├── .coveragerc ├── .editorconfig ├── .github ├── dependabot.yml └── workflows │ ├── check-dependencies.yaml │ ├── main.yaml │ ├── pypi-publish.yaml │ └── test-upstream.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── CONTRIBUTING.md ├── LICENSE ├── Makefile ├── README.md ├── checkout_outputs.sh ├── codecov.yml ├── hide_test_changes.sh ├── linkml_runtime ├── __init__.py ├── dumpers │ ├── __init__.py │ ├── csv_dumper.py │ ├── delimited_file_dumper.py │ ├── dumper_root.py │ ├── json_dumper.py │ ├── rdf_dumper.py │ ├── rdflib_dumper.py │ ├── tsv_dumper.py │ └── yaml_dumper.py ├── exceptions.py ├── index │ ├── __init__.py │ └── object_index.py ├── linkml_model │ ├── README.md │ ├── __init__.py │ ├── annotations.py │ ├── array.py │ ├── datasets.py │ ├── excel │ │ └── meta.xlsx │ ├── extensions.py │ ├── graphql │ │ ├── README.md │ │ └── meta.graphql │ ├── json │ │ ├── README.md │ │ ├── annotations.json │ │ ├── datasets.json │ │ ├── extensions.json │ │ ├── mappings.json │ │ ├── meta.json │ │ ├── types.json │ │ ├── units.json │ │ └── validation.json │ ├── jsonld │ │ ├── README.md │ │ ├── annotations.context.jsonld │ │ ├── annotations.model.context.jsonld │ │ ├── context.jsonld │ │ ├── datasets.context.jsonld │ │ ├── datasets.model.context.jsonld │ │ ├── extensions.context.jsonld │ │ ├── extensions.model.context.jsonld │ │ ├── mappings.context.jsonld │ │ ├── mappings.model.context.jsonld │ │ ├── meta.context.jsonld │ │ ├── meta.jsonld │ │ ├── meta.model.context.jsonld │ │ ├── types.context.jsonld │ │ ├── types.model.context.jsonld │ │ ├── units.context.jsonld │ │ ├── units.model.context.jsonld │ │ ├── validation.context.jsonld │ │ └── validation.model.context.jsonld │ ├── jsonschema │ │ ├── README.md │ │ ├── annotations.schema.json │ │ ├── datasets.schema.json │ │ ├── extensions.schema.json │ │ ├── mappings.schema.json │ │ ├── meta.schema.json │ │ ├── types.schema.json │ │ ├── units.schema.json │ │ └── validation.schema.json │ ├── linkml_files.py │ ├── mappings.py │ ├── meta.py │ ├── model │ │ ├── README.md │ │ ├── docs │ │ │ ├── credits.md │ │ │ ├── home.md │ │ │ └── specification │ │ │ │ ├── 00preamble.md │ │ │ │ ├── 01introduction.md │ │ │ │ ├── 02instances.md │ │ │ │ ├── 03schemas.md │ │ │ │ ├── 04derived-schemas.md │ │ │ │ ├── 05validation.md │ │ │ │ ├── 06mapping.md │ │ │ │ ├── 07codegen.md │ │ │ │ └── index.md │ │ ├── import_map.json │ │ └── schema │ │ │ ├── README.md │ │ │ ├── annotations.yaml │ │ │ ├── array.yaml │ │ │ ├── datasets.yaml │ │ │ ├── extensions.yaml │ │ │ ├── mappings.yaml │ │ │ ├── meta.yaml │ │ │ ├── types.yaml │ │ │ ├── units.yaml │ │ │ └── validation.yaml │ ├── owl │ │ ├── README.md │ │ └── meta.owl.ttl │ ├── prefixmap │ │ └── meta.yaml │ ├── protobuf │ │ └── meta.proto │ ├── rdf │ │ ├── README.md │ │ ├── annotations.model.ttl │ │ ├── annotations.ttl │ │ ├── datasets.model.ttl │ │ ├── datasets.ttl │ │ ├── extensions.model.ttl │ │ ├── extensions.ttl │ │ ├── mappings.model.ttl │ │ ├── mappings.ttl │ │ ├── meta.model.ttl │ │ ├── meta.ttl │ │ ├── types.model.ttl │ │ ├── types.ttl │ │ ├── units.model.ttl │ │ ├── units.ttl │ │ ├── validation.model.ttl │ │ └── validation.ttl │ ├── shacl │ │ └── meta.shacl.ttl │ ├── shex │ │ ├── README.md │ │ ├── annotations.shex │ │ ├── annotations.shexj │ │ ├── datasets.shex │ │ ├── datasets.shexj │ │ ├── extensions.shex │ │ ├── extensions.shexj │ │ ├── mappings.shex │ │ ├── mappings.shexj │ │ ├── meta.shex │ │ ├── meta.shexj │ │ ├── types.shex │ │ ├── types.shexj │ │ ├── units.shex │ │ ├── units.shexj │ │ ├── validation.shex │ │ └── validation.shexj │ ├── sqlddl │ │ └── meta.sql │ ├── sqlschema │ │ └── meta.sql │ ├── types.py │ ├── units.py │ └── validation.py ├── loaders │ ├── __init__.py │ ├── context_flattener.py │ ├── csv_loader.py │ ├── delimited_file_loader.py │ ├── json_loader.py │ ├── loader_root.py │ ├── rdf_loader.py │ ├── rdflib_loader.py │ ├── requests_ssl_patch.py │ ├── tsv_loader.py │ └── yaml_loader.py ├── processing │ ├── referencevalidator.py │ ├── validation_datamodel.py │ └── validation_datamodel.yaml └── utils │ ├── __init__.py │ ├── comparefiles.py │ ├── compile_python.py │ ├── context_utils.py │ ├── csvutils.py │ ├── curienamespace.py │ ├── dataclass_extensions_376.py │ ├── dictutils.py │ ├── distroutils.py │ ├── enumerations.py │ ├── eval_utils.py │ ├── formatutils.py │ ├── inference_utils.py │ ├── introspection.py │ ├── metamodelcore.py │ ├── namespaces.py │ ├── pattern.py │ ├── ruleutils.py │ ├── schema_as_dict.py │ ├── schema_builder.py │ ├── schemaops.py │ ├── schemaview.py │ ├── schemaview_cli.py │ ├── slot.py │ ├── strictness.py │ ├── uri_validator.py │ ├── walker_utils.py │ └── yamlutils.py ├── notebooks ├── SchemaView_BioLink.ipynb ├── SchemaView_MIxS.ipynb └── SchemaView_Monarch.ipynb ├── pyproject.toml ├── show_test_changes.sh ├── tests ├── Testing.md ├── __init__.py ├── conftest.py ├── environment.py ├── support │ ├── __init__.py │ ├── clicktestcase.py │ ├── compare_rdf.py │ ├── dirutils.py │ ├── filters.py │ ├── mismatchlog.py │ └── test_environment.py ├── test_config.ini.example ├── test_enumerations │ ├── __init__.py │ └── environment.py ├── test_index │ ├── __init__.py │ ├── input │ │ ├── container_test.yaml │ │ └── object-indexer-data.yaml │ ├── model │ │ ├── __init__.py │ │ └── container_test.py │ └── test_object_index.py ├── test_issues │ ├── __init__.py │ ├── environment.py │ ├── input │ │ ├── __init__.py │ │ ├── include_core.yaml │ │ ├── include_schema.yaml │ │ ├── issue_355.py │ │ ├── issue_368.context.jsonld │ │ ├── issue_368.py │ │ ├── issue_368_imports.py │ │ ├── issue_8.yaml │ │ └── issue_8a.yaml │ ├── test_include_schema.py │ ├── test_issue_355.py │ ├── test_issue_368_enums.py │ └── test_issue_8.py ├── test_linkml_model │ ├── __init__.py │ └── test_linkml_files.py ├── test_loaders_dumpers │ ├── README.md │ ├── __init__.py │ ├── environment.py │ ├── input │ │ ├── README.md │ │ ├── bacteria-taxon-class.ttl │ │ ├── blank_node_test.ttl │ │ ├── book_series_lotr.json │ │ ├── book_series_lotr.yaml │ │ ├── book_series_lotr_json.yaml │ │ ├── book_series_lotr_yaml.yaml │ │ ├── books_normalized_01.yaml │ │ ├── books_normalized_02.yaml │ │ ├── complex_range_example.yaml │ │ ├── enum_union_type_test.ttl │ │ ├── example_personinfo_data.ttl │ │ ├── example_personinfo_data.yaml │ │ ├── example_personinfo_test_issue_429_data.yaml │ │ ├── issue_1040.yaml │ │ ├── issue_450.yaml │ │ ├── issue_576.yaml │ │ ├── issue_576_data.yaml │ │ ├── kitchen_sink_inst_01.json │ │ ├── kitchen_sink_inst_01.yaml │ │ ├── kitchen_sink_normalized_inst_01.json │ │ ├── kitchen_sink_normalized_inst_01.yaml │ │ ├── kitchen_sink_normalized_inst_01_json.yaml │ │ ├── kitchen_sink_normalized_inst_01_yaml.yaml │ │ ├── kitchen_sink_person_01.json │ │ ├── kitchen_sink_person_01.yaml │ │ ├── obo_sample.json │ │ ├── obo_sample.jsonld │ │ ├── obo_sample.ttl │ │ ├── obo_sample.yaml │ │ ├── personinfo.yaml │ │ ├── personinfo_test_issue_429.yaml │ │ ├── phenopackets │ │ │ ├── any.yaml │ │ │ ├── base.yaml │ │ │ ├── biosample.yaml │ │ │ ├── constants.yaml │ │ │ ├── cv_terms.yaml │ │ │ ├── dicts.yaml │ │ │ ├── disease.yaml │ │ │ ├── genome.yaml │ │ │ ├── individual.yaml │ │ │ ├── interpretation.yaml │ │ │ ├── measurement.yaml │ │ │ ├── medical_action.yaml │ │ │ ├── meta_data.yaml │ │ │ ├── pedigree.yaml │ │ │ ├── phenopackets.yaml │ │ │ ├── phenotypic_feature.yaml │ │ │ ├── timestamp.yaml │ │ │ ├── vrs.yaml │ │ │ └── vrsatile.yaml │ │ ├── table-inlined.tsv │ │ ├── table-json.tsv │ │ ├── unmapped_predicates_test.ttl │ │ └── unmapped_type_test.ttl │ ├── jsonld_context │ │ ├── Dockerfile │ │ ├── README.md │ │ ├── db.sh │ │ ├── dr.sh │ │ ├── ds.sh │ │ ├── jsonld_10 │ │ │ └── termci_schema.context.jsonld │ │ ├── jsonld_11 │ │ │ ├── ConceptReference.context.jsonld │ │ │ ├── ConceptSystem.context.jsonld │ │ │ ├── Package.context.jsonld │ │ │ ├── termci_namespaces.context.jsonld │ │ │ ├── termci_schema.frame.jsonld │ │ │ └── termci_schema_inlined.context.jsonld │ │ └── nginx │ │ │ ├── context_server.crt │ │ │ ├── context_server.key │ │ │ ├── localhost.cnf │ │ │ ├── mime.types │ │ │ └── nginx.conf │ ├── loaderdumpertestcase.py │ ├── models │ │ ├── __init__.py │ │ ├── books_normalized.py │ │ ├── books_normalized.yaml │ │ ├── books_normalized_pydantic.py │ │ ├── core.yaml │ │ ├── enum_model.py │ │ ├── enum_model.yaml │ │ ├── issue_576.py │ │ ├── kitchen_sink.yaml │ │ ├── kitchen_sink_pydantic.py │ │ ├── model_817.py │ │ ├── node_object.py │ │ ├── personinfo.py │ │ ├── personinfo_test_issue_429.py │ │ ├── phenopackets.py │ │ ├── table.py │ │ ├── table.yaml │ │ └── termci_schema.py │ ├── output │ │ ├── dump │ │ │ ├── generated │ │ │ ├── obo_sample.json │ │ │ ├── obo_sample.jsonld │ │ │ ├── obo_sample.ttl │ │ │ ├── obo_sample.yaml │ │ │ └── obo_sample_context.json │ │ ├── dumps │ │ │ ├── generated │ │ │ ├── obo_sample.json │ │ │ ├── obo_sample.ttl │ │ │ ├── obo_sample.yaml │ │ │ └── obo_sample_context.json │ │ └── load │ │ │ ├── generated │ │ │ ├── obo_sample_json.yaml │ │ │ └── obo_sample_yaml.yaml │ ├── test_csv_tsv_loader_dumper.py │ ├── test_dumpers.py │ ├── test_dumpers_pydantic.py │ ├── test_enum.py │ ├── test_loaders.py │ ├── test_loaders_dumpers.py │ ├── test_loaders_no_namespace.py │ ├── test_loaders_pydantic.py │ ├── test_rdflib_dumper.py │ └── test_yaml_loader_dumper.py ├── test_processing │ ├── __init__.py │ ├── input │ │ ├── array_example.yaml │ │ └── array_example_data.yaml │ ├── test_arrays.py │ └── test_referencevalidator.py └── test_utils │ ├── __init__.py │ ├── environment.py │ ├── input │ ├── DJ_controller_schema.yaml │ ├── attribute_edge_cases.yaml │ ├── core.yaml │ ├── cycles.yaml │ ├── imports │ │ ├── README.md │ │ ├── main.yaml │ │ ├── s1.yaml │ │ ├── s1_1.yaml │ │ ├── s1_2.yaml │ │ ├── s1_2_1.yaml │ │ ├── s1_2_1_1.yaml │ │ ├── s1_2_1_1_1.yaml │ │ ├── s1_2_1_1_2.yaml │ │ ├── s2.yaml │ │ ├── s2_1.yaml │ │ ├── s2_2.yaml │ │ ├── s3.yaml │ │ ├── s3_1.yaml │ │ └── s3_2.yaml │ ├── imports_relative │ │ ├── L0_0 │ │ │ ├── L1_0_0 │ │ │ │ ├── L2_0_0_0 │ │ │ │ │ └── child.yaml │ │ │ │ ├── L2_0_0_1 │ │ │ │ │ └── child.yaml │ │ │ │ ├── L2_0_0_2 │ │ │ │ │ ├── four.yaml │ │ │ │ │ ├── one.yaml │ │ │ │ │ ├── stepchild.yaml │ │ │ │ │ ├── three.yaml │ │ │ │ │ └── two.yaml │ │ │ │ ├── main.yaml │ │ │ │ └── neighbor.yaml │ │ │ ├── L1_0_1 │ │ │ │ ├── L2_0_1_0 │ │ │ │ │ └── grandchild.yaml │ │ │ │ └── dupe.yaml │ │ │ ├── neighborhood_parent.yaml │ │ │ └── parent.yaml │ │ ├── L0_1 │ │ │ ├── L1_1_0 │ │ │ │ ├── L2_1_0_0 │ │ │ │ │ ├── apple.yaml │ │ │ │ │ └── index.yaml │ │ │ │ ├── L2_1_0_1 │ │ │ │ │ ├── banana.yaml │ │ │ │ │ └── index.yaml │ │ │ │ └── index.yaml │ │ │ └── cousin.yaml │ │ ├── L0_2 │ │ │ ├── L2_2_0 │ │ │ │ ├── L3_2_0_0 │ │ │ │ │ ├── L4_2_0_0_0 │ │ │ │ │ │ └── greatgrandchild.yaml │ │ │ │ │ └── grandchild.yaml │ │ │ │ └── child.yaml │ │ │ └── main.yaml │ │ └── README.md │ ├── inference-example.yaml │ ├── inlined_as_dict.py │ ├── inlined_as_dict.yaml │ ├── inlined_as_list.py │ ├── inlined_as_list.yaml │ ├── issue_1126.yaml │ ├── issue_478.yaml │ ├── issue_590.yaml │ ├── kitchen_sink.yaml │ ├── kitchen_sink_noimports.yaml │ ├── list_strings.yaml │ ├── mcc │ │ ├── creature_basics.yaml │ │ ├── creature_schema.yaml │ │ ├── creature_schema_local.yaml │ │ ├── creature_schema_remote.yaml │ │ ├── creature_subsets.yaml │ │ └── creature_types.yaml │ ├── pattern-example.yaml │ ├── range_importer.yaml │ ├── range_local.yaml │ ├── rules-example.yaml │ ├── schema1.yaml │ ├── schema6.json │ ├── schema6.yaml │ ├── schemaview_is_inlined.yaml │ ├── yaml1.yaml │ └── yaml2.yaml │ ├── model │ └── inference_example.py │ ├── output │ └── README.md │ ├── test_compile_python.py │ ├── test_context_utils.py │ ├── test_csv_utils.py │ ├── test_curienamespace.py │ ├── test_dataclass_extensions_376.py │ ├── test_dict_utils.py │ ├── test_distroutils.py │ ├── test_eval_utils.py │ ├── test_formatutils.py │ ├── test_inference_utils.py │ ├── test_inlined_as_dict_forms.py │ ├── test_inlined_as_list_forms.py │ ├── test_introspection.py │ ├── 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