Index

A

Abstract (in module ts_ids_core.annotations) AbstractAnnotation (class in ts_ids_core.annotations) acquired (RawSampleTime attribute) (RawTime attribute), [1] (SampleTime attribute) (Time attribute)

algorithm (Checksum attribute), [1] all_abstract_fields_implemented() (IdsElement class method), [1] assay (ProjectAttributes attribute), [1]

B

barcode (Batch attribute), [1] (Holder attribute), [1] (Sample attribute), [1] batch (Sample attribute), [1] body (MappingTable attribute)

body_to_dataframe() (MappingTable method) BOOLEAN (ValueDataType attribute), [1] boolean_value (Parameter attribute), [1] (Property attribute), [1] bucket (Pointer attribute), [1]

C

canonical_id (Concept attribute), [1] canonical_term (Concept attribute), [1] checksum (RelatedFile attribute), [1] column (Location attribute), [1] column_name (Column attribute) compound (Sample attribute), [1] consistent_number_of_dimensions() (DataCube method), [1] construct_body_from_dataframe() (in module ts_ids_core.mapping_table.mapping_table) construct_header_from_columns() (in module ts_ids_core.mapping_table.mapping_table)

construct_mapping_table_body_from_paths() (in module ts_ids_core.mapping_table.mapping_table) convert_programmatic_ids_to_jsonschema() (in module ts_ids_core.scripts.programmatic_ids_to_jsonschema) create_mapping_table_json() (in module ts_ids_core.mapping_table.sync) create_readme() (in module ts_ids_core.mapping_table.sync) create_record_from_existing_record() (in module ts_ids_core.mapping_table.mapping_table) created (RawSampleTime attribute) (RawTime attribute), [1] (SampleTime attribute) (Time attribute)

D

DataCubeDict (class in ts_ids_core.schema) dataframe_to_markdown_lines() (in module ts_ids_core.mapping_table.convert) DecimalNumber (in module ts_ids_core.annotations) DecimalString (in module ts_ids_core.annotations) default_header() (in module ts_ids_core.mapping_table.mapping_table) default_schema() (IdsSchemaGenerator method) deindexed_path (SchemaPath property) description (Assay attribute), [1] (Experiment attribute), [1] (Project attribute), [1]

dict() (IdsElement method), [1] dimensions (DataCube attribute), [1] (DataCubeDict attribute) (DataCubeMetadata attribute), [1] duration (RawSampleTime attribute) (RawTime attribute), [1] (SampleTime attribute) (Time attribute)

E

enum_schema() (IdsSchemaGenerator method) experiment (ProjectAttributes attribute), [1]

export_schema_cmd() (in module ts_ids_core.scripts.programmatic_ids_to_jsonschema) extra_field_validator() (Record method) extra_keys (MappingTable property)

F

file_id (DataCubeMetadata attribute), [1] fileId (Pointer attribute), [1] fileKey (Pointer attribute), [1] firmware (System.Firmware attribute), [1] fixed_length() (in module ts_ids_core.annotations)

ForeignKey (class in ts_ids_core.annotations) format_table_lines() (in module ts_ids_core.mapping_table.convert) from_dict() (Record class method) from_str() (Index static method) (PathPart static method) (SchemaPath static method)

G

generate() (IdsSchemaGenerator method) get_deindexed_path_to_records_map() (MappingTable method) get_docs_url() (in module ts_ids_core.scripts.docs) get_field_paths() (in module ts_ids_core.mapping_table.locate) get_header_line_index() (in module ts_ids_core.mapping_table.locate)

get_line_index_with_pattern() (in module ts_ids_core.mapping_table.locate) get_module_classes() (in module ts_ids_core.scripts.programmatic_ids_to_jsonschema) get_table_indexes() (in module ts_ids_core.mapping_table.locate) get_table_lines() (in module ts_ids_core.mapping_table.locate) GREATER_THAN (ModifierType attribute), [1] GREATER_THAN_OR_EQUAL (ModifierType attribute), [1]

H

handle_ref_overrides() (IdsSchemaGenerator method)

header (MappingTable attribute) holder (Location attribute), [1]

I

id (Assay attribute), [1] (Experiment attribute), [1] (Project attribute), [1] id_ (Batch attribute), [1] (Compound attribute), [1] (Run attribute), [1] (Sample attribute), [1] (Set attribute), [1] (System.Id attribute), [1] (User attribute), [1] ids_field_arg (ForeignKey attribute) ids_model_init() (in module ts_ids_core.base.meta) ids_namespace (IdsSchema attribute), [1] ids_type (IdsSchema attribute), [1] IDS_UNDEFINED (in module ts_ids_core.base.ids_undefined_type) ids_version (IdsSchema attribute), [1] IdsField() (in module ts_ids_core.base.ids_field) (in module ts_ids_core.schema)

IdsSchemaGenerator (class in ts_ids_core.base.ids_element) IdsUndefinedType (class in ts_ids_core.base.ids_undefined_type) import_schema_cmd() (in module ts_ids_core.scripts.jsonschema_to_programmatic_ids) Index (class in ts_ids_core.mapping_table.schema_path_models) index (DataCubeMetadata attribute), [1] (Location attribute), [1] indices (PathPart attribute) IntStr (in module ts_ids_core.annotations) InvalidArrayShape InvalidField InvalidForeignKeyField InvalidForeignKeySchema InvalidNonMandatoryField InvalidPrimaryKeyField InvalidSchemaMetadata InvalidTypeError is_valid_version_string() (IdsSchema class method), [1]

J

JSON_SCHEMA_TYPE (IdsUndefinedType attribute)

json_string_to_dict() (in module ts_ids_core.mapping_table.convert)

K

key (Column attribute) (Parameter attribute), [1]

key_to_column_map (MappingTable property) keys (MappingTable property)

L

labels (Sample attribute), [1] last_updated (RawSampleTime attribute) (RawTime attribute), [1] (SampleTime attribute) (Time attribute) legacy_import() (in module ts_ids_core.scripts.cli) LESS_THAN (ModifierType attribute), [1]

LESS_THAN_OR_EQUAL (ModifierType attribute), [1] literal_schema() (IdsSchemaGenerator method) location (Sample attribute), [1] logs (Run attribute), [1] lookup (RawSampleTime attribute), [1] (RawTime attribute), [1] (SampleTime attribute) (Time attribute)

M

main() (in module ts_ids_core.scripts.jsonschema_to_programmatic_ids) mapping_table_to_markdown_lines() (in module ts_ids_core.mapping_table.convert) markdown_table_lines_to_dataframe() (in module ts_ids_core.mapping_table.convert) measures (DataCube attribute), [1] (DataCubeDict attribute) (DataCubeMetadata attribute), [1] MissingLineError model (System attribute), [1] model_dump() (IdsElement method), [1] model_dump_json() (IdsElement method), [1] model_json_schema() (IdsElement class method), [1] modified (RawSampleTime attribute) (RawTime attribute), [1] (SampleTime attribute) (Time attribute) modifier (Modifier attribute), [1] ModifierType (class in ts_ids_core.schema) (class in ts_ids_core.schema.modifier) module ts_ids_core ts_ids_core.annotations ts_ids_core.base ts_ids_core.base.ids_element ts_ids_core.base.ids_field ts_ids_core.base.ids_undefined_type ts_ids_core.base.meta ts_ids_core.errors ts_ids_core.mapping_table ts_ids_core.mapping_table.constants ts_ids_core.mapping_table.convert ts_ids_core.mapping_table.locate ts_ids_core.mapping_table.mapping_table ts_ids_core.mapping_table.schema_path_models ts_ids_core.mapping_table.sync ts_ids_core.schema ts_ids_core.schema.datacube ts_ids_core.schema.dimension ts_ids_core.schema.ids_schema ts_ids_core.schema.measure ts_ids_core.schema.modifier ts_ids_core.schema.parameter ts_ids_core.schema.project ts_ids_core.schema.related_file ts_ids_core.schema.run ts_ids_core.schema.sample ts_ids_core.schema.semantic ts_ids_core.schema.semantic.concept ts_ids_core.schema.system ts_ids_core.schema.time_ ts_ids_core.schema.user ts_ids_core.schema.value_unit ts_ids_core.scripts ts_ids_core.scripts.cli ts_ids_core.scripts.docs ts_ids_core.scripts.jsonschema_to_programmatic_ids ts_ids_core.scripts.mapping_table ts_ids_core.scripts.programmatic_ids_to_jsonschema ts_ids_core.scripts.schema_diff

MultipleTypesError

N

name (Assay attribute), [1] (Batch attribute), [1] (Compound attribute), [1] (DataCube attribute), [1] (DataCubeDict attribute) (DataCubeMetadata attribute), [1] (Dimension attribute) (DimensionMetadata attribute), [1] (Experiment attribute), [1] (Firmware attribute), [1] (Holder attribute), [1] (Label attribute), [1] (Measure attribute) (MeasureMetadata attribute), [1] (PathPart attribute) (Pattern attribute) (Project attribute), [1] (Property attribute), [1] (RelatedFile attribute), [1] (Run attribute), [1] (RunStatus attribute), [1] (Sample attribute), [1] (Set attribute), [1] (Software attribute), [1] (Source attribute), [1] (System.Name attribute), [1] (User attribute), [1]

NULL (ModifierType attribute), [1] Nullable (in module ts_ids_core.annotations) nullable_schema() (IdsSchemaGenerator method) NullableBoolean (in module ts_ids_core.annotations) NullableInt (in module ts_ids_core.annotations) NullableNumber (in module ts_ids_core.annotations) NullableReferenceError NullableString (in module ts_ids_core.annotations) num_dimensions (Measure attribute), [1] NUMBER (ValueDataType attribute), [1] numerical_value (Parameter attribute), [1] (Property attribute), [1] numerical_value_unit (Parameter attribute), [1] (Property attribute), [1]

P

parts (SchemaPath attribute) path (Record attribute) (RelatedFile attribute), [1] path_is_first_column() (MappingTable method) PathPart (class in ts_ids_core.mapping_table.schema_path_models) Pattern (class in ts_ids_core.mapping_table.locate) pk_metadata_field (PrimaryKey attribute)

pk_reference_field (ForeignKey attribute) pointer (RelatedFile attribute), [1] position (Location attribute), [1] PrimaryKey (class in ts_ids_core.annotations) project (ProjectAttributes attribute), [1] properties (Sample attribute), [1] PYDANTIC_UNDEFINED (in module ts_ids_core.base.ids_undefined_type)

R

raw (SampleTime attribute), [1] (Time attribute), [1] raw_value (RawValueUnit attribute), [1] readme_lines_to_mapping_table() (in module ts_ids_core.mapping_table.convert) readme_to_mapping_table() (in module ts_ids_core.mapping_table.convert) ref_template (IdsSchemaGenerator attribute)

regex (Pattern attribute) replace_mapping_table_in_readme_lines() (in module ts_ids_core.mapping_table.sync) Required (in module ts_ids_core.annotations) RequiredAnnotation (class in ts_ids_core.annotations) resolve_length_annotation_metadata() (in module ts_ids_core.annotations) row (Location attribute), [1]

S

scale (Dimension attribute), [1] schema() (IdsElement class method), [1] schema_dialect (IdsSchemaGenerator attribute) schema_extra_metadata (IdsElement attribute), [1] (IdsSchema attribute), [1] schema_json() (IdsElement class method), [1] SchemaExtraMetadataType (in module ts_ids_core.base.ids_element) SchemaPath (class in ts_ids_core.mapping_table.schema_path_models) SchemaValidationError serial_number (System.SerialNumber attribute), [1] set_ (Sample attribute), [1] size (RelatedFile attribute), [1] software (System.Software attribute), [1] sort_records() (in module ts_ids_core.mapping_table.mapping_table)

source (Label attribute), [1] (Property attribute), [1] start (RawSampleTime attribute) (RawTime attribute), [1] (SampleTime attribute) (Time attribute) stop (RawSampleTime attribute) (RawTime attribute), [1] (SampleTime attribute) (Time attribute) STRING (ValueDataType attribute), [1] string_value (Parameter attribute), [1] (Property attribute), [1] sync_mapping_table_with_schema() (in module ts_ids_core.mapping_table.mapping_table)

T

TableError time (Label attribute), [1] (Property attribute), [1] to_snakecase() (in module ts_ids_core.mapping_table.mapping_table) ts_ids_core module ts_ids_core.annotations module ts_ids_core.base module ts_ids_core.base.ids_element module ts_ids_core.base.ids_field module ts_ids_core.base.ids_undefined_type module ts_ids_core.base.meta module ts_ids_core.errors module ts_ids_core.mapping_table module ts_ids_core.mapping_table.constants module ts_ids_core.mapping_table.convert module ts_ids_core.mapping_table.locate module ts_ids_core.mapping_table.mapping_table module ts_ids_core.mapping_table.schema_path_models module ts_ids_core.mapping_table.sync module ts_ids_core.schema module ts_ids_core.schema.datacube module ts_ids_core.schema.dimension module ts_ids_core.schema.ids_schema module ts_ids_core.schema.measure module

ts_ids_core.schema.modifier module ts_ids_core.schema.parameter module ts_ids_core.schema.project module ts_ids_core.schema.related_file module ts_ids_core.schema.run module ts_ids_core.schema.sample module ts_ids_core.schema.semantic module ts_ids_core.schema.semantic.concept module ts_ids_core.schema.system module ts_ids_core.schema.time_ module ts_ids_core.schema.user module ts_ids_core.schema.value_unit module ts_ids_core.scripts module ts_ids_core.scripts.cli module ts_ids_core.scripts.docs module ts_ids_core.scripts.jsonschema_to_programmatic_ids module ts_ids_core.scripts.mapping_table module ts_ids_core.scripts.programmatic_ids_to_jsonschema module ts_ids_core.scripts.schema_diff module type_ (Holder attribute), [1] (Pointer attribute), [1] (Source attribute), [1] (System attribute), [1] (User attribute), [1]

U

UnexpectedJsonError UnimplementedAbstractField union_schema() (IdsSchemaGenerator method) unit (Dimension attribute) (DimensionMetadata attribute), [1] (Measure attribute) (MeasureMetadata attribute), [1] (RawValueUnit attribute) (ValueUnit attribute), [1]

user_facing_display (Concept attribute), [1] UUIDForeignKey (in module ts_ids_core.annotations) UUIDPrimaryKey (in module ts_ids_core.annotations) UUIDStr (in module ts_ids_core.annotations) UUIDValidator (in module ts_ids_core.annotations)

V

validate_code_gen_import() (in module ts_ids_core.scripts.cli) validate_uuid() (in module ts_ids_core.annotations) value (Checksum attribute), [1] (Index attribute) (Label attribute), [1] (Measure attribute), [1] (Modifier attribute), [1] (Parameter attribute), [1] (Property attribute), [1] (RawValueUnit attribute) (RunStatus attribute), [1] (ValueUnit attribute), [1]

value_data_type (Parameter attribute), [1] (Property attribute), [1] ValueDataType (class in ts_ids_core.schema) (class in ts_ids_core.schema.sample) vendor (System attribute), [1] version (Firmware attribute), [1] (Pointer attribute), [1] (Software attribute), [1] visible (Record attribute)

W

WrongConstantError