Opened 5 years ago

Closed 5 years ago

#1206 closed enhancement (fixed)

The MIPs aliquot importer should handle some values as special cases

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: minor Milestone: Reggie v4.24.1
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Some of the columns in the file used for importing MIPs aliquots sometimes have special values that should be treated differently. This used to be a manual curation process before importing the file to BASE. Manually changing values is error prone so it would be a lot better to do this in the importer instead.

All full list cases is not yet available. Here is what we know so far:

  • The NormalTumor columns can have values that should be translated: NA --> null; TUMOR --> T. Other values are kept as is.
  • Variant: 0 --> null. Other values are kept as is.
  • More...

Change History (3)

comment:1 by Nicklas Nordborg, 5 years ago

Summary: The MIPs aliquot importer should be able to handle som special values → The MIPs aliquot importer should handle some values as special cases

comment:2 by Nicklas Nordborg, 5 years ago

In 5757:

References #1206: The MIPs aliquot importer should handle some values as special cases

Implemented the NormalTumor and Variant translations.

comment:3 by Nicklas Nordborg, 5 years ago

Resolution: → fixed
Status: new → closed

Closing this for now since we need to release the other bugfixes. If there are more special cases a new ticket should be opened.

Note: See TracTickets for help on using tickets.