LC/MS support in ChemSpectra#264
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This reverts commit 61c5d7c.
…poser, update dependencies to Flask 2.x and Gunicorn 22.x, and remove obsolete LCMS files. Introduce new chemotion converter profiles for LCMS.
Co-authored-by: Cursor <cursoragent@cursor.com>
…S image generation from peak.jdx files
…e ZIP responses with JCAMP and images
…t helper functions in share.py for improved filename handling
…ms functions, and clean up related code in chemotion_converter_lcms.py to streamline LCMS processing.
…improve retention of retention time source
…params functions, and implement data extraction for MS peaks in chemotion_converter_lcms.py to enhance LCMS processing.
…by refining active MS threshold handling and implementing conditional coloring for MS peaks based on the threshold. Default to 5% when the threshold is missing or uninitialized.
…upport for lcms_mz_page header extraction and conditional inclusion in JCAMP output.
… requests and refresh logic, enhancing data integrity checks and file reading methods. Update TransformerModel to ensure robust filename handling when retrieving JCAMP files.
…ra. Consolidate LCMS response building into dedicated helper functions, streamline parameter extraction, and enhance file handling for improved data integrity. Update configuration settings and remove unused code to optimize performance.
…Update to_zip_flat_bagit_response for single-level zips, enhancing file naming conventions and entry stem management. Adjust tests to reflect changes in UV/Vis handling within LCMS composer path.
…SConverterAppComposer for improved file response generation. Update TransformerModel to utilize build_lcms_composer for LC/MS file processing, ensuring robust handling of various data types. Refactor LCMSConverterAppComposer to include tf_csv method and optimize image preview logic.
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What this feature does
ChemSpectra can now process LC/MS data from OpenLab and ChemStation JCAMP exports (typical
.jdxworkflows from those stacks). The backend reads the.jdxfiles, builds previews and structured output for the UI.User-facing behaviour
Upload formats:
bagit.txtand spectra underdata/)..jdxfiles: same JCAMPs packaged without BagIt - either at the root of the zip or in one top-level folder (typical export layout).When LC/MS processing fails:
Technical scope (short)
Per-file JCAMP typing (MS / NI / LC/MS) drives routing. LC/MS files are merged through a dedicated composer and preview path; combined “multi-curve” images follow the same rules as for other BagIt content (LC/MS composers are excluded where needed).
LCMS-related request parameters (e.g. wavelength / mz page) are passed through in a clear, isolated way for the UI and processing.