LICENSE
README.md
pyproject.toml
config/__init__.py
config/directory_structure.json
config/experiment_patterns.json
config/factor_extraction_rules.json
config/fcs_markers.json
config/investigation_defaults.json
config/people.json
config/profile.json
config/protein_names.json
config/settings.json
gui/__init__.py
gui/app.py
gui/main.py
gui/main_window.py
gui/dialogs/__init__.py
gui/dialogs/add_parameter_dialog.py
gui/dialogs/assay_dialog.py
gui/dialogs/image_converter.py
gui/dialogs/investigation_dialog.py
gui/dialogs/material_dialog.py
gui/dialogs/material_selection_dialog.py
gui/dialogs/parameter_dialog.py
gui/dialogs/study_wizard.py
gui/dialogs/template_editor.py
gui/pages/__init__.py
gui/pages/assays.py
gui/pages/base_page.py
gui/pages/dashboard.py
gui/pages/files.py
gui/pages/images.py
gui/pages/materials.py
gui/pages/ontology_browser.py
gui/pages/process_sequence.py
gui/pages/settings.py
gui/pages/studies.py
gui/pages/templates.py
gui/resources/styles/dark.qss
gui/resources/styles/light.qss
gui/widgets/__init__.py
gui/widgets/collapsible_group_box.py
gui/widgets/common.py
gui/widgets/file_attachment_widget.py
gui/widgets/graph_widget.py
gui/widgets/path_picker.py
gui/widgets/sidebar.py
gui/widgets/status_bar.py
gui/widgets/url_line_edit.py
isa_json_steward.egg-info/PKG-INFO
isa_json_steward.egg-info/SOURCES.txt
isa_json_steward.egg-info/dependency_links.txt
isa_json_steward.egg-info/entry_points.txt
isa_json_steward.egg-info/requires.txt
isa_json_steward.egg-info/top_level.txt
tests/test_directory_manager.py
tests/test_dna_conversion.py
tests/test_file_converter.py
tests/test_file_manager.py
tests/test_file_manager_extended.py
tests/test_lab_book_xml_parser.py
tests/test_link_microscopy_files.py
tests/test_material_manager.py
tests/test_parse_excel_metadata.py
tests/test_parse_microscopy_docx.py
tests/test_process_sequence_manager.py
tests/test_sequence_file_attachment.py
tests/test_validation.py
utils/__init__.py
utils/config_loader.py
utils/constants.py
utils/directory_manager.py
utils/file_converter.py
utils/file_manager.py
utils/file_type_validator.py
utils/graph_builder.py
utils/isa_json_exporter.py
utils/isa_json_preview_helpers.py
utils/logging_config.py
utils/material_handover_validator.py
utils/material_manager.py
utils/ontology_manager.py
utils/process_sequence_manager.py
utils/template_index.py
utils/validation.py
utils/batch/__init__.py
utils/batch/__main__.py
utils/batch/batch_processor.py
utils/batch/experiment_classifier.py
utils/batch/file_organizer.py
utils/batch/folder_scanner.py
utils/batch/format_converter.py
utils/batch/isa_json_generator.py
utils/batch/metadata_extractor.py
utils/batch/validator.py