from metabolights_utils.common import CamelCaseModel
from metabolights_utils.isatab import Reader, Writer
from metabolights_utils.isatab.default.assay_file import DefaultAssayFileReader
from metabolights_utils.isatab.default.assignment_file import (
    DefaultAssignmentFileReader,
)
from metabolights_utils.isatab.default.factory import (
    DefaultIsaTabReaderFactory,
    DefaultIsaTabWriterFactory,
)
from metabolights_utils.isatab.default.investigation_file import (
    DefaultInvestigationFileReader,
    DefaultInvestigationFileWriter,
)
from metabolights_utils.isatab.default.parser.isa_table_parser import (
    assay_file_expected_patterns,
    samples_file_expected_patterns,
)
from metabolights_utils.isatab.default.sample_file import DefaultSampleFileReader
from metabolights_utils.isatab.default.writer import DefaultIsaTableFileWriter
from metabolights_utils.isatab.reader import (
    InvestigationFileReader,
    InvestigationFileReaderResult,
    IsaTableFileReader,
    IsaTableFileReaderResult,
    IsaTabReaderFactory,
)
from metabolights_utils.isatab.writer import (
    InvestigationFileWriter,
    IsaTableFileWriter,
    IsaTabWriterFactory,
)
from metabolights_utils.models.common import GenericMessage, MetabolightsBaseModel
from metabolights_utils.models.enums import GenericMessageType
from metabolights_utils.models.isa.assay_file import AssayFile
from metabolights_utils.models.isa.assignment_file import AssignmentFile
from metabolights_utils.models.isa.common import (
    AssayTechnique,
    Comment,
    IsaAbstractModel,
    IsaTable,
    IsaTableColumn,
    IsaTableFile,
    NumericItem,
    OntologyItem,
    OrganismAndOrganismPartPair,
)
from metabolights_utils.models.isa.enums import (
    ColumnsStructure,
    IsaTableAdditionalColumn,
)
from metabolights_utils.models.isa.investigation_file import (
    Assay,
    BaseSection,
    Factor,
    Investigation,
    InvestigationContacts,
    InvestigationPublications,
    OntologyAnnotation,
    OntologySourceReference,
    OntologySourceReferences,
    Person,
    Protocol,
    Publication,
    Study,
    StudyAssays,
    StudyContacts,
    StudyFactors,
    StudyProtocols,
    StudyPublications,
    ValueTypeAnnotation,
)
from metabolights_utils.models.metabolights.metabolights_study import (
    BaseMetabolightsStudyModel,
)
from metabolights_utils.models.parser.common import ParserMessage, ParserReport
from metabolights_utils.models.parser.enums import ParserMessageType
from metabolights_utils.tsv.actions.add_column import AddColumnsTsvAction
from metabolights_utils.tsv.actions.add_row import AddRowsTsvAction
from metabolights_utils.tsv.actions.base import BaseTsvAction, TsvActionException
from metabolights_utils.tsv.actions.copy_column import CopyColumnTsvAction
from metabolights_utils.tsv.actions.copy_row import CopyRowTsvAction
from metabolights_utils.tsv.actions.delete_column import DeleteColumnsTsvAction
from metabolights_utils.tsv.actions.delete_row import DeleteRowsTsvAction
from metabolights_utils.tsv.actions.move_column import MoveColumnTsvAction
from metabolights_utils.tsv.actions.update_cell import UpdateCellsTsvAction
from metabolights_utils.tsv.actions.update_column import UpdateColumnsTsvAction
from metabolights_utils.tsv.actions.update_column_header import (
    UpdateColumnHeadersTsvAction,
)
from metabolights_utils.tsv.actions.update_row import UpdateRowsTsvAction
from metabolights_utils.tsv.filter import (
    BetweenEqualCustomFilter,
    ContainsFilter,
    CustomFilter,
    EmptyFilter,
    EndsWithFilter,
    EnumContainsCustomFilter,
    Filter,
    FilterDataType,
    FilterOperation,
    FilterRegistry,
    GreaterEqualFilter,
    GreaterFilter,
    LessEqualFilter,
    LessFilter,
    RegexFilter,
    StartsWithFilter,
    TsvFileFilterOption,
    TsvFilterException,
    ValidDatetimeCustomFilter,
    ValidNumberCustomFilter,
)
from metabolights_utils.tsv.model import (
    TsvAction,
    TsvActionReport,
    TsvActionResult,
    TsvActionType,
    TsvAddColumnsAction,
    TsvAddRowsAction,
    TsvCellData,
    TsvColumnData,
    TsvCopyColumnAction,
    TsvCopyRowAction,
    TsvDeleteColumnsAction,
    TsvDeleteRowsAction,
    TsvMoveColumnAction,
    TsvMoveRowAction,
    TsvRowData,
    TsvUpdateCellsAction,
    TsvUpdateColumnHeaderAction,
    TsvUpdateColumnsAction,
    TsvUpdateRowsAction,
)
from metabolights_utils.tsv.sort import (
    AbstractSorter,
    CustomSorter,
    DateTimeSorter,
    EnumSorter,
    FloatSorter,
    IntegerSorter,
    Sorter,
    SorterRegistry,
    SortType,
    SortValueClassification,
    StringSorter,
    TsvFileSortOption,
    TsvFileSortValueOrder,
    TsvSortException,
)
from metabolights_utils.tsv.tsv_file_updater import TSV_FILE_ACTIONS, TsvFileUpdater
from metabolights_utils.utils.audit_utils import MetabolightsAuditUtils
from metabolights_utils.utils.filename_utils import MetabolightsFileNamehUtils
from metabolights_utils.utils.hash_utils import (
    EMPTY_FILE_HASH,
    IsaMetadataFolderHash,
    MetabolightsHashUtils,
)
from metabolights_utils.utils.search_utils import MetabolightsSearchUtils

__all__ = [
    "Assay",
    "BaseSection",
    "Factor",
    "Investigation",
    "InvestigationContacts",
    "InvestigationPublications",
    "OntologyAnnotation",
    "OntologySourceReference",
    "OntologySourceReferences",
    "Person",
    "Protocol",
    "Publication",
    "Study",
    "StudyAssays",
    "StudyContacts",
    "StudyFactors",
    "StudyProtocols",
    "StudyPublications",
    "ValueTypeAnnotation",
    "ColumnsStructure",
    "IsaTableAdditionalColumn",
    "IsaAbstractModel",
    "NumericItem",
    "AssayFile",
    "AssignmentFile",
    "GenericMessage",
    "GenericMessageType",
    "MetabolightsBaseModel",
    "CamelCaseModel",
    "AssayTechnique",
    "Comment",
    "IsaTable",
    "IsaTableColumn",
    "IsaTableFile",
    "OntologyItem",
    "OrganismAndOrganismPartPair",
    "BaseMetabolightsStudyModel",
    "ParserMessage",
    "ParserMessageType",
    "ParserReport",
    "Reader",
    "DefaultAssayFileReader",
    "InvestigationFileReader",
    "DefaultAssignmentFileReader",
    "IsaTableFileReader",
    "InvestigationFileReaderResult",
    "IsaTableFileReaderResult",
    "DefaultIsaTabReaderFactory",
    "DefaultIsaTabWriterFactory",
    "DefaultInvestigationFileReader",
    "DefaultInvestigationFileWriter",
    "assay_file_expected_patterns",
    "samples_file_expected_patterns",
    "DefaultSampleFileReader",
    "DefaultIsaTableFileWriter",
    "IsaTabReaderFactory",
    "Writer",
    "InvestigationFileWriter",
    "IsaTableFileWriter",
    "IsaTabWriterFactory",
    # TSV
    "TsvAction",
    "TsvActionReport",
    "TsvActionResult",
    "TsvActionType",
    "TsvAddColumnsAction",
    "TsvAddRowsAction",
    "TsvCellData",
    "TsvColumnData",
    "TsvCopyColumnAction",
    "TsvCopyRowAction",
    "TsvDeleteColumnsAction",
    "TsvDeleteRowsAction",
    "TsvMoveColumnAction",
    "TsvMoveRowAction",
    "TsvRowData",
    "TsvUpdateCellsAction",
    "TsvUpdateColumnHeaderAction",
    "TsvUpdateColumnsAction",
    "TsvUpdateRowsAction",
    "Filter",
    "FilterDataType",
    "FilterOperation",
    "TsvFileFilterOption",
    "TsvFilterException",
    "CustomFilter",
    "FilterRegistry",
    "ContainsFilter",
    "StartsWithFilter",
    "EndsWithFilter",
    "GreaterFilter",
    "GreaterEqualFilter",
    "LessFilter",
    "LessEqualFilter",
    "EmptyFilter",
    "RegexFilter",
    "ValidNumberCustomFilter",
    "ValidDatetimeCustomFilter",
    "EnumContainsCustomFilter",
    "BetweenEqualCustomFilter",
    "AbstractSorter",
    "CustomSorter",
    "DateTimeSorter",
    "EnumSorter",
    "FloatSorter",
    "IntegerSorter",
    "Sorter",
    "SorterRegistry",
    "SortType",
    "SortValueClassification",
    "StringSorter",
    "TsvFileSortOption",
    "TsvFileSortValueOrder",
    "TsvSortException",
    "TSV_FILE_ACTIONS",
    "TsvFileUpdater",
    "TsvActionException",
    "BaseTsvAction",
    "AddColumnsTsvAction",
    "AddRowsTsvAction",
    "CopyColumnTsvAction",
    "CopyRowTsvAction",
    "DeleteColumnsTsvAction",
    "DeleteRowsTsvAction",
    "MoveColumnTsvAction",
    "UpdateCellsTsvAction",
    "UpdateColumnsTsvAction",
    "UpdateColumnHeadersTsvAction",
    "UpdateRowsTsvAction",
    # utils
    "MetabolightsAuditUtils",
    "MetabolightsSearchUtils",
    "MetabolightsFileNamehUtils",
    # hash utils
    "MetabolightsHashUtils",
    "IsaMetadataFolderHash",
    "EMPTY_FILE_HASH",
]
