Convert variants annotations to TEXT type

[Nicklas Nordborg]

The annotation types are currently created with STRING type (see #1229 [5872]). The problem with this is that the STRING data type has a limit of 255 characters. If several variants are found in the same gene the value can be longer than this. For example, we got the following error message:

Error: String too long. The 'PTEN_Variants' mustn't be longer than 255 characters. 
The supplied value 'chr10:87864283:G>T,...' is 418 characters.

Unfortunately it is not possible to change the value type for annotation types. We need to remove all existing annotations and delete the existing annotation types before we can re-create annotation types and run the batch importer again.

1. Export a file with the ID of all variant call raw bioassays. No other columns are needed. The Excel format can be used.
2. Add headers to the exported file for each of the 21 variant annotation types:

   AKT1_Variants
   ARHGAP35_Variants
   ARID1A_Variants
   CBFB_Variants
   CDH1_Variants
   ERBB2_Variants
   ESR1_ResistanceVariants
   FOXA1_Variants
   GATA3_Variants
   KMT2C_Variants
   MAP3K1_Variants
   NFIC_Variants
   PIK3CA_Variants
   PLEC_Variants
   PTEN_Variants
   RNF213_Variants
   RUNX1_Variants
   SF3B1_Variants
   TBX3_Variants
   TP53_Variants
   TRPS1_Variants
   

Use the attachment:headers-for-import.txt​ file as template.

3. Upload the file to BASE and run the Annotation importer plug-in. Make sure that Identification method=Internal ID, that all columns are mapped correctly and that the Remove existing option is enabled in the third step.
4. When all annotations have been deleted it should be possible to delete the 21 annotation types as well.
5. Also delete the Import variants from existing variant calls item list.
6. Empty the trashcan so that the 21 annotation types and item list is properly removed.
7. Update Reggie and run the Installation wizard.
8. Run the Import variants for existing variant call raw bioassays.

[Nicklas Nordborg]

A tab-separated file with headers to use in the import step

[Nicklas Nordborg]

In 5912:

Fixes #1238: Convert variants annotations to TEXT type