wiki:net.sf.basedb.reggie.notes27

Updating to Reggie 2.7

Updating to Reggie 2.7 require some manual changes to the NoSpecimen items that already exists. This is required since we have not stored the LATERALITY for those items. We need to check the laterality on the parent Case item and copy that information to the NoSpecimen items that doesn't have a value. For more information see ticket:399.

Follow this procedure:

1. Update to Reggie 2.7

2. Generate a list of all NoSpecimen items without laterality

  • Go to the samples list page and filter on `NoSpecimen?' and no laterality.
  • Export the name and parent of all items found and save that to the local computer.
  • Create a biomaterial list with Member type=Sample and the Include pooled option checked. This should create a list with all NoSpecimen items and their parent Case items.

3. Generate a list of all Case items

  • Change the filter on the samples list page to list Case items. Remove all other filters.
  • Display the Biomaterial list column and use the biomaterial list created above as a filter.
  • Export the name and laterality for all cases that are found and save that to the local computer.

4. Use Excel/OpenOffice or compatible to map laterality to NoSpecimen

  • The two files that has been exported should include all information that is needed to find the laterality for a given NoSpecimen item. With a spreadsheet program as Excel it should be possible to create a formula to do this.
  • OpenOffice has the LOOKUP formula that can be used. Open both files and copy the information to two sheets in the same document. In the sheet with the NoSpecimen items create a formula that uses LOOKUP on the Case name to find the laterality from the other sheet.
  • Save the result as a tab separated text file, upload it to BASE and use the annotation importer to import the laterality values.
Last modified 5 years ago Last modified on May 31, 2012, 11:42:53 AM