diff --git a/.github/workflows/deploy-docs.yaml b/.github/workflows/deploy-docs.yaml index fefd8707..8e0013a9 100644 --- a/.github/workflows/deploy-docs.yaml +++ b/.github/workflows/deploy-docs.yaml @@ -1,29 +1,27 @@ --- - name: Auto-deployment of Schema Documentation - on: - push: - branches: [main] - jobs: - build-docs: - runs-on: ubuntu-latest - permissions: - contents: write - pull-requests: write - steps: - - name: Checkout - uses: actions/checkout@main - with: - fetch-depth: 0 +name: Auto-deployment of Schema Documentation +on: + push: + branches: [main] +jobs: + build-docs: + runs-on: ubuntu-latest + permissions: + contents: write + pull-requests: write + steps: + - name: Checkout + uses: actions/checkout@main - - name: Set up Python 3. - uses: actions/setup-python@main - with: - python-version: 3.13 + - name: Set up Python 3. + uses: actions/setup-python@main + with: + python-version: 3.13 - - name: Install uv - uses: astral-sh/setup-uv@v7 + - name: Install uv + uses: astral-sh/setup-uv@v7 - - name: Build documentation. - run: | - uv sync - make gendoc-gh + - name: Build documentation. + run: | + uv sync + make gendoc-gh diff --git a/pyproject.toml b/pyproject.toml index f06f1f6b..71b11e4b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "cdm-schema" -version = "0.1.1" +version = "0.1.2" description = "CDM Schema repo" readme = "README.md" requires-python = ">=3.13" @@ -9,12 +9,12 @@ authors = [ ] dependencies = [ - "linkml>=1.9.6", - "linkml-runtime>=1.9.5", - "mkdocs-material>=9.7.1", + "linkml>=1.10.0", + "linkml-runtime>=1.10.0", + "mkdocs-material>=9.7.6", "mkdocs-mermaid2-plugin>=1.2.3", "pyspark>=4.1.1", - "ruff>=0.15.1", + "ruff>=0.15.8", ] [build-system] diff --git a/src/cdm_schema/kbase_cdm_pydantic.py b/src/cdm_schema/kbase_cdm_pydantic.py index c9f6cc04..d5bdd75a 100644 --- a/src/cdm_schema/kbase_cdm_pydantic.py +++ b/src/cdm_schema/kbase_cdm_pydantic.py @@ -19,8 +19,8 @@ ) -metamodel_version = "None" -version = "0.1.1" +metamodel_version = "1.7.0" +version = "0.1.2" class ConfiguredBaseModel(BaseModel): @@ -35,19 +35,6 @@ class ConfiguredBaseModel(BaseModel): strict=False, ) - @model_serializer(mode="wrap", when_used="unless-none") - def treat_empty_lists_as_none( - self, handler: SerializerFunctionWrapHandler, info: SerializationInfo - ) -> dict[str, Any]: - if info.exclude_none: - _instance = self.model_copy() - for field, field_info in type(_instance).model_fields.items(): - if getattr(_instance, field) == [] and not (field_info.is_required()): - setattr(_instance, field, None) - else: - _instance = self - return handler(_instance, info) - class LinkMLMeta(RootModel): root: dict[str, Any] = {} @@ -1126,6 +1113,7 @@ class ClusterMember(Table): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -1467,6 +1455,7 @@ class Entity(Table): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -1486,6 +1475,7 @@ class Entity(Table): "linkml_meta": { "domain_of": [ "Entity", + "Entity_x_SourceFile", "Contributor_x_DataSource", "DataSource", "DataSourceNew", @@ -1557,6 +1547,7 @@ class Identifier(Table): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -1650,6 +1641,7 @@ class Name(Table): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -1753,6 +1745,59 @@ class EntityIdentifiers(LinkerTable): pass +class EntityXSourceFile(Table): + """ + Captures information about the source file for a given entity. + """ + + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "http://kbase.github.io/cdm-schema/linkml/cdm_base"}) + + entity_id: str = Field( + default=..., + description="""Internal (CDM) unique identifier for an entity.""", + json_schema_extra={ + "linkml_meta": { + "domain_of": [ + "ClusterMember", + "Entity", + "Identifier", + "Name", + "Entity_x_SourceFile", + "EntityMixin", + "Sequence", + "Association_x_SupportingObject", + ] + } + }, + ) + data_source_id: str = Field( + default=..., + description="""Internal (CDM) unique identifier for a data source. +From the Entity table: entity_id where entity_type == 'DataSource'. +""", + json_schema_extra={ + "linkml_meta": { + "domain_of": [ + "Entity", + "Entity_x_SourceFile", + "Contributor_x_DataSource", + "DataSource", + "DataSourceNew", + "DataSource_x_Description", + "DataSource_x_FundingReference", + "DataSource_x_License", + "DataSource_x_Title", + ] + } + }, + ) + source_file: Optional[str] = Field( + default=None, + description="""Path to a file in the local file system from which data was parsed.""", + json_schema_extra={"linkml_meta": {"domain_of": ["Entity_x_SourceFile"]}}, + ) + + class AttributeMixin(ConfiguredBaseModel): """ The attribute in an attribute-value pair. One of `attribute_cv_id`, `attribute_cv_label`, and `attribute_string` is required. @@ -1808,6 +1853,7 @@ class EntityMixin(ConfiguredBaseModel): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -1914,6 +1960,7 @@ class AttributeValue(EntityMixin, AttributeMixin): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -2055,6 +2102,7 @@ class EntityAttributeValue(UnitMixin, EntityMixin, AttributeMixin): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -2191,6 +2239,7 @@ class QuantityValue(AttributeValue, UnitMixin): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -2319,6 +2368,7 @@ class QuantityRangeValue(AttributeValue, UnitMixin): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -2408,6 +2458,7 @@ class DateTimeValue(AttributeValue): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -2498,6 +2549,7 @@ class Geolocation(AttributeValue): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -2586,6 +2638,7 @@ class ControlledTermValue(AttributeValue): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -2685,6 +2738,7 @@ class ControlledVocabularyTermValue(AttributeValue): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -2786,6 +2840,7 @@ class TextValue(AttributeValue): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -2948,7 +3003,7 @@ class ContributorAffiliation(LinkerTable): }, ) affiliation_id: Optional[list[str]] = Field( - default=[], + default=None, description="""The ID of the organization to which a contributor belongs. Should be the ID of another contributor.""", json_schema_extra={ "linkml_meta": {"aliases": ["affiliation_contributor_id"], "domain_of": ["ContributorAffiliation"]} @@ -3001,6 +3056,7 @@ class ContributorXDataSource(LinkerTable): "linkml_meta": { "domain_of": [ "Entity", + "Entity_x_SourceFile", "Contributor_x_DataSource", "DataSource", "DataSourceNew", @@ -3089,6 +3145,7 @@ class DataSource(Table): "linkml_meta": { "domain_of": [ "Entity", + "Entity_x_SourceFile", "Contributor_x_DataSource", "DataSource", "DataSourceNew", @@ -3158,6 +3215,7 @@ class DataSourceNew(Table): "linkml_meta": { "domain_of": [ "Entity", + "Entity_x_SourceFile", "Contributor_x_DataSource", "DataSource", "DataSourceNew", @@ -3297,6 +3355,7 @@ class DataSourceXDescription(LinkerTable): "linkml_meta": { "domain_of": [ "Entity", + "Entity_x_SourceFile", "Contributor_x_DataSource", "DataSource", "DataSourceNew", @@ -3333,6 +3392,7 @@ class DataSourceXFundingReference(LinkerTable): "linkml_meta": { "domain_of": [ "Entity", + "Entity_x_SourceFile", "Contributor_x_DataSource", "DataSource", "DataSourceNew", @@ -3371,6 +3431,7 @@ class DataSourceXLicense(LinkerTable): "linkml_meta": { "domain_of": [ "Entity", + "Entity_x_SourceFile", "Contributor_x_DataSource", "DataSource", "DataSourceNew", @@ -3408,6 +3469,7 @@ class DataSourceXTitle(LinkerTable): "linkml_meta": { "domain_of": [ "Entity", + "Entity_x_SourceFile", "Contributor_x_DataSource", "DataSource", "DataSourceNew", @@ -5467,6 +5529,7 @@ class Sequence(Table): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -5524,6 +5587,7 @@ class AssociationXSupportingObject(LinkerTable): "Entity", "Identifier", "Name", + "Entity_x_SourceFile", "EntityMixin", "Sequence", "Association_x_SupportingObject", @@ -6025,317 +6089,317 @@ class Schema(ConfiguredBaseModel): ) entities: Optional[list[str]] = Field( - default=[], + default=None, description="""All entities in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) names: Optional[list[Name]] = Field( - default=[], + default=None, description="""All names in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) identifiers: Optional[list[Identifier]] = Field( - default=[], + default=None, description="""All identifiers in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) entity_names: Optional[list[EntityNames]] = Field( - default=[], + default=None, description="""All name x entity records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) entity_identifiers: Optional[list[EntityIdentifiers]] = Field( - default=[], + default=None, description="""All identifier x entity records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) entity_attribute_values: Optional[list[EntityAttributeValue]] = Field( - default=[], + default=None, description="""All entity attribute values in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) associations: Optional[list[str]] = Field( - default=[], + default=None, description="""All associations in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) clusters: Optional[list[str]] = Field( - default=[], + default=None, description="""All clusters in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) cluster_members: Optional[list[ClusterMember]] = Field( - default=[], + default=None, description="""All cluster members in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) events: Optional[list[str]] = Field( - default=[], + default=None, description="""All events in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) gold_environmental_contexts: Optional[list[str]] = Field( - default=[], + default=None, description="""All GOLD environmental contexts in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) mixs_environmental_contexts: Optional[list[str]] = Field( - default=[], + default=None, description="""All MIxS environmental contexts in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contributors: Optional[list[str]] = Field( - default=[], + default=None, description="""All contributors in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contributor_affiliations: Optional[list[ContributorAffiliation]] = Field( - default=[], + default=None, description="""All contributor affiliations in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contributor_x_role_x_project: Optional[list[ContributorXRoleXProject]] = Field( - default=[], + default=None, description="""All contributor x role x project records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) data_sources: Optional[list[str]] = Field( - default=[], + default=None, description="""All data sources in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) data_source_x_descriptions: Optional[list[DataSourceXDescription]] = Field( - default=[], + default=None, description="""All data source descriptions in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) data_source_x_funding_references: Optional[list[DataSourceXFundingReference]] = Field( - default=[], + default=None, description="""All data source x funding reference records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) data_source_x_licenses: Optional[list[DataSourceXLicense]] = Field( - default=[], + default=None, description="""All data source x license records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) data_source_x_titles: Optional[list[DataSourceXTitle]] = Field( - default=[], + default=None, description="""All data source x title records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) funding_references: Optional[list[str]] = Field( - default=[], + default=None, description="""All funding references in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) licenses: Optional[list[str]] = Field( - default=[], + default=None, description="""All licenses in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) projects: Optional[list[str]] = Field( - default=[], + default=None, description="""All projects in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) publications: Optional[list[str]] = Field( - default=[], + default=None, description="""All publications in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) resource_descriptions: Optional[list[ResourceDescription]] = Field( - default=[], + default=None, description="""All resource descriptions in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) resource_titles: Optional[list[ResourceTitle]] = Field( - default=[], + default=None, description="""All resource titles in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) prefixes: Optional[list[Prefix]] = Field( - default=[], + default=None, description="""The prefix mappings for the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) statements: Optional[list[Statement]] = Field( - default=[], + default=None, description="""All statements in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) entailed_edges: Optional[list[EntailedEdge]] = Field( - default=[], + default=None, description="""All entailed edges in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contigs: Optional[list[str]] = Field( - default=[], + default=None, description="""All contigs in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contig_collections: Optional[list[str]] = Field( - default=[], + default=None, description="""All contig collections in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) encoded_features: Optional[list[str]] = Field( - default=[], + default=None, description="""All encoded features in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) features: Optional[list[str]] = Field( - default=[], + default=None, description="""All features in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) proteins: Optional[list[str]] = Field( - default=[], + default=None, description="""All proteins in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) samples: Optional[list[str]] = Field( - default=[], + default=None, description="""All samples in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) sequences: Optional[list[Sequence]] = Field( - default=[], + default=None, description="""All sequences in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) experiments: Optional[list[str]] = Field( - default=[], + default=None, description="""All experiments in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) experiment_conditions: Optional[list[str]] = Field( - default=[], + default=None, description="""All experiment conditions in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) experiment_condition_sets: Optional[list[ExperimentConditionSet]] = Field( - default=[], + default=None, description="""All experiment condition sets in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) measurements: Optional[list[str]] = Field( - default=[], + default=None, description="""All measurements in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) measurement_sets: Optional[list[str]] = Field( - default=[], + default=None, description="""All measurement sets in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) ordered_protocol_steps: Optional[list[OrderedProtocolStep]] = Field( - default=[], + default=None, description="""All ordered protocol steps in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) parameters: Optional[list[str]] = Field( - default=[], + default=None, description="""All parameters in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) protocols: Optional[list[str]] = Field( - default=[], + default=None, description="""All protocols in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) protocol_executions: Optional[list[str]] = Field( - default=[], + default=None, description="""All protocol executions in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) protocol_inputs: Optional[list[str]] = Field( - default=[], + default=None, description="""All protocol inputs in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) protocol_input_sets: Optional[list[str]] = Field( - default=[], + default=None, description="""All protocol input sets in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) protocol_outputs: Optional[list[str]] = Field( - default=[], + default=None, description="""All protocol outputs in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) protocol_steps: Optional[list[str]] = Field( - default=[], + default=None, description="""All protocol steps in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) protocol_variables: Optional[list[ProtocolVariable]] = Field( - default=[], + default=None, description="""All protocol variables in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) variables: Optional[list[str]] = Field( - default=[], + default=None, description="""All variables in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) variable_values: Optional[list[str]] = Field( - default=[], + default=None, description="""All variable values in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) association_x_supporting_objects: Optional[list[AssociationXSupportingObject]] = Field( - default=[], + default=None, description="""All association x supporting object records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contig_x_contig_collections: Optional[list[ContigXContigCollection]] = Field( - default=[], + default=None, description="""All contig x contig collection records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contig_x_encoded_features: Optional[list[ContigXEncodedFeature]] = Field( - default=[], + default=None, description="""All contig x encoded feature records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contig_x_features: Optional[list[ContigXFeature]] = Field( - default=[], + default=None, description="""All contig x feature records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contig_x_proteins: Optional[list[ContigXProtein]] = Field( - default=[], + default=None, description="""All contig x protein records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contig_collection_x_encoded_features: Optional[list[ContigCollectionXEncodedFeature]] = Field( - default=[], + default=None, description="""All contig collection x encoded feature records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contig_collection_x_features: Optional[list[ContigCollectionXFeature]] = Field( - default=[], + default=None, description="""All contig collection x feature records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) contig_collection_x_proteins: Optional[list[ContigCollectionXProtein]] = Field( - default=[], + default=None, description="""All contig collection x protein records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) encoded_feature_x_features: Optional[list[EncodedFeatureXFeature]] = Field( - default=[], + default=None, description="""All encoded feature x feature records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) encoded_feature_x_proteins: Optional[list[EncodedFeatureXProtein]] = Field( - default=[], + default=None, description="""All encoded feature x protein records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) feature_x_proteins: Optional[list[FeatureXProtein]] = Field( - default=[], + default=None, description="""All feature x protein records in the schema.""", json_schema_extra={"linkml_meta": {"domain_of": ["Schema"]}}, ) @@ -6356,6 +6420,7 @@ class Schema(ConfiguredBaseModel): Name.model_rebuild() EntityNames.model_rebuild() EntityIdentifiers.model_rebuild() +EntityXSourceFile.model_rebuild() AttributeMixin.model_rebuild() EntityMixin.model_rebuild() UnitMixin.model_rebuild() diff --git a/src/cdm_schema/kbase_cdm_pyspark.py b/src/cdm_schema/kbase_cdm_pyspark.py index 4891fde0..9452f6e0 100644 --- a/src/cdm_schema/kbase_cdm_pyspark.py +++ b/src/cdm_schema/kbase_cdm_pyspark.py @@ -1,6 +1,6 @@ """Automated conversion of cdm_schema to PySpark. -cdm_schema version: 0.1.1 +cdm_schema version: 0.1.2 """ import re @@ -288,6 +288,13 @@ def convert_to_snake_case(name: str) -> str: StructField("updated", DateType(), nullable=False), ] ), + "Entity_x_SourceFile": StructType( + [ + StructField("entity_id", StringType(), nullable=False), + StructField("data_source_id", StringType(), nullable=False), + StructField("source_file", StringType(), nullable=True), + ] + ), "Event": StructType( [ StructField("event_id", StringType(), nullable=False), diff --git a/src/jsonschema/kbase_cdm.schema.json b/src/jsonschema/kbase_cdm.schema.json index 3905777b..fe0f1961 100644 --- a/src/jsonschema/kbase_cdm.schema.json +++ b/src/jsonschema/kbase_cdm.schema.json @@ -1476,6 +1476,35 @@ "title": "EntityType", "type": "string" }, + "EntityXSourceFile": { + "additionalProperties": false, + "description": "Captures information about the source file for a given entity.", + "properties": { + "data_source_id": { + "description": "Internal (CDM) unique identifier for a data source.\nFrom the Entity table: entity_id where entity_type == 'DataSource'.\n", + "pattern": "^CDM:dsrc-[0-9a-f]{8}([0-9a-f]{4}){3}-[0-9a-f]{12}$", + "type": "string" + }, + "entity_id": { + "description": "Internal (CDM) unique identifier for an entity.", + "pattern": "^CDM:[a-zA-Z]{2,4}-[0-9a-f]{8}([0-9a-f]{4}){3}-[0-9a-f]{12}$", + "type": "string" + }, + "source_file": { + "description": "Path to a file in the local file system from which data was parsed.", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "entity_id", + "data_source_id" + ], + "title": "EntityXSourceFile", + "type": "object" + }, "Event": { "additionalProperties": false, "description": "Something that happened.", @@ -3187,6 +3216,6 @@ "metamodel_version": "1.7.0", "title": "cdm_schema", "type": "object", - "version": "0.1.1" + "version": "0.1.2" } diff --git a/src/linkml/cdm_base.yaml b/src/linkml/cdm_base.yaml index c36496f6..c5c9832a 100644 --- a/src/linkml/cdm_base.yaml +++ b/src/linkml/cdm_base.yaml @@ -44,6 +44,8 @@ slots: source: description: The source for a specific piece of information; should be a CDM internal ID of a source in the DataSource table. range: cdm_data_source_id + source_file: + description: Path to a file in the local file system from which data was parsed. classes: @@ -165,6 +167,13 @@ classes: - Entity.entity_id one:many Identifier.entity_id - one entity can have multiple identifiers, and one identifier can be associated with multiple entities. + Entity_x_SourceFile: + is_a: Table + description: Captures information about the source file for a given entity. + slots: + - entity_id + - data_source_id + - source_file enums: EntityType: diff --git a/src/linkml/cdm_join_tables.yaml b/src/linkml/cdm_join_tables.yaml index 67f2581a..70272ce1 100644 --- a/src/linkml/cdm_join_tables.yaml +++ b/src/linkml/cdm_join_tables.yaml @@ -145,7 +145,6 @@ classes: - feature_id description: Captures the relationship between a feature and its transcription product. - EncodedFeature_x_Protein: is_a: LinkerTable represents_relationship: true diff --git a/src/linkml/cdm_schema.yaml b/src/linkml/cdm_schema.yaml index 92c8c616..7aca90a2 100644 --- a/src/linkml/cdm_schema.yaml +++ b/src/linkml/cdm_schema.yaml @@ -3,7 +3,7 @@ id: http://kbase.github.io/cdm-schema/linkml/cdm_schema name: cdm_schema description: Schema for KBase CDM -version: 0.1.1 +version: 0.1.2 prefixes: kb_cdm: 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