= Updating to Reggie 2.13 =

'''IMPORTANT! ''' Item 1 must be done '''BEFORE''' installing the update. Items 2-4 can be done after upgrading.


=== 1. Make sure that pools have been registered ===

Make sure that all created pools have been completed in the lab and registered. Eg. the '''Lab protocols for pooling''' and '''Register pooled libraries''' wizards should display (0) items waiting for registration. Otherwise the lab protocols will show incorrect mixing values.

=== 2. 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.

=== 3. 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: `=5 * <quantity> / 1000`
 6. Save the results as a tab-separated file and upload it to BASE.
 7. Use the annotation importer to update the '''!PoolConc''' values.

=== 4. 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.