Multiple MAF file Produced by GDC are not able to be imported into the GDC

[rosibaj]

1. Go to the collab test environment, and upload variants for HCM-BROD-0002-C71 (http://hcmi.cancercollaboratory.org/admin/model/HCM-BROD-0002-C71). You will see the multiple MAF error:

2. Investigating the model on GDC link here, you can see that there are 3 open MAF files:

   • First is Primary Tumour sample type
   • Second is Expanded Next Generation Cancer Model sample type
   • Third is Next Generation Cancer Model sample type

While both of these values are allowed (code reference for Next Generation Cancer Model files, having both on a single model is indistinguishable as to which one the importer should pick.

Questions:

1. Is there a precedence between open-MAFS selected between Expanded Next Generation Cancer Model vs Next Generation Cancer Model
2. It was deisded on June 06, 2020 that the design presented by OICR that accounted for this issue should not be used. An import should only proceed if in fact a model had one and only one uniquely identifiable file from GDC. The original design presented by OICR was like so in the event that a model had > 1 NGCM MAFs available from the GDC API. Is it better to instead return to the original design? This would need to be worked into bulk import designs.

[rosibaj]

Closing this ticket as it has been addressed with the several other tickets in this epic.