Opened 4 months ago

Closed 4 months ago

#1252 closed defect (fixed)

Convert SSP score annotations to TEXT type

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v4.27.2
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

It is the same problem as in #1238. The SSP_*_Scores annotations should be defined as TEXT type. Existing SSP annotations need to be removed, and the SSP plug-in re-executed.

The update process involves some manual steps:

  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.
  2. Add headers to the exported file for all SSP annotation types:
    SSP_CC15
    SSP_CC15_Scores
    SSP_ER
    SSP_ER_Scores
    SSP_ERBB2
    SSP_ERBB2_ERn
    SSP_ERBB2_ERn_Scores
    SSP_ERBB2_ERp
    SSP_ERBB2_ERp_Scores
    SSP_ERBB2_Scores
    SSP_IntClust10
    SSP_IntClust10_Scores
    SSP_Ki67
    SSP_Ki67_Scores
    SSP_NHG
    SSP_NHG_Scores
    SSP_PAM50subtype
    SSP_PAM50subtype_Scores
    SSP_PR
    SSP_PR_Scores
    SSP_RORasT0
    SSP_RORasT0_Scores
    SSP_Subtype
    SSP_Subtype_Scores
    

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

  1. 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.
  2. 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.
  3. Update Reggie and run the Installation wizard. The SSP annotation types should be re-created.
  4. All existing StringTie raw bioassays need to be re-analyzed by the SSP plug-in.

Attachments (1)

headers-for-import.txt (356 bytes) - added by Nicklas Nordborg 4 months ago.

Download all attachments as: .zip

Change History (5)

comment:1 Changed 4 months ago by Nicklas Nordborg

Description: modified (diff)

Changed 4 months ago by Nicklas Nordborg

Attachment: headers-for-import.txt added

comment:2 Changed 4 months ago by Nicklas Nordborg

In 5963:

References #1252: Convert SSP score annotations to TEXT type

Annotation types for SSP scores are now created with the TEXT type.

comment:3 Changed 4 months ago by Nicklas Nordborg

Description: modified (diff)

comment:4 Changed 4 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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