= Updating to Reggie 2.13 = The following items should be performed after updating to Reggie 2.13. === 1. Flag some libraries and their parent RNA item === Due to a bug (see #508), libraries which got a Qubit concentration measurement of '''0 ng/µl''' have been left in a dead end state. To ensure that new RNA is extracted in the future, a flag must be set manually and the parent RNA items must be added to the '''Flagged RNA''' list. 1. To find the libraries in question go to the '''Biomaterial LIMS->Extracts''' page and filter on '''Type=Library''' and '''CA_Molarity=0'''. 2. Edit each library item and set the annotation: '''Flag=!ExcludedFromPool'''. 3. Find the parent RNA item for each library and set the annotation: '''Flag=!ExcludedFromPool'''. 4. Add all parent RNA items to the '''Flagged RNA''' biomaterial list. 5. Check that the selection list in the '''Create pooled libraries''' no longer include already registered library plates. === 2. Fix !PoolConc values for all *.dil extracts === Due to a bug (see #507), all `*.dil` extracts have been registered with an incorrect value for the '''!PoolConc''' annotation. This need to be fixed by a manual export/import procedure. 1. To find the libraries in question go to the '''Biomaterial LIMS->Extracts''' page and filter on '''name=%.dil'''. 2. To avoid rounding errors in the exported data go to '''BASE->Preferences''' and set '''Decimals=all'''. 3. Use the '''Table exporter''' plug-in to export a tab-separated file with '''Name''' and '''Original quantity''' columns. 4. Download the exported file to your computer and open in a spreadsheet program. 5. Add a new column '''!PoolConc''' and use the following formula to calculate the values: `=1000 * / 5` 6. Save the results as a tab-separated file and upload it to BASE. 7. Use the annotation importer to update the '''!PoolConc''' values. === 3. Copy missing consent information from blood to case items === Due to a bug (see #511) consent information that has already been registered on blood samples with '''!BloodSample=!PreNeo''' has not been copied to cases that was registered at a later time. To fix this a manual crossmatch is required to find which cases are missing consent information that is available on a blood item. 1. Find all cases with missing consent information. Export a list with the case names to a tab-separated file. 2. Find all '''!PreNeo''' blood items that has consent information. Export the blood name, '''Consent''' and '''!ConsentDate''' columns to a tab-separated file. 3. Use a spreadsheet program to crossmatch the case names with the blood names. 4. Copy the found consent information to new columns in the list with cases. 5. Save the result as a tab-separated file and upload it to BASE. 6. Use the annotation importer to import values for '''Consent''' and '''!ConsentDate''' to the cases.