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R/qtl2 bundles can contain more than one file, of the same type. When
errors are encountered in any of the files, we need to be able to
inform the user which file it is, in addition to the line and column
number.
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The number columns in each contents line should be equal to the nember
of columns in the header line.
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Remove the old code that relied on exceptions to parse errors in the
uploaded files.
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- replace `line_number` with `line` and `column_number` with `column`
to save on slot name lengths.
- Fix the type name for the `DuplicateHeading` namedtuple type
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This commit adds a number of functions that return the error object
when an error is found, or `None` otherwise. It avoids the use of
exceptions as control flow constructs.
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* qc_app/entry.py: Pass filetype onward to parsing endpoint
* qc_app/parse.py: Call the function(s) necessary to parse a file
* quality_control/errors.py: Fix argument passing to super class
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* Improve tests that ensure parsing fails in case the file has errors
* Add strains.csv file
* Implement minimum viable functionality that passes the implemented tests
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Change the exception name to be more descriptive.
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* Add tests to check for validity of the headers
* Add stubs for the tests
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