Add support for xia2.multiplex data processing in pdb_deposition - #91
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Add support for xia2.multiplex data processing in pdb_deposition#91tdudgeon wants to merge 2 commits into
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The SoakDB DataProcessingProgram value for xia2.multiplex crystals is "xia2.multiplex <group>" (free-text suffix), and its logfile is an HTML report rather than a plain-text log, both of which caused pdb_deposition to fail. Normalize the program name, add a matching xia2/DIALS software template, and add an HTML table parser for the processing stats. Also add unit tests covering all data-processing types dispatched by scrape_processing_stats.handle_file (autoproc, autoproc_staraniso, xia_3dii, xia2-multiplex), using real excerpts pulled from data/std_test. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
pdb_depositionfailed on crystals processed withxia2.multiplex: the SoakDBDataProcessingProgramvalue is free text ("xia2.multiplex <group>"), its logfile is an HTML report rather than a plain-text log, and there was no matching_softwaretemplate — normalize the program name toxia2-multiplex, add an HTML table parser for its processing stats, and add a matching xia2/DIALS software template.scrape_processing_stats.handle_file(autoproc,autoproc_staraniso,xia_3dii,xia2-multiplex), using real excerpts pulled fromdata/std_test.Test plan
pytest tests/test_scrape_processing_stats.py(20 new tests, all passing)pytest tests/(excluding the slow integration test) — 79 tests passingpython -m pdbdepo.pdb_depositionend-to-end against theRFKAT2B-x0002(nr23571-141) collator output — completes with zero errors/warnings, and the generated_struc.cifhas correct_software/_reflns/_reflns_shellvalues matching the sourcexia2.multiplex.htmlreport.black/pylintpre-commit hooks pass🤖 Generated with Claude Code