fairspec-metadata 0.0.0.dev0__py3-none-any.whl

fairspec_metadata/__init__.py

@@ -0,0 +1,504 @@
+from .actions.column.create import create_column_from_property
+from .actions.column.property import (
+    get_base_property_type,
+    get_column_properties,
+    get_is_nullable_property_type,
+)
+from .actions.data_schema.assert_ import assert_data_schema
+from .actions.data_schema.load import load_data_schema
+from .actions.data_schema.resolve import resolve_data_schema
+from .actions.data_schema.save import save_data_schema
+from .actions.data_schema.validate import (
+    DataSchemaValidationResult,
+    validate_data_schema,
+)
+from .actions.dataset.assert_ import assert_dataset
+from .actions.dataset.denormalize import denormalize_dataset
+from .actions.dataset.load import load_dataset_descriptor
+from .actions.dataset.normalize import normalize_dataset
+from .actions.dataset.save import save_dataset_descriptor
+from .actions.dataset.validate import (
+    DatasetValidationResult,
+    validate_dataset_descriptor,
+)
+from .actions.descriptor.copy import copy_descriptor
+from .actions.descriptor.general import get_is_descriptor
+from .actions.descriptor.load import load_descriptor
+from .actions.descriptor.parse import parse_descriptor
+from .actions.descriptor.save import save_descriptor
+from .actions.descriptor.stringify import stringify_descriptor
+from .actions.descriptor.validate import validate_descriptor
+from .actions.file_dialect.assert_ import assert_file_dialect
+from .actions.file_dialect.infer import infer_file_dialect_format
+from .actions.file_dialect.load import load_file_dialect
+from .actions.file_dialect.resolve import resolve_file_dialect
+from .actions.file_dialect.save import save_file_dialect
+from .actions.file_dialect.support import get_supported_file_dialect
+from .actions.file_dialect.validate import (
+    FileDialectValidationResult,
+    validate_file_dialect,
+)
+from .actions.json.inspect import inspect_json
+from .actions.json_schema.assert_ import assert_json_schema
+from .actions.json_schema.inspect import inspect_json_schema
+from .actions.json_schema.load import load_json_schema
+from .actions.json_schema.resolve import resolve_json_schema
+from .actions.json_schema.save import save_json_schema
+from .actions.path.basepath import get_basepath, resolve_basepath
+from .actions.path.denormalize import denormalize_path
+from .actions.path.general import (
+    get_file_basename,
+    get_file_extension,
+    get_file_name,
+    get_file_name_slug,
+    get_file_protocol,
+    get_is_remote_path,
+)
+from .actions.path.normalize import normalize_path
+from .actions.profile.assert_ import assert_profile
+from .actions.profile.load import load_profile
+from .actions.profile.registry import profile_registry
+from .actions.report.create import create_report
+from .actions.resource.data import (
+    get_data_first_path,
+    get_data_path,
+    get_data_paths,
+    get_data_records,
+    get_data_value,
+)
+from .actions.resource.denormalize import denormalize_resource
+from .actions.resource.general import get_is_remote_resource
+from .actions.resource.infer import infer_resource_name
+from .actions.resource.normalize import normalize_resource
+from .actions.table_schema.assert_ import assert_table_schema
+from .actions.table_schema.column import get_columns
+from .actions.table_schema.load import load_table_schema
+from .actions.table_schema.resolve import resolve_table_schema
+from .actions.table_schema.save import save_table_schema
+from .actions.table_schema.validate import (
+    TableSchemaValidationResult,
+    validate_table_schema,
+)
+from .models.base import FairspecModel
+from .models.catalog import Catalog, CatalogDataset
+from .models.datacite.alternate_identifier import (
+    AlternateIdentifier,
+    AlternateIdentifiers,
+)
+from .models.datacite.common import (
+    ContributorType,
+    ContentTypeGeneral,
+    CreatorNameType,
+    DateType,
+    DescriptionType,
+    FunderIdentifierType,
+    Latitude,
+    Longitude,
+    NumberType,
+    RelatedIdentifierType,
+    RelationType,
+    TitleType,
+)
+from .models.datacite.content_type import ContentTypes
+from .models.datacite.contributor import Contributor, Contributors
+from .models.datacite.creator import (
+    Creator,
+    CreatorAffiliation,
+    CreatorNameIdentifier,
+    Creators,
+)
+from .models.datacite.date import DataciteDate, DateValue, Dates
+from .models.datacite.description import DataciteDescription, Descriptions
+from .models.datacite.formats import Formats
+from .models.datacite.funding_reference import FundingReference, FundingReferences
+from .models.datacite.geo_location import (
+    GeoLocation,
+    GeoLocationBox,
+    GeoLocationPoint,
+    GeoLocationPolygonItem,
+    GeoLocations,
+)
+from .models.datacite.identifier import Doi, DoiPrefix, DoiSuffix
+from .models.datacite.language import Language
+from .models.datacite.publication_year import PublicationYear
+from .models.datacite.publisher import Publisher
+from .models.datacite.related_identifier import (
+    RelatedIdentifier,
+    RelatedIdentifiers,
+    RelatedObject,
+)
+from .models.datacite.related_item import (
+    RelatedItem,
+    RelatedItemIdentifier,
+    RelatedItems,
+)
+from .models.datacite.rights import Rights, RightsList
+from .models.datacite.size import Sizes
+from .models.datacite.subject import Subject, Subjects
+from .models.datacite.title import Title, Titles
+from .models.datacite.version import Version
+from .models.column.array import ArrayColumn, ArrayColumnProperty
+from .models.column.base import BaseColumn, BaseColumnProperty, BasePropertyType
+from .models.column.base64 import Base64Column, Base64ColumnProperty
+from .models.column.boolean import BooleanColumn, BooleanColumnProperty
+from .models.column.categorical import (
+    CategoricalColumn,
+    IntegerCategoricalColumnProperty,
+    IntegerCategoryItem,
+    StringCategoricalColumnProperty,
+    StringCategoryItem,
+)
+from .models.column.column import Column, ColumnProperty, ColumnType
+from .models.column.date import DateColumn, DateColumnProperty
+from .models.column.date_time import DateTimeColumn, DateTimeColumnProperty
+from .models.column.decimal import DecimalColumn, DecimalColumnProperty
+from .models.column.duration import DurationColumn, DurationColumnProperty
+from .models.column.email import EmailColumn, EmailColumnProperty
+from .models.column.geojson import GeojsonColumn, GeojsonColumnProperty
+from .models.column.hex import HexColumn, HexColumnProperty
+from .models.column.integer import IntegerColumn, IntegerColumnProperty
+from .models.column.list import ListColumn, ListColumnProperty
+from .models.column.number import NumberColumn, NumberColumnProperty
+from .models.column.object import ObjectColumn, ObjectColumnProperty
+from .models.column.string import StringColumn, StringColumnProperty
+from .models.column.time import TimeColumn, TimeColumnProperty
+from .models.column.topojson import TopojsonColumn, TopojsonColumnProperty
+from .models.column.unknown import UnknownColumn, UnknownColumnProperty
+from .models.column.url import UrlColumn, UrlColumnProperty
+from .models.column.wkb import WkbColumn, WkbColumnProperty
+from .models.column.wkt import WktColumn, WktColumnProperty
+from .models.data import Data, ResourceData, ResourceDataPath, ResourceDataValue
+from .models.data_schema import DataSchema, RenderDataSchemaOptions
+from .models.datacite.datacite import Datacite
+from .models.dataset import (
+    ConvertDatasetFromOptions,
+    ConvertDatasetToOptions,
+    Dataset,
+    RenderDatasetOptions,
+)
+from .models.descriptor import Descriptor
+from .models.error.base import BaseError
+from .models.error.cell import (
+    CellConstError,
+    CellEnumError,
+    CellError,
+    CellExclusiveMaximumError,
+    CellExclusiveMinimumError,
+    CellJsonError,
+    CellMaximumError,
+    CellMaxItemsError,
+    CellMaxLengthError,
+    CellMinimumError,
+    CellMinItemsError,
+    CellMinLengthError,
+    CellMissingError,
+    CellMultipleOfError,
+    CellPatternError,
+    CellTypeError,
+    CellUniqueError,
+)
+from .models.error.column import ColumnError, ColumnMissingError, ColumnTypeError
+from .models.error.data import DataError
+from .models.error.error import FairspecError
+from .models.error.file import FileError, IntegrityError, TextualError
+from .models.error.foreign_key import ForeignKeyError
+from .models.error.metadata import MetadataError
+from .models.error.resource import (
+    ResourceError,
+    ResourceMissingError,
+    ResourceTypeError,
+)
+from .models.error.row import RowError, RowPrimaryKeyError, RowUniqueKeyError
+from .models.error.table import TableError
+from .models.exception import FairspecException
+from .models.file_dialect.common import RowType
+from .models.file_dialect.arrow import ArrowFileDialect
+from .models.file_dialect.csv import CsvFileDialect
+from .models.file_dialect.file_dialect import FileDialect
+from .models.file_dialect.json import JsonFileDialect
+from .models.file_dialect.jsonl import JsonlFileDialect
+from .models.file_dialect.ods import OdsFileDialect
+from .models.file_dialect.parquet import ParquetFileDialect
+from .models.file_dialect.sqlite import SqliteFileDialect
+from .models.file_dialect.tsv import TsvFileDialect
+from .models.file_dialect.unknown import UnknownFileDialect
+from .models.file_dialect.xlsx import XlsxFileDialect
+from .models.foreign_key import ForeignKey, ForeignKeyReference
+from .models.integrity import Integrity, IntegrityType
+from .models.json_schema import JsonSchema
+from .models.path import ExternalPath, InternalPath, Path
+from .models.profile import Profile, ProfileRegistry, ProfileType
+from .models.report import Report
+from .models.resource import Resource
+from .models.table_schema import (
+    ConvertTableSchemaFromOptions,
+    ConvertTableSchemaToOptions,
+    RenderTableSchemaOptions,
+    TableSchema,
+    TableSchemaMissingValueItem,
+)
+from .models.unique_key import UniqueKey
+from .plugin import MetadataPlugin
+from .settings import FAIRSPEC_VERSION
+
+__all__ = [
+    "ArrowFileDialect",
+    "assert_data_schema",
+    "assert_dataset",
+    "assert_file_dialect",
+    "assert_json_schema",
+    "assert_profile",
+    "assert_table_schema",
+    "copy_descriptor",
+    "create_column_from_property",
+    "create_report",
+    "DataSchemaValidationResult",
+    "DatasetValidationResult",
+    "denormalize_dataset",
+    "denormalize_path",
+    "denormalize_resource",
+    "FileDialectValidationResult",
+    "get_base_property_type",
+    "get_basepath",
+    "get_column_properties",
+    "get_columns",
+    "get_data_first_path",
+    "get_data_path",
+    "get_data_paths",
+    "get_data_records",
+    "get_data_value",
+    "get_file_basename",
+    "get_file_extension",
+    "get_file_name",
+    "get_file_name_slug",
+    "get_file_protocol",
+    "get_is_descriptor",
+    "get_is_nullable_property_type",
+    "get_is_remote_path",
+    "get_is_remote_resource",
+    "get_supported_file_dialect",
+    "infer_file_dialect_format",
+    "infer_resource_name",
+    "inspect_json",
+    "inspect_json_schema",
+    "load_data_schema",
+    "load_dataset_descriptor",
+    "load_descriptor",
+    "load_file_dialect",
+    "load_json_schema",
+    "load_profile",
+    "load_table_schema",
+    "normalize_dataset",
+    "normalize_path",
+    "normalize_resource",
+    "parse_descriptor",
+    "profile_registry",
+    "resolve_basepath",
+    "resolve_data_schema",
+    "resolve_file_dialect",
+    "resolve_json_schema",
+    "resolve_table_schema",
+    "save_data_schema",
+    "save_dataset_descriptor",
+    "save_descriptor",
+    "save_file_dialect",
+    "save_json_schema",
+    "save_table_schema",
+    "stringify_descriptor",
+    "TableSchemaValidationResult",
+    "validate_data_schema",
+    "validate_dataset_descriptor",
+    "validate_descriptor",
+    "validate_file_dialect",
+    "validate_table_schema",
+    "AlternateIdentifier",
+    "AlternateIdentifiers",
+    "ArrayColumn",
+    "ArrayColumnProperty",
+    "Base64Column",
+    "Base64ColumnProperty",
+    "BaseColumn",
+    "BaseColumnProperty",
+    "BaseError",
+    "BasePropertyType",
+    "BooleanColumn",
+    "BooleanColumnProperty",
+    "Catalog",
+    "CatalogDataset",
+    "CategoricalColumn",
+    "CellConstError",
+    "CellEnumError",
+    "CellError",
+    "CellExclusiveMaximumError",
+    "CellExclusiveMinimumError",
+    "CellJsonError",
+    "CellMaxItemsError",
+    "CellMaxLengthError",
+    "CellMaximumError",
+    "CellMinItemsError",
+    "CellMinLengthError",
+    "CellMinimumError",
+    "CellMissingError",
+    "CellMultipleOfError",
+    "CellPatternError",
+    "CellTypeError",
+    "CellUniqueError",
+    "Column",
+    "ColumnError",
+    "ContentTypeGeneral",
+    "ContentTypes",
+    "Contributor",
+    "Contributors",
+    "ContributorType",
+    "ConvertDatasetFromOptions",
+    "ConvertDatasetToOptions",
+    "ConvertTableSchemaFromOptions",
+    "ConvertTableSchemaToOptions",
+    "ColumnMissingError",
+    "ColumnProperty",
+    "ColumnType",
+    "ColumnTypeError",
+    "Creator",
+    "CreatorAffiliation",
+    "CreatorNameIdentifier",
+    "CreatorNameType",
+    "Creators",
+    "CsvFileDialect",
+    "Data",
+    "DataError",
+    "DataSchema",
+    "Datacite",
+    "DataciteDate",
+    "DataciteDescription",
+    "Dataset",
+    "DateColumn",
+    "DateColumnProperty",
+    "DateTimeColumn",
+    "DateTimeColumnProperty",
+    "Dates",
+    "DateType",
+    "DateValue",
+    "DecimalColumn",
+    "DecimalColumnProperty",
+    "Descriptions",
+    "DescriptionType",
+    "Descriptor",
+    "Doi",
+    "DoiPrefix",
+    "DoiSuffix",
+    "DurationColumn",
+    "DurationColumnProperty",
+    "EmailColumn",
+    "EmailColumnProperty",
+    "ExternalPath",
+    "FAIRSPEC_VERSION",
+    "FairspecError",
+    "FairspecModel",
+    "FairspecException",
+    "FileDialect",
+    "FileError",
+    "ForeignKey",
+    "ForeignKeyError",
+    "ForeignKeyReference",
+    "Formats",
+    "FunderIdentifierType",
+    "FundingReference",
+    "FundingReferences",
+    "GeoLocation",
+    "GeoLocationBox",
+    "GeoLocationPoint",
+    "GeoLocationPolygonItem",
+    "GeoLocations",
+    "GeojsonColumn",
+    "GeojsonColumnProperty",
+    "HexColumn",
+    "HexColumnProperty",
+    "Integrity",
+    "IntegerCategoricalColumnProperty",
+    "IntegerCategoryItem",
+    "IntegerColumn",
+    "IntegerColumnProperty",
+    "IntegrityError",
+    "IntegrityType",
+    "InternalPath",
+    "JsonFileDialect",
+    "JsonSchema",
+    "JsonlFileDialect",
+    "Language",
+    "Latitude",
+    "ListColumn",
+    "ListColumnProperty",
+    "Longitude",
+    "MetadataError",
+    "MetadataPlugin",
+    "NumberColumn",
+    "NumberColumnProperty",
+    "NumberType",
+    "ObjectColumn",
+    "ObjectColumnProperty",
+    "OdsFileDialect",
+    "ParquetFileDialect",
+    "Path",
+    "Profile",
+    "ProfileRegistry",
+    "ProfileType",
+    "PublicationYear",
+    "Publisher",
+    "RelatedIdentifier",
+    "RelatedIdentifierType",
+    "RelatedIdentifiers",
+    "RelatedItem",
+    "RelatedItemIdentifier",
+    "RelatedItems",
+    "RelatedObject",
+    "RelationType",
+    "RenderDataSchemaOptions",
+    "RenderDatasetOptions",
+    "RenderTableSchemaOptions",
+    "Report",
+    "Resource",
+    "ResourceData",
+    "ResourceDataPath",
+    "ResourceDataValue",
+    "ResourceError",
+    "ResourceMissingError",
+    "ResourceTypeError",
+    "Rights",
+    "RightsList",
+    "RowError",
+    "RowPrimaryKeyError",
+    "RowType",
+    "RowUniqueKeyError",
+    "Sizes",
+    "SqliteFileDialect",
+    "StringCategoricalColumnProperty",
+    "StringCategoryItem",
+    "StringColumn",
+    "StringColumnProperty",
+    "Subject",
+    "Subjects",
+    "TableError",
+    "TableSchema",
+    "TableSchemaMissingValueItem",
+    "TextualError",
+    "TimeColumn",
+    "TimeColumnProperty",
+    "Title",
+    "Titles",
+    "TitleType",
+    "TopojsonColumn",
+    "TopojsonColumnProperty",
+    "TsvFileDialect",
+    "UniqueKey",
+    "UnknownColumn",
+    "UnknownColumnProperty",
+    "UnknownFileDialect",
+    "UrlColumn",
+    "UrlColumnProperty",
+    "Version",
+    "WkbColumn",
+    "WkbColumnProperty",
+    "WktColumn",
+    "WktColumnProperty",
+    "XlsxFileDialect",
+]

fairspec_metadata/actions/column/create.py

@@ -0,0 +1,175 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, cast
+
+from fairspec_metadata.models.column.array import ArrayColumn, ArrayColumnProperty
+from fairspec_metadata.models.column.base import BaseColumn, BaseColumnProperty
+from fairspec_metadata.models.column.base64 import Base64Column, Base64ColumnProperty
+from fairspec_metadata.models.column.boolean import (
+    BooleanColumn,
+    BooleanColumnProperty,
+)
+from fairspec_metadata.models.column.categorical import (
+    CategoricalColumn,
+    IntegerCategoricalColumnProperty,
+    StringCategoricalColumnProperty,
+)
+from fairspec_metadata.models.column.column import ColumnType
+from fairspec_metadata.models.column.date import DateColumn, DateColumnProperty
+from fairspec_metadata.models.column.date_time import (
+    DateTimeColumn,
+    DateTimeColumnProperty,
+)
+from fairspec_metadata.models.column.decimal import DecimalColumn, DecimalColumnProperty
+from fairspec_metadata.models.column.duration import (
+    DurationColumn,
+    DurationColumnProperty,
+)
+from fairspec_metadata.models.column.email import EmailColumn, EmailColumnProperty
+from fairspec_metadata.models.column.geojson import GeojsonColumn, GeojsonColumnProperty
+from fairspec_metadata.models.column.hex import HexColumn, HexColumnProperty
+from fairspec_metadata.models.column.integer import IntegerColumn, IntegerColumnProperty
+from fairspec_metadata.models.column.list import ListColumn, ListColumnProperty
+from fairspec_metadata.models.column.number import NumberColumn, NumberColumnProperty
+from fairspec_metadata.models.column.object import ObjectColumn, ObjectColumnProperty
+from fairspec_metadata.models.column.string import StringColumn, StringColumnProperty
+from fairspec_metadata.models.column.time import TimeColumn, TimeColumnProperty
+from fairspec_metadata.models.column.topojson import (
+    TopojsonColumn,
+    TopojsonColumnProperty,
+)
+from fairspec_metadata.models.column.unknown import UnknownColumn, UnknownColumnProperty
+from fairspec_metadata.models.column.url import UrlColumn, UrlColumnProperty
+from fairspec_metadata.models.column.wkb import WkbColumn, WkbColumnProperty
+from fairspec_metadata.models.column.wkt import WktColumn, WktColumnProperty
+
+from .property import get_base_property_type, get_is_nullable_property_type
+
+if TYPE_CHECKING:
+    from fairspec_metadata.models.column.column import Column
+    from fairspec_metadata.models.descriptor import Descriptor
+
+_COLUMN_CLASS_MAP: dict[
+    ColumnType, tuple[type[BaseColumn], type[BaseColumnProperty]]
+] = {
+    ColumnType.array: (ArrayColumn, ArrayColumnProperty),
+    ColumnType.base64: (Base64Column, Base64ColumnProperty),
+    ColumnType.boolean: (BooleanColumn, BooleanColumnProperty),
+    ColumnType.date: (DateColumn, DateColumnProperty),
+    ColumnType.date_time: (DateTimeColumn, DateTimeColumnProperty),
+    ColumnType.decimal: (DecimalColumn, DecimalColumnProperty),
+    ColumnType.duration: (DurationColumn, DurationColumnProperty),
+    ColumnType.email: (EmailColumn, EmailColumnProperty),
+    ColumnType.geojson: (GeojsonColumn, GeojsonColumnProperty),
+    ColumnType.hex: (HexColumn, HexColumnProperty),
+    ColumnType.integer: (IntegerColumn, IntegerColumnProperty),
+    ColumnType.list: (ListColumn, ListColumnProperty),
+    ColumnType.number: (NumberColumn, NumberColumnProperty),
+    ColumnType.object: (ObjectColumn, ObjectColumnProperty),
+    ColumnType.string: (StringColumn, StringColumnProperty),
+    ColumnType.time: (TimeColumn, TimeColumnProperty),
+    ColumnType.topojson: (TopojsonColumn, TopojsonColumnProperty),
+    ColumnType.unknown: (UnknownColumn, UnknownColumnProperty),
+    ColumnType.url: (UrlColumn, UrlColumnProperty),
+    ColumnType.wkb: (WkbColumn, WkbColumnProperty),
+    ColumnType.wkt: (WktColumn, WktColumnProperty),
+}
+
+_CATEGORICAL_PROPERTY_MAP: dict[str | None, type[BaseColumnProperty]] = {
+    "integer": IntegerCategoricalColumnProperty,
+    "string": StringCategoricalColumnProperty,
+}
+
+
+def create_column_from_property(name: str, property: Descriptor) -> Column:
+    base_type = get_base_property_type(property.get("type"))
+    format = property.get("format")
+    nullable = get_is_nullable_property_type(property.get("type")) or None
+    column_type = _get_column_type(base_type, format)
+
+    if column_type == ColumnType.categorical:
+        cat_property_cls = _CATEGORICAL_PROPERTY_MAP.get(
+            base_type, StringCategoricalColumnProperty
+        )
+        property_model = cat_property_cls.model_validate(property)
+        # Upcast concrete subclass to Column union (type checker can't infer this)
+        return cast(
+            "Column",
+            CategoricalColumn.model_validate(
+                {
+                    "type": column_type,
+                    "name": name,
+                    "nullable": nullable,
+                    "property": property_model,
+                }
+            ),
+        )
+
+    column_cls, property_cls = _COLUMN_CLASS_MAP[column_type]
+    property_model = property_cls.model_validate(property)
+    # Upcast concrete subclass to Column union (type checker can't infer this)
+    return cast(
+        "Column",
+        column_cls.model_validate(
+            {
+                "type": column_type,
+                "name": name,
+                "nullable": nullable,
+                "property": property_model,
+            }
+        ),
+    )
+
+
+def _get_column_type(base_type: str | None, format: str | None) -> ColumnType:
+    match base_type:
+        case "boolean":
+            return ColumnType.boolean
+        case "integer":
+            if format == "categorical":
+                return ColumnType.categorical
+            return ColumnType.integer
+        case "number":
+            return ColumnType.number
+        case "string":
+            match format:
+                case "categorical":
+                    return ColumnType.categorical
+                case "decimal":
+                    return ColumnType.decimal
+                case "list":
+                    return ColumnType.list
+                case "base64":
+                    return ColumnType.base64
+                case "hex":
+                    return ColumnType.hex
+                case "email":
+                    return ColumnType.email
+                case "url":
+                    return ColumnType.url
+                case "date-time":
+                    return ColumnType.date_time
+                case "date":
+                    return ColumnType.date
+                case "time":
+                    return ColumnType.time
+                case "duration":
+                    return ColumnType.duration
+                case "wkt":
+                    return ColumnType.wkt
+                case "wkb":
+                    return ColumnType.wkb
+                case _:
+                    return ColumnType.string
+        case "array":
+            return ColumnType.array
+        case "object":
+            match format:
+                case "geojson":
+                    return ColumnType.geojson
+                case "topojson":
+                    return ColumnType.topojson
+                case _:
+                    return ColumnType.object
+        case _:
+            return ColumnType.unknown