLhm5z-e3BhrLJpY2xoW1yuD8Y7QPNtVg,2093
-linkml-1.8.0.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
-linkml-1.8.0.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-linkml-1.8.0.dist-info/METADATA,sha256=ImZiqQezJfM8leU0WgCimYjcJXydh1XO8T22tlC9zpw,3724
-linkml-1.8.0.dist-info/RECORD,,
+linkml-1.8.1.dist-info/entry_points.txt,sha256=7haDkIbyC7ZLhm5z-e3BhrLJpY2xoW1yuD8Y7QPNtVg,2093
+linkml-1.8.1.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
+linkml-1.8.1.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
+linkml-1.8.1.dist-info/METADATA,sha256=-Nk6qRvku2ysnCvxuObK_ILTulyQzPAKyvbbUbzSSfk,3724
+linkml-1.8.1.dist-info/RECORD,,