Added get_approx_sample_header_replacement_regex which returns a regex to heuristically convert common sample headers into database sample names.
Added build_lcms_dict to turn sample headers from a peak annotation file and mzXML file names into an LCMS dict keyed on the unique header name and containing dicts whose keys are headers of the LCMS metadata format.
Modified form_valid to call build_lcms_dict with the appropriate arguments.
Created a class attribute to hold common header suffixes.
Modified set_files to build the file names if not supplied.
Added tests for the new methods.
Affected Issues/Pull Requests
Partially addresses #829
Partially addresses #888
Merges into #918
Next PR: #922
Review Notes
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Checklist
This pull request will be merged once the following requirements are met. The
author and/or reviewers should uncheck any unmet requirements:
Review requirements
Minimum approvals: 1
No changes requested
All blocking issues resolved by reviewers
Specific reviewers: @add_username_here
Review period: 2 days
Associated issue/pull request requirements:
[x] All requirements in affected issues marked "resolved" are satisfied
[x] All required pull requests are merged (or none)
Summary Change Description
Affected Issues/Pull Requests
Review Notes
See comments in-line.
Checklist
This pull request will be merged once the following requirements are met. The author and/or reviewers should uncheck any unmet requirements:
changelog.md
(or no change)