This was the direction I started in WRT #976. I basically was cleaning up the get_msrun_sequence method and cleared up some of the if conditionals that did not previously distinguish between lines from the input file that had no sequence name versus mzXML file loads that were not present in the infile. In fact, then code originally was written to avoid potential errors from the sequence defaults provided on the commentd line if in fact the defaults were not actually needed (i.e. everything was provided with values in --infile).
While I was at it, I finished a half-assed attempt I had never completed due to a change in direction: and that was the ability to supply only some of the options: --instrument, --operator, --date, and --lc-protocol-name. I'd realized part-way through the original effort that it's pretty likely that for example, only the date was enough to uniquely identify a sequence. That's why I added an exception in this effort called MultipleRecordsReturned (which inherits from both InfileError and MultipleObjectsReturned).
Affected Issues/Pull Requests
Partially addresses #976
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)
Summary Change Description
This was the direction I started in WRT #976. I basically was cleaning up the
get_msrun_sequencemethod and cleared up some of theifconditionals that did not previously distinguish between lines from the input file that had no sequence name versus mzXML file loads that were not present in the infile. In fact, then code originally was written to avoid potential errors from the sequence defaults provided on the commentd line if in fact the defaults were not actually needed (i.e. everything was provided with values in--infile).While I was at it, I finished a half-assed attempt I had never completed due to a change in direction: and that was the ability to supply only some of the options:
--instrument,--operator,--date, and--lc-protocol-name. I'd realized part-way through the original effort that it's pretty likely that for example, only the date was enough to uniquely identify a sequence. That's why I added an exception in this effort calledMultipleRecordsReturned(which inherits from bothInfileErrorandMultipleObjectsReturned).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)