6 Configure File Watcher Support

The Oracle Health Sciences Data Management Workbench (Oracle DMW) File Watcher feature detects data files in locations you specify and loads the data when it finds files that meet requirements you specify. For further information see the clinical data models chapter of the Oracle Health Sciences Data Management Workbench User's Guide.

Do the following to support File Watcher:

• Section 6.1, "Secure Files in Watched Locations"

• Section 6.2, "Configure Server Time Zone Settings"

6.1 Secure Files in Watched Locations

On the computers where labs or other data sources will post data files, restrict access to data files in to prevent investigators and others from seeing data they should not see, such as blinded data.

1. Set up a secure file transfer method:

   • Transfer files using a secure system process such as SFTP or a secure file synchronization service.

   • Isolate the file share from direct user access by using an indirect method of conveying files to the file share such as a dropbox.

2. Use UNIX/Linux file system security by creating a UNIX/Linux file system group and assigning user IDs that require access to the group:

   • The OS user ID that executes the DP Server that is running File Watcher.

   • OS user IDs that place files in the file share (using SFTP, for example)

   • The OS user ID that executes a program that places files in the file share (an automated file transfer or file synchronization program)

3. Restrict access to the file share. Only the file owner and group should have any permissions. The other permissions should be empty. If the user ID running the DP Server is the same as the user ID used to transfer all files, then only owner file permissions are needed. Assuming this is not the case, grant permissions to both the file owner and group as follows.

   In /etc/bashrc or /etc/profile, set umask:

   umask 007

   This has the same effect as the following settings:

Table 6-1 Recommended Operating System Permissions

File Type	Description	Symbolic	Numeric
Directory	Owner and Group have Read, Write, and Execute; others have no permissions.	drwxrwx---	770
File	Owner and Group have Read and Write; others have no permissions.	-rw-rw----	660

6.2 Configure Server Time Zone Settings

For File Watcher to load the data files it detects in a timely manner, the date and time settings on your servers—database server, the middle tier server where the WebLogic Server is installed, and the middle tier server(s) where the Oracle LSH Distributed Processing (DP) Server is installed—must all have the same date and time setting.

If your servers are located in different time zones, do one of the following:

• Section 6.2.1, "Set the TZ Environment Variable Manually"

• Section 6.2.2, "Set the TZ Environment Variable Automatically"

To determine valid values for the TZ environment variable, see Section 6.2.3, "Use the tzselect Utility".

Finally, follow Section 6.2.4, "Verify the Time Zone Setting Used by Java Virtual Machine (JVM)".

6.2.1 Set the TZ Environment Variable Manually

You can set the TZ environment variable as follows:

TZ='<correct timezone>'export TZ

For example, to set the time zone to the US Pacific time zone:

TZ='America/Los_Angeles'export TZ

To determine a valid TZ value, see Section 6.2.3, "Use the tzselect Utility".

6.2.2 Set the TZ Environment Variable Automatically

You can set the TZ environment variable automatically by one of the following methods:

• Set the TZ variable in the startup configuration file (.profile or .cshrc file) for the operating system user that runs the DP Server process or the Web Logic Server process on the respective middle tier.

• Set the TZ variable in the shell script that starts the process:

  • For the DP Server, set the TZ variable in the DP Server Home/cdr_apps_dpserver.sh shell script, or in a shell script that invokes cdr_apps_dpserver.sh; see the Oracle Life Sciences Data Hub Installation Guide for information

  • For the Web Logic Server, set the TZ variable in the setDomainEnv.sh script from your Web Logic installation in a full path similar to /app/product/middleware/user_projects/domains/base_domain/bin/setDomainEnv.sh.

To determine a valid TZ value, see Section 6.2.3, "Use the tzselect Utility".

6.2.3 Use the tzselect Utility

Many UNIX systems provide the tzselect utility to aid in selecting a Posix standard time zone format. You enter this command at the UNIX command prompt with no arguments and it prompts you to select a continent or ocean and then a time zone region. It returns the string to use in the TZ command.

See your operating system documentation for more information about this command in your specific environment.

6.2.4 Verify the Time Zone Setting Used by Java Virtual Machine (JVM)

On the middle tier servers DMW is implemented using Java, and you must confirm that the Java Virtual Machine (JVM) is using the correct time zone

Note that a correct return from the UNIX date command does NOT mean that the Java Virtual Machine (JVM) is using the correct time zone. The JVM looks for the time zone settings as follows. This can vary in different implementations of UNIX/Linux, so check your operating system documentation for further information:

1. JVM uses the environment variable TZ if it is set.

2. If TZ is not set, then JVM looks for the file /etc/sysconfig/clock and finds the ZONE entry.

3. If neither TZ nor ZONE is set, JVM compares the contents of /etc/localtime to the files in /usr/share/zoneinfo looking for a match. The matching path and filename under /usr/share/zoneinfo provides the time zone.

Check the time zone that the DP Server and Web Logic Server are actually using by reading the time zone information displayed at the beginning of most lines in their log files:

• DP Server: The log file is located in the directory: DP Server Home/log.

• Web Logic Server: The log file is located in a full path similar to: /app/product/middleware/user_projects/domains/base_domain/servers/DMWServer/logs.