Warnings and errors are not always reflected in the UI

[williamdlees]

Ideally, all warnings or errors should be available from the UI, so that the utility can be run on an unattended server and accessed over the web. However some are not. As an example, I inadvertently ran the tool on a changeo file instead of an airr file. The reported error in the UI was 'Error: 'x' must be numeric but there was a much more informative error in the console:

Warning in validate_airr(data, schema = schema) :
Warning: File is missing AIRR mandatory field(s): sequence_id, sequence, rev_comp, productive, v_call, d_call, j_call, sequence_alignment, germline_alignment, junction, junction_aa, v_cigar, d_cigar, j_cigar

Also - perhaps processing should have stopped at this point?

[ssnn-airr]

There is a lot of error/warning/message handling to do. I made a specific issue for not AIRR-C compliant files.