tempo-mpgen column names inconsistent with schema

[anoronh4]

I have looked into a couple of column names and found that they change a bit from IGO to SMILE to tempo-mpgen and just wanted clarify and get it on your radar.

IGO	SMILE	tempo-mpgen python	Voyager	sample_tracker.txt	Example value
cmoSampleName	sampleType	sample_class	sampleType	not shown	Adjacent Tissue
specimenType	sampleClass	specimen_type	sampleClass	Sample_Class_(T/N) and sampleClass	RapidAutopsy
tumorOrNormal	tumorOrNormal	tumorOrNormal	tumorOrNormal	tumorOrNormal	Tumor

One issue with the first item is that this column is used in pairing to define whether a sample is normal or tumor, but it is not available in table form for downstream inspection or displaying in the tracker. tumorOrNormal is included in the sample_tracker.txt, but not used at all for pairing. This is creating some confusion with PMs when trying to debug.

I found the names used in tempo-mpgen code here:
https://github.com/mskcc/beagle/blob/master/runner/operator/tempo_mpgen_operator/bin/tempo_sample.py#L30-L31
Although voyager's names match the Schema v2.0, i found that using different names in beagle code made it more difficult to trace how samples are being organized with tempo-mpgen.

[allanbolipata]

Unfortunately, a lot of this is my fault - the field names across the different databases are so similar that it's become convoluted and lost a lot of meaning.

We can, however, re-map them to something more suitable for a future release. If you have a preference on column names and value mapping, let us know.