As part of installing required components, you need to install a database server. You can use either PostgreSQL or Microsoft SQL Server. This topic covers the process of setting up a Windows machine to use Microsoft SQL Server. 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:

Additional Topics:

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.

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.

To enable this feature on SQL Server 2017 Express, select the Custom installation option and proceed through the wizard accepting defaults until the Database Engine Configuration step.

Keep track of the user name and password; LabKey Server uses it to authenticate to SQL Server. It must be provided in plaintext in labkey.xml or in your mssql.properties file later.

If you've already installed SQL Server without enabling SQL Server Authentication then see How to: Change Server Authentication Mode in the Microsoft SQL Server documentation.

Configure TCP/IP

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

  • Launch the SQL Server Configuration Manager.
  • Under the SQL Server Network Configuration node, select Protocols for <servername>.
  • In the right pane, right-click on TCP/IP and choose Enable.
  • Right-click on TCP/IP and choose Properties.
  • Switch to the IP Addresses tab.
  • Scroll down to the IPAll section, clear the value next to TCP Dynamic Ports and set the value for TCP Port to 1433 and click OK. By default, SQL Server will choose a random port number each time it starts, but the JDBC driver expects SQL Server to be listening on port 1433.
  • Click OK
  • Restart the service by selecting the SQL Server Services node in the left pane, selecting SQL Server <edition name> in the right pane, and choosing Restart from the Action menu (or use the Restart button on the toolbar).

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:

  • Run SQL Server Management Studio.
  • Connect to the database.
  • Under Security > Logins, add a new login, using SQL Server authentication.
  • Enter the user name and password.
  • Use this password to configure the data source below.

LabKey Configuration File

Next edit the LabKey Server configuration file, by default named labkey.xml, to configure the jTDS JDBC driver for Microsoft SQL Server, which is included in the LabKey Server installation. You should comment out the Resource tag that specifies the PostgreSQL configuration. This Resource tag can be identified by the driverClassName "org.postgresql.Driver". After commenting out this resource tag, it should look similar to the following:

Comment out PostgreSQL Resource Tag

<!--
<Resource name="jdbc/labkeyDataSource" auth="Container"
type="javax.sql.DataSource"
username="postgres"
password="sa"
driverClassName="org.postgresql.Driver"
url="jdbc:postgresql://localhost:5433/labkey162"
maxTotal="20"
maxIdle="10"
accessToUnderlyingConnectionAllowed="true"
validationQuery="SELECT 1"
/>
-->

Add MS SQL Server Resource Tag

Use the following template for configuring a MS SQL Server data source. Replace USERNAME, PASSWORD, and DATABASE_NAME to fit the particulars of your target data source. The following template applies to Tomcat 8 and above. See an earlier version of this topic for a Tomcat 7 template.

<Resource name="jdbc/labkeyDataSource" auth="Container"
type="javax.sql.DataSource"
username="USERNAME"
password="PASSWORD"
driverClassName="net.sourceforge.jtds.jdbc.Driver"
url="jdbc:jtds:sqlserver://localhost:1433/DATABASE_NAME"
maxTotal="20"
maxIdle="10"
accessToUnderlyingConnectionAllowed="true"
validationQuery="SELECT 1"/>

Documentation for this driver is available on SourceForge. Other JDBC drivers for Microsoft SQL Server have not been tested.

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.

For Premium Editions, you may also need to install the PremiumStats CLR functions separately. For details see PremiumStats Install.

Premium 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

VirtualBox Deployment

On Mac or Linux (or Windows), you can set up a VirtualBox VM running Windows and install SQL Server there. These Mac-specific instructions, combined with the documentation above should get you running.

Linux Deployment

Starting with SQL Server 2017, Microsoft has started distributing a native Linux version:

Docker Deployment

The Linux edition of SQL Server is also available within a Docker container. This will work on Mac, Linux, or Windows.
You will need to install a separate visual database management tool:

Related Topics

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