diff --git a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py index c7d6ade7f..d46f2905e 100644 --- a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py +++ b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py @@ -4082,7 +4082,54 @@ class SourceMultiGlob(ConfiguredBaseModel): class DefaultSource(ConfiguredBaseModel): """ - A generalized source class with glob finders. + A default source class that all source classes inherit from. + """ + + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) + + exclude: Optional[List[str]] = Field( + None, + description="""Exclude files from the source that match (regexes).""", + json_schema_extra={ + "linkml_meta": { + "alias": "exclude", + "domain_of": [ + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", + "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", + ], + } + }, + ) + + +class StandardSource(DefaultSource): + """ + A generalized source class with glob finders. Inherited by a majority of source classes. """ linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) @@ -4094,10 +4141,12 @@ class DefaultSource(ConfiguredBaseModel): "linkml_meta": { "alias": "destination_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -4116,10 +4165,12 @@ class DefaultSource(ConfiguredBaseModel): "linkml_meta": { "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -4138,9 +4189,11 @@ class DefaultSource(ConfiguredBaseModel): "linkml_meta": { "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -4152,65 +4205,56 @@ class DefaultSource(ConfiguredBaseModel): } }, ) - exclude: Optional[List[str]] = Field( + literal: Optional[StandardLiteral] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "literal", "domain_of": [ - "DefaultSource", - "AnnotationSource", - "AnnotationParentFilters", - "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "StandardSource", + "DatasetKeyPhotoSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", + "VoxelSpacingSource", + "DatasetSource", + "DepositionSource", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", - "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - - -class DefaultLiteralEntity(ConfiguredBaseModel): - """ - Used as a mixin with root-level classes that contain sources that have literals. - """ - - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) - - literal: Optional[DefaultLiteral] = Field( + exclude: Optional[List[str]] = Field( None, - description="""A literal class with a value attribute.""", + description="""Exclude files from the source that match (regexes).""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "exclude", "domain_of": [ - "DefaultLiteralEntity", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "VoxelSpacingSource", + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -4218,13 +4262,14 @@ class DefaultLiteralEntity(ConfiguredBaseModel): "RunSource", "TiltSeriesSource", "TomogramSource", + "VoxelSpacingSource", ], } }, ) -class DefaultLiteral(ConfiguredBaseModel): +class StandardLiteral(ConfiguredBaseModel): """ A literal class with a value attribute. """ @@ -4236,7 +4281,10 @@ class DefaultLiteral(ConfiguredBaseModel): description="""The value for the literal.""", min_length=1, json_schema_extra={ - "linkml_meta": {"alias": "value", "domain_of": ["DefaultLiteral", "KeyPhotoLiteral", "VoxelSpacingLiteral"]} + "linkml_meta": { + "alias": "value", + "domain_of": ["StandardLiteral", "KeyPhotoLiteral", "VoxelSpacingLiteral"], + } }, ) @@ -4252,7 +4300,10 @@ class KeyPhotoLiteral(ConfiguredBaseModel): ..., description="""A set of paths to representative images of a piece of data.""", json_schema_extra={ - "linkml_meta": {"alias": "value", "domain_of": ["DefaultLiteral", "KeyPhotoLiteral", "VoxelSpacingLiteral"]} + "linkml_meta": { + "alias": "value", + "domain_of": ["StandardLiteral", "KeyPhotoLiteral", "VoxelSpacingLiteral"], + } }, ) @@ -4307,7 +4358,7 @@ class AnnotationEntity(ConfiguredBaseModel): ) -class AnnotationSource(ConfiguredBaseModel): +class AnnotationSource(DefaultSource): """ An annotation source. """ @@ -4370,31 +4421,32 @@ class AnnotationSource(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -4439,31 +4491,32 @@ class AnnotationParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -4601,14 +4654,12 @@ class DatasetEntity(ConfiguredBaseModel): ) -class DatasetSource(DefaultLiteralEntity, DefaultSource): +class DatasetSource(StandardSource): """ A dataset source. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta( - {"from_schema": "cdp-ingestion-config", "mixins": ["DefaultSource", "DefaultLiteralEntity"]} - ) + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) parent_filters: Optional[DatasetParentFilters] = Field( None, @@ -4633,54 +4684,43 @@ class DatasetSource(DefaultLiteralEntity, DefaultSource): } }, ) - exclude: Optional[List[str]] = Field( + destination_glob: Optional[DestinationGlob] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A glob class for finding files in the output / destination directory.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "destination_glob", "domain_of": [ - "DefaultSource", - "AnnotationSource", - "AnnotationParentFilters", + "StandardSource", + "VoxelSpacingSource", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", - "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - destination_glob: Optional[DestinationGlob] = Field( + source_glob: Optional[SourceGlob] = Field( None, - description="""A glob class for finding files in the output / destination directory.""", + description="""A glob class for finding files in the source directory.""", json_schema_extra={ "linkml_meta": { - "alias": "destination_glob", + "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -4692,17 +4732,18 @@ class DatasetSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_glob: Optional[SourceGlob] = Field( + source_multi_glob: Optional[SourceMultiGlob] = Field( None, - description="""A glob class for finding files in the source directory.""", + description="""A glob class for finding files in the source directory (with multiple globs).""", json_schema_extra={ "linkml_meta": { - "alias": "source_glob", + "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", - "VoxelSpacingSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -4714,14 +4755,17 @@ class DatasetSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_multi_glob: Optional[SourceMultiGlob] = Field( + literal: Optional[StandardLiteral] = Field( None, - description="""A glob class for finding files in the source directory (with multiple globs).""", + description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { - "alias": "source_multi_glob", + "alias": "literal", "domain_of": [ - "DefaultSource", + "StandardSource", + "DatasetKeyPhotoSource", + "DepositionKeyPhotoSource", + "VoxelSpacingSource", "DatasetSource", "DepositionSource", "FrameSource", @@ -4735,19 +4779,32 @@ class DatasetSource(DefaultLiteralEntity, DefaultSource): } }, ) - literal: Optional[DefaultLiteral] = Field( + exclude: Optional[List[str]] = Field( None, - description="""A literal class with a value attribute.""", + description="""Exclude files from the source that match (regexes).""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "exclude", "domain_of": [ - "DefaultLiteralEntity", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "VoxelSpacingSource", + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -4755,6 +4812,7 @@ class DatasetSource(DefaultLiteralEntity, DefaultSource): "RunSource", "TiltSeriesSource", "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -4799,31 +4857,32 @@ class DatasetParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -4894,65 +4953,99 @@ class DatasetKeyPhotoEntity(ConfiguredBaseModel): } }, ) - exclude: Optional[List[str]] = Field( + + +class DatasetKeyPhotoSource(StandardSource): + """ + A key photo source. + """ + + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) + + literal: Optional[KeyPhotoLiteral] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A literal for a key photo.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "literal", + "domain_of": [ + "StandardSource", + "DatasetKeyPhotoSource", + "DepositionKeyPhotoSource", + "VoxelSpacingSource", + "DatasetSource", + "DepositionSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + ], + } + }, + ) + parent_filters: Optional[DatasetKeyPhotoParentFilters] = Field( + None, + description="""Types of parent filters for a key photo source.""", + json_schema_extra={ + "linkml_meta": { + "alias": "parent_filters", "domain_of": [ - "DefaultSource", "AnnotationSource", - "AnnotationParentFilters", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - - -class DatasetKeyPhotoSource(ConfiguredBaseModel): - """ - A key photo source. - """ - - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) - - literal: Optional[KeyPhotoLiteral] = Field( + destination_glob: Optional[DestinationGlob] = Field( None, - description="""A literal for a key photo.""", + description="""A glob class for finding files in the output / destination directory.""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "destination_glob", "domain_of": [ - "DefaultLiteralEntity", + "StandardSource", + "VoxelSpacingSource", + "DatasetSource", "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + ], + } + }, + ) + source_glob: Optional[SourceGlob] = Field( + None, + description="""A glob class for finding files in the source directory.""", + json_schema_extra={ + "linkml_meta": { + "alias": "source_glob", + "domain_of": [ + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -4964,16 +5057,54 @@ class DatasetKeyPhotoSource(ConfiguredBaseModel): } }, ) - parent_filters: Optional[DatasetKeyPhotoParentFilters] = Field( + source_multi_glob: Optional[SourceMultiGlob] = Field( None, - description="""Types of parent filters for a key photo source.""", + description="""A glob class for finding files in the source directory (with multiple globs).""", json_schema_extra={ "linkml_meta": { - "alias": "parent_filters", + "alias": "source_multi_glob", + "domain_of": [ + "StandardSource", + "DatasetSource", + "DatasetKeyPhotoSource", + "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + ], + } + }, + ) + exclude: Optional[List[str]] = Field( + None, + description="""Exclude files from the source that match (regexes).""", + json_schema_extra={ + "linkml_meta": { + "alias": "exclude", "domain_of": [ + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", "AnnotationSource", "DatasetSource", "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", "FrameSource", "GainSource", @@ -5027,31 +5158,32 @@ class DatasetKeyPhotoParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -5140,14 +5272,12 @@ class DepositionEntity(ConfiguredBaseModel): ) -class DepositionSource(DefaultLiteralEntity, DefaultSource): +class DepositionSource(StandardSource): """ A deposition source. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta( - {"from_schema": "cdp-ingestion-config", "mixins": ["DefaultSource", "DefaultLiteralEntity"]} - ) + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) destination_glob: Optional[DestinationGlob] = Field( None, @@ -5156,10 +5286,12 @@ class DepositionSource(DefaultLiteralEntity, DefaultSource): "linkml_meta": { "alias": "destination_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -5178,10 +5310,12 @@ class DepositionSource(DefaultLiteralEntity, DefaultSource): "linkml_meta": { "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -5200,9 +5334,11 @@ class DepositionSource(DefaultLiteralEntity, DefaultSource): "linkml_meta": { "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -5214,56 +5350,56 @@ class DepositionSource(DefaultLiteralEntity, DefaultSource): } }, ) - exclude: Optional[List[str]] = Field( + literal: Optional[StandardLiteral] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "literal", "domain_of": [ - "DefaultSource", - "AnnotationSource", - "AnnotationParentFilters", - "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "StandardSource", + "DatasetKeyPhotoSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", + "VoxelSpacingSource", + "DatasetSource", + "DepositionSource", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", - "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - literal: Optional[DefaultLiteral] = Field( + exclude: Optional[List[str]] = Field( None, - description="""A literal class with a value attribute.""", + description="""Exclude files from the source that match (regexes).""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "exclude", "domain_of": [ - "DefaultLiteralEntity", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "VoxelSpacingSource", + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -5271,6 +5407,7 @@ class DepositionSource(DefaultLiteralEntity, DefaultSource): "RunSource", "TiltSeriesSource", "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -5311,7 +5448,7 @@ class DepositionKeyPhotoEntity(ConfiguredBaseModel): ) -class DepositionKeyPhotoSource(ConfiguredBaseModel): +class DepositionKeyPhotoSource(StandardSource): """ A key photo source. """ @@ -5325,7 +5462,7 @@ class DepositionKeyPhotoSource(ConfiguredBaseModel): "linkml_meta": { "alias": "literal", "domain_of": [ - "DefaultLiteralEntity", + "StandardSource", "DatasetKeyPhotoSource", "DepositionKeyPhotoSource", "VoxelSpacingSource", @@ -5365,6 +5502,77 @@ class DepositionKeyPhotoSource(ConfiguredBaseModel): } }, ) + destination_glob: Optional[DestinationGlob] = Field( + None, + description="""A glob class for finding files in the output / destination directory.""", + json_schema_extra={ + "linkml_meta": { + "alias": "destination_glob", + "domain_of": [ + "StandardSource", + "VoxelSpacingSource", + "DatasetSource", + "DatasetKeyPhotoSource", + "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + ], + } + }, + ) + source_glob: Optional[SourceGlob] = Field( + None, + description="""A glob class for finding files in the source directory.""", + json_schema_extra={ + "linkml_meta": { + "alias": "source_glob", + "domain_of": [ + "StandardSource", + "VoxelSpacingSource", + "DatasetSource", + "DatasetKeyPhotoSource", + "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + ], + } + }, + ) + source_multi_glob: Optional[SourceMultiGlob] = Field( + None, + description="""A glob class for finding files in the source directory (with multiple globs).""", + json_schema_extra={ + "linkml_meta": { + "alias": "source_multi_glob", + "domain_of": [ + "StandardSource", + "DatasetSource", + "DatasetKeyPhotoSource", + "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + ], + } + }, + ) exclude: Optional[List[str]] = Field( None, description="""Exclude files from the source that match (regexes).""", @@ -5373,31 +5581,32 @@ class DepositionKeyPhotoSource(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -5442,31 +5651,32 @@ class DepositionKeyPhotoParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -5539,14 +5749,12 @@ class FrameEntity(ConfiguredBaseModel): ) -class FrameSource(DefaultLiteralEntity, DefaultSource): +class FrameSource(StandardSource): """ A frame source. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta( - {"from_schema": "cdp-ingestion-config", "mixins": ["DefaultSource", "DefaultLiteralEntity"]} - ) + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) parent_filters: Optional[FrameParentFilters] = Field( None, @@ -5571,54 +5779,43 @@ class FrameSource(DefaultLiteralEntity, DefaultSource): } }, ) - exclude: Optional[List[str]] = Field( + destination_glob: Optional[DestinationGlob] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A glob class for finding files in the output / destination directory.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "destination_glob", "domain_of": [ - "DefaultSource", - "AnnotationSource", - "AnnotationParentFilters", + "StandardSource", + "VoxelSpacingSource", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", - "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - destination_glob: Optional[DestinationGlob] = Field( + source_glob: Optional[SourceGlob] = Field( None, - description="""A glob class for finding files in the output / destination directory.""", + description="""A glob class for finding files in the source directory.""", json_schema_extra={ "linkml_meta": { - "alias": "destination_glob", + "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -5630,17 +5827,18 @@ class FrameSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_glob: Optional[SourceGlob] = Field( + source_multi_glob: Optional[SourceMultiGlob] = Field( None, - description="""A glob class for finding files in the source directory.""", + description="""A glob class for finding files in the source directory (with multiple globs).""", json_schema_extra={ "linkml_meta": { - "alias": "source_glob", + "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", - "VoxelSpacingSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -5652,14 +5850,17 @@ class FrameSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_multi_glob: Optional[SourceMultiGlob] = Field( + literal: Optional[StandardLiteral] = Field( None, - description="""A glob class for finding files in the source directory (with multiple globs).""", + description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { - "alias": "source_multi_glob", + "alias": "literal", "domain_of": [ - "DefaultSource", + "StandardSource", + "DatasetKeyPhotoSource", + "DepositionKeyPhotoSource", + "VoxelSpacingSource", "DatasetSource", "DepositionSource", "FrameSource", @@ -5673,19 +5874,32 @@ class FrameSource(DefaultLiteralEntity, DefaultSource): } }, ) - literal: Optional[DefaultLiteral] = Field( + exclude: Optional[List[str]] = Field( None, - description="""A literal class with a value attribute.""", + description="""Exclude files from the source that match (regexes).""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "exclude", "domain_of": [ - "DefaultLiteralEntity", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "VoxelSpacingSource", + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -5693,6 +5907,7 @@ class FrameSource(DefaultLiteralEntity, DefaultSource): "RunSource", "TiltSeriesSource", "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -5737,31 +5952,32 @@ class FrameParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -5873,14 +6089,12 @@ class GainEntity(ConfiguredBaseModel): ) -class GainSource(DefaultLiteralEntity, DefaultSource): +class GainSource(StandardSource): """ A gain source. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta( - {"from_schema": "cdp-ingestion-config", "mixins": ["DefaultSource", "DefaultLiteralEntity"]} - ) + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) parent_filters: Optional[GainParentFilters] = Field( None, @@ -5905,54 +6119,43 @@ class GainSource(DefaultLiteralEntity, DefaultSource): } }, ) - exclude: Optional[List[str]] = Field( + destination_glob: Optional[DestinationGlob] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A glob class for finding files in the output / destination directory.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "destination_glob", "domain_of": [ - "DefaultSource", - "AnnotationSource", - "AnnotationParentFilters", + "StandardSource", + "VoxelSpacingSource", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", - "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - destination_glob: Optional[DestinationGlob] = Field( + source_glob: Optional[SourceGlob] = Field( None, - description="""A glob class for finding files in the output / destination directory.""", + description="""A glob class for finding files in the source directory.""", json_schema_extra={ "linkml_meta": { - "alias": "destination_glob", + "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -5964,17 +6167,18 @@ class GainSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_glob: Optional[SourceGlob] = Field( + source_multi_glob: Optional[SourceMultiGlob] = Field( None, - description="""A glob class for finding files in the source directory.""", + description="""A glob class for finding files in the source directory (with multiple globs).""", json_schema_extra={ "linkml_meta": { - "alias": "source_glob", + "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", - "VoxelSpacingSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -5986,14 +6190,17 @@ class GainSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_multi_glob: Optional[SourceMultiGlob] = Field( + literal: Optional[StandardLiteral] = Field( None, - description="""A glob class for finding files in the source directory (with multiple globs).""", + description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { - "alias": "source_multi_glob", + "alias": "literal", "domain_of": [ - "DefaultSource", + "StandardSource", + "DatasetKeyPhotoSource", + "DepositionKeyPhotoSource", + "VoxelSpacingSource", "DatasetSource", "DepositionSource", "FrameSource", @@ -6007,19 +6214,32 @@ class GainSource(DefaultLiteralEntity, DefaultSource): } }, ) - literal: Optional[DefaultLiteral] = Field( + exclude: Optional[List[str]] = Field( None, - description="""A literal class with a value attribute.""", + description="""Exclude files from the source that match (regexes).""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "exclude", "domain_of": [ - "DefaultLiteralEntity", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "VoxelSpacingSource", + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -6027,6 +6247,7 @@ class GainSource(DefaultLiteralEntity, DefaultSource): "RunSource", "TiltSeriesSource", "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -6071,31 +6292,32 @@ class GainParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -6207,14 +6429,12 @@ class KeyImageEntity(ConfiguredBaseModel): ) -class KeyImageSource(DefaultLiteralEntity, DefaultSource): +class KeyImageSource(StandardSource): """ A key image source. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta( - {"from_schema": "cdp-ingestion-config", "mixins": ["DefaultSource", "DefaultLiteralEntity"]} - ) + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) parent_filters: Optional[KeyImageParentFilters] = Field( None, @@ -6239,54 +6459,43 @@ class KeyImageSource(DefaultLiteralEntity, DefaultSource): } }, ) - exclude: Optional[List[str]] = Field( + destination_glob: Optional[DestinationGlob] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A glob class for finding files in the output / destination directory.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "destination_glob", "domain_of": [ - "DefaultSource", - "AnnotationSource", - "AnnotationParentFilters", + "StandardSource", + "VoxelSpacingSource", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", - "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - destination_glob: Optional[DestinationGlob] = Field( + source_glob: Optional[SourceGlob] = Field( None, - description="""A glob class for finding files in the output / destination directory.""", + description="""A glob class for finding files in the source directory.""", json_schema_extra={ "linkml_meta": { - "alias": "destination_glob", + "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -6298,17 +6507,18 @@ class KeyImageSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_glob: Optional[SourceGlob] = Field( + source_multi_glob: Optional[SourceMultiGlob] = Field( None, - description="""A glob class for finding files in the source directory.""", + description="""A glob class for finding files in the source directory (with multiple globs).""", json_schema_extra={ "linkml_meta": { - "alias": "source_glob", + "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", - "VoxelSpacingSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -6320,14 +6530,17 @@ class KeyImageSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_multi_glob: Optional[SourceMultiGlob] = Field( + literal: Optional[StandardLiteral] = Field( None, - description="""A glob class for finding files in the source directory (with multiple globs).""", + description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { - "alias": "source_multi_glob", + "alias": "literal", "domain_of": [ - "DefaultSource", + "StandardSource", + "DatasetKeyPhotoSource", + "DepositionKeyPhotoSource", + "VoxelSpacingSource", "DatasetSource", "DepositionSource", "FrameSource", @@ -6341,19 +6554,32 @@ class KeyImageSource(DefaultLiteralEntity, DefaultSource): } }, ) - literal: Optional[DefaultLiteral] = Field( + exclude: Optional[List[str]] = Field( None, - description="""A literal class with a value attribute.""", + description="""Exclude files from the source that match (regexes).""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "exclude", "domain_of": [ - "DefaultLiteralEntity", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "VoxelSpacingSource", + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -6361,6 +6587,7 @@ class KeyImageSource(DefaultLiteralEntity, DefaultSource): "RunSource", "TiltSeriesSource", "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -6405,31 +6632,32 @@ class KeyImageParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", "AnnotationSource", - "AnnotationParentFilters", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, @@ -6556,14 +6784,12 @@ class RawTiltEntity(ConfiguredBaseModel): ) -class RawTiltSource(DefaultLiteralEntity, DefaultSource): +class RawTiltSource(StandardSource): """ A raw tilt source. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta( - {"from_schema": "cdp-ingestion-config", "mixins": ["DefaultSource", "DefaultLiteralEntity"]} - ) + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) parent_filters: Optional[RawTiltParentFilters] = Field( None, @@ -6588,54 +6814,43 @@ class RawTiltSource(DefaultLiteralEntity, DefaultSource): } }, ) - exclude: Optional[List[str]] = Field( + destination_glob: Optional[DestinationGlob] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A glob class for finding files in the output / destination directory.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "destination_glob", "domain_of": [ - "DefaultSource", - "AnnotationSource", - "AnnotationParentFilters", + "StandardSource", + "VoxelSpacingSource", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", - "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - destination_glob: Optional[DestinationGlob] = Field( + source_glob: Optional[SourceGlob] = Field( None, - description="""A glob class for finding files in the output / destination directory.""", + description="""A glob class for finding files in the source directory.""", json_schema_extra={ "linkml_meta": { - "alias": "destination_glob", + "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -6647,17 +6862,18 @@ class RawTiltSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_glob: Optional[SourceGlob] = Field( + source_multi_glob: Optional[SourceMultiGlob] = Field( None, - description="""A glob class for finding files in the source directory.""", + description="""A glob class for finding files in the source directory (with multiple globs).""", json_schema_extra={ "linkml_meta": { - "alias": "source_glob", + "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", - "VoxelSpacingSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -6669,14 +6885,17 @@ class RawTiltSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_multi_glob: Optional[SourceMultiGlob] = Field( + literal: Optional[StandardLiteral] = Field( None, - description="""A glob class for finding files in the source directory (with multiple globs).""", + description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { - "alias": "source_multi_glob", + "alias": "literal", "domain_of": [ - "DefaultSource", + "StandardSource", + "DatasetKeyPhotoSource", + "DepositionKeyPhotoSource", + "VoxelSpacingSource", "DatasetSource", "DepositionSource", "FrameSource", @@ -6690,19 +6909,32 @@ class RawTiltSource(DefaultLiteralEntity, DefaultSource): } }, ) - literal: Optional[DefaultLiteral] = Field( + exclude: Optional[List[str]] = Field( None, - description="""A literal class with a value attribute.""", + description="""Exclude files from the source that match (regexes).""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "exclude", "domain_of": [ - "DefaultLiteralEntity", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "VoxelSpacingSource", + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -6710,6 +6942,7 @@ class RawTiltSource(DefaultLiteralEntity, DefaultSource): "RunSource", "TiltSeriesSource", "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -6754,31 +6987,32 @@ class RawTiltParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -6890,14 +7124,12 @@ class RunEntity(ConfiguredBaseModel): ) -class RunSource(DefaultLiteralEntity, DefaultSource): +class RunSource(StandardSource): """ A run source. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta( - {"from_schema": "cdp-ingestion-config", "mixins": ["DefaultSource", "DefaultLiteralEntity"]} - ) + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) parent_filters: Optional[RunParentFilters] = Field( None, @@ -6922,54 +7154,43 @@ class RunSource(DefaultLiteralEntity, DefaultSource): } }, ) - exclude: Optional[List[str]] = Field( + destination_glob: Optional[DestinationGlob] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A glob class for finding files in the output / destination directory.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "destination_glob", "domain_of": [ - "DefaultSource", - "AnnotationSource", - "AnnotationParentFilters", + "StandardSource", + "VoxelSpacingSource", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", - "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - destination_glob: Optional[DestinationGlob] = Field( + source_glob: Optional[SourceGlob] = Field( None, - description="""A glob class for finding files in the output / destination directory.""", + description="""A glob class for finding files in the source directory.""", json_schema_extra={ "linkml_meta": { - "alias": "destination_glob", + "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -6981,17 +7202,18 @@ class RunSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_glob: Optional[SourceGlob] = Field( + source_multi_glob: Optional[SourceMultiGlob] = Field( None, - description="""A glob class for finding files in the source directory.""", + description="""A glob class for finding files in the source directory (with multiple globs).""", json_schema_extra={ "linkml_meta": { - "alias": "source_glob", + "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", - "VoxelSpacingSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -7003,14 +7225,17 @@ class RunSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_multi_glob: Optional[SourceMultiGlob] = Field( + literal: Optional[StandardLiteral] = Field( None, - description="""A glob class for finding files in the source directory (with multiple globs).""", + description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { - "alias": "source_multi_glob", + "alias": "literal", "domain_of": [ - "DefaultSource", + "StandardSource", + "DatasetKeyPhotoSource", + "DepositionKeyPhotoSource", + "VoxelSpacingSource", "DatasetSource", "DepositionSource", "FrameSource", @@ -7024,19 +7249,32 @@ class RunSource(DefaultLiteralEntity, DefaultSource): } }, ) - literal: Optional[DefaultLiteral] = Field( + exclude: Optional[List[str]] = Field( None, - description="""A literal class with a value attribute.""", + description="""Exclude files from the source that match (regexes).""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "exclude", "domain_of": [ - "DefaultLiteralEntity", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "VoxelSpacingSource", + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -7044,6 +7282,7 @@ class RunSource(DefaultLiteralEntity, DefaultSource): "RunSource", "TiltSeriesSource", "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -7088,31 +7327,32 @@ class RunParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -7260,71 +7500,32 @@ class TiltSeriesEntity(ConfiguredBaseModel): ) -class TiltSeriesSource(DefaultLiteralEntity, DefaultSource): +class TiltSeriesSource(StandardSource): """ A tilt series source. """ - - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta( - {"from_schema": "cdp-ingestion-config", "mixins": ["DefaultSource", "DefaultLiteralEntity"]} - ) - - parent_filters: Optional[TiltSeriesParentFilters] = Field( - None, - description="""Types of parent filters for a tilt series source.""", - json_schema_extra={ - "linkml_meta": { - "alias": "parent_filters", - "domain_of": [ - "AnnotationSource", - "DatasetSource", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "FrameSource", - "GainSource", - "KeyImageSource", - "RawTiltSource", - "RunSource", - "TiltSeriesSource", - "TomogramSource", - "VoxelSpacingSource", - ], - } - }, - ) - exclude: Optional[List[str]] = Field( + + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) + + parent_filters: Optional[TiltSeriesParentFilters] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""Types of parent filters for a tilt series source.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "parent_filters", "domain_of": [ - "DefaultSource", "AnnotationSource", - "AnnotationParentFilters", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, @@ -7336,10 +7537,12 @@ class TiltSeriesSource(DefaultLiteralEntity, DefaultSource): "linkml_meta": { "alias": "destination_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -7358,10 +7561,12 @@ class TiltSeriesSource(DefaultLiteralEntity, DefaultSource): "linkml_meta": { "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -7380,9 +7585,11 @@ class TiltSeriesSource(DefaultLiteralEntity, DefaultSource): "linkml_meta": { "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -7394,14 +7601,14 @@ class TiltSeriesSource(DefaultLiteralEntity, DefaultSource): } }, ) - literal: Optional[DefaultLiteral] = Field( + literal: Optional[StandardLiteral] = Field( None, description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { "alias": "literal", "domain_of": [ - "DefaultLiteralEntity", + "StandardSource", "DatasetKeyPhotoSource", "DepositionKeyPhotoSource", "VoxelSpacingSource", @@ -7418,6 +7625,44 @@ class TiltSeriesSource(DefaultLiteralEntity, DefaultSource): } }, ) + exclude: Optional[List[str]] = Field( + None, + description="""Exclude files from the source that match (regexes).""", + json_schema_extra={ + "linkml_meta": { + "alias": "exclude", + "domain_of": [ + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", + "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", + ], + } + }, + ) class TiltSeriesParentFilters(ConfiguredBaseModel): @@ -7458,31 +7703,32 @@ class TiltSeriesParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -7610,14 +7856,12 @@ class TomogramEntity(ConfiguredBaseModel): ) -class TomogramSource(DefaultLiteralEntity, DefaultSource): +class TomogramSource(StandardSource): """ A tomogram source. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta( - {"from_schema": "cdp-ingestion-config", "mixins": ["DefaultSource", "DefaultLiteralEntity"]} - ) + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({"from_schema": "cdp-ingestion-config"}) parent_filters: Optional[TomogramParentFilters] = Field( None, @@ -7642,54 +7886,43 @@ class TomogramSource(DefaultLiteralEntity, DefaultSource): } }, ) - exclude: Optional[List[str]] = Field( + destination_glob: Optional[DestinationGlob] = Field( None, - description="""Exclude files from the source that match (regexes).""", + description="""A glob class for finding files in the output / destination directory.""", json_schema_extra={ "linkml_meta": { - "alias": "exclude", + "alias": "destination_glob", "domain_of": [ - "DefaultSource", - "AnnotationSource", - "AnnotationParentFilters", + "StandardSource", + "VoxelSpacingSource", "DatasetSource", - "DatasetParentFilters", - "DatasetKeyPhotoEntity", - "DatasetKeyPhotoParentFilters", + "DatasetKeyPhotoSource", + "DepositionSource", "DepositionKeyPhotoSource", - "DepositionKeyPhotoParentFilters", "FrameSource", - "FrameParentFilters", "GainSource", - "GainParentFilters", "KeyImageSource", - "KeyImageParentFilters", "RawTiltSource", - "RawTiltParentFilters", "RunSource", - "RunParentFilters", "TiltSeriesSource", - "TiltSeriesParentFilters", "TomogramSource", - "TomogramParentFilters", - "VoxelSpacingSource", - "VoxelSpacingParentFilters", - "DepositionSource", ], } }, ) - destination_glob: Optional[DestinationGlob] = Field( + source_glob: Optional[SourceGlob] = Field( None, - description="""A glob class for finding files in the output / destination directory.""", + description="""A glob class for finding files in the source directory.""", json_schema_extra={ "linkml_meta": { - "alias": "destination_glob", + "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -7701,17 +7934,18 @@ class TomogramSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_glob: Optional[SourceGlob] = Field( + source_multi_glob: Optional[SourceMultiGlob] = Field( None, - description="""A glob class for finding files in the source directory.""", + description="""A glob class for finding files in the source directory (with multiple globs).""", json_schema_extra={ "linkml_meta": { - "alias": "source_glob", + "alias": "source_multi_glob", "domain_of": [ - "DefaultSource", - "VoxelSpacingSource", + "StandardSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -7723,14 +7957,17 @@ class TomogramSource(DefaultLiteralEntity, DefaultSource): } }, ) - source_multi_glob: Optional[SourceMultiGlob] = Field( + literal: Optional[StandardLiteral] = Field( None, - description="""A glob class for finding files in the source directory (with multiple globs).""", + description="""A literal class with a value attribute.""", json_schema_extra={ "linkml_meta": { - "alias": "source_multi_glob", + "alias": "literal", "domain_of": [ - "DefaultSource", + "StandardSource", + "DatasetKeyPhotoSource", + "DepositionKeyPhotoSource", + "VoxelSpacingSource", "DatasetSource", "DepositionSource", "FrameSource", @@ -7744,19 +7981,32 @@ class TomogramSource(DefaultLiteralEntity, DefaultSource): } }, ) - literal: Optional[DefaultLiteral] = Field( + exclude: Optional[List[str]] = Field( None, - description="""A literal class with a value attribute.""", + description="""Exclude files from the source that match (regexes).""", json_schema_extra={ "linkml_meta": { - "alias": "literal", + "alias": "exclude", "domain_of": [ - "DefaultLiteralEntity", - "DatasetKeyPhotoSource", - "DepositionKeyPhotoSource", - "VoxelSpacingSource", + "DefaultSource", + "AnnotationParentFilters", + "DatasetParentFilters", + "DatasetKeyPhotoParentFilters", + "DepositionKeyPhotoParentFilters", + "FrameParentFilters", + "GainParentFilters", + "KeyImageParentFilters", + "RawTiltParentFilters", + "RunParentFilters", + "TiltSeriesParentFilters", + "TomogramParentFilters", + "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -7764,6 +8014,7 @@ class TomogramSource(DefaultLiteralEntity, DefaultSource): "RunSource", "TiltSeriesSource", "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -7808,31 +8059,32 @@ class TomogramParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -7954,7 +8206,7 @@ class VoxelSpacingEntity(ConfiguredBaseModel): ) -class VoxelSpacingSource(ConfiguredBaseModel): +class VoxelSpacingSource(DefaultSource): """ A voxel spacing source. """ @@ -7968,10 +8220,12 @@ class VoxelSpacingSource(ConfiguredBaseModel): "linkml_meta": { "alias": "destination_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -7990,10 +8244,12 @@ class VoxelSpacingSource(ConfiguredBaseModel): "linkml_meta": { "alias": "source_glob", "domain_of": [ - "DefaultSource", + "StandardSource", "VoxelSpacingSource", "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", "FrameSource", "GainSource", "KeyImageSource", @@ -8012,7 +8268,7 @@ class VoxelSpacingSource(ConfiguredBaseModel): "linkml_meta": { "alias": "literal", "domain_of": [ - "DefaultLiteralEntity", + "StandardSource", "DatasetKeyPhotoSource", "DepositionKeyPhotoSource", "VoxelSpacingSource", @@ -8065,31 +8321,32 @@ class VoxelSpacingSource(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -8134,31 +8391,32 @@ class VoxelSpacingParentFilters(ConfiguredBaseModel): "alias": "exclude", "domain_of": [ "DefaultSource", - "AnnotationSource", "AnnotationParentFilters", - "DatasetSource", "DatasetParentFilters", - "DatasetKeyPhotoEntity", "DatasetKeyPhotoParentFilters", - "DepositionKeyPhotoSource", "DepositionKeyPhotoParentFilters", - "FrameSource", "FrameParentFilters", - "GainSource", "GainParentFilters", - "KeyImageSource", "KeyImageParentFilters", - "RawTiltSource", "RawTiltParentFilters", - "RunSource", "RunParentFilters", - "TiltSeriesSource", "TiltSeriesParentFilters", - "TomogramSource", "TomogramParentFilters", - "VoxelSpacingSource", "VoxelSpacingParentFilters", + "StandardSource", + "AnnotationSource", + "DatasetSource", + "DatasetKeyPhotoSource", "DepositionSource", + "DepositionKeyPhotoSource", + "FrameSource", + "GainSource", + "KeyImageSource", + "RawTiltSource", + "RunSource", + "TiltSeriesSource", + "TomogramSource", + "VoxelSpacingSource", ], } }, @@ -8248,7 +8506,10 @@ class VoxelSpacingLiteral(ConfiguredBaseModel): description="""The value for the voxel spacing literal.""", min_length=1, json_schema_extra={ - "linkml_meta": {"alias": "value", "domain_of": ["DefaultLiteral", "KeyPhotoLiteral", "VoxelSpacingLiteral"]} + "linkml_meta": { + "alias": "value", + "domain_of": ["StandardLiteral", "KeyPhotoLiteral", "VoxelSpacingLiteral"], + } }, ) @@ -8337,8 +8598,8 @@ class TomogramHeader(ConfiguredBaseModel): SourceGlob.model_rebuild() SourceMultiGlob.model_rebuild() DefaultSource.model_rebuild() -DefaultLiteralEntity.model_rebuild() -DefaultLiteral.model_rebuild() +StandardSource.model_rebuild() +StandardLiteral.model_rebuild() KeyPhotoLiteral.model_rebuild() AnnotationEntity.model_rebuild() AnnotationSource.model_rebuild() diff --git a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json index 2802dacc3..97da73a5f 100644 --- a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json +++ b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json @@ -1292,16 +1292,6 @@ "additionalProperties": false, "description": "A dataset key photo entity.", "properties": { - "exclude": { - "description": "Exclude files from the source that match (regexes).", - "items": { - "type": "string" - }, - "type": [ - "array", - "null" - ] - }, "sources": { "description": "A key photo source.", "items": { @@ -1369,6 +1359,27 @@ "additionalProperties": false, "description": "A key photo source.", "properties": { + "destination_glob": { + "anyOf": [ + { + "$ref": "#/$defs/DestinationGlob" + }, + { + "type": "null" + } + ], + "description": "A glob class for finding files in the output / destination directory." + }, + "exclude": { + "description": "Exclude files from the source that match (regexes).", + "items": { + "type": "string" + }, + "type": [ + "array", + "null" + ] + }, "literal": { "anyOf": [ { @@ -1390,6 +1401,28 @@ } ], "description": "Types of parent filters for a key photo source." + }, + "source_glob": { + "anyOf": [ + { + "$ref": "#/$defs/SourceGlob" + }, + { + "type": "null" + } + ], + "description": "A glob class for finding files in the source directory." + }, + "source_multi_glob": { + "anyOf": [ + { + "$ref": "#/$defs/SourceMultiGlob" + }, + { + "type": "null" + } + ], + "description": "A glob class for finding files in the source directory (with multiple globs)." } }, "title": "DatasetKeyPhotoSource", @@ -1471,7 +1504,7 @@ "literal": { "anyOf": [ { - "$ref": "#/$defs/DefaultLiteral" + "$ref": "#/$defs/StandardLiteral" }, { "type": "null" @@ -1559,59 +1592,10 @@ "title": "DateStampedEntity", "type": "object" }, - "DefaultLiteral": { - "additionalProperties": false, - "description": "A literal class with a value attribute.", - "properties": { - "value": { - "description": "The value for the literal.", - "items": { - "$ref": "#/$defs/Any" - }, - "minItems": 1, - "type": "array" - } - }, - "required": [ - "value" - ], - "title": "DefaultLiteral", - "type": "object" - }, - "DefaultLiteralEntity": { - "additionalProperties": false, - "description": "Used as a mixin with root-level classes that contain sources that have literals.", - "properties": { - "literal": { - "anyOf": [ - { - "$ref": "#/$defs/DefaultLiteral" - }, - { - "type": "null" - } - ], - "description": "A literal class with a value attribute." - } - }, - "title": "DefaultLiteralEntity", - "type": "object" - }, "DefaultSource": { "additionalProperties": false, - "description": "A generalized source class with glob finders.", + "description": "A default source class that all source classes inherit from.", "properties": { - "destination_glob": { - "anyOf": [ - { - "$ref": "#/$defs/DestinationGlob" - }, - { - "type": "null" - } - ], - "description": "A glob class for finding files in the output / destination directory." - }, "exclude": { "description": "Exclude files from the source that match (regexes).", "items": { @@ -1621,28 +1605,6 @@ "array", "null" ] - }, - "source_glob": { - "anyOf": [ - { - "$ref": "#/$defs/SourceGlob" - }, - { - "type": "null" - } - ], - "description": "A glob class for finding files in the source directory." - }, - "source_multi_glob": { - "anyOf": [ - { - "$ref": "#/$defs/SourceMultiGlob" - }, - { - "type": "null" - } - ], - "description": "A glob class for finding files in the source directory (with multiple globs)." } }, "title": "DefaultSource", @@ -1809,6 +1771,17 @@ "additionalProperties": false, "description": "A key photo source.", "properties": { + "destination_glob": { + "anyOf": [ + { + "$ref": "#/$defs/DestinationGlob" + }, + { + "type": "null" + } + ], + "description": "A glob class for finding files in the output / destination directory." + }, "exclude": { "description": "Exclude files from the source that match (regexes).", "items": { @@ -1840,6 +1813,28 @@ } ], "description": "Types of parent filters for a key photo source." + }, + "source_glob": { + "anyOf": [ + { + "$ref": "#/$defs/SourceGlob" + }, + { + "type": "null" + } + ], + "description": "A glob class for finding files in the source directory." + }, + "source_multi_glob": { + "anyOf": [ + { + "$ref": "#/$defs/SourceMultiGlob" + }, + { + "type": "null" + } + ], + "description": "A glob class for finding files in the source directory (with multiple globs)." } }, "title": "DepositionKeyPhotoSource", @@ -1873,7 +1868,7 @@ "literal": { "anyOf": [ { - "$ref": "#/$defs/DefaultLiteral" + "$ref": "#/$defs/StandardLiteral" }, { "type": "null" @@ -2162,7 +2157,7 @@ "literal": { "anyOf": [ { - "$ref": "#/$defs/DefaultLiteral" + "$ref": "#/$defs/StandardLiteral" }, { "type": "null" @@ -2362,7 +2357,7 @@ "literal": { "anyOf": [ { - "$ref": "#/$defs/DefaultLiteral" + "$ref": "#/$defs/StandardLiteral" }, { "type": "null" @@ -2542,7 +2537,7 @@ "literal": { "anyOf": [ { - "$ref": "#/$defs/DefaultLiteral" + "$ref": "#/$defs/StandardLiteral" }, { "type": "null" @@ -2846,7 +2841,7 @@ "literal": { "anyOf": [ { - "$ref": "#/$defs/DefaultLiteral" + "$ref": "#/$defs/StandardLiteral" }, { "type": "null" @@ -2996,7 +2991,7 @@ "literal": { "anyOf": [ { - "$ref": "#/$defs/DefaultLiteral" + "$ref": "#/$defs/StandardLiteral" }, { "type": "null" @@ -3104,6 +3099,87 @@ "title": "SourceMultiGlob", "type": "object" }, + "StandardLiteral": { + "additionalProperties": false, + "description": "A literal class with a value attribute.", + "properties": { + "value": { + "description": "The value for the literal.", + "items": { + "$ref": "#/$defs/Any" + }, + "minItems": 1, + "type": "array" + } + }, + "required": [ + "value" + ], + "title": "StandardLiteral", + "type": "object" + }, + "StandardSource": { + "additionalProperties": false, + "description": "A generalized source class with glob finders. Inherited by a majority of source classes.", + "properties": { + "destination_glob": { + "anyOf": [ + { + "$ref": "#/$defs/DestinationGlob" + }, + { + "type": "null" + } + ], + "description": "A glob class for finding files in the output / destination directory." + }, + "exclude": { + "description": "Exclude files from the source that match (regexes).", + "items": { + "type": "string" + }, + "type": [ + "array", + "null" + ] + }, + "literal": { + "anyOf": [ + { + "$ref": "#/$defs/StandardLiteral" + }, + { + "type": "null" + } + ], + "description": "A literal class with a value attribute." + }, + "source_glob": { + "anyOf": [ + { + "$ref": "#/$defs/SourceGlob" + }, + { + "type": "null" + } + ], + "description": "A glob class for finding files in the source directory." + }, + "source_multi_glob": { + "anyOf": [ + { + "$ref": "#/$defs/SourceMultiGlob" + }, + { + "type": "null" + } + ], + "description": "A glob class for finding files in the source directory (with multiple globs)." + } + }, + "title": "StandardSource", + "type": "object" + }, "StandardizationConfig": { "additionalProperties": false, "description": "A standardization configuration.", @@ -3553,7 +3629,7 @@ "literal": { "anyOf": [ { - "$ref": "#/$defs/DefaultLiteral" + "$ref": "#/$defs/StandardLiteral" }, { "type": "null" @@ -4040,7 +4116,7 @@ "literal": { "anyOf": [ { - "$ref": "#/$defs/DefaultLiteral" + "$ref": "#/$defs/StandardLiteral" }, { "type": "null" diff --git a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml index 13f2bdd15..aae99667b 100644 --- a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml +++ b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml @@ -945,17 +945,48 @@ classes: minimum_cardinality: 1 DefaultSource: name: DefaultSource - description: A generalized source class with glob finders. + description: A default source class that all source classes inherit from. from_schema: cdp-ingestion-config + attributes: + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: DefaultSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true + inlined: true + inlined_as_list: true + StandardSource: + name: StandardSource + description: A generalized source class with glob finders. Inherited by a majority + of source classes. + from_schema: cdp-ingestion-config + is_a: DefaultSource attributes: destination_glob: name: destination_glob description: A glob class for finding files in the output / destination directory. from_schema: cdp-ingestion-config alias: destination_glob - owner: DefaultSource + owner: StandardSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -965,9 +996,9 @@ classes: description: A glob class for finding files in the source directory. from_schema: cdp-ingestion-config alias: source_glob - owner: DefaultSource + owner: StandardSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -978,70 +1009,52 @@ classes: multiple globs). from_schema: cdp-ingestion-config alias: source_multi_glob - owner: DefaultSource + owner: StandardSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true + literal: + name: literal + description: A literal class with a value attribute. + from_schema: cdp-ingestion-config + alias: literal + owner: StandardSource + domain_of: + - StandardSource + - DatasetKeyPhotoSource + - DepositionKeyPhotoSource + - VoxelSpacingSource + range: StandardLiteral + inlined: true + inlined_as_list: true exclude: name: exclude description: Exclude files from the source that match (regexes). from_schema: cdp-ingestion-config alias: exclude - owner: DefaultSource + owner: StandardSource domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: string multivalued: true inlined: true inlined_as_list: true - DefaultLiteralEntity: - name: DefaultLiteralEntity - description: Used as a mixin with root-level classes that contain sources that - have literals. - from_schema: cdp-ingestion-config - attributes: - literal: - name: literal - description: A literal class with a value attribute. - from_schema: cdp-ingestion-config - alias: literal - owner: DefaultLiteralEntity - domain_of: - - DefaultLiteralEntity - - DatasetKeyPhotoSource - - DepositionKeyPhotoSource - - VoxelSpacingSource - range: DefaultLiteral - inlined: true - inlined_as_list: true - DefaultLiteral: - name: DefaultLiteral + StandardLiteral: + name: StandardLiteral description: A literal class with a value attribute. from_schema: cdp-ingestion-config attributes: @@ -1050,9 +1063,9 @@ classes: description: The value for the literal. from_schema: cdp-ingestion-config alias: value - owner: DefaultLiteral + owner: StandardLiteral domain_of: - - DefaultLiteral + - StandardLiteral - KeyPhotoLiteral - VoxelSpacingLiteral range: Any @@ -1073,7 +1086,7 @@ classes: alias: value owner: KeyPhotoLiteral domain_of: - - DefaultLiteral + - StandardLiteral - KeyPhotoLiteral - VoxelSpacingLiteral range: PicturePath @@ -1131,6 +1144,7 @@ classes: name: AnnotationSource description: An annotation source. from_schema: cdp-ingestion-config + is_a: DefaultSource attributes: InstanceSegmentation: name: InstanceSegmentation @@ -1222,29 +1236,17 @@ classes: owner: AnnotationSource domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: string multivalued: true @@ -1289,29 +1291,17 @@ classes: owner: AnnotationParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: AnnotationParent inlined: true @@ -1454,9 +1444,7 @@ classes: name: DatasetSource description: A dataset source. from_schema: cdp-ingestion-config - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: name: parent_filters @@ -1480,42 +1468,6 @@ classes: range: DatasetParentFilters inlined: true inlined_as_list: true - exclude: - name: exclude - description: Exclude files from the source that match (regexes). - from_schema: cdp-ingestion-config - alias: exclude - owner: DatasetSource - domain_of: - - DefaultSource - - AnnotationSource - - AnnotationParentFilters - - DatasetSource - - DatasetParentFilters - - DatasetKeyPhotoEntity - - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - - DepositionKeyPhotoParentFilters - - FrameSource - - FrameParentFilters - - GainSource - - GainParentFilters - - KeyImageSource - - KeyImageParentFilters - - RawTiltSource - - RawTiltParentFilters - - RunSource - - RunParentFilters - - TiltSeriesSource - - TiltSeriesParentFilters - - TomogramSource - - TomogramParentFilters - - VoxelSpacingSource - - VoxelSpacingParentFilters - range: string - multivalued: true - inlined: true - inlined_as_list: true destination_glob: name: destination_glob description: A glob class for finding files in the output / destination directory. @@ -1523,7 +1475,7 @@ classes: alias: destination_glob owner: DatasetSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -1535,7 +1487,7 @@ classes: alias: source_glob owner: DatasetSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -1548,7 +1500,7 @@ classes: alias: source_multi_glob owner: DatasetSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true @@ -1559,11 +1511,35 @@ classes: alias: literal owner: DatasetSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource - range: DefaultLiteral + range: StandardLiteral + inlined: true + inlined_as_list: true + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: DatasetSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true inlined: true inlined_as_list: true DatasetParentFilters: @@ -1605,29 +1581,17 @@ classes: owner: DatasetParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: DatasetParent inlined: true @@ -1694,46 +1658,11 @@ classes: inlined: true inlined_as_list: true minimum_cardinality: 1 - exclude: - name: exclude - description: Exclude files from the source that match (regexes). - from_schema: cdp-ingestion-config - alias: exclude - owner: DatasetKeyPhotoEntity - domain_of: - - DefaultSource - - AnnotationSource - - AnnotationParentFilters - - DatasetSource - - DatasetParentFilters - - DatasetKeyPhotoEntity - - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - - DepositionKeyPhotoParentFilters - - FrameSource - - FrameParentFilters - - GainSource - - GainParentFilters - - KeyImageSource - - KeyImageParentFilters - - RawTiltSource - - RawTiltParentFilters - - RunSource - - RunParentFilters - - TiltSeriesSource - - TiltSeriesParentFilters - - TomogramSource - - TomogramParentFilters - - VoxelSpacingSource - - VoxelSpacingParentFilters - range: string - multivalued: true - inlined: true - inlined_as_list: true DatasetKeyPhotoSource: name: DatasetKeyPhotoSource description: A key photo source. from_schema: cdp-ingestion-config + is_a: StandardSource attributes: literal: name: literal @@ -1742,7 +1671,7 @@ classes: alias: literal owner: DatasetKeyPhotoSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource @@ -1771,6 +1700,66 @@ classes: range: DatasetKeyPhotoParentFilters inlined: true inlined_as_list: true + destination_glob: + name: destination_glob + description: A glob class for finding files in the output / destination directory. + from_schema: cdp-ingestion-config + alias: destination_glob + owner: DatasetKeyPhotoSource + domain_of: + - StandardSource + - VoxelSpacingSource + range: DestinationGlob + inlined: true + inlined_as_list: true + source_glob: + name: source_glob + description: A glob class for finding files in the source directory. + from_schema: cdp-ingestion-config + alias: source_glob + owner: DatasetKeyPhotoSource + domain_of: + - StandardSource + - VoxelSpacingSource + range: SourceGlob + inlined: true + inlined_as_list: true + source_multi_glob: + name: source_multi_glob + description: A glob class for finding files in the source directory (with + multiple globs). + from_schema: cdp-ingestion-config + alias: source_multi_glob + owner: DatasetKeyPhotoSource + domain_of: + - StandardSource + range: SourceMultiGlob + inlined: true + inlined_as_list: true + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: DatasetKeyPhotoSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true + inlined: true + inlined_as_list: true DatasetKeyPhotoParentFilters: name: DatasetKeyPhotoParentFilters description: Types of parent filters for a key photo source. @@ -1810,29 +1799,17 @@ classes: owner: DatasetKeyPhotoParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: DatasetKeyPhotoParent inlined: true @@ -1918,9 +1895,7 @@ classes: name: DepositionSource description: A deposition source. from_schema: cdp-ingestion-config - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: destination_glob: name: destination_glob @@ -1929,7 +1904,7 @@ classes: alias: destination_glob owner: DepositionSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -1941,7 +1916,7 @@ classes: alias: source_glob owner: DepositionSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -1954,10 +1929,24 @@ classes: alias: source_multi_glob owner: DepositionSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true + literal: + name: literal + description: A literal class with a value attribute. + from_schema: cdp-ingestion-config + alias: literal + owner: DepositionSource + domain_of: + - StandardSource + - DatasetKeyPhotoSource + - DepositionKeyPhotoSource + - VoxelSpacingSource + range: StandardLiteral + inlined: true + inlined_as_list: true exclude: name: exclude description: Exclude files from the source that match (regexes). @@ -1966,48 +1955,22 @@ classes: owner: DepositionSource domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: string multivalued: true inlined: true inlined_as_list: true - literal: - name: literal - description: A literal class with a value attribute. - from_schema: cdp-ingestion-config - alias: literal - owner: DepositionSource - domain_of: - - DefaultLiteralEntity - - DatasetKeyPhotoSource - - DepositionKeyPhotoSource - - VoxelSpacingSource - range: DefaultLiteral - inlined: true - inlined_as_list: true DepositionKeyPhotoEntity: name: DepositionKeyPhotoEntity description: A deposition key photo entity. @@ -2043,6 +2006,7 @@ classes: name: DepositionKeyPhotoSource description: A key photo source. from_schema: cdp-ingestion-config + is_a: StandardSource attributes: literal: name: literal @@ -2051,7 +2015,7 @@ classes: alias: literal owner: DepositionKeyPhotoSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource @@ -2080,6 +2044,42 @@ classes: range: DepositionKeyPhotoParentFilters inlined: true inlined_as_list: true + destination_glob: + name: destination_glob + description: A glob class for finding files in the output / destination directory. + from_schema: cdp-ingestion-config + alias: destination_glob + owner: DepositionKeyPhotoSource + domain_of: + - StandardSource + - VoxelSpacingSource + range: DestinationGlob + inlined: true + inlined_as_list: true + source_glob: + name: source_glob + description: A glob class for finding files in the source directory. + from_schema: cdp-ingestion-config + alias: source_glob + owner: DepositionKeyPhotoSource + domain_of: + - StandardSource + - VoxelSpacingSource + range: SourceGlob + inlined: true + inlined_as_list: true + source_multi_glob: + name: source_multi_glob + description: A glob class for finding files in the source directory (with + multiple globs). + from_schema: cdp-ingestion-config + alias: source_multi_glob + owner: DepositionKeyPhotoSource + domain_of: + - StandardSource + range: SourceMultiGlob + inlined: true + inlined_as_list: true exclude: name: exclude description: Exclude files from the source that match (regexes). @@ -2088,29 +2088,17 @@ classes: owner: DepositionKeyPhotoSource domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: string multivalued: true @@ -2155,29 +2143,17 @@ classes: owner: DepositionKeyPhotoParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: DepositionKeyPhotoParent inlined: true @@ -2248,9 +2224,7 @@ classes: name: FrameSource description: A frame source. from_schema: cdp-ingestion-config - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: name: parent_filters @@ -2274,42 +2248,6 @@ classes: range: FrameParentFilters inlined: true inlined_as_list: true - exclude: - name: exclude - description: Exclude files from the source that match (regexes). - from_schema: cdp-ingestion-config - alias: exclude - owner: FrameSource - domain_of: - - DefaultSource - - AnnotationSource - - AnnotationParentFilters - - DatasetSource - - DatasetParentFilters - - DatasetKeyPhotoEntity - - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - - DepositionKeyPhotoParentFilters - - FrameSource - - FrameParentFilters - - GainSource - - GainParentFilters - - KeyImageSource - - KeyImageParentFilters - - RawTiltSource - - RawTiltParentFilters - - RunSource - - RunParentFilters - - TiltSeriesSource - - TiltSeriesParentFilters - - TomogramSource - - TomogramParentFilters - - VoxelSpacingSource - - VoxelSpacingParentFilters - range: string - multivalued: true - inlined: true - inlined_as_list: true destination_glob: name: destination_glob description: A glob class for finding files in the output / destination directory. @@ -2317,7 +2255,7 @@ classes: alias: destination_glob owner: FrameSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -2329,7 +2267,7 @@ classes: alias: source_glob owner: FrameSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -2342,7 +2280,7 @@ classes: alias: source_multi_glob owner: FrameSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true @@ -2353,11 +2291,35 @@ classes: alias: literal owner: FrameSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource - range: DefaultLiteral + range: StandardLiteral + inlined: true + inlined_as_list: true + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: FrameSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true inlined: true inlined_as_list: true FrameParentFilters: @@ -2397,29 +2359,17 @@ classes: owner: FrameParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: FrameParent inlined: true @@ -2531,9 +2481,7 @@ classes: name: GainSource description: A gain source. from_schema: cdp-ingestion-config - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: name: parent_filters @@ -2557,42 +2505,6 @@ classes: range: GainParentFilters inlined: true inlined_as_list: true - exclude: - name: exclude - description: Exclude files from the source that match (regexes). - from_schema: cdp-ingestion-config - alias: exclude - owner: GainSource - domain_of: - - DefaultSource - - AnnotationSource - - AnnotationParentFilters - - DatasetSource - - DatasetParentFilters - - DatasetKeyPhotoEntity - - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - - DepositionKeyPhotoParentFilters - - FrameSource - - FrameParentFilters - - GainSource - - GainParentFilters - - KeyImageSource - - KeyImageParentFilters - - RawTiltSource - - RawTiltParentFilters - - RunSource - - RunParentFilters - - TiltSeriesSource - - TiltSeriesParentFilters - - TomogramSource - - TomogramParentFilters - - VoxelSpacingSource - - VoxelSpacingParentFilters - range: string - multivalued: true - inlined: true - inlined_as_list: true destination_glob: name: destination_glob description: A glob class for finding files in the output / destination directory. @@ -2600,7 +2512,7 @@ classes: alias: destination_glob owner: GainSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -2612,7 +2524,7 @@ classes: alias: source_glob owner: GainSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -2625,7 +2537,7 @@ classes: alias: source_multi_glob owner: GainSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true @@ -2636,11 +2548,35 @@ classes: alias: literal owner: GainSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource - range: DefaultLiteral + range: StandardLiteral + inlined: true + inlined_as_list: true + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: GainSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true inlined: true inlined_as_list: true GainParentFilters: @@ -2680,29 +2616,17 @@ classes: owner: GainParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: GainParent inlined: true @@ -2814,9 +2738,7 @@ classes: name: KeyImageSource description: A key image source. from_schema: cdp-ingestion-config - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: name: parent_filters @@ -2840,42 +2762,6 @@ classes: range: KeyImageParentFilters inlined: true inlined_as_list: true - exclude: - name: exclude - description: Exclude files from the source that match (regexes). - from_schema: cdp-ingestion-config - alias: exclude - owner: KeyImageSource - domain_of: - - DefaultSource - - AnnotationSource - - AnnotationParentFilters - - DatasetSource - - DatasetParentFilters - - DatasetKeyPhotoEntity - - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - - DepositionKeyPhotoParentFilters - - FrameSource - - FrameParentFilters - - GainSource - - GainParentFilters - - KeyImageSource - - KeyImageParentFilters - - RawTiltSource - - RawTiltParentFilters - - RunSource - - RunParentFilters - - TiltSeriesSource - - TiltSeriesParentFilters - - TomogramSource - - TomogramParentFilters - - VoxelSpacingSource - - VoxelSpacingParentFilters - range: string - multivalued: true - inlined: true - inlined_as_list: true destination_glob: name: destination_glob description: A glob class for finding files in the output / destination directory. @@ -2883,7 +2769,7 @@ classes: alias: destination_glob owner: KeyImageSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -2895,7 +2781,7 @@ classes: alias: source_glob owner: KeyImageSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -2908,7 +2794,7 @@ classes: alias: source_multi_glob owner: KeyImageSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true @@ -2919,11 +2805,35 @@ classes: alias: literal owner: KeyImageSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource - range: DefaultLiteral + range: StandardLiteral + inlined: true + inlined_as_list: true + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: KeyImageSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true inlined: true inlined_as_list: true KeyImageParentFilters: @@ -2965,29 +2875,17 @@ classes: owner: KeyImageParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: KeyImageParent inlined: true @@ -3128,9 +3026,7 @@ classes: name: RawTiltSource description: A raw tilt source. from_schema: cdp-ingestion-config - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: name: parent_filters @@ -3154,42 +3050,6 @@ classes: range: RawTiltParentFilters inlined: true inlined_as_list: true - exclude: - name: exclude - description: Exclude files from the source that match (regexes). - from_schema: cdp-ingestion-config - alias: exclude - owner: RawTiltSource - domain_of: - - DefaultSource - - AnnotationSource - - AnnotationParentFilters - - DatasetSource - - DatasetParentFilters - - DatasetKeyPhotoEntity - - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - - DepositionKeyPhotoParentFilters - - FrameSource - - FrameParentFilters - - GainSource - - GainParentFilters - - KeyImageSource - - KeyImageParentFilters - - RawTiltSource - - RawTiltParentFilters - - RunSource - - RunParentFilters - - TiltSeriesSource - - TiltSeriesParentFilters - - TomogramSource - - TomogramParentFilters - - VoxelSpacingSource - - VoxelSpacingParentFilters - range: string - multivalued: true - inlined: true - inlined_as_list: true destination_glob: name: destination_glob description: A glob class for finding files in the output / destination directory. @@ -3197,7 +3057,7 @@ classes: alias: destination_glob owner: RawTiltSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -3209,7 +3069,7 @@ classes: alias: source_glob owner: RawTiltSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -3222,7 +3082,7 @@ classes: alias: source_multi_glob owner: RawTiltSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true @@ -3233,11 +3093,35 @@ classes: alias: literal owner: RawTiltSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource - range: DefaultLiteral + range: StandardLiteral + inlined: true + inlined_as_list: true + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: RawTiltSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true inlined: true inlined_as_list: true RawTiltParentFilters: @@ -3279,29 +3163,17 @@ classes: owner: RawTiltParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: RawTiltParent inlined: true @@ -3413,9 +3285,7 @@ classes: name: RunSource description: A run source. from_schema: cdp-ingestion-config - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: name: parent_filters @@ -3439,42 +3309,6 @@ classes: range: RunParentFilters inlined: true inlined_as_list: true - exclude: - name: exclude - description: Exclude files from the source that match (regexes). - from_schema: cdp-ingestion-config - alias: exclude - owner: RunSource - domain_of: - - DefaultSource - - AnnotationSource - - AnnotationParentFilters - - DatasetSource - - DatasetParentFilters - - DatasetKeyPhotoEntity - - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - - DepositionKeyPhotoParentFilters - - FrameSource - - FrameParentFilters - - GainSource - - GainParentFilters - - KeyImageSource - - KeyImageParentFilters - - RawTiltSource - - RawTiltParentFilters - - RunSource - - RunParentFilters - - TiltSeriesSource - - TiltSeriesParentFilters - - TomogramSource - - TomogramParentFilters - - VoxelSpacingSource - - VoxelSpacingParentFilters - range: string - multivalued: true - inlined: true - inlined_as_list: true destination_glob: name: destination_glob description: A glob class for finding files in the output / destination directory. @@ -3482,7 +3316,7 @@ classes: alias: destination_glob owner: RunSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -3494,7 +3328,7 @@ classes: alias: source_glob owner: RunSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -3507,7 +3341,7 @@ classes: alias: source_multi_glob owner: RunSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true @@ -3518,11 +3352,35 @@ classes: alias: literal owner: RunSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource - range: DefaultLiteral + range: StandardLiteral + inlined: true + inlined_as_list: true + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: RunSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true inlined: true inlined_as_list: true RunParentFilters: @@ -3562,29 +3420,17 @@ classes: owner: RunParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: RunParent inlined: true @@ -3764,9 +3610,7 @@ classes: name: TiltSeriesSource description: A tilt series source. from_schema: cdp-ingestion-config - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: name: parent_filters @@ -3790,42 +3634,6 @@ classes: range: TiltSeriesParentFilters inlined: true inlined_as_list: true - exclude: - name: exclude - description: Exclude files from the source that match (regexes). - from_schema: cdp-ingestion-config - alias: exclude - owner: TiltSeriesSource - domain_of: - - DefaultSource - - AnnotationSource - - AnnotationParentFilters - - DatasetSource - - DatasetParentFilters - - DatasetKeyPhotoEntity - - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - - DepositionKeyPhotoParentFilters - - FrameSource - - FrameParentFilters - - GainSource - - GainParentFilters - - KeyImageSource - - KeyImageParentFilters - - RawTiltSource - - RawTiltParentFilters - - RunSource - - RunParentFilters - - TiltSeriesSource - - TiltSeriesParentFilters - - TomogramSource - - TomogramParentFilters - - VoxelSpacingSource - - VoxelSpacingParentFilters - range: string - multivalued: true - inlined: true - inlined_as_list: true destination_glob: name: destination_glob description: A glob class for finding files in the output / destination directory. @@ -3833,7 +3641,7 @@ classes: alias: destination_glob owner: TiltSeriesSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -3845,7 +3653,7 @@ classes: alias: source_glob owner: TiltSeriesSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -3858,7 +3666,7 @@ classes: alias: source_multi_glob owner: TiltSeriesSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true @@ -3869,11 +3677,35 @@ classes: alias: literal owner: TiltSeriesSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource - range: DefaultLiteral + range: StandardLiteral + inlined: true + inlined_as_list: true + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: TiltSeriesSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true inlined: true inlined_as_list: true TiltSeriesParentFilters: @@ -3915,29 +3747,17 @@ classes: owner: TiltSeriesParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: TiltSeriesParent inlined: true @@ -4064,9 +3884,7 @@ classes: name: TomogramSource description: A tomogram source. from_schema: cdp-ingestion-config - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: name: parent_filters @@ -4090,42 +3908,6 @@ classes: range: TomogramParentFilters inlined: true inlined_as_list: true - exclude: - name: exclude - description: Exclude files from the source that match (regexes). - from_schema: cdp-ingestion-config - alias: exclude - owner: TomogramSource - domain_of: - - DefaultSource - - AnnotationSource - - AnnotationParentFilters - - DatasetSource - - DatasetParentFilters - - DatasetKeyPhotoEntity - - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - - DepositionKeyPhotoParentFilters - - FrameSource - - FrameParentFilters - - GainSource - - GainParentFilters - - KeyImageSource - - KeyImageParentFilters - - RawTiltSource - - RawTiltParentFilters - - RunSource - - RunParentFilters - - TiltSeriesSource - - TiltSeriesParentFilters - - TomogramSource - - TomogramParentFilters - - VoxelSpacingSource - - VoxelSpacingParentFilters - range: string - multivalued: true - inlined: true - inlined_as_list: true destination_glob: name: destination_glob description: A glob class for finding files in the output / destination directory. @@ -4133,7 +3915,7 @@ classes: alias: destination_glob owner: TomogramSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -4145,7 +3927,7 @@ classes: alias: source_glob owner: TomogramSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -4158,7 +3940,7 @@ classes: alias: source_multi_glob owner: TomogramSource domain_of: - - DefaultSource + - StandardSource range: SourceMultiGlob inlined: true inlined_as_list: true @@ -4169,11 +3951,35 @@ classes: alias: literal owner: TomogramSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource - range: DefaultLiteral + range: StandardLiteral + inlined: true + inlined_as_list: true + exclude: + name: exclude + description: Exclude files from the source that match (regexes). + from_schema: cdp-ingestion-config + alias: exclude + owner: TomogramSource + domain_of: + - DefaultSource + - AnnotationParentFilters + - DatasetParentFilters + - DatasetKeyPhotoParentFilters + - DepositionKeyPhotoParentFilters + - FrameParentFilters + - GainParentFilters + - KeyImageParentFilters + - RawTiltParentFilters + - RunParentFilters + - TiltSeriesParentFilters + - TomogramParentFilters + - VoxelSpacingParentFilters + range: string + multivalued: true inlined: true inlined_as_list: true TomogramParentFilters: @@ -4215,29 +4021,17 @@ classes: owner: TomogramParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: TomogramParent inlined: true @@ -4365,6 +4159,7 @@ classes: name: VoxelSpacingSource description: A voxel spacing source. from_schema: cdp-ingestion-config + is_a: DefaultSource attributes: destination_glob: name: destination_glob @@ -4373,7 +4168,7 @@ classes: alias: destination_glob owner: VoxelSpacingSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: DestinationGlob inlined: true @@ -4385,7 +4180,7 @@ classes: alias: source_glob owner: VoxelSpacingSource domain_of: - - DefaultSource + - StandardSource - VoxelSpacingSource range: SourceGlob inlined: true @@ -4397,7 +4192,7 @@ classes: alias: literal owner: VoxelSpacingSource domain_of: - - DefaultLiteralEntity + - StandardSource - DatasetKeyPhotoSource - DepositionKeyPhotoSource - VoxelSpacingSource @@ -4445,29 +4240,17 @@ classes: owner: VoxelSpacingSource domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: string multivalued: true @@ -4512,29 +4295,17 @@ classes: owner: VoxelSpacingParentFilters domain_of: - DefaultSource - - AnnotationSource - AnnotationParentFilters - - DatasetSource - DatasetParentFilters - - DatasetKeyPhotoEntity - DatasetKeyPhotoParentFilters - - DepositionKeyPhotoSource - DepositionKeyPhotoParentFilters - - FrameSource - FrameParentFilters - - GainSource - GainParentFilters - - KeyImageSource - KeyImageParentFilters - - RawTiltSource - RawTiltParentFilters - - RunSource - RunParentFilters - - TiltSeriesSource - TiltSeriesParentFilters - - TomogramSource - TomogramParentFilters - - VoxelSpacingSource - VoxelSpacingParentFilters range: VoxelSpacingParent inlined: true @@ -4623,7 +4394,7 @@ classes: alias: value owner: VoxelSpacingLiteral domain_of: - - DefaultLiteral + - StandardLiteral - KeyPhotoLiteral - VoxelSpacingLiteral range: float diff --git a/schema/ingestion_config/v1.0.0/ingestion_config_models.yaml b/schema/ingestion_config/v1.0.0/ingestion_config_models.yaml index 924090213..dbf83bed3 100644 --- a/schema/ingestion_config/v1.0.0/ingestion_config_models.yaml +++ b/schema/ingestion_config/v1.0.0/ingestion_config_models.yaml @@ -150,7 +150,19 @@ classes: required: true DefaultSource: - description: A generalized source class with glob finders. + description: A default source class that all source classes inherit from. + attributes: + # Would also have parent_filters here, but sometimes parent_filters doesn't apply (e.g., Deposition) and + # for other cases the permitted entries in parent_filters are different for different source classes + # so we have individual ParentFiltersEntity instead + exclude: + description: Exclude files from the source that match (regexes). + range: string + multivalued: true + + StandardSource: + description: A generalized source class with glob finders. Inherited by a majority of source classes. + is_a: DefaultSource attributes: destination_glob: description: The glob object for the destination file. @@ -161,22 +173,11 @@ classes: source_multi_glob: description: The glob object for the source file (with multiple globs). range: SourceMultiGlob - # Would also have literal here, but literal schema varies by class, so we have DefaultLiteralEntity instead - # Would also have parent_filters here, but sometimes parent_filters doesn't apply (e.g., Dataset), - # so we have individual ParentFiltersEntity instead - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true - - DefaultLiteralEntity: - description: Used as a mixin with root-level classes that contain sources that have literals. - attributes: literal: description: A literal class with a value attribute. - range: DefaultLiteral + range: StandardLiteral - DefaultLiteral: + StandardLiteral: description: A literal class with a value attribute. attributes: value: @@ -211,6 +212,7 @@ classes: AnnotationSource: description: An annotation source. + is_a: DefaultSource attributes: InstanceSegmentation: description: The instance segmentation annotation source. @@ -230,11 +232,6 @@ classes: parent_filters: description: Filters for the parent of a source. range: AnnotationParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true - AnnotationParentFilters: description: Filters for the parent of an annotation source. @@ -266,17 +263,11 @@ classes: DatasetSource: description: A dataset source. - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: description: Permitted parent filters for a dataset source. range: DatasetParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true DatasetParentFilters: description: Types of parent filters for a dataset source. @@ -300,13 +291,10 @@ classes: multivalued: true range: DatasetKeyPhotoSource required: true - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true DatasetKeyPhotoSource: description: A key photo source. + is_a: StandardSource attributes: literal: description: A literal for a key photo. @@ -342,9 +330,7 @@ classes: DepositionSource: description: A deposition source. - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource # No ParentFiltersEntity because parent_filters doesn't apply to Deposition DepositionKeyPhotoEntity: @@ -357,6 +343,7 @@ classes: DepositionKeyPhotoSource: description: A key photo source. + is_a: StandardSource attributes: literal: description: A literal for a key photo. @@ -364,10 +351,6 @@ classes: parent_filters: description: Permitted parent filters for a key photo source. range: DepositionKeyPhotoParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true DepositionKeyPhotoParentFilters: description: Types of parent filters for a key photo source. @@ -394,17 +377,11 @@ classes: FrameSource: description: A frame source. - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: description: Permitted parent filters for a frame source. range: FrameParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true FrameParentFilters: description: Types of parent filters for a frame source. @@ -433,17 +410,11 @@ classes: GainSource: description: A gain source. - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: description: Permitted parent filters for a gain source. range: GainParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true GainParentFilters: description: Types of parent filters for a gain source. @@ -472,17 +443,11 @@ classes: KeyImageSource: description: A key image source. - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: description: Permitted parent filters for a key image source. range: KeyImageParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true KeyImageParentFilters: description: Types of parent filters for a key image source. @@ -513,17 +478,11 @@ classes: RawTiltSource: description: A raw tilt source. - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: description: Permitted parent filters for a raw tilt source. range: RawTiltParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true RawTiltParentFilters: description: Types of parent filters for a raw tilt source. @@ -552,17 +511,11 @@ classes: RunSource: description: A run source. - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: description: Permitted parent filters for a run source. range: RunParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true RunParentFilters: description: Types of parent filters for a run source. @@ -616,17 +569,11 @@ classes: TiltSeriesSource: description: A tilt series source. - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: description: Permitted parent filters for a tilt series source. range: TiltSeriesParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true TiltSeriesParentFilters: description: Types of parent filters for a tilt series source. @@ -657,17 +604,11 @@ classes: TomogramSource: description: A tomogram source. - mixins: - - DefaultSource - - DefaultLiteralEntity + is_a: StandardSource attributes: parent_filters: description: Permitted parent filters for a tomogram source. range: TomogramParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true TomogramParentFilters: description: Types of parent filters for a tomogram source. @@ -695,8 +636,9 @@ classes: range: VoxelSpacingSource required: true - # Can't use DefaultSource since it doesn't permit source_multi_glob + # Can't use StandardSource since VoxelSpacingImporter doesn't permit source_multi_glob VoxelSpacingSource: + is_a: DefaultSource description: A voxel spacing source. attributes: destination_glob: @@ -713,10 +655,6 @@ classes: parent_filters: description: Permitted parent filters for a voxel spacing source. range: VoxelSpacingParentFilters - exclude: - description: Exclude files from the source that match (regexes). - range: string - multivalued: true VoxelSpacingParentFilters: description: Types of parent filters for a voxel spacing source.