The Peak Annotations files all use El-Maven style labels, and I wanted to put that parsing code in a utilities file. The accucor loader doesn't use the isotopeLabel column (even though it's there), and I wanted to make it universal, so I made all the peak annotation loaders use the same code, so I added a parse_isotope_label method to the (poorly named) infusate_name_parser.py utils file. (I wanted to rename that file, but I couldn't think of a good name, so I left it alone).
Some of the parsing exception names were changed to make these changes durable (so that the accucor loader still works).
Note, the PR associated with this change does not (by itself) need to merge into the converted table loader branch, but the changes in this PR and the next PR are all needed (along with the PRs thus far) by the peak annotations loader PR. That's why this and the next PR are a part of the chain - because you can't merge into multiple PRs.
Affected Issues/Pull Requests
Partially addresses #825
Merges into #994
Next PR: #996
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:
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)
hepcat72
commented
2 months ago
Summary Change Description
The Peak Annotations files all use El-Maven style labels, and I wanted to put that parsing code in a utilities file. The accucor loader doesn't use the
isotopeLabelcolumn (even though it's there), and I wanted to make it universal, so I made all the peak annotation loaders use the same code, so I added a parse_isotope_label method to the (poorly named) infusate_name_parser.py utils file. (I wanted to rename that file, but I couldn't think of a good name, so I left it alone).Some of the parsing exception names were changed to make these changes durable (so that the accucor loader still works).
Note, the PR associated with this change does not (by itself) need to merge into the converted table loader branch, but the changes in this PR and the next PR are all needed (along with the PRs thus far) by the peak annotations loader PR. That's why this and the next PR are a part of the chain - because you can't merge into multiple PRs.
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)