Changes between Initial Version and Version 1 of Ticket #1252


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Timestamp:
Jun 4, 2020, 1:45:06 PM (5 years ago)
Author:
Nicklas Nordborg
Comment:

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  • Ticket #1252 – Description

    initial v1  
    1 It is the same problem as in #1238. The `SSP_*_SCORE` annotations should be defined as TEXT type. Existing SSP annotations need to be removed, and the SSP plug-in re-executed.
     1It is the same problem as in #1238. The `SSP_*_SCORE` annotations should be defined as TEXT type. Existing SSP annotations need to be removed, and the SSP plug-in re-executed.
     2
     3The update process involves some manual steps:
     4
     5 1. Export a file with the ID of all !StringTie raw bioassays that already have one or more SSP annotaions. No other columns are needed. The Excel format can be used. Save to exported file to the local computer.
     6 2. Add headers to the exported file for all SSP annotation types:
     7{{{
     8SSP_CC15
     9SSP_CC15_Scores
     10SSP_ER
     11SSP_ER_Scores
     12SSP_ERBB2
     13SSP_ERBB2_ERn
     14SSP_ERBB2_ERn_Scores
     15SSP_ERBB2_ERp
     16SSP_ERBB2_ERp_Scores
     17SSP_ERBB2_Scores
     18SSP_IntClust10
     19SSP_IntClust10_Scores
     20SSP_Ki67
     21SSP_Ki67_Scores
     22SSP_NHG
     23SSP_NHG_Scores
     24SSP_PAM50subtype
     25SSP_PAM50subtype_Scores
     26SSP_PR
     27SSP_PR_Scores
     28SSP_RORasT0
     29SSP_RORasT0_Scores
     30SSP_Subtype
     31SSP_Subtype_Scores
     32}}}
     33Use the attachment:headers-for-import.txt file as template.
     34
     35 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.
     36 4. When all annotations have been deleted it should be possible to delete all SSP_* annotation types as well. Do not forget to empty the trashcan.
     37 5. Update Reggie and run the **Installation wizard**. The SSP annotation types should be re-created.
     38 6. All existing !StringTie raw bioassays need to be re-analyzed by the SSP plug-in.