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Oracle® Health Sciences Empirica Healthcare Analysis Installation Guide Installation Guide Release 1.0.2.1 E71220-01 |
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# 4 Setting up the Empirica Healthcare Analysis software

This chapter includes the following topics:

- Configuring properties files

## Configuring properties files

This section describes how to configure properties files in the Empirica Healthcare Analysis software.

### Reviewing the webvdme.properties file

Prerequisites: If you intend to configure the Empirica Healthcare Analysis software to use single sign-on (SSO) with Oracle Access Manager (OAM), refer to Appendix A, "Single sign-on (SSO) - Oracle Access Manager (OAM) setup" for configuration details.

Perform these steps on the application server using the non-privileged user account.

The `webvdme.properties` file stores database connection information for the Empirica Healthcare Analysis software.

1. In a command shell, create a directory that will be used for temporary files created by the Empirica Healthcare Analysis application, such as:

   `/u01/app/oracle/product/Healthcare/temp`

   Make sure to create this directory so that the non-privileged user account has write access to it.

2. Navigate to the following directory:

   `<`INSTALL_DIR`>/Healthcare/WEB-INF/classes`

3. Make a copy of the `template_webvdme.properties` file in the same directory with the name webvdme.properties. For example, use the following command:

   `$ cp template_webvdme.properties webvdme.properties`

4. Using a text editor, open the webvdme.properties file.

5. Review the settings for the following values in the file, changing the values as appropriate for your installation.

   1. `connect=jdbc:oracle:thin:@//host:port/service_name`

      where:

      - host is the IP address or fully qualified name of the database server.

      - port is the port number used by the database listener.

      - service_name is the database service name.

      Example: `connect=jdbc:oracle:thin:@//198.168.0.1:1521/ORCL`

   2. `sqlldr_connect=tnsnames_alias`

      Example: `sqlldr_connect=orcl`

6. Modify the temp_dir entry so that it points to the temporary directory that you created in step 1.

7. Optionally, configure the Empirica Healthcare Analysis software for single sign-on (SSO):

   1. In the `webvdme.properties` file, uncomment the following properties:

      - `sso.plugins=com.oracle.hsgbu.empirica.sso.EmpiricaSsoPlugin`

      - `sso.EmpiricaSsoPlugin.username.header=oam-remote-user`

      Note: The value of the `sso.EmpiricaSsoPlugin.username.header` property depends on your OAM configuration.

   2. Specify the SSO logout URL by uncommenting the following property and replacing the bold sample URL with the appropriate value. You obtain the SSO logout URL in Information to collect before you begin.

      - `sso.EmpiricaSsoPlugin.logoutRedirectUrl=``https://ssoServer:port/oamsso/logout.jsp`

   3. Update the session timeout value:

      1. Navigate to the following directory:

         `<`INSTALL_DIR`>/Healthcare/WEB-INF`

      2. Open the `web.xml` file.

      3. Set the value of the session-timeout parameter so that it is greater than the session timeout for the single sign-on setup in the organization.

8. Save the file, and exit the editor.

### Reviewing the listener.properties file

Perform these steps on the application server using the non-privileged user account.

The `listener.properties` file stores information used for analysis runs.

1. Navigate to the following directory:

   `<`INSTALL_DIR`>/Healthcare/WEB-INF/classes`

   The directory contains the `template_listener.properties` file.

2. Make a copy of the `template_listener.properties` file in the same directory with the name `listener.properties`. For example, use the following command:

   `$ cp template_listener.properties listener.properties`

3. Using a text editor, open the `listener.properties` file.

4. Edit the `sqlldr_path` path settings as needed.

   Note: If R version 3.0.1 is installed on your application server, set the property r_path to the path of the R executable.

5. Save and close the file.

### Creating the webvdme-fonts.properties file

Perform these steps on the application server using the non-privileged user account.

The `webvdme-fonts.properties` file stores font information.

1. Navigate to the following directory:

   `<`INSTALL_DIR`>/Healthcare/WEB-INF/classes`

   The directory contains the `template_webvdme-fonts.properties` file.

2. Make a copy of the `template_webvdme-fonts.properties` file in the same directory with the name `webvdme-fonts.properties`. For example, use the following command:

   `$ cp template_webvdme-fonts.properties webvdme-fonts.properties`

### Setting up the log4j.properties file

Perform these steps on the application server using the non-privileged user account.

1. Navigate to the following directory:

   `<`INSTALL_DIR`>/Healthcare/WEB-INF/classes`

2. Open the `log4j.properties` file, and update the following property with the location for storing the application log file. Make sure the non-privileged user account has write access to the folder.

   `log4j.appender.defaultAppender.File`

3. Save and close the file.

### Installing the pharmacoepi.jar file

- Copy the pharmacoepi jar file from the following location:

  `/u01/stage/toolbox/java`

  to

  `$INSTALL-DIR/Healthcare/WEB-INF/lib`

### Preparing the LTI.jar file for the patient timelines applet

If you do not perform these steps, security-related dialog boxes appear for end users when they work with single-patient and multi-patient timelines in applet mode, and the applets might be blocked by a client machine's security settings.

Prerequisite: Make sure you have access to the jar and jarsigner commands, and that you know your company's jar signing process.

1. From the <INSTALL_DIR>`/Healthcare/AppJars/DataMontage` directory, copy the following file into any empty directory that is outside the <INSTALL_DIR>`/Healthcare` directory:

   - `lti.jar`

2. Update the manifest in the JAR file:

   1. Create a text file in the same directory as your copied JAR file, and save it. The example later in this procedure uses the name MANIFEST.MF.

   2. In the file, insert two lines of text with the fully qualified domain name of the application server and the WebLogic connection port.

      You can use an asterisk (*) as a wildcard for the most specific part of the domain name, or you can use the IP address of the server.

      To name more than one server in each entry, use a space as the delimiter. For example, if you support connections by way of both SSL on port 7004 and SSO on port 7777 within the example.com domain, you might include entries similar to the following lines in the `MANIFEST.MF` file:

      `Codebase: <server_name>.example.com:7004 <server_name>.example.com:7777`

      `Caller-Allowable-Codebase: <server_name>.example.com:7004 <server_name>.example.com:7777`

      `Application-Library-Allowable-Codebase: <server_name>.example.com:7004 <server_name>.example.com:7777`

      Note: Information that is specific to a single server and port improves the security of the application deployment.

   3. Insert a line break after the last line of text, and save and close the file.

   4. Open a command shell and navigate to the directory containing the text file you created and the JAR file.

   5. In the command shell, issue the following command, replacing `MANIFEST.MF` with the name of the text file you created:

      `jar –ufm lti.jar MANIFEST.MF`

3. Sign the modified JAR file so it will work correctly within the Empirica Healthcare Analysis application. Use your company's jar signing process to perform this signing task, which typically includes using java's jarsigner utility. For information about this utility, see:

   `http://docs.oracle.com/javase/7/docs/technotes/tools/windows/jarsigner.html`

4. Copy the signed JAR file to the <INSTALL_DIR>`/Healthcare/AppJars/DataMontage` directory, replacing the original file.