#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 Changed 12 months ago by Nicklas Nordborg

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

comment:2 Changed 12 months ago by Nicklas Nordborg

In 5757:

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

Implemented the NormalTumor and Variant translations.

comment:3 Changed 12 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed

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

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