This topic is provided to help administrators and developers migrate specific features to the current release.

Extract-Transform-Load (ETL)

The ETL module has been removed from the Community Edition and the functionality has migrated to the dataintegration module, available with all Premium Editions. Premium clients will not experience any change in functionality or interruption in service.

Premium subscribers have access to a variety of LabKey features outside of the community edition as well as professional support. Learn more about LabKey Premium Editions.

The announcement made on the Developer Forum about this change can be found here.

Developers with premium clients who have enlisted in the version control project and will be using ETLs in 18.3 and beyond will need to take the following steps in order to continue to use the premium 'dataintegration' module from Git. (Learn more about working with Git modules here).

  1. To obtain access, you will need to provide your LabKey Account Manager with the username of your GitHub account if you have not already done so.
  2. Clone the dataintegration module into your optionalModules directory.
  3. Sync your svn enlistment to remove the old svn module.
  4. Add a line like this to your settings.gradle file:
include ":server:optionalModules:dataintegration"
  1. Execute these two commands in this order to ensure that you clear out the old copy and are solely building and running the module from Git:
gradlew cleanBuild
gradlew deployApp

Create Chart View

The deprecated chart creation tool was removed in 18.3. Existing chart views created by users will be automatically migrated to the current JavaScript visualization implementation in version 19.1.

Windows Installer Decommission

The LabKey Server Windows-only Graphical Installer will be decommissioned as part of the 18.3 release in November 2018. Moving forward, virtual machine images will be provided with each release as an alternate method for evaluating LabKey Server on-premise. We encourage new users looking to evaluate LabKey Server to take advantage of the cloud-hosted trial version of LabKey Server.

Upgrading Servers Installed with the Graphical Installer

If you used the Windows graphical installer in the past and want to update your LabKey Server, complete these steps:

  1. Backup your database to be safe and notify any users that the server will be down for a period of time. Place the database backup in the C:\labkey\backup\ location suggested and save the pg_dumpall output in the Notepad for use below.
  2. Create the recommended folder structure for your future LabKey installations.
  3. Set the environment variable CATALINA_HOME to the location of your tomcat installation. Following our recommended folder structure, this would be the following (substituting your actual version numbers for the # symbols):
    CATALINA_HOME = C:\labkey\apps\apache\apache-tomcat-#.#.##
  4. Backup the files in your previous installation: Open the C:\Program Files (x86)\LabKey Server directory. Right click on the files folder and select Send To > Compressed (zipped) folder to create a zip file. Move this zip file to C:\labkey\backup\.
  5. Delete the uninstaller, uninst.exe, that was bundled with the windows installer. You can find it under the C:\Program Files (x86)\LabKey Server directory.
  6. Confirm that you are running the recommended versions of Java, Tomcat, and Postgres. If you are upgrading any component, you should also delete the LabKey tomcat service LabKeyTomcat7 using the registry editor (regedit).
You should now be able to follow the procedures to upgrade your LabKey installation as if it was originally installed manually, using this topic: If you encounter any difficulties, the following details may be helpful.

Restoring PostgreSQl User and Backup

During the migration process, you can avoid making manual changes to the labkey.xml file and restore the database backup by completing these steps to configure the new installation after you have upgraded LabKey.

  1. After installing the new PostgreSQL version, locate the pgAdmin4.# utility and run it.
  2. Locate your server within pgAdmin. It will likely prompt you for the postgres user. Enter the password you found in the labkey.xml file.
  3. Double click on the "postgres" database to open it.
  4. Now right click on the postgres database and select the option for the Query tool.
  5. Copy the SQL that you saved when you did the pg_dumpall during backup, specifically the "Roles" section. It will look something like this:
    CREATE ROLE databaseusername;
    ALTER ROLE databaseusername WITH SUPERUSER INHERIT CREATEROLE CREATEDB LOGIN NOREPLICATION NOBYPASSRLS PASSWORD 'long-md5-32-character-password-hash';
  6. Paste these CREATE ROLE and ALTER ROLE lines from your notepad into the Query tool and click on the lightning bolt button to run the SQL. This will recreate the database user from your previous labkey.xml file with the same password so you don't need to edit the file again.
  7. Right click on 'databases' and select the option to create a new database. Name it "labkey". Make sure to assign the new user you just created as the owner of this new database.
  8. After the database is created, right-click on it again and select the option to restore the database. Select your backup file from C:\labkey\backup\labkey_migration_backup.bak and restore it.

Install LabKey and Restore Files Backup

  1. Follow the installation steps, making sure you install to the <LABKEY_HOME> directory (i.e. C:\labkey\labkey)
  2. Copy the listed JAR files from the tomcat-lib directory in the unzipped distribution to <CATALINA_HOME>\lib (Note: <CATALINA_HOME> is the location of your Tomcat installation.)
  3. Create the new directory C:\labkey\labkey\files
  4. Start the new Tomcat service and confirm that your new instance of LabKey is accessible.
  5. Once you've started the server, point the file root at the new location in order to automatically move the files to the new location.
    • Select (Admin) > Site > Admin Console.
    • Click Admin Console Links.
    • Under Configuration, click Files.
    • Change the Site-Level File Root to C:\labkey\labkey\files.
    • Click Save and the files will be moved for you.

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