Version 1 (modified by 12 years ago) ( diff ) | ,
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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 theInclude pooled
option checked. This should create a list with allNoSpecimen
items and their parentCase
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.
- TODO -- how to create a formula
- Save the result as a tab separated text file, upload it to BASE and use the annotation importer to import the laterality values.
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