.gitignore
LICENSE
README.rst
pyproject.toml
requirements.txt
setup.py
.github/workflows/codecov.yml
.github/workflows/documentation.yml
.github/workflows/package_release.yml
.github/workflows/pull_request.yml
.github/workflows/pypi.yml
.github/workflows/tests.yml
docs/Makefile
docs/api.rst
docs/cli.rst
docs/common_conventions.rst
docs/conf.py
docs/conversion_directives.rst
docs/experiment_description_specification.rst
docs/guide.rst
docs/index.rst
docs/license.rst
docs/make.bat
docs/mouse_diagram.png
docs/protocol_dependent_schema.rst
docs/requirements.txt
docs/supported_formats.rst
docs/tagging.rst
docs/todo.rst
docs/tutorial.rst
docs/_static/css/custom_css.css
examples/Full_mwtab_example/MS/CESB/convert/README.txt
examples/Full_mwtab_example/MS/CESB/convert/extracted_result.json
examples/Full_mwtab_example/MS/CESB/convert/output.json
examples/Full_mwtab_example/MS/CESB/convert/output.txt
examples/Full_mwtab_example/MS/CESB/extract/MS_colon_measurements.xlsx
examples/Full_mwtab_example/MS/CESB/extract/README.txt
examples/Full_mwtab_example/MS/CESB/extract/extracted_result.json
examples/Full_mwtab_example/MS/CESB/extract/mouse_experiment_metadata.xlsx
examples/Full_mwtab_example/MS/CESB/validate/README.txt
examples/Full_mwtab_example/MS/CESB/validate/extracted_result.json
examples/Full_mwtab_example/MS/CESB/validate/protocol-dependent_schema.json
examples/Full_mwtab_example/MS/West_Coast/README.txt
examples/Full_mwtab_example/MS/West_Coast/convert/README.txt
examples/Full_mwtab_example/MS/West_Coast/convert/biogenic_amines_neg_extraction.json
examples/Full_mwtab_example/MS/West_Coast/convert/biogenic_amines_neg_mwtab.json
examples/Full_mwtab_example/MS/West_Coast/convert/biogenic_amines_neg_mwtab.txt
examples/Full_mwtab_example/MS/West_Coast/convert/biogenic_amines_pos_extraction.json
examples/Full_mwtab_example/MS/West_Coast/convert/biogenic_amines_pos_mwtab.json
examples/Full_mwtab_example/MS/West_Coast/convert/biogenic_amines_pos_mwtab.txt
examples/Full_mwtab_example/MS/West_Coast/convert/lipids_neg_extraction.json
examples/Full_mwtab_example/MS/West_Coast/convert/lipids_neg_mwtab.json
examples/Full_mwtab_example/MS/West_Coast/convert/lipids_neg_mwtab.txt
examples/Full_mwtab_example/MS/West_Coast/convert/lipids_pos_extraction.json
examples/Full_mwtab_example/MS/West_Coast/convert/lipids_pos_mwtab.json
examples/Full_mwtab_example/MS/West_Coast/convert/lipids_pos_mwtab.txt
examples/Full_mwtab_example/MS/West_Coast/convert/metabolism_extraction.json
examples/Full_mwtab_example/MS/West_Coast/convert/metabolism_mwtab.json
examples/Full_mwtab_example/MS/West_Coast/convert/metabolism_mwtab.txt
examples/Full_mwtab_example/MS/West_Coast/convert/mwtab_ms_conversion_directives.json
examples/Full_mwtab_example/MS/West_Coast/extract/README.txt
examples/Full_mwtab_example/MS/West_Coast/extract/biogenic_amines_end_modify.xlsx
examples/Full_mwtab_example/MS/West_Coast/extract/biogenic_amines_neg_extraction.json
examples/Full_mwtab_example/MS/West_Coast/extract/biogenic_amines_pos_extraction.json
examples/Full_mwtab_example/MS/West_Coast/extract/lipids_end_modify.xlsx
examples/Full_mwtab_example/MS/West_Coast/extract/lipids_neg_extraction.json
examples/Full_mwtab_example/MS/West_Coast/extract/lipids_pos_extraction.json
examples/Full_mwtab_example/MS/West_Coast/extract/metabolism_end_modify.xlsx
examples/Full_mwtab_example/MS/West_Coast/extract/metabolism_extraction.json
examples/Full_mwtab_example/MS/West_Coast/extract/metabolomics_biogenic_amines_neg.xlsx
examples/Full_mwtab_example/MS/West_Coast/extract/metabolomics_biogenic_amines_pos.xlsx
examples/Full_mwtab_example/MS/West_Coast/extract/metabolomics_lipidomics_neg.xlsx
examples/Full_mwtab_example/MS/West_Coast/extract/metabolomics_lipidomics_pos.xlsx
examples/Full_mwtab_example/MS/West_Coast/extract/metabolomics_primary_metabolism.xlsx
examples/Full_mwtab_example/MS/West_Coast/extract/sample_list.xlsx
examples/Full_mwtab_example/MS/West_Coast/original_data/metabolomics_biogenic_amines.xlsx
examples/Full_mwtab_example/MS/West_Coast/original_data/metabolomics_lipidomics.xlsx
examples/Full_mwtab_example/MS/West_Coast/original_data/metabolomics_primary_metabolism.xlsx
examples/Full_mwtab_example/MS/West_Coast/original_data/sample_list.xlsx
examples/Full_mwtab_example/MS/West_Coast/validate/README.txt
examples/Full_mwtab_example/MS/West_Coast/validate/biogenic_amines_neg_extraction.json
examples/Full_mwtab_example/MS/West_Coast/validate/biogenic_amines_pos_extraction.json
examples/Full_mwtab_example/MS/West_Coast/validate/lipids_neg_extraction.json
examples/Full_mwtab_example/MS/West_Coast/validate/lipids_pos_extraction.json
examples/Full_mwtab_example/MS/West_Coast/validate/metabolism_extraction.json
examples/Full_mwtab_example/MS/West_Coast/validate/protocol-dependent_schema.xlsx
examples/Full_mwtab_example/NMR/convert/README.txt
examples/Full_mwtab_example/NMR/convert/extracted_result.json
examples/Full_mwtab_example/NMR/convert/output.json
examples/Full_mwtab_example/NMR/convert/output.txt
examples/Full_mwtab_example/NMR/extract/NMR_colon_measurements.xlsx
examples/Full_mwtab_example/NMR/extract/README.txt
examples/Full_mwtab_example/NMR/extract/extracted_result.json
examples/Full_mwtab_example/NMR/extract/mouse_experiment_metadata.xlsx
examples/Full_mwtab_example/NMR/validate/README.txt
examples/Full_mwtab_example/NMR/validate/extracted_result.json
examples/Full_mwtab_example/NMR/validate/protocol-dependent_schema.json
examples/convert/generic/MS_base_input.json
examples/convert/generic/MS_output.json
examples/convert/generic/README.txt
examples/convert/generic/mwtab_ms_conversion_directives.json
examples/convert/mwtab/MS/MS_base_input.json
examples/convert/mwtab/MS/MS_output.json
examples/convert/mwtab/MS/MS_output.txt
examples/convert/mwtab/MS/README.txt
examples/convert/mwtab/NMR/NMR_base_input.json
examples/convert/mwtab/NMR/NMR_output.json
examples/convert/mwtab/NMR/NMR_output.txt
examples/convert/mwtab/NMR/README.txt
examples/convert/mwtab/NMR Binned/NMR_binned_base_input.json
examples/convert/mwtab/NMR Binned/NMR_binned_output.json
examples/convert/mwtab/NMR Binned/NMR_binned_output.txt
examples/convert/mwtab/NMR Binned/README.txt
examples/convert/mwtab/Saved Directives/README.txt
examples/convert/mwtab/Saved Directives/mwtab_ms_conversion_directives.csv
examples/convert/mwtab/Saved Directives/mwtab_ms_conversion_directives.json
examples/convert/mwtab/Saved Directives/mwtab_ms_conversion_directives.xlsx
examples/convert/mwtab/Saved Directives/mwtab_nmr_binned_conversion_directives.csv
examples/convert/mwtab/Saved Directives/mwtab_nmr_binned_conversion_directives.json
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examples/convert/mwtab/Saved Directives/mwtab_nmr_conversion_directives.csv
examples/convert/mwtab/Saved Directives/mwtab_nmr_conversion_directives.json
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examples/extract/MS_colon_measurements_truncated.xlsx
examples/extract/README.txt
examples/extract/measurements.json
examples/extract/metadata.json
examples/extract/metadata_and_measurements.json
examples/extract/mouse_experiment_metadata.xlsx
examples/validate/PDS_errors/PDS_base_bad_type.json
examples/validate/PDS_errors/PDS_base_no_parent_table.json
examples/validate/PDS_errors/PDS_base_parent_protocol_errors.json
examples/validate/PDS_errors/README.txt
examples/validate/base_schema_errors/README.txt
examples/validate/base_schema_errors/simplified_base_input_base_errors.json
examples/validate/cd-to-json-schema/README.txt
examples/validate/cd-to-json-schema/directives_template.json
examples/validate/cd-to-json-schema/mwtab_ms_conversion_directives.json
examples/validate/mwtab_format_errors/MS_base_input_truncated_mwtab_errors.json
examples/validate/mwtab_format_errors/README.txt
examples/validate/pds-to-json/README.txt
examples/validate/pds-to-json/protocol-dependent_schema.json
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examples/validate/pds-to-table/README.txt
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examples/validate/pds-to-table/protocol-dependent_schema.json
src/messes/.gitignore
src/messes/__init__.py
src/messes/__main__.py
src/messes/_version.py
src/messes.egg-info/PKG-INFO
src/messes.egg-info/SOURCES.txt
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src/messes/convert/convert_schema.py
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src/messes/convert/mwtab_functions.py
src/messes/convert/user_input_checking.py
src/messes/extract/__init__.py
src/messes/extract/cythonized_tagSheet.c
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src/messes/validate/__init__.py
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src/messes/validate/validate_schema.py
tests/test_convert/test_convert_CLI.py
tests/test_convert/test_convert_tags.py
tests/test_convert/test_mwtab_tag_functions.py
tests/test_convert/test_user_input_checking.py
tests/test_convert/testing_files/MS_base_input.json
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tests/test_convert/testing_files/NMR_base_input.json
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tests/test_extract/testing_files/star_operator_not_at_beginning_no_tag_error.xlsx
tests/test_extract/testing_files/star_operator_not_at_beginning_no_tokens_error.xlsx
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tests/test_extract/testing_files/table_tag_without_assignment_no_word_error.xlsx
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tests/test_extract/testing_files/tandem_operators_error.xlsx
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tests/test_extract/testing_files/tracking_no_equal_sign_error.xlsx
tests/test_extract/testing_files/tracking_not_enough_tokens_error.xlsx
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tests/test_extract/testing_files/tracking_test3.xlsx
tests/test_extract/testing_files/transpose_test.xlsx
tests/test_extract/testing_files/two_child_fields_without_id_error.xlsx
tests/test_extract/testing_files/undefined_table_name_error.xlsx
tests/test_extract/testing_files/untracking_malformed_field_error.xlsx
tests/test_extract/testing_files/untracking_no_equal_sign_error.xlsx
tests/test_extract/testing_files/untracking_not_enough_tokens_error.xlsx
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tests/test_extract/testing_files/unused_tag.xlsx
tests/test_extract/testing_files/variable_operand_test.xlsx
tests/test_extract/testing_files/variable_operand_test_error.xlsx
tests/test_extract/testing_files/~$modification_error.xlsx
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tests/test_extract/testing_files/main_dir/base_directives.json
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tests/test_validate/test_validate_print_better_error_messages.py
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tests/test_validate/testing_files/MS_base_input_truncated_mwtab_error.json
tests/test_validate/testing_files/MS_base_input_truncated_mwtab_extra_error.json
tests/test_validate/testing_files/MS_base_input_truncated_mwtab_extra_error_2.json
tests/test_validate/testing_files/NMR_base_input_mwtab_error.json
tests/test_validate/testing_files/NMR_binned_base_input_mwtab_error.json
tests/test_validate/testing_files/PDS_base.csv
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tests/test_validate/testing_files/PDS_base_bad_sheet_name.xlsx
tests/test_validate/testing_files/PDS_base_boolean_keyword.json
tests/test_validate/testing_files/PDS_base_format_conversion_check.json
tests/test_validate/testing_files/PDS_base_format_conversion_check2.json
tests/test_validate/testing_files/PDS_base_invalid.json
tests/test_validate/testing_files/bad_JSON_file.json
tests/test_validate/testing_files/base_schema.json
tests/test_validate/testing_files/invalid_JSON_Schema.json
tests/test_validate/testing_files/mwtab_ms_conversion_directives.json
tests/test_validate/testing_files/mwtab_ms_conversion_directives_error.json
tests/test_validate/testing_files/output.json
tests/test_validate/testing_files/simplified_base_input.json
tests/test_validate/testing_files/simplified_base_input_SS_protocol_errors.json
tests/test_validate/testing_files/simplified_base_input_base_error.json
tests/test_validate/testing_files/simplified_base_input_boolean_keyword.json
tests/test_validate/testing_files/simplified_base_input_extra_and_base_error.json
tests/test_validate/testing_files/simplified_base_input_extra_error.json
tests/test_validate/testing_files/simplified_base_input_factor_errors.json
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tests/test_validate/testing_files/simplified_base_input_measurement_bad_protocol.json
tests/test_validate/testing_files/simplified_base_input_no_factors_table.json
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tests/test_validate/testing_files/simplified_base_input_parent_id_errors.json
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tests/test_validate/testing_files/simplified_base_input_protocol_pds_warning.json
tests/test_validate/testing_files/simplified_base_input_protocol_problems.json
tests/test_validate/testing_files/simplified_base_input_protocol_same_descriptions.json
tests/test_validate/testing_files/simplified_base_input_str_format_errors.json
tests/test_validate/testing_files/simplified_base_input_warnings.json
tests/test_validate/testing_files/bad_PDSs/PDS_base_bad_type.json
tests/test_validate/testing_files/bad_PDSs/PDS_base_no_parent_table.json
tests/test_validate/testing_files/bad_PDSs/PDS_base_parent_protocol_errors.json
tests/test_validate/testing_files/main_dir/MS_directives_schema.json
tests/test_validate/testing_files/main_dir/PDS_JSON_Schema.json
tests/test_validate/testing_files/main_dir/base_schema.json
tests/test_validate/testing_files/main_dir/base_schema_plus_pds.json
tests/test_validate/testing_files/main_dir/base_schema_plus_pds_plus_input.json
tests/test_validate/testing_files/main_dir/base_schema_plus_pds_plus_input2.json
tests/test_validate/testing_files/main_dir/mwtab_schema.json
tests/test_validate/testing_files/main_dir/pds_to_json.json
tests/test_validate/testing_files/main_dir/pds_to_table.csv
tests/test_validate/testing_files/main_dir/pds_to_table.xlsx