As part of installing required components, you need to install a database server. You can use either PostgreSQL or Microsoft SQL Server as the primary database with a Premium Edition of LabKey Server. This topic covers the process of setting up a Windows machine to use Microsoft SQL Server as the primary database. Information about other environments is provided below.

Install and Configure Microsoft SQL Server

For current supported versions of Microsoft SQL Server, see Supported Technologies.

Basic Installation Topics:

• Install Microsoft SQL Server
• Configure During Installation
• Using SQL Server with a Local Development Machine
• Configure TCP/IP
• SQL Server Management Studio
• Set Up a Login
• LabKey Configuration File
• Add MS SQL Server Resource Tag

• Install CLR Functions (GROUP_CONCAT)
• SQL Server Synonyms
• Installation on Other Platforms
• Linux Deployment
• Docker Deployment on Mac/OSX
• Docker Deployment on Windows
• Using Windows/Domain Authentication
• Switch from jTDS to Microsoft JDBC Driver

Install Microsoft SQL Server

If you already have a licensed version of Microsoft SQL Server in a supported version, follow the installation instructions noting the requirements outlined for installing an express edition below.

If you don't have a licensed version of Microsoft SQL Server, you can download a free Express Edition. Note that the Express Edition has database size limitations that generally make it inappropriate for production deployments. You can also use the Developer Edition; details may differ slightly from instructions in this topic.

• Microsoft SQL Server 2019 Express: https://www.microsoft.com/en-us/download/details.aspx?id=101064

Configure During Installation

During installation, configure Microsoft SQL Server to accept both Windows Authentication and SQL Server Authentication, ("Mixed Mode"), and specify a user name and password for the administrative account.

Using SQL Server with a Local Development Machine

Follow the general steps to set up a development machine, with a few exceptions noted below:

• Set Up a Development Machine

2. Instead of configuring your pg.properties file, use the one for use with Microsoft SQL Server (mssql.properties), specifying JDBC settings, including URL, port, username, password, etc.

3. Instead of running "gradlew pickPg" to pick up the properties file, run:

gradlew pickMSSQL

Configure TCP/IP

After you've installed SQL Server, you'll need to configure it to use TCP/IP. Follow these steps:

SQL Server Management Studio

Download the SQL Server Management Studio graphical database management tool.

Set Up a Login

You may want to set up a new login (in addition to the "sa" system administrator) for LabKey Server to use to connect to SQL Server:

LabKey Configuration File

Edit the LabKey Server configuration file (usually named labkey.xml or ROOT.xml) to configure the JDBC driver for Microsoft SQL Server, available with Premium Editions of LabKey Server.

Comment out the Resource tag that specifies the PostgreSQL configuration. This Resource tag can be identified by the driverClassName "org.postgresql.Driver". Use "<!--" and "-->" to comment it out, similar to the following:

Comment out PostgreSQL Resource Tag

<!--
    <Resource name="jdbc/labkeyDataSource" auth="Container"
        type="javax.sql.DataSource"
        username="postgres"
 ...
        validationQuery="SELECT 1"
        />
-->

Add MS SQL Server Resource Tag

Use the following template for configuring a MS SQL Server data source. Replace USERNAME, PASSWORD, SERVER_NAME, and DATABASE_NAME to fit the particulars of your target data source. If your SQL Server is not using port 1433 (the default), edit that part of the URL as well.

<Resource name="jdbc/labkeyDataSource" auth="Container"
  type="javax.sql.DataSource"
  username="USERNAME"
  password="PASSWORD"
  driverClassName="com.microsoft.sqlserver.jdbc.SQLServerDriver"
url="jdbc:sqlserver://SERVER_NAME:1433;databaseName=DATABASE_NAME;trustServerCertificate=true;applicationName=LabKey Server;"
  maxTotal="20"
  maxIdle="10" 
  maxWaitMillis="120000" 
  accessToUnderlyingConnectionAllowed="true"
  validationQuery="SELECT 1"
/>

Note: In the url parameter, "trustServerCertificate=true" is needed if SQL Server is using a self-signed cert that Java hasn't been configured to trust. The applicationName isn't required but identifies the client to SQL Server to show in connection usage and other reports. For production environments, adding the certificate to a trust store enable it validation. See the driver documentation for details on these configuration options.

Note: The maxWaitMillis parameter is provided to prevent server deadlocks. Waiting threads will time out when no connections are available rather than hang the server indefinitely.

Install CLR Functions (GROUP_CONCAT)

When setting up SQL Server, you may need to separately install the GROUP_CONCAT Common Language Runtime (CLR) function. For details see GROUP_CONCAT Install.

You may also need to install the PremiumStats CLR functions separately. For details see PremiumStats Install.

EHR users may also need to install LDKNaturalize, following similar methods.

SQL Server Synonyms

LabKey Server supports the use of SQL Server Synonyms. These alternative names function like shortcuts or symlinks, allowing you to "mount" tables and views which actually exist in another schema or database. For more information, see SQL Synonyms.

Installation on Other Platforms

Linux Deployment

Microsoft distributes a native Linux version. Obtain it and follow the documentation available here:

• https://www.microsoft.com/en-us/sql-server/sql-server-downloads

Docker Deployment on Mac/OSX

1. Install Docker.

2. Load the SQL Server docker image. Learn more about this here.

• Note that M1/arm64 MacBooks aren't compatible with Docker-based SQL Server but can use Azure SQL Edge.

  docker pull mcr.microsoft.com/mssql/server:2019-latest

docker run -e 'ACCEPT_EULA=Y' -e 'MSSQL_SA_PASSWORD=Strong!Passw0rd' -p 1401:1433 --name mssql -d mcr.microsoft.com/mssql/server:2019-latest

• Use a strong password (not the password shown above, or something simple like 'sa').
• Specify whatever available port you want (1401 here)
• Give it whatever name you want. This will be how you start/stop the Docker container (mssql here)

gradlew pickMSSQL

5. Start tomcat.

Docker Deployment on Windows

The Linux edition of SQL Server is also available within a Docker container:

• https://www.microsoft.com/en-us/sql-server/sql-server-downloads.

Steps to deploy SQL Server in Docker on a Windows machine:

1. Install a stable version of Docker for Windows, accepting the default settings in the installer dialog.

2. Restart your PC, if it does not automatically restart.

• Note that you may see a warning about Hyper-V not being enabled yet. If so, click cancel. We will enable it manually.

DOCKER_CERT_PATH=C:
DOCKER_HOST=tcp://192..xx.xx.xxx:2376
DOCKER_MACHINE_NAME=default
DOCKER_TLS_VERIFY=1

4. Enable Hyper-V by going to Turn Windows features on or off and checking all Hyper-V boxes. Click OK.

5. Make sure Virtualization is enabled by checking your Windows Task Manager. Find it on the Performance tab under the grid for CPU usage. If it is not enabled, check the troubleshooting documentation available from Docker.

6. Restart your PC. Docker should start during this reboot. Follow status from the icon on the taskbar.

7. Use Windows Powershell to test the installation:

docker run hello-world

8. If the test is unsuccessful, install Docker Toolbox for Windows and restart, then try again.

9. Once the test is successful, you can pull the SQL Server image for linux from the Docker registry. Find the specific featured tag to pull on this page. For example:

docker pull mcr.microsoft.com/mssql/server:2019-latest

10. Once completed, run:

docker image ls

11. You should now see microsoft/mssql-server-linux listed in the Docker image cache.

12. Run SQL Server:

docker run -e 'ACCEPT_EULA=Y' -e 'MSSQL_SA_PASSWORD=<your strong password>' -p 1401:1433 --name mssql -d microsoft/mssql-server-linux:2019-latest

13. View your SQL Server container up and running:

docker ps -a

14. Connect to SQL Server via SQL Server Management Studio using:

• Server name: your Server name followed by a comma and the port number
• Authentication: Login "sa" with your new strong password

16. If desired, you can use disable the automatic start of Docker by editing the settings.

For troubleshooting assistance with this process, review the Docker documentation.

Using Windows/Domain Authentication

In some organizations, you may want or need to use Windows/Domain Authentication instead of SQL Server Authentication. This option should be considered carefully, as access to LabKey Server will depend on a successful login in the domain/Active Directory. If a problem occurs, like an expired profile or if Active Directory is either down or having issues, this will prevent the Windows-based authentication to SQL Server.

In order to use Windows/Domain Authentication you need to add the integratedSecurty parameter to the URL string in your data source tag:

url="jdbc:sqlserver://localhost:1433;databaseName=DATABASE_NAME;trustServerCertificate=true;applicationName=LabKey Server;integratedSecurity=true"

In addition, you need to install the MSSQL JDBC Auth DLL file within the driver package; it is not included by default. You can download the matching version of the full driver from Microsoft directly. The error message you see will guide you to the expected version and specific file name. Find the DLL in the auth > x64 subfolder, download it, and put it into the Windows/System32 directory.

If this DLL is not present, you'll see an error message similar to:

Message: This driver is not configured for integrated authentication. ClientConnectionId:##### SQLState: 08S01 ErrorCode: 0
com.microsoft.sqlserver.jdbc.SQLServerException: This driver is not configured for integrated authentication. ClientConnectionId:#####
...
java.lang.UnsatisfiedLinkError: Unable to load authentication DLL mssql-jdbc_auth-10.2.1.x64

Switch from jTDS to Microsoft JDBC Driver

Support for the jTDS driver was removed in 23.3 (March 2023).

If you are currently using the jTDS driver with a development machine, the next time you pull from develop and run 'gradlew pickMSSQL' you'll start using the new driver. If you need to switch back for some reason, you can use the target 'gradlew pickJtds' to return to using the jTDS driver.

For other instances, you will need to update the data source driver's class and URL in the labkey.xml/ROOT.xml file. See the configuration template above, particularly the driverClassName and url lines. We recommend that you first upgrade your staging (and/or test) instance(s), and upgrade production after testing is completed.

Note that if you are using Windows domain authentication, you will need to obtain and install a different DLL than you needed for the jTDS driver.

Related Topics

• Supported Technologies
• Install on Linux: Main Components
• Set Up a Development Machine