linkml 1.5.5__tar.gz → 1.5.7__tar.gz

{linkml-1.5.5 → linkml-1.5.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.5.5
+Version: 1.5.7
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -33,7 +33,7 @@ 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 (>=1.5.3)
+Requires-Dist: linkml-runtime (>=1.5.4)
 Requires-Dist: openpyxl
 Requires-Dist: parse
 Requires-Dist: prefixcommons (>=0.1.7)

{linkml-1.5.5 → linkml-1.5.7}/linkml/__init__.py

@@ -20,9 +20,7 @@ MODULE_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
 LOCAL_METAMODEL_YAML_FILE = linkml_files.LOCAL_PATH_FOR(Source.META, Format.YAML)
 LOCAL_TYPES_YAML_FILE = linkml_files.LOCAL_PATH_FOR(Source.TYPES, Format.YAML)
 LOCAL_MAPPINGS_YAML_FILE = linkml_files.LOCAL_PATH_FOR(Source.MAPPINGS, Format.YAML)
-LOCAL_ANNOTATIONS_YAML_FILE = linkml_files.LOCAL_PATH_FOR(
-    Source.ANNOTATIONS, Format.YAML
-)
+LOCAL_ANNOTATIONS_YAML_FILE = linkml_files.LOCAL_PATH_FOR(Source.ANNOTATIONS, Format.YAML)
 LOCAL_EXTENSIONS_YAML_FILE = linkml_files.LOCAL_PATH_FOR(Source.EXTENSIONS, Format.YAML)
 
 # Local location of jsonld and context.jsonld files
@@ -30,9 +28,7 @@ LOCAL_METAMODEL_LDCONTEXT_FILE = linkml_files.LOCAL_PATH_FOR(Source.META, Format
 LOCAL_METAMODEL_JSONLD_FILE = linkml_files.LOCAL_PATH_FOR(Source.META, Format.JSON)
 LOCAL_TYPES_LDCONTEXT_FILE = linkml_files.LOCAL_PATH_FOR(Source.TYPES, Format.JSONLD)
 LOCAL_TYPES_JSONLD_FILE = linkml_files.LOCAL_PATH_FOR(Source.TYPES, Format.JSON)
-LOCAL_MAPPINGS_LDCONTEXT_FILE = linkml_files.LOCAL_PATH_FOR(
-    Source.MAPPINGS, Format.JSONLD
-)
+LOCAL_MAPPINGS_LDCONTEXT_FILE = linkml_files.LOCAL_PATH_FOR(Source.MAPPINGS, Format.JSONLD)
 LOCAL_MAPPINGS_JSONLD_FILE = linkml_files.LOCAL_PATH_FOR(Source.MAPPINGS, Format.JSON)
 
 # Local location of metamodel shex file

{linkml-1.5.5 → linkml-1.5.7}/linkml/_version.py

@@ -3,7 +3,7 @@ try:
 except ImportError:
     # Python < 3.8
     import importlib_metadata as metadata  # pragma: no cover
-                
+
 try:
     __version__ = metadata.version(__package__)
 except metadata.PackageNotFoundError:

{linkml-1.5.5 → linkml-1.5.7}/linkml/generators/PythonGenNotes.md

@@ -122,7 +122,7 @@ the builtin type `int`.  Four class variables are included in the generation:
 * `type_name` - the non-mangled name assigned to the type in the original definition
 * `type_model_uri` - the URIRef of the type definition in the default LinkML namespace
 
-The python then emits a class definition for the `Integers` classe, where we have defined four slot type permutations:
+The python then emits a class definition for the `Integers` class, where we have defined four slot type permutations:
 
 1) `mand_integer` - a single valued required type:
 
@@ -189,7 +189,7 @@ The python then emits a class definition for the `Integers` classe, where we hav
     
         `opt_multi_integer: Optional[Union[int, List[int]]] = empty_list()`
         
-    * The absence of a list property is always represented as an emtpy list:
+    * The absence of a list property is always represented as an empty list:
         ```        
         if self.opt_multi_integer is None:
             self.opt_multi_integer = []
@@ -1232,7 +1232,7 @@ dictionary.  You can construct a list of integers with a single value:
 ```python
     my_entries = ListOfIntegers(17)
 ```
-Which would, if the class `ListOfIntegers`'s first variable was a multivalued slot with a range of intgers, result in
+Which would, if the class `ListOfIntegers`'s first variable was a multivalued slot with a range of integers, result in
 `my_entries.v == [17]`.  When dealing with classes, however, the following:
 ```python
     my_entries = ListOfClasses(dict(name='element1', value=17))
@@ -1243,7 +1243,7 @@ The final line in the `__post_init__` section:
 ```python
     self._normalize_inlined_slot(slot_name="v1", slot_type=IdentifiedThreeElementClass, key_name="name", inlined_as_list=True, keyed=True)
 ```
-passes the remainder of the post initilization normalization to a function defined in `YAMLRoot`.  
+passes the remainder of the post initialization normalization to a function defined in `YAMLRoot`.  
 
 
 The final case, Case 2.4 (Inlined as dictionary) is essentially the same, with the exception that the target type is

linkml-1.5.7/linkml/generators/__init__.py

@@ -0,0 +1,53 @@
+"""
+Generators translate between a SchemaDefinition and an alternative
+representation such as JsonSchema
+"""
+
+from linkml.generators.javagen import JavaGenerator
+from linkml.generators.jsonschemagen import JsonSchemaGenerator
+from linkml.generators.owlgen import OwlSchemaGenerator
+from linkml.generators.pydanticgen import PydanticGenerator
+from linkml.generators.pythongen import PythonGenerator
+from linkml.generators.shaclgen import ShaclGenerator
+from linkml.generators.shexgen import ShExGenerator
+from linkml.generators.sqlalchemygen import SQLAlchemyGenerator
+from linkml.generators.sqltablegen import SQLTableGenerator
+
+__all__ = [
+    "csvgen",
+    "dotgen",
+    "docgen",
+    "golrgen",
+    "graphqlgen",
+    "javagen",
+    "jsonldcontextgen",
+    "jsonldgen",
+    "jsonschemagen",
+    "markdowngen",
+    "namespacegen",
+    "owlgen",
+    "protogen",
+    "pythongen",
+    "pydanticgen",
+    "rdfgen",
+    "shexgen",
+    "shaclgen",
+    "sssomgen",
+    "summarygen",
+    "yamlgen",
+    "yumlgen",
+    "OwlSchemaGenerator",
+    "PydanticGenerator",
+    "PythonGenerator",
+    "JavaGenerator",
+    "JsonSchemaGenerator",
+    "ShaclGenerator",
+    "ShExGenerator",
+    "SQLAlchemyGenerator",
+    "SQLTableGenerator",
+]
+
+# TODO: deprecate usage of these
+# GENERATOR_BASE = "0.9"
+
+# PYTHON_GEN_VERSION = GENERATOR_BASE + ".0"

linkml-1.5.7/linkml/generators/common/type_designators.py

@@ -0,0 +1,49 @@
+from typing import List
+
+from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
+from linkml_runtime.utils.schemaview import SchemaView
+
+
+def get_type_designator_value(
+    sv: SchemaView, type_designator_slot: SlotDefinition, class_def: ClassDefinition
+) -> str:
+    """
+    returns the correct value for a type designator field for a given class, depending on its range
+    this implements the logic described in https://github.com/linkml/linkml/issues/945:
+    """
+    slot_types = set(sv.type_ancestors(type_designator_slot.range))
+    if "uri" in slot_types:
+        return sv.get_uri(class_def, expand=True, native=False)
+    elif "uriorcurie" in slot_types:
+        return sv.get_uri(class_def, expand=False, native=False)
+    elif "string" in slot_types:
+        return class_def.name
+    else:
+        return sv.get_uri(class_def, expand=False, native=False)
+
+
+def get_accepted_type_designator_values(
+    sv: SchemaView, type_designator_slot: SlotDefinition, class_def: ClassDefinition
+) -> List[str]:
+    """
+    returns the accepted values for a type designator field for a given class, depending on its range
+    this implements the logic described in https://github.com/linkml/linkml/issues/945:
+    """
+    accepted_uri_values = [
+        sv.get_uri(class_def, expand=True, native=True),
+        sv.get_uri(class_def, expand=True, native=False),
+        sv.get_uri(class_def, expand=False, native=True),
+        sv.get_uri(class_def, expand=False, native=False),
+    ]
+    # unique, but with order preserved (https://stackoverflow.com/a/17016257)
+    accepted_uri_values = list(dict.fromkeys(accepted_uri_values))
+
+    slot_types = set(sv.type_ancestors(type_designator_slot.range))
+    uri_types = ["uri", "uriorcurie"]
+
+    if slot_types.intersection(uri_types):
+        return accepted_uri_values
+    elif type_designator_slot.range == "string":
+        return [class_def.name]
+    else:
+        return accepted_uri_values

{linkml-1.5.5 → linkml-1.5.7}/linkml/generators/csvgen.py

@@ -5,12 +5,10 @@ import os
 import sys
 from csv import DictWriter
 from dataclasses import dataclass
-from typing import List, Optional, Set, TextIO, Union
+from typing import List, Optional, Set
 
 import click
-from linkml_runtime.linkml_model.meta import (ClassDefinition,
-                                              ClassDefinitionName,
-                                              SchemaDefinition)
+from linkml_runtime.linkml_model.meta import ClassDefinition, ClassDefinitionName
 from linkml_runtime.utils.formatutils import be, underscore
 
 from linkml._version import __version__
@@ -37,9 +35,7 @@ class CsvGenerator(Generator):
     sep: Optional[str] = None
     """Separator for columns"""
 
-    closure: Optional[
-        Set[ClassDefinitionName]
-    ] = None
+    closure: Optional[Set[ClassDefinitionName]] = None
     """List of classes to include in output"""
 
     writer: Optional[DictWriter] = None
@@ -69,9 +65,7 @@ class CsvGenerator(Generator):
                 self.closure.update(self.ancestors(self.schema.classes[clsname]))
 
         dialect: str = "excel" if self.format == "csv" else "excel-tab"
-        self.writer = DictWriter(
-            sys.stdout, ["id", "mappings", "description"], dialect=dialect
-        )
+        self.writer = DictWriter(sys.stdout, ["id", "mappings", "description"], dialect=dialect)
         self.writer.writeheader()
 
     def visit_class(self, cls: ClassDefinition) -> bool:

{linkml-1.5.5 → linkml-1.5.7}/linkml/generators/docgen/class.md.jinja2

@@ -18,7 +18,14 @@ _{{ element_description_line }}_
 
 URI: {{ gen.uri_link(element) }}
 
+
+{% if diagram_type == "er_diagram" %}
+```{{ gen.mermaid_directive() }}
+{{ gen.mermaid_diagram([element.name]) }}
+```
+{% else %}
 {% include "class_diagram.md.jinja2" %}
+{% endif %}
 
 {% if schemaview.class_parents(element.name) or schemaview.class_children(element.name, mixins=False) %}
 

{linkml-1.5.5 → linkml-1.5.7}/linkml/generators/docgen/class_diagram.md.jinja2

@@ -1,8 +1,3 @@
-{% if diagram_type == "er_diagram" %}
-```{{ gen.mermaid_directive() }}
-{{ gen.mermaid_diagram([element.name]) }}
-```
-{% else %}
 {% if schemaview.class_parents(element.name) and schemaview.class_children(element.name) %}
 ```{{ gen.mermaid_directive() }}
  classDiagram
@@ -61,5 +56,4 @@
         {% endif %}
       {% endfor %}
 ```
-{% endif %}
 {% endif %}

linkml-1.5.7/linkml/generators/docgen/subset.md.jinja2

@@ -0,0 +1,106 @@
+# Subset: {{ gen.name(element) }}
+
+{%- if header -%}
+{{ header }}
+{%- endif -%}
+
+{% if element.description %}
+{% set element_description_lines = element.description.split('\n') %}
+{% for element_description_line in element_description_lines %}
+_{{ element_description_line }}_
+{% endfor %}
+{% endif %}
+
+URI: {{ gen.uri_link(element) }}
+
+{% include "common_metadata.md.jinja2" %}
+
+{% set classes_in_subset = [] %}
+{% set slots_in_subset = [] %}
+{% set enums_in_subset = [] %}
+
+{# Collect classes, slots, and enumerations in subset #}
+{% for c in gen.all_class_objects()|sort(attribute=sort_by) %}
+    {%- if element.name in c.in_subset %}
+        {% set _ = classes_in_subset.append(c) %}
+    {%- endif %}
+{% endfor %}
+
+{% for s in gen.all_slot_objects()|sort(attribute=sort_by) %}
+    {%- if element.name in s.in_subset %}
+        {% set _ = slots_in_subset.append(s) %}
+    {%- endif %}
+{% endfor %}
+
+{% for e in schemaview.all_enums().values() %}
+    {%- if element.name in e.in_subset %}
+        {% set _ = enums_in_subset.append(e) %}
+    {%- endif %}
+{% endfor %}
+
+{% if classes_in_subset %}
+## Classes in subset
+
+| Class | Description |
+| --- | --- |
+{% for c in gen.all_class_objects()|sort(attribute=sort_by) -%}
+{%- if element.name in c.in_subset -%}
+| {{gen.link(c)}} | {{c.description|enshorten}} |
+{% endif -%}
+{% endfor %}
+
+{% for c in gen.all_class_objects()|sort(attribute=sort_by) -%}
+{%- if element.name in c.in_subset -%}
+### {{ gen.name(c) }}
+
+{{c.description}}
+
+{%- set filtered_slots = [] -%}
+
+{%- for s in induced_slots|sort(attribute=sort_by) -%}
+    {%- if element.name in s.in_subset or element.name in schemaview.get_slot(s.name).in_subset -%}
+        {% set _ = filtered_slots.append(s) %}
+    {%- endif -%}
+{%- endfor %}
+
+{%- if filtered_slots|length > 0 -%}
+| Name | Cardinality and Range  | Description  |
+| ---  | ---  | --- |
+{% for s in filtered_slots -%}
+| {{gen.link(s)}} | {{ gen.cardinality(s) }} <br/> {{gen.link(s.range)}}  | {{s.description|enshorten}} {% if s.identifier %}**identifier**{% endif %}  |
+{% endfor %}
+{%- endif %}
+
+
+{%- endif %}
+{% endfor %}
+
+{%- endif %}
+
+
+{% if slots_in_subset %}
+## Slots in subset
+
+| Slot | Description |
+| --- | --- |
+{% for s in slots_in_subset|sort(attribute=sort_by) -%}
+{%- if element.name in s.in_subset -%}
+| {{ gen.link(s) }} | {{ s.description|enshorten }} |
+{%- endif %}
+{% endfor %}
+
+{%- endif %}
+
+
+{% if enums_in_subset %}
+## Enumerations in subset
+
+| Enumeration | Description |
+| --- | --- |
+{% for e in enums_in_subset|sort(attribute='name') -%}
+{%- if element.name in e.in_subset %}
+| {{ gen.link(e) }} | {{ e.description|enshorten }} |
+{%- endif %}
+{% endfor %}
+
+{%- endif %}