Changes between Initial Version and Version 1 of net.sf.basedb.reggie.notes27

May 31, 2012, 11:27:56 AM (11 years ago)
Nicklas Nordborg

Adding page about updating to reggie 2.7


  • net.sf.basedb.reggie.notes27

    v1 v1  
     1= Updating to Reggie 2.7 =
     3Updating 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.
     5Follow this procedure:
     7== 1. Update to Reggie 2.7 ==
     9== 2. Generate a list of all `NoSpecimen` items without laterality ==
     11 * Go to the samples list page and filter on `NoSpecimen' and no laterality.
     12 * Export the name and parent of all items found and save that to the local computer.
     13 * 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.
     15== 3. Generate a list of all `Case` items ==
     17 * Change the filter on the samples list page to list `Case` items. Remove all other filters.
     18 * Display the `Biomaterial list` column and use the biomaterial list created above as a filter.
     19 * Export the name and laterality for all cases that are found and save that to the local computer.
     21== 4. Use Excel/OpenOffice or compatible to map laterality to `NoSpecimen` ==
     23 * 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.
     25 * TODO -- how to create a formula
     27 * Save the result as a tab separated text file, upload it to BASE and use the annotation importer to import the laterality values.