linkml 1.7.5__py3-none-any.whl → 1.7.6__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- linkml/generators/__init__.py +2 -0
- linkml/generators/docgen/class.md.jinja2 +15 -2
- linkml/generators/docgen/slot.md.jinja2 +14 -1
- linkml/generators/docgen.py +17 -3
- linkml/generators/jsonldcontextgen.py +9 -6
- linkml/generators/jsonldgen.py +3 -1
- linkml/generators/owlgen.py +14 -0
- linkml/generators/prefixmapgen.py +5 -4
- linkml/generators/projectgen.py +14 -2
- linkml/generators/pydanticgen/__init__.py +29 -0
- linkml/generators/{pydanticgen.py → pydanticgen/pydanticgen.py} +192 -299
- linkml/generators/pydanticgen/template.py +504 -0
- linkml/generators/pydanticgen/templates/attribute.py.jinja +10 -0
- linkml/generators/pydanticgen/templates/base_model.py.jinja +27 -0
- linkml/generators/pydanticgen/templates/class.py.jinja +21 -0
- linkml/generators/pydanticgen/templates/conditional_import.py.jinja +9 -0
- linkml/generators/pydanticgen/templates/enum.py.jinja +16 -0
- linkml/generators/pydanticgen/templates/footer.py.jinja +13 -0
- linkml/generators/pydanticgen/templates/imports.py.jinja +31 -0
- linkml/generators/pydanticgen/templates/module.py.jinja +27 -0
- linkml/generators/pydanticgen/templates/validator.py.jinja +15 -0
- linkml/generators/pythongen.py +13 -7
- linkml/generators/shacl/__init__.py +3 -0
- linkml/generators/shacl/ifabsent_processor.py +41 -0
- linkml/generators/shacl/shacl_data_type.py +40 -0
- linkml/generators/shaclgen.py +105 -82
- linkml/generators/shexgen.py +1 -1
- linkml/generators/sqlalchemygen.py +1 -1
- linkml/generators/sqltablegen.py +32 -22
- linkml/generators/terminusdbgen.py +7 -1
- linkml/linter/config/datamodel/config.py +8 -0
- linkml/linter/rules.py +11 -2
- linkml/utils/generator.py +7 -6
- linkml/utils/ifabsent_functions.py +7 -9
- linkml/utils/schemaloader.py +1 -9
- linkml/utils/sqlutils.py +39 -25
- {linkml-1.7.5.dist-info → linkml-1.7.6.dist-info}/METADATA +4 -1
- {linkml-1.7.5.dist-info → linkml-1.7.6.dist-info}/RECORD +41 -27
- {linkml-1.7.5.dist-info → linkml-1.7.6.dist-info}/LICENSE +0 -0
- {linkml-1.7.5.dist-info → linkml-1.7.6.dist-info}/WHEEL +0 -0
- {linkml-1.7.5.dist-info → linkml-1.7.6.dist-info}/entry_points.txt +0 -0
linkml/utils/sqlutils.py
CHANGED
@@ -324,9 +324,15 @@ def main(verbose: int, quiet: bool, csv_field_size_limit: int):
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show_default=True,
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help="Force creation of a database if it does not exist",
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)
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@click.
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@click.option(
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"--glob/--no-glob",
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default=False,
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show_default=True,
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help="Treat input as a quoted glob expression, e.g. 'data/*.json'",
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)
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@click.argument("inputs", nargs=-1)
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def dump(
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inputs,
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module,
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db,
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target_class,
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@@ -334,6 +340,7 @@ def dump(
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schema=None,
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validate=None,
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force: bool = None,
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glob: bool = None,
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index_slot=None,
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) -> None:
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"""
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@@ -359,34 +366,41 @@ def dump(
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if target_class is None:
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raise Exception("target class not specified and could not be inferred")
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py_target_class = python_module.__dict__[target_class]
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input_format = _get_format(input, input_format)
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loader = get_loader(input_format)
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inargs = {}
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if datautils._is_rdf_format(input_format):
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if sv is None:
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raise Exception("Must pass schema arg")
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inargs["schemaview"] = sv
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inargs["fmt"] = input_format
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if _is_xsv(input_format):
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if index_slot is None:
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index_slot = infer_index_slot(sv, target_class)
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if index_slot is None:
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raise Exception("--index-slot is required for CSV input")
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inargs["index_slot"] = index_slot
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inargs["schema"] = schema
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obj = loader.load(source=input, target_class=py_target_class, **inargs)
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if validate:
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if schema is None:
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raise Exception("--schema must be passed in order to validate. Suppress with --no-validate")
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# TODO: use validator framework
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validation.validate_object(obj, schema)
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endpoint = SQLStore(schema, database_path=db, include_schema_in_database=False)
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endpoint.native_module = python_module
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endpoint.db_exists(force=force)
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endpoint.compile()
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if glob:
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import glob
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inputs = [item for input in inputs for item in glob.glob(input)]
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for input in inputs:
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logging.info(f"Loading: {input}")
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input_format = _get_format(input, input_format)
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loader = get_loader(input_format)
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inargs = {}
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if datautils._is_rdf_format(input_format):
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if sv is None:
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raise Exception("Must pass schema arg")
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inargs["schemaview"] = sv
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inargs["fmt"] = input_format
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if _is_xsv(input_format):
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if index_slot is None:
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index_slot = infer_index_slot(sv, target_class)
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if index_slot is None:
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raise Exception("--index-slot is required for CSV input")
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inargs["index_slot"] = index_slot
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inargs["schema"] = schema
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obj = loader.load(source=input, target_class=py_target_class, **inargs)
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if validate:
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if schema is None:
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raise Exception("--schema must be passed in order to validate. Suppress with --no-validate")
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# TODO: use validator framework
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validation.validate_object(obj, schema)
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endpoint.dump(obj)
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@main.command()
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.1
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Name: linkml
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Version: 1.7.
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Version: 1.7.6
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Summary: Linked Open Data Modeling Language
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Home-page: https://linkml.io/linkml/
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Keywords: schema,linked data,data modeling,rdf,owl,biolink
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@@ -22,6 +22,8 @@ Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.8
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Topic :: Software Development :: Libraries :: Python Modules
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Provides-Extra: shacl
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Provides-Extra: tests
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Requires-Dist: antlr4-python3-runtime (>=4.9.0,<4.10)
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Requires-Dist: click (>=7.0)
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Requires-Dist: graphviz (>=0.10.1)
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@@ -38,6 +40,7 @@ Requires-Dist: prefixcommons (>=0.1.7)
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Requires-Dist: prefixmaps (>=0.1.3)
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Requires-Dist: pydantic (>=1.0.0,<3.0.0)
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Requires-Dist: pyjsg (>=0.11.6)
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Requires-Dist: pyshacl (>=0.25.0,<0.26.0) ; extra == "shacl" or extra == "tests"
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Requires-Dist: pyshex (>=0.7.20)
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Requires-Dist: pyshexc (>=0.8.3)
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Requires-Dist: python-dateutil
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@@ -2,21 +2,21 @@ linkml/__init__.py,sha256=jwtUdhwmquj-0fCR6VwPH5_RfSpuG94hLWdre_W_FD4,3327
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linkml/_version.py,sha256=udxv6OEqcE89DTVMYPtetXYg8IA8Sgc6yW26-6f8C3M,310
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linkml/generators/PythonGenNotes.md,sha256=wb9BPLLhF6378OKLbwSBAwmniLpwrcT5_bbfCHfLme8,51006
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linkml/generators/README.md,sha256=RMzT8EblC_GEdPy5WyfXHDBXlFI6k6mz3Cx2sdpcyWI,4438
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linkml/generators/__init__.py,sha256=
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linkml/generators/__init__.py,sha256=dQ2EUKy_MctEVEzbC3XzEJL5YmYwjYfsa44mG2zKn7g,1517
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linkml/generators/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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linkml/generators/common/type_designators.py,sha256=lgVcIRJJ-yCvVGeP9U_gQZpm77UmJBQo9Bh3lGJITno,1956
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linkml/generators/csvgen.py,sha256=X0f4qKXahSDtkzM9Y47rwWqdseP1O6PTZ_WKiOqOrQI,2956
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linkml/generators/docgen/class.md.jinja2,sha256=
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linkml/generators/docgen/class.md.jinja2,sha256=bz5A46HOIPkUVbzPGorg64NNhr66zK0hCCekSfRPErY,3787
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linkml/generators/docgen/class_diagram.md.jinja2,sha256=lLU_0sQZBttOX5Wiup2oZwrxHuiQtbU9ZgLi66aJvOo,2538
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linkml/generators/docgen/common_metadata.md.jinja2,sha256=zy8Ua3gDtAAq8VA3e3O3ft9W7eJopVZaq5efP8LU_hU,1321
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linkml/generators/docgen/enum.md.jinja2,sha256=mXnUrRkleY2bOTEyAZ5c4pcUnqhs6BNa8a-4LVve-eo,1014
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linkml/generators/docgen/index.md.jinja2,sha256=wXUYTmayPLFltC0vbGE_Mf6m3GkkWav7FOEjCvEpHp4,1466
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linkml/generators/docgen/index.tex.jinja2,sha256=Go_EA-_N4JUpbOYbk3OY11mz5yV70VF2l2sMtgIPWw4,501
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linkml/generators/docgen/schema.md.jinja2,sha256=xlENfnzNRYgPT_0tdqNFxgklVM4Qf5BuzhFVvSMDuxs,70
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linkml/generators/docgen/slot.md.jinja2,sha256=
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linkml/generators/docgen/slot.md.jinja2,sha256=HcLu32FiyIRy0AaV-GwBPUwEbTCY-KkPDhOZk3OKfqg,3226
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linkml/generators/docgen/subset.md.jinja2,sha256=fTNIpAkml5RKFbbtLore3IAzFN1cISVsyL1ru2-Z4oA,2665
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linkml/generators/docgen/type.md.jinja2,sha256=QmCMJZrFwP33eHkggBVtypbyrxTb-XZn9vHOYojVaYk,635
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linkml/generators/docgen.py,sha256=
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linkml/generators/docgen.py,sha256=dz7OWxclX306EweVIgC765h3NKtJTRg0TPnqmltWygs,34347
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linkml/generators/dotgen.py,sha256=kzp1EYtF8bBqOuycJokDmsvHVDVkkW-J-6-MiUhwJH0,5013
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linkml/generators/erdiagramgen.py,sha256=xCnxIldDYZ7xnQ-vLaXlH3FH8MH3cxu-E0j8it-lyJE,10153
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linkml/generators/excelgen.py,sha256=3ILAeIHeYngNpPf3Ad7CXoHOLQ9KSiYcX5HdwHhQeQE,7696
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@@ -26,34 +26,48 @@ linkml/generators/graphqlgen.py,sha256=6qZpI0rwg3ypsv_KrLVzXgdsJfR8LNPqgMwaRwzwn
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linkml/generators/javagen/example_template.java.jinja2,sha256=ec4CVTv_0zS7V5Y-1E6H4lRraya10gfX7BEMBlu38X4,444
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linkml/generators/javagen/java_record_template.jinja2,sha256=OQZffLSy_xR3FIhQMltvrYyVeut7l2Q-tzK7AOiVmWs,1729
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linkml/generators/javagen.py,sha256=KxwupMztyCRHcSsbtTnOovuj1WamsAny0mxbYWvTiDs,5324
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linkml/generators/jsonldcontextgen.py,sha256=
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linkml/generators/jsonldgen.py,sha256=
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linkml/generators/jsonldcontextgen.py,sha256=048kzs28xooik86A8OQ0NIbXxyJZGkqH1ZMxg17mcf4,8073
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linkml/generators/jsonldgen.py,sha256=pk8Gmh2gSvXt_o7MTuJ71thNfIJuHUGkNl3yl3RIdsE,7728
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linkml/generators/jsonschemagen.py,sha256=XOsYIrpA6BwtAcfh8GNGduIjpuPAsF2f_PQ1mghj_WU,27455
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linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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linkml/generators/linkmlgen.py,sha256=1_Kt_7rD42WvCTjq0yaq1Of7jEDZR_uusyzAT-qWMHk,3471
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linkml/generators/markdowngen.py,sha256=dDMyusNXLvM2raIW-_vd2AQBhDHn0P_rMeDq3QFuacs,32926
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linkml/generators/namespacegen.py,sha256=vVcIyM0zlKd7XRvtdzwTwHjG4Pg49801gy4FUmjJlqQ,6450
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linkml/generators/oocodegen.py,sha256=r73QI08ajbTZTobc9OIG6BMWZft3zdu76vKVR33pyYg,7774
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linkml/generators/owlgen.py,sha256=
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linkml/generators/owlgen.py,sha256=FMzdiK85CND8wnLiXPmylpayUTGpuydgD_g4hFjyez4,54374
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linkml/generators/plantumlgen.py,sha256=tk-_XJtBA5EqYJSUTc3bdMdCwqlC-rc9VYO9A2V_HpM,14895
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linkml/generators/prefixmapgen.py,sha256
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linkml/generators/projectgen.py,sha256=
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linkml/generators/prefixmapgen.py,sha256=L9TccwKNHEguW0ox5qgf_GhIuqauYTI8d4jSjeqdkWo,4720
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linkml/generators/projectgen.py,sha256=OuT_AneoZFNMCn50GllfZafadUHt50u61JcftM2eed4,9750
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linkml/generators/protogen.py,sha256=5UxThsFDVyDTzzTDh77Z0anx4-tLgz8kQQ-e7ywIqwI,2290
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linkml/generators/pydanticgen.py,sha256=
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linkml/generators/
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linkml/generators/pydanticgen/__init__.py,sha256=uKGaaQSaeKqinHImXGFE448i-t8Oi0No8suIO76sep8,629
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linkml/generators/pydanticgen/pydanticgen.py,sha256=ZUi9fE5ZiQbW5V4Ckth8hysMghHh9H2RpqLZa3m8PfQ,27598
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linkml/generators/pydanticgen/template.py,sha256=e2PYQFRlDR1Nva_xy-NlsttpW79L8n6e63QKHZzoXH8,17016
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linkml/generators/pydanticgen/templates/attribute.py.jinja,sha256=AlH_QFJJkONpzXQRGqnW4ufmjp9s9E7Q9W5r8ykNGeQ,443
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linkml/generators/pydanticgen/templates/base_model.py.jinja,sha256=eYKNI-4itB6lYW5yhfIWngtMcHZnuEaic9Dv56XKX4M,797
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linkml/generators/pydanticgen/templates/class.py.jinja,sha256=RIdkqdZS9rDILUuVqDIAWK_vATGkirLbPhdHSyHDAbY,565
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linkml/generators/pydanticgen/templates/conditional_import.py.jinja,sha256=YheknDrxvepiJUzeItSL5aSbAkCdR1k0a6m6aTA4qNM,240
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linkml/generators/pydanticgen/templates/enum.py.jinja,sha256=572XFQyEMZfL-G_Cj68T-NI_mUnDoFOAVJOGIKu2Hb8,338
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linkml/generators/pydanticgen/templates/footer.py.jinja,sha256=WuWGJjkWDQcEPL2bGk5fdGuhO0gQRUJzpo4CQHHxQNQ,385
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linkml/generators/pydanticgen/templates/imports.py.jinja,sha256=d1XFna2eOpkH8cgJML3vXwqGcocczvOcrbg6jjd4kP0,945
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linkml/generators/pydanticgen/templates/module.py.jinja,sha256=SkmtWtQS7D-xBiZI-sFiYC3WYPKi3VJCj_KtaMVxexM,438
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linkml/generators/pydanticgen/templates/validator.py.jinja,sha256=Yo4dubQal-HwEoJKztQkLYM5qCz1I8na2oaDlXuEpwU,532
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linkml/generators/pythongen.py,sha256=AvOQZJ-OT8lMYeaT2bdexHuRPRfTK7wpbmgAdfc2lW4,52805
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linkml/generators/rdfgen.py,sha256=L6F08iDUqVemXXrRbJmcOxvJTt14hR0oo8WLoqf4npw,2656
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linkml/generators/
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linkml/generators/
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linkml/generators/shacl/__init__.py,sha256=O-M-wndKw8rMW-U8X3QCNHal-ErXP6uXZqxiQSa77l4,108
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linkml/generators/shacl/ifabsent_processor.py,sha256=I7zvSjZzB7tZjcXRE0UE3DUmF5sY7QrKbXblYvpRwkc,1746
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linkml/generators/shacl/shacl_data_type.py,sha256=BT3C9tdFyBQnuucPN7YQiFAKEa9yuzy-Q26X6dmOXgo,1827
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linkml/generators/shaclgen.py,sha256=mTkHziEIKoMTr-Vl6nwOdqxk-97cJzTsFG7ViMiFhMs,8308
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linkml/generators/shexgen.py,sha256=KzhaL-A4R4peSdhY6nlDWmS-DPfnZMxMzrXhHGnA_Ag,9874
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linkml/generators/sparqlgen.py,sha256=c7x8GFChKWprBx4rToSnu9qN8OleWTCenVUdZ8XSTWM,6138
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linkml/generators/sqlalchemy/__init__.py,sha256=mb9AC1rIFkSiNZhhG0TAk45ol9PjS1XvsrvCjgfVUpQ,249
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linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py,sha256=X_Ws1NUBikMI5HuNgEhl_PIeWM-B-c2B0W9KUBH4QTg,2542
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linkml/generators/sqlalchemy/sqlalchemy_imperative_template.py,sha256=u4ZpponG1h6XROrOHGOf_0H2e6xL1_s8twAOA-gx94A,1622
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linkml/generators/terminusdbgen.py,sha256=
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linkml/generators/yamlgen.py,sha256=PKssrY5VHpdbOU54PVwLVLbsRqHwoOgOImlMb6DVcXM,1614
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linkml/generators/yumlgen.py,sha256=lnHcLY0VwlU_i8QporSmwR62CXSV4aOCXKxRDw5AxUk,12196
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linkml/linter/config/recommended.yaml,sha256=hxrRSlCZzFXr3WndWAxs2RKwuSwQxRjrvRQi-zteiYQ,198
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linkml/linter/rules.py,sha256=
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linkml/linter/rules.py,sha256=EuZTHtrU9YndAf2vw6QknGZSVFgsbydStsQmrUCwTKk,11502
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linkml/reporting/__init__.py,sha256=Jo0V_nyEcnWhMukMW-bqW9dlbgCfaRlWm3CO-XzgU84,92
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linkml/reporting/model.py,sha256=-10yNfk8wuRC48ZI-akrWvtlJ9a6RYWET2TzlZV3XXo,8622
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linkml/transformers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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linkml/utils/datautils.py,sha256=QlbzwXykh5Fphfe5KxPo6_ekXfniLbHiEGJtLWjUrvY,3742
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linkml/utils/datavalidator.py,sha256=kBdWaVi8IZT1bOwEJgJYx-wZAb_PTBObB9nHpYORfKA,472
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linkml/utils/execute_tutorial.py,sha256=T4kHTSyz3ItJGEUZxVjR-3yLVKnOr5Ix4NMGE47-IuE,6912
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linkml/utils/generator.py,sha256=8-5JpMmvkWyLMeK5qSRv3XuOpfAmi2quNQ4Mo6nNCA0,38362
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linkml/utils/helpers.py,sha256=yR8n4zFA5wPcYC7xzRuNF3wO16vG80v6j7DM3qTNmIc,447
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linkml/utils/ifabsent_functions.py,sha256=
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linkml/utils/ifabsent_functions.py,sha256=IkcBcmRYu8sllx7_mTCqu4aHfTxX2AnQoccZ1KOODds,5843
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linkml/utils/logictools.py,sha256=GSmBiobC49TcQjE08RtXEE3JwJEOV7eEREio25uJiFs,21184
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linkml/utils/mergeutils.py,sha256=QVm2iQB4v_L2rSvPBsPe9C865R03BgV3TzlPoTTTwWQ,9044
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linkml/utils/rawloader.py,sha256=QB7Rdvy4o4ZJEWBWa2_2xzz2TOh_6Oe4slvUn8IBVIc,4329
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linkml/utils/schema_builder.py,sha256=4qhrur8O0xRZnPm7H1h2BZmTkut5R4q-IE_1KKiHy_c,9937
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linkml/utils/schemaloader.py,sha256=
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linkml/utils/schemasynopsis.py,sha256=jKf5ZJxpNgSZ5x9oAcdGO3m1IwzcIU2Ni1ugm0SQq1g,18447
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linkml/utils/typereferences.py,sha256=8Yfuz9-HAwOPoJLbIcO_sY9zf32hvPRzGeSOzECfMWA,2232
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linkml/validator/__init__.py,sha256=djKc1IyxGKvVYaX5jSxsqjfcEYaw3rFgKbFJxI2wDNk,5002
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linkml-1.7.6.dist-info/entry_points.txt,sha256=7haDkIbyC7ZLhm5z-e3BhrLJpY2xoW1yuD8Y7QPNtVg,2093
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linkml-1.7.6.dist-info/METADATA,sha256=PaI8ylnY-nUYjDrS-44yWh-r6UsiLNLQ_cYYDBNZHX8,3588
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linkml-1.7.6.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
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linkml-1.7.6.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
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linkml-1.7.6.dist-info/RECORD,,
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