linkml 1.6.9__tar.gz → 1.7.0rc2__tar.gz

{linkml-1.6.9 → linkml-1.7.0rc2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.6.9
+Version: 1.7.0rc2
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -31,7 +31,7 @@ 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 (>=1.6.0)
+Requires-Dist: linkml-runtime (>=1.7.0rc1)
 Requires-Dist: openpyxl
 Requires-Dist: parse
 Requires-Dist: prefixcommons (>=0.1.7)

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/__init__.py

@@ -4,6 +4,7 @@ representation such as JsonSchema
 """
 
 from linkml.generators.javagen import JavaGenerator
+from linkml.generators.jsonldcontextgen import ContextGenerator
 from linkml.generators.jsonschemagen import JsonSchemaGenerator
 from linkml.generators.owlgen import OwlSchemaGenerator
 from linkml.generators.pydanticgen import PydanticGenerator
@@ -41,6 +42,7 @@ __all__ = [
     "PydanticGenerator",
     "PythonGenerator",
     "JavaGenerator",
+    "ContextGenerator",
     "JsonSchemaGenerator",
     "ShaclGenerator",
     "ShExGenerator",

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/csvgen.py

@@ -1,6 +1,7 @@
 """
 Generate CSVs
 """
+
 import os
 import sys
 from csv import DictWriter

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/dotgen.py

@@ -1,6 +1,7 @@
 """
 Generate dotfiles
 """
+
 import os
 from dataclasses import dataclass
 from typing import List, Optional

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/golrgen.py

@@ -6,6 +6,7 @@ These can be converted to solr schema-xml, and used in amigo-bbop tools
 See the golr-views directory in this repo for examples
 
 """
+
 import os
 from dataclasses import dataclass
 from typing import List, Optional

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/javagen.py

@@ -70,6 +70,7 @@ class JavaGenerator(OOCodeGenerator):
     generatorname = os.path.basename(__file__)
     generatorversion = "0.0.1"
     valid_formats = ["java"]
+    file_extension = "java"
 
     # ObjectVars
     generate_records: bool = False

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/jsonldcontextgen.py

@@ -2,6 +2,7 @@
 Generate JSON-LD contexts
 
 """
+
 import os
 import re
 from dataclasses import dataclass, field
@@ -37,6 +38,7 @@ class ContextGenerator(Generator):
     visit_all_class_slots = False
     uses_schemaloader = True
     requires_metamodel = True
+    file_extension = "context.jsonld"
 
     # ObjectVars
     emit_prefixes: Set[str] = field(default_factory=lambda: set())

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/jsonldgen.py

@@ -1,6 +1,7 @@
 """ Generate JSONld
 
 """
+
 import os
 from copy import deepcopy
 from dataclasses import dataclass
@@ -99,13 +100,15 @@ class JSONLDGenerator(Generator):
             return (
                 ClassDefinitionName(camelcase(node))
                 if node in self.schema.classes
-                else SlotDefinitionName(underscore(node))
-                if node in self.schema.slots
-                else SubsetDefinitionName(camelcase(node))
-                if node in self.schema.subsets
-                else TypeDefinitionName(underscore(node))
-                if node in self.schema.types
-                else None
+                else (
+                    SlotDefinitionName(underscore(node))
+                    if node in self.schema.slots
+                    else (
+                        SubsetDefinitionName(camelcase(node))
+                        if node in self.schema.subsets
+                        else TypeDefinitionName(underscore(node)) if node in self.schema.types else None
+                    )
+                )
             )
         return None
 

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/jsonschemagen.py

@@ -193,6 +193,9 @@ class JsonSchemaGenerator(Generator):
     Note that if the range of a slot has a type designator, descendants will always be included.
     """
 
+    title_from: str = "name"
+    """The slot from which to populate JSONSchema title annotation."""
+
     top_level_schema: JsonSchema = None
 
     def __post_init__(self):
@@ -215,7 +218,7 @@ class JsonSchemaGenerator(Generator):
                 "$id": self.schema.id,
                 "metamodel_version": metamodel_version,
                 "version": self.schema.version if self.schema.version else None,
-                "title": self.schema.name,
+                "title": self.schema.title if self.title_from == "title" and self.schema.title else self.schema.name,
                 "type": "object",
                 "additionalProperties": self.not_closed,
             }
@@ -238,6 +241,8 @@ class JsonSchemaGenerator(Generator):
                 "description": be(cls.description),
             }
         )
+        if self.title_from == "title" and cls.title:
+            class_subschema["title"] = cls.title
 
         for slot_definition in self.schemaview.class_induced_slots(cls.name):
             self.handle_class_slot(subschema=class_subschema, cls=cls, slot=slot_definition)
@@ -364,6 +369,9 @@ class JsonSchemaGenerator(Generator):
                 "description": be(enum.description),
             }
         )
+        if self.title_from == "title" and enum.title:
+            enum_schema["title"] = enum.title
+
         if permissible_values_texts:
             enum_schema["enum"] = permissible_values_texts
         self.top_level_schema.add_def(enum.name, enum_schema)
@@ -480,6 +488,8 @@ class JsonSchemaGenerator(Generator):
                     prop = JsonSchema.array_of(prop)
 
         prop.add_keyword("description", slot.description)
+        if self.title_from == "title" and slot.title:
+            prop.add_keyword("title", slot.title)
 
         own_constraints = self.get_value_constraints_for_slot(slot)
 
@@ -619,6 +629,14 @@ If this is a positive number the resulting JSON will be pretty-printed with that
 disable pretty-printing and return the most compact JSON representation
 """,
 )
+@click.option(
+    "--title-from",
+    type=click.Choice(["name", "title"], case_sensitive=False),
+    default="name",
+    help="""
+Specify from which slot are JSON Schema 'title' annotations generated.
+""",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **kwargs):
     """Generate JSON Schema representation of a LinkML model"""

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/markdowngen.py

@@ -456,11 +456,11 @@ class MarkdownGenerator(Generator):
         filename = (
             self.formatted_element_name(obj)
             if isinstance(obj, ClassDefinition)
-            else underscore(obj.name)
-            if isinstance(obj, SlotDefinition)
-            else underscore(obj.name)
-            if isinstance(obj, EnumDefinition)
-            else camelcase(obj.name)
+            else (
+                underscore(obj.name)
+                if isinstance(obj, SlotDefinition)
+                else underscore(obj.name) if isinstance(obj, EnumDefinition) else camelcase(obj.name)
+            )
         )
         subdir = "/types" if isinstance(obj, TypeDefinition) and not self.no_types_dir else ""
         return f"{self.directory}{subdir}/{filename}.md"

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/owlgen.py

@@ -1,4 +1,5 @@
 """Generate OWL ontology representation of a LinkML schema."""
+
 import logging
 import os
 from collections import defaultdict
@@ -1219,6 +1220,12 @@ class OwlSchemaGenerator(Generator):
     show_default=True,
     help="If true, then mixins are represented as existential expressions",
 )
+@click.option(
+    "--use-native-uris/--no-use-native-uris",
+    default=True,
+    show_default=True,
+    help="Use model URIs rather than class/slot URIs",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, metadata_profile: str, **kwargs):
     """Generate an OWL representation of a LinkML model
@@ -1238,7 +1245,8 @@ def cli(yamlfile, metadata_profile: str, **kwargs):
         metadata_profiles = [MetadataProfile(metadata_profile)]
     else:
         metadata_profiles = [MetadataProfile.linkml]
-    print(OwlSchemaGenerator(yamlfile, metadata_profiles=metadata_profiles, **kwargs).serialize(**kwargs))
+    gen = OwlSchemaGenerator(yamlfile, metadata_profiles=metadata_profiles, **kwargs)
+    print(gen.serialize(**kwargs))
 
 
 if __name__ == "__main__":

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/plantumlgen.py

@@ -3,6 +3,7 @@
 https://plantuml.com/
 
 """
+
 import base64
 import os
 import zlib

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/prefixmapgen.py

@@ -2,6 +2,7 @@
 Generate JSON-LD contexts
 
 """
+
 import csv
 import os
 from dataclasses import dataclass, field

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/rdfgen.py

@@ -4,6 +4,7 @@ YAML Schema to RDF Generator
 Generate a JSON LD representation of the model
 
 """
+
 import os
 import urllib.parse as urlparse
 from dataclasses import dataclass, field

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/shaclgen.py

@@ -116,6 +116,7 @@ class ShaclGenerator(Generator):
                     prop_pv_literal(SH.minCount, 1)
                 prop_pv_literal(SH.minInclusive, s.minimum_value)
                 prop_pv_literal(SH.maxInclusive, s.maximum_value)
+                prop_pv_literal(SH.hasValue, s.equals_number)
                 r = s.range
                 if r in sv.all_classes():
                     range_ref = sv.get_uri(r, expand=True)

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/shexgen.py

@@ -1,6 +1,7 @@
 """Generate ShEx definition of a model
 
 """
+
 import os
 import urllib.parse as urlparse
 from dataclasses import dataclass, field

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/sqlddlgen.py

@@ -1,4 +1,5 @@
 """DEPRECATED: Use SQLTableGenerator instead"""
+
 import logging
 import os
 from contextlib import redirect_stdout

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/summarygen.py

@@ -1,6 +1,7 @@
 """Generate Summary Spreadsheets
 
 """
+
 import os
 import sys
 from csv import DictWriter

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/yamlgen.py

@@ -1,6 +1,7 @@
 """Validate linkml input and optionally emit completely resolved biolink yaml output
 
 """
+
 import os
 from dataclasses import dataclass, field
 

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/generators/yumlgen.py

@@ -3,6 +3,7 @@
 https://yuml.me/diagram/scruffy/class/samples
 
 """
+
 import os
 from dataclasses import dataclass, field
 from typing import Callable, List, Optional, Set, cast

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/transformers/logical_model_transformer.py

@@ -12,6 +12,7 @@ of constraints in both classes hold.
 These logical constraints are then simplified by translating to disjunctive normal form,
 and applying simplification rules.
 """
+
 import logging
 from copy import deepcopy
 from dataclasses import dataclass

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/utils/generator.py

@@ -14,6 +14,7 @@ New generators should always using the latter approach
 See: https://github.com/linkml/linkml/issues/923
 
 """
+
 import abc
 import logging
 import os
@@ -453,9 +454,11 @@ class Generator(metaclass=abc.ABCMeta):
         return (
             None
             if element.is_a is None
-            else self.schema.classes[element.is_a]
-            if isinstance(element, ClassDefinition)
-            else self.schema.slots[element.is_a]
+            else (
+                self.schema.classes[element.is_a]
+                if isinstance(element, ClassDefinition)
+                else self.schema.slots[element.is_a]
+            )
         )
 
     def ancestors(self, element: Union[ClassDefinition, SlotDefinition]) -> List[ElementName]:
@@ -904,7 +907,7 @@ def shared_arguments(g: Type[Generator]) -> Callable[[Command], Command]:
                 ("--useuris/--metauris",),
                 default=True,
                 show_default=True,
-                help="Include metadata in output",
+                help="Use class and slot URIs over model uris",
             )
         )
         f.params.append(Option(("--importmap", "-im"), type=click.File(), help="Import mapping file"))

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/utils/ifabsent_functions.py

@@ -113,7 +113,13 @@ default_library: List[
 
 def isabsent_match(
     txt: Text,
-) -> Optional[Tuple[Match[str], bool, Callable[[Match[str], SchemaLoader, ClassDefinition, SlotDefinition], str],]]:
+) -> Optional[
+    Tuple[
+        Match[str],
+        bool,
+        Callable[[Match[str], SchemaLoader, ClassDefinition, SlotDefinition], str],
+    ]
+]:
     txt = str(txt)
     for pattern, postinit, f in default_library:
         m = re.match(pattern + "$", txt)

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/utils/schemasynopsis.py

@@ -120,13 +120,11 @@ class SchemaSynopsis:
         self.add_ref(
             SlotType,
             k,
-            ClassType
-            if v.range in self.schema.classes
-            else EnumType
-            if v.range in self.schema.enums
-            else TypeType
-            if v.range in self.schema.types
-            else None,
+            (
+                ClassType
+                if v.range in self.schema.classes
+                else EnumType if v.range in self.schema.enums else TypeType if v.range in self.schema.types else None
+            ),
             v.range,
         )
 

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/validator/__init__.py

@@ -3,6 +3,7 @@ The ``linkml.validator`` package contains a new LinkML validation framework that
 than the ``linkml.validators`` package. While that package still exists, it may become deprecated
 in the future.
 """
+
 import os
 from pathlib import Path
 from typing import Any, Optional, Union

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/validator/loaders/__init__.py

@@ -4,6 +4,7 @@ instance from a source. Instances of these classes are passed to
 :meth:`linkml.validator.Validator.validate_source` and
 :meth:`linkml.validator.Validator.iter_results_from_source`
 """
+
 import os
 from typing import Union
 

linkml-1.7.0rc2/linkml/validator/plugins/shacl_validation_plugin.py

@@ -0,0 +1,93 @@
+import os
+from typing import Any, Iterator, Optional
+
+import rdflib
+from linkml_runtime.dumpers import rdflib_dumper
+
+from linkml.generators import PythonGenerator, ShaclGenerator
+from linkml.validator.plugins.validation_plugin import ValidationPlugin
+from linkml.validator.report import Severity, ValidationResult
+from linkml.validator.validation_context import ValidationContext
+
+SH = rdflib.Namespace("http://www.w3.org/ns/shacl#")
+
+
+class ShaclValidationPlugin(ValidationPlugin):
+    """A validation plugin which validates instances using SHACL.
+
+    :param shacl_path: If provided, SHACL will not be generated from the schema,
+        instead it will be read from this path.
+    :param closed: If ``True``, additional properties are not allowed on instances.
+        Defaults to ``False``.
+    :param raise_on_conversion_error: If ``True``, raise an exception if the instance
+        cannot be converted to a Python class. Otherwise, treat as a ValidationError.
+        Defaults to ``False``.
+    """
+
+    def __init__(
+        self,
+        *,
+        closed: bool = False,
+        shacl_path: Optional[os.PathLike] = None,
+        raise_on_conversion_error: bool = False,
+    ) -> None:
+        self.closed = closed
+        self.shacl_path = shacl_path
+        self.raise_on_conversion_error = raise_on_conversion_error
+
+    def _shacl_graph(self, context: ValidationContext) -> Optional[rdflib.Graph]:
+        g = rdflib.Graph()
+        if self.shacl_path:
+            g.parse(str(self.shacl_path))
+        else:
+            gen = ShaclGenerator(context._schema)
+            g = gen.as_graph()
+        return g
+
+    def process(self, instance: Any, context: ValidationContext) -> Iterator[ValidationResult]:
+        """Perform JSON Schema validation on the provided instance
+
+        :param instance: The instance to validate
+        :param context: The validation context which provides a JSON Schema artifact
+        :return: Iterator over validation results
+        :rtype: Iterator[ValidationResult]
+        """
+        import pyshacl
+
+        shacl_graph = self._shacl_graph(context)
+        if isinstance(instance, dict):
+            pygen = PythonGenerator(context._schema)
+            mod = pygen.compile_module()
+            py_cls = getattr(mod, context._target_class)
+            if self.raise_on_conversion_error:
+                instance = py_cls(**instance)
+            else:
+                try:
+                    instance = py_cls(**instance)
+                except (ValueError, TypeError):
+                    yield ValidationResult(
+                        type="shacl validation",
+                        severity=Severity.ERROR,
+                        instance=instance,
+                        instantiates=context.target_class,
+                        message="failed at class instantiation stage",
+                    )
+                    return
+        data_graph = rdflib_dumper.as_rdf_graph(instance, schemaview=context.schema_view)
+        validator = pyshacl.Validator(
+            shacl_graph=shacl_graph,
+            data_graph=data_graph,
+            inference="rdfs",
+        )
+        conforms, report_graph, report_text = validator.run()
+        for s, _, o in report_graph.triples((None, SH.result, None)):
+            msg = ""
+            for p, o2 in report_graph.predicate_objects(o):
+                msg += f"{p} {o2}\n"
+            yield ValidationResult(
+                type="shacl validation",
+                severity=Severity.ERROR,
+                instance=instance,
+                instantiates=context.target_class,
+                message=f"{msg}",
+            )

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/validator/validator.py

@@ -29,7 +29,7 @@ class Validator:
         schema: Union[str, dict, TextIO, Path, SchemaDefinition],
         validation_plugins: Optional[List[ValidationPlugin]] = None,
         *,
-        strict: bool = False
+        strict: bool = False,
     ) -> None:
         if isinstance(schema, Path):
             schema = str(schema)

{linkml-1.6.9 → linkml-1.7.0rc2}/linkml/workspaces/example_runner.py

@@ -1,6 +1,7 @@
 """Iterate through all examples in a folder testing them for validity.
 
 """
+
 import glob
 import json
 import logging

{linkml-1.6.9 → linkml-1.7.0rc2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "linkml"
-version = "1.6.9"
+version = "1.7.0rc2"
 description = "Linked Open Data Modeling Language"
 authors = [
     "Chris Mungall <cjmungall@lbl.gov>",
@@ -106,7 +106,7 @@ jinja2 = ">= 3.1.0"
 jsonasobj2 = "==1.*,>=1.0.0,>=1.0.3"
 jsonschema = {extras = ["format"], version = ">=4.0.0"}
 linkml-dataops = "*"
-linkml-runtime = ">=1.6.0"
+linkml-runtime = ">=1.7.0rc1"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
@@ -143,6 +143,10 @@ pytest = "^7.4.0"
 pytest-subtests = "^0.11.0"
 numpy = ">=1.24.3"
 
+
+[tool.poetry.group.shacl.dependencies]
+pyshacl = "^0.25.0"
+
 [tool.poetry.extras]
 docs = ["Sphinx", "sphinxcontrib-mermaid", "furo"]
 
@@ -152,7 +156,7 @@ build-backend = "poetry_dynamic_versioning.backend"
 
 [tool.codespell]
 # TODO: bring in tests in too
-skip = '.git,*.pdf,*.svg,./tests,pyproject.toml,*.dill'
+skip = '.git,*.pdf,*.svg,./tests,pyproject.toml,*.dill,poetry.lock'
 # Ignore table where words could be split across rows
 # Ignore shortcut specifications like [Ff]alse
 ignore-regex = '(\|.*\|.*\|.*\||\[[A-Z][a-z]\][a-z][a-z])'
@@ -161,7 +165,7 @@ quiet-level = 3
 
 [tool.black]
 line-length = 120
-target-versions = ["py38", "py39", "py310", "py311"]
+target-version = ["py38", "py39", "py310", "py311"]
 force-exclude = '''
 /(
   # default exclude

{linkml-1.6.9 → linkml-1.7.0rc2}/setup.py

@@ -35,7 +35,7 @@ install_requires = \
  'jsonasobj2>=1.0.3,<2.0.0',
  'jsonschema[format]>=4.0.0',
  'linkml-dataops',
- 'linkml-runtime>=1.6.0',
+ 'linkml-runtime>=1.7.0rc1',
  'openpyxl',
  'parse',
  'prefixcommons>=0.1.7',
@@ -109,7 +109,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'linkml',
-    'version': '1.6.9',
+    'version': '1.7.0rc2',
     'description': 'Linked Open Data Modeling Language',
     'long_description': '[![Pyversions](https://img.shields.io/pypi/pyversions/linkml.svg)](https://pypi.python.org/pypi/linkml)\n![](https://github.com/linkml/linkml/workflows/Build/badge.svg)\n[![PyPi](https://img.shields.io/pypi/v/linkml.svg)](https://pypi.python.org/pypi/linkml)\n[![badge](https://img.shields.io/badge/launch-binder-579ACA.svg)](https://mybinder.org/v2/gh/linkml/linkml/main?filepath=notebooks)\n[![DOI](https://zenodo.org/badge/13996/linkml/linkml.svg)](https://zenodo.org/badge/latestdoi/13996/linkml/linkml)\n[![PyPIDownloadsTotal](https://pepy.tech/badge/linkml)](https://pepy.tech/project/linkml)\n[![PyPIDownloadsMonth](https://img.shields.io/pypi/dm/linkml?logo=PyPI&color=blue)](https://pypi.org/project/linkml)\n[![codecov](https://codecov.io/gh/linkml/linkml/branch/main/graph/badge.svg?token=WNQNG986UN)](https://codecov.io/gh/linkml/linkml)\n\n\n# LinkML - Linked Data Modeling Language\n\nLinkML is a linked data modeling language following object-oriented and ontological principles. LinkML models are typically authored in YAML, and can be converted to other schema representation formats such as JSON or RDF.\n\nThis repo holds the tools for generating and working with LinkML. For the LinkML schema (metamodel), please see https://github.com/linkml/linkml-model\n\nThe complete documentation for LinkML can be found here:\n\n - [linkml.io/linkml](https://linkml.io/linkml)\n',
     'author': 'Chris Mungall',