Improves form merging, cli output, & table mapping#67
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- Now also checks which columns in the mapping file are not contained in the REDCap input - this is useful especially when there are updates to the REDCap schema
- Reduces read_csv verbosity by setting show_col_types to False - Adds header & cleans get_overflow_mapping_table cli output
- Updates cli output accordingly - Adds incomplete key (previously hard-coded) & notes_cols to config file
- The way uncertainty is captured in REDCap has been updated and an improved mapping is now possible - Uses raw col names to be consistent with previous mapping
- These have been replaced with different columns following the uncertainty capturing update in REDCap
- Parameter uncertainty - single type & Parameter uncertainty - single value were swapped
sangeetabhatia03
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Apr 17, 2025
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sangeetabhatia03
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sangeetabhatia03
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thanks @tristan-myles
The changes look very good; I have not checked the code or the outputs, just made sure the tasks ran for me and the output messages made sense.
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Adds smarter merging of articles when there are form continuations.
Updates the mapping_table using Zika raw column names, reflecting the REDCap uncertainty-capturing update.
Fixes Pathogen filtering bug - NA pathogen columns were erroneously included.
Improves cli output of prepare_redcap.