feat: handle zip lcms

[baolanlequang]

No description provided.

[Copilot]

Pull Request Overview

This PR introduces support for LCMS (Liquid Chromatography–Mass Spectrometry) data by adding a new converter (LCMSBaseConverter), composer (LCMSComposer), integrating them into the transformer model and API endpoint, and providing unit tests to validate the end-to-end flow.

• Added tests/lib/converter/lcms/test_lcms_converter.py to verify raw CSV reading into structured data.
• Added tests/lib/composer/test_lcms_composer.py to ensure JCAMP-DX generation for TIC, UV-VIS, and m/z spectra.
• Updated TransformerModel, transform_api.py, and new composer/converter modules to wire LCMS support into the existing pipeline.

Reviewed Changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/lib/converter/lcms/test_lcms_converter.py	New unit tests for LCMSBaseConverter
tests/lib/composer/test_lcms_composer.py	New unit tests for LCMSComposer
chem_spectra/model/transformer.py	Integrated LCMS detection and dispatch in TransformerModel
chem_spectra/lib/converter/lcms/base.py	Implemented LCMSBaseConverter for reading LCMS CSV files
chem_spectra/lib/composer/lcms.py	Implemented LCMSComposer for JCAMP-DX output
chem_spectra/controller/transform_api.py	Extended API to handle LCMSComposer responses

Comments suppressed due to low confidence (4)

tests/lib/converter/lcms/test_lcms_converter.py:5

• There's a typo in the alias: LCMSConveter should be LCMSConverter to match the class name.

from chem_spectra.lib.converter.lcms.base import LCMSBaseConverter as LCMSConveter

tests/lib/composer/test_lcms_composer.py:92

• This test function duplicates the name of the positive m/z test defined at line 77; rename one to test_lcms_composer_mz_spectra_negative to avoid collision.

def test_lcms_composer_mz_spectra_positive(zip_file):

chem_spectra/controller/transform_api.py:83

• [nitpick] The spc_type for LCMSComposer is set to 'hplc', which may be confusing. Consider using 'lcms' to reflect the actual data type.

rsp.headers['X-Extra-Info-JSON'] = json.dumps({'spc_type': 'hplc', 'invalid_molfile': invalid_molfile})

chem_spectra/lib/converter/lcms/base.py:31

• There's a typo in the variable name tic_postive_data; it should be tic_positive_data to maintain consistency and avoid confusion.

tic_postive_data = data_frame.to_dict(orient='list')

[Copilot]

Concatenating a string into a list using += will split it into characters. Use msspc.append(my_content) or msspc += [my_content] instead.

Suggested change

	msspc += my_content
	msspc.append(my_content)

[Copilot]

The m/z spectra composer mistakenly includes the UVVIS category header. Replace this line with the appropriate category variable or remove it to avoid conflicting headers.

Suggested change

'##$CSCATEGORY=UVVIS SPECTRUM\n',