Various improvements to support the build-a-submission interface.
Details:
PeakAnnotationFilesLoader
To support auto-fill of compounds parsed from the peak annotation files without loading, None records were included in the compound return from the parsing of the compound column so that the interface could decide whether to use the given string for the peak group name or the primary compound names.
Added a get_default_sequence_details method split off from load_peak_annotations method on the PeakAnnotationFilesLoader, so that other code could re-use the parsing code for the sequence name columns loacated in different sheets.
TableLoader
Added an option to TableLoader's methods: check_dataframe_headers and check_dataframe_values to be able to return the status without raising or buffering an error. This allows us to just read the file without buffering errors or loading anything, which facilitates the autofill-only mode.
Added a private class version of TableLoader's get_column_types so that files could be read with types without having to build an object just to get the types for the pandas' reading methods.
Affected Issues/Pull Requests
Partially addresses #829
Merges into: #1019
Next PR: #1021
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 is the second PR split off from #1015.
Various improvements to support the build-a-submission interface.
Details:
PeakAnnotationFilesLoaderNonerecords were included in the compound return from the parsing of the compound column so that the interface could decide whether to use the given string for the peak group name or the primary compound names.get_default_sequence_detailsmethod split off fromload_peak_annotationsmethod on thePeakAnnotationFilesLoader, so that other code could re-use the parsing code for the sequence name columns loacated in different sheets.TableLoaderTableLoader's methods:check_dataframe_headersandcheck_dataframe_valuesto be able to return the status without raising or buffering an error. This allows us to just read the file without buffering errors or loading anything, which facilitates the autofill-only mode.TableLoader'sget_column_typesso that files could be read with types without having to build an object just to get the types for the pandas' reading methods.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)