From cadbafdb1fea5f95556a04f1855af287bb2935c0 Mon Sep 17 00:00:00 2001
From: ozgury <ozgury@ebi.ac.uk>
Date: Fri, 6 Dec 2024 09:42:22 +0000
Subject: [PATCH] refactor: refactor code to export modules

---
 .gitignore                                    |   2 +-
 metabolights_utils/__init__.py                | 608 +++++++++---------
 metabolights_utils/commands/__init__.py       |   0
 metabolights_utils/isa_file_utils.py          | 105 +++
 metabolights_utils/isatab/__init__.py         |  13 +
 metabolights_utils/isatab/default/__init__.py |  23 +
 .../isatab/default/parser/__init__.py         |  11 +
 metabolights_utils/models/__init__.py         |   9 +
 metabolights_utils/models/isa/__init__.py     |  17 +
 .../models/metabolights/__init__.py           |   4 +
 metabolights_utils/models/parser/__init__.py  |   3 +
 metabolights_utils/provider/__init__.py       |  23 +
 .../provider/async_provider/__init__.py       |   3 +
 metabolights_utils/provider/ftp/__init__.py   |  11 +
 metabolights_utils/tsv/__init__.py            |   3 +
 metabolights_utils/tsv/actions/__init__.py    |  31 +
 metabolights_utils/utils/__init__.py          |  13 +
 17 files changed, 583 insertions(+), 296 deletions(-)
 create mode 100644 metabolights_utils/commands/__init__.py
 create mode 100644 metabolights_utils/isa_file_utils.py
 create mode 100644 metabolights_utils/provider/__init__.py
 create mode 100644 metabolights_utils/provider/async_provider/__init__.py
 create mode 100644 metabolights_utils/provider/ftp/__init__.py
 create mode 100644 metabolights_utils/utils/__init__.py

diff --git a/.gitignore b/.gitignore
index b4216bb..c33ff7b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,7 +5,7 @@ test-temp
 __pycache__/
 *.py[cod]
 *$py.class
-
+.DS_Store
 # C extensions
 *.so
 
diff --git a/metabolights_utils/__init__.py b/metabolights_utils/__init__.py
index bc3aef7..5ba8624 100644
--- a/metabolights_utils/__init__.py
+++ b/metabolights_utils/__init__.py
@@ -1,301 +1,319 @@
-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.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 MetabolightsFileNameUtils
+# from metabolights_utils.utils.hash_utils import (
+#     EMPTY_FILE_HASH,
+#     IsaMetadataFolderHash,
+#     MetabolightsHashUtils,
+# )
+# from metabolights_utils.utils.search_utils import MetabolightsSearchUtils
+from metabolights_utils import (
+    isatab,
+    commands,
+    models,
+    provider,
+    tsv,
+    utils,
+    common,
+    isa_file_utils,
 )
-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 MetabolightsFileNameUtils
-from metabolights_utils.utils.hash_utils import (
-    EMPTY_FILE_HASH,
-    IsaMetadataFolderHash,
-    MetabolightsHashUtils,
-)
-from metabolights_utils.utils.search_utils import MetabolightsSearchUtils
 
 __VERSION__ = "1.3.7"
 
 __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",
-    "MetabolightsFileNameUtils",
-    # hash utils
-    "MetabolightsHashUtils",
-    "IsaMetadataFolderHash",
-    "EMPTY_FILE_HASH",
+    "commands",
+    "isatab",
+    "models",
+    "provider",
+    "tsv",
+    "utils",
+    "common",
+    "isa_file_utils",
+    # "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",
+    # "MetabolightsFileNameUtils",
+    # # hash utils
+    # "MetabolightsHashUtils",
+    # "IsaMetadataFolderHash",
+    # "EMPTY_FILE_HASH",
 ]
diff --git a/metabolights_utils/commands/__init__.py b/metabolights_utils/commands/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/metabolights_utils/isa_file_utils.py b/metabolights_utils/isa_file_utils.py
new file mode 100644
index 0000000..88844d9
--- /dev/null
+++ b/metabolights_utils/isa_file_utils.py
@@ -0,0 +1,105 @@
+import logging
+import os
+from typing import Any, Union
+
+from metabolights_utils.isatab import Writer
+from metabolights_utils.models.isa.common import IsaTableFile
+from metabolights_utils.models.metabolights.model import MetabolightsStudyModel
+
+logger = logging.getLogger(__name__)
+
+
+class IsaFileUtils:
+
+    @staticmethod
+    async def save_metabolights_study_model(
+        mtbls_model: MetabolightsStudyModel,
+        output_dir: str,
+        values_in_quotation_mark: bool = False,
+        investigation_module_name: Union[None, str] = None,
+    ):
+        if not os.path.exists(output_dir):
+            logger.info(f"Study save folder % is created", output_dir)
+            os.makedirs(output_dir, exist_ok=True)
+        i_file_name = mtbls_model.investigation_file_path
+        logger.info("Saving investigation file: %s", i_file_name)
+        Writer.get_investigation_file_writer().write(
+            mtbls_model.investigation,
+            f"{output_dir}/{mtbls_model.investigation_file_path}",
+            values_in_quotation_mark=values_in_quotation_mark,
+            investigation_module_name=investigation_module_name,
+        )
+        for isa_table_files in (
+            mtbls_model.samples,
+            mtbls_model.assays,
+            mtbls_model.metabolite_assignments,
+        ):
+            for isa_table_file in isa_table_files.values():
+                i_file_name = isa_table_file.file_path
+                await IsaFileUtils.save_isa_table(
+                    isa_table_file,
+                    f"{output_dir}/{isa_table_file.file_path}",
+                    values_in_quotation_mark=values_in_quotation_mark,
+                )
+
+    @staticmethod
+    def sanitise_data(self, value: Union[None, Any]):
+        if isinstance(value, list):
+            for idx, val in enumerate(value):
+                value[idx] = IsaFileUtils.sanitise_single_value(val)
+            return value
+        return IsaFileUtils.sanitise_single_value(value)
+
+    @staticmethod
+    def sanitise_single_value(self, value: Union[None, Any]):
+        if value is None:
+            return ""
+        return (
+            str(value).replace("\n", " ").replace("\r", " ").replace("\t", " ").strip()
+        )
+
+    @staticmethod
+    async def save_isa_table(
+        isa_table_file: IsaTableFile,
+        file_path: str,
+        values_in_quotation_mark=False,
+    ):
+        column_order_map = {}
+        column_header_map = {}
+        data = isa_table_file.table.data
+        for column_model in isa_table_file.table.headers:
+            column_order_map[column_model.column_index] = column_model.column_name
+            column_header_map[column_model.column_index] = column_model.column_header
+        parent_dir = os.path.dirname(file_path)
+        basename = os.path.dirname(file_path)
+        if not os.path.exists(parent_dir):
+            logger.info(f"Study save folder % is created", parent_dir)
+            os.makedirs(parent_dir, exist_ok=True)
+
+        logger.info("Saving file: %s", basename)
+        with open(file_path, "w") as f:
+            if values_in_quotation_mark:
+                header = [
+                    f'"{column_header_map[idx]}"'
+                    for idx in range(len(column_header_map))
+                ]
+            else:
+                header = [
+                    column_header_map[idx].strip('"')
+                    for idx in range(len(column_header_map))
+                ]
+            f.write("\t".join(header) + "\n")
+
+            column_names = [
+                column_order_map[idx] for idx in range(len(column_order_map))
+            ]
+            for row_idx in range(len(data[column_names[0]])):
+                row = [data[column_name][row_idx] for column_name in column_names]
+                for idx, cell in enumerate(row):
+                    cell = IsaFileUtils.sanitise_data(cell) if row[idx] else ""
+                    if values_in_quotation_mark:
+                        cell = f'"{cell}"'
+                    else:
+                        cell = cell.strip('"')
+                    row[idx] = cell
+                f.write("\t".join(row) + "\n")
diff --git a/metabolights_utils/isatab/__init__.py b/metabolights_utils/isatab/__init__.py
index 5eec434..601199c 100644
--- a/metabolights_utils/isatab/__init__.py
+++ b/metabolights_utils/isatab/__init__.py
@@ -15,6 +15,8 @@
     IsaTabWriterFactory,
 )
 
+from metabolights_utils.isatab import default, reader, writer
+
 
 @lru_cache
 def get_reader_factory():
@@ -72,3 +74,14 @@ def get_sample_file_writer(cls) -> IsaTableFileWriter:
     @classmethod
     def get_assignment_file_writer(cls) -> IsaTableFileWriter:
         return cls.writer_factory.get_sample_file_writer()
+
+
+__all__ = [
+    "reader",
+    "default",
+    "writer",
+    "Reader",
+    "Writer",
+    "get_reader_factory",
+    "get_writer_factory",
+]
diff --git a/metabolights_utils/isatab/default/__init__.py b/metabolights_utils/isatab/default/__init__.py
index e69de29..307015d 100644
--- a/metabolights_utils/isatab/default/__init__.py
+++ b/metabolights_utils/isatab/default/__init__.py
@@ -0,0 +1,23 @@
+from metabolights_utils.isatab.default import (
+    parser,
+    assay_file,
+    assignment_file,
+    base_isa_table_file,
+    base_isa_file,
+    factory,
+    investigation_file,
+    sample_file,
+    writer,
+)
+
+__all__ = [
+    "parser",
+    "assay_file",
+    "assignment_file",
+    "base_isa_table_file",
+    "base_isa_file",
+    "factory",
+    "investigation_file",
+    "sample_file",
+    "writer",
+]
diff --git a/metabolights_utils/isatab/default/parser/__init__.py b/metabolights_utils/isatab/default/parser/__init__.py
index e69de29..f5fb890 100644
--- a/metabolights_utils/isatab/default/parser/__init__.py
+++ b/metabolights_utils/isatab/default/parser/__init__.py
@@ -0,0 +1,11 @@
+from metabolights_utils.isatab.default.parser import (
+    common,
+    investigation_parser,
+    isa_table_parser,
+)
+
+__all__ = [
+    "common",
+    "investigation_parser",
+    "isa_table_parser",
+]
diff --git a/metabolights_utils/models/__init__.py b/metabolights_utils/models/__init__.py
index e69de29..60b7325 100644
--- a/metabolights_utils/models/__init__.py
+++ b/metabolights_utils/models/__init__.py
@@ -0,0 +1,9 @@
+from metabolights_utils.models import common, enums, isa, metabolights, parser
+
+__all__ = [
+    "common",
+    "enums",
+    "isa",
+    "metabolights",
+    "parser",
+]
diff --git a/metabolights_utils/models/isa/__init__.py b/metabolights_utils/models/isa/__init__.py
index e69de29..edc82f1 100644
--- a/metabolights_utils/models/isa/__init__.py
+++ b/metabolights_utils/models/isa/__init__.py
@@ -0,0 +1,17 @@
+from metabolights_utils.models.isa import (
+    assay_file,
+    assignment_file,
+    common,
+    enums,
+    investigation_file,
+    samples_file,
+)
+
+__all__ = [
+    "assay_file",
+    "assignment_file",
+    "common",
+    "enums",
+    "investigation_file",
+    "samples_file",
+]
diff --git a/metabolights_utils/models/metabolights/__init__.py b/metabolights_utils/models/metabolights/__init__.py
index 66850c0..7777174 100644
--- a/metabolights_utils/models/metabolights/__init__.py
+++ b/metabolights_utils/models/metabolights/__init__.py
@@ -1,6 +1,7 @@
 import json
 import os
 from typing import Dict, Union
+from metabolights_utils.models.metabolights import metabolights_study, model
 
 
 def get_study_model_schema(schema_path: Union[str, None] = None) -> Dict:
@@ -12,3 +13,6 @@ def get_study_model_schema(schema_path: Union[str, None] = None) -> Dict:
     with open(schema_path, "r", encoding="utf-8") as sf:
         study_model_jsonschema = json.load(sf)
     return study_model_jsonschema
+
+
+__all__ = ["metabolights_study", "model", "get_study_model_schema"]
diff --git a/metabolights_utils/models/parser/__init__.py b/metabolights_utils/models/parser/__init__.py
index e69de29..af559c6 100644
--- a/metabolights_utils/models/parser/__init__.py
+++ b/metabolights_utils/models/parser/__init__.py
@@ -0,0 +1,3 @@
+from metabolights_utils.models.parser import common, enums
+
+__all__ = ["common", "enums"]
diff --git a/metabolights_utils/provider/__init__.py b/metabolights_utils/provider/__init__.py
new file mode 100644
index 0000000..611f82e
--- /dev/null
+++ b/metabolights_utils/provider/__init__.py
@@ -0,0 +1,23 @@
+from metabolights_utils.provider import (
+    ftp,
+    async_provider,
+    definitions,
+    ftp_repository,
+    local_folder_metadata_collector,
+    study_provider,
+    submission_model,
+    submission_repository,
+    utils,
+)
+
+__all__ = [
+    "ftp",
+    "async_provider",
+    "definitions",
+    "ftp_repository",
+    "local_folder_metadata_collector",
+    "study_provider",
+    "submission_model",
+    "submission_repository",
+    "utils",
+]
diff --git a/metabolights_utils/provider/async_provider/__init__.py b/metabolights_utils/provider/async_provider/__init__.py
new file mode 100644
index 0000000..2b4ec02
--- /dev/null
+++ b/metabolights_utils/provider/async_provider/__init__.py
@@ -0,0 +1,3 @@
+from metabolights_utils.provider.async_provider import study_provider
+
+__all__ = ["study_provider"]
diff --git a/metabolights_utils/provider/ftp/__init__.py b/metabolights_utils/provider/ftp/__init__.py
new file mode 100644
index 0000000..26ba826
--- /dev/null
+++ b/metabolights_utils/provider/ftp/__init__.py
@@ -0,0 +1,11 @@
+from metabolights_utils.provider.ftp import (
+    default_ftp_client,
+    folder_metadata_collector,
+    model,
+)
+
+__all__ = [
+    "default_ftp_client",
+    "folder_metadata_collector",
+    "model",
+]
diff --git a/metabolights_utils/tsv/__init__.py b/metabolights_utils/tsv/__init__.py
index e69de29..450ef4d 100644
--- a/metabolights_utils/tsv/__init__.py
+++ b/metabolights_utils/tsv/__init__.py
@@ -0,0 +1,3 @@
+from metabolights_utils.tsv import actions, filter, model, sort, tsv_file_updater
+
+__all__ = ["actions", "filter", "model", "sort", "tsv_file_updater"]
diff --git a/metabolights_utils/tsv/actions/__init__.py b/metabolights_utils/tsv/actions/__init__.py
index e69de29..29535f8 100644
--- a/metabolights_utils/tsv/actions/__init__.py
+++ b/metabolights_utils/tsv/actions/__init__.py
@@ -0,0 +1,31 @@
+from metabolights_utils.tsv.actions import (
+    add_column,
+    add_row,
+    base,
+    copy_column,
+    copy_row,
+    delete_column,
+    delete_row,
+    move_column,
+    move_row,
+    update_cell,
+    update_column_header,
+    update_column,
+    update_row,
+)
+
+__all__ = [
+    "add_column",
+    "add_row",
+    "base",
+    "copy_column",
+    "copy_row",
+    "delete_column",
+    "delete_row",
+    "move_column",
+    "move_row",
+    "update_cell",
+    "update_column_header",
+    "update_column",
+    "update_row",
+]
diff --git a/metabolights_utils/utils/__init__.py b/metabolights_utils/utils/__init__.py
new file mode 100644
index 0000000..c6a5ca8
--- /dev/null
+++ b/metabolights_utils/utils/__init__.py
@@ -0,0 +1,13 @@
+from metabolights_utils.utils import (
+    audit_utils,
+    filename_utils,
+    hash_utils,
+    search_utils,
+)
+
+__all__ = [
+    "audit_utils",
+    "filename_utils",
+    "hash_utils",
+    "search_utils",
+]