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Fast Data Transfer is a utility developed by CalTech and CERN. See http://monalisa.cern.ch/FDT/.

GNomEx can be configured with FDT, which is equipped to deal with the transfer of large data files over the internet. NOTE: At this time, FDT in GNomEx is set up to work with the application server running on Unix and Linux based systems. If you are running GNomEx on a Windows server, GNomEx is is not yet configured to work.

fdt_home is the path to the FDT home directory.fdt_download is the unzipped fdt distribution downloaded from SourceForge.fdt_stage is staging area where FDT uploads and downloads occur. The FDT server has access to this directory. For downloads, there will be links from the staging directory back to the experiment and analysis files.fdt_filedaemon is the directory that runs a daemon to move uploaded files from the FDT staging directory to their target experiment/analysis directories.

1. Download and unzip the fdt download. http://sourceforge.net/projects/gnomex/files/fdt_1.1.zip/download

2. Copy /path/to/fdt_download/fdtServer.jar to /path/to/fdt_home

>cp /path/to/fdt_download/fdtServer.jar /path/to/fdt_home/
>cp /path/to/fdt_download/start_fdt.sh /path/to/fdt_home/

3. Make sure port 54321 is not blocked by the firewall.

4. Make a directory for fdt_stage. This will be the directory that stages the files for the fdt uploads and downloads.

VERY IMPORTANT: the fdt_stage directory should be a sandbox directory that ONLY contains temporary fdt directories and files. Make sure that this directory does not contain any files or subdirectories that should be restricted from FDT transfers.

5. Modify start_fdt.sh. Change the /path/t0/fdt_stage to your directory for fdt staging. For now, don’t worry about the second argument for fdtapplogger.

6. Start the fdt server in the background.

>cd /path/to/fdt_home  >sh start_fdt.sh

7. Copy fdtClient.jar to your default web directory. (For example, create a directory called fdt under var/www/html/ if your system is running the standard apache server.)

>mkdir /var/www/html/fdt  >cp /path/to/fdt_download/fdtClient.jar /var/www/html/fdt/

8. Make a directory for the fdtfiledaemon and copy the files located in the fdt distribution:

>mkdir /path/to/fdtfiledaemon  >mkdir /path/to/fdtfieldaemon/tasks
>cp /path/to/fdt_download/fdtfiledaemon/*.* /path/to/fdtfiledaemon/

9. Modify start_fdtfiledaemon.sh. Edit /path/to/fdt_stage to point to your file path location for fdt_stage.

10. Start the fdt file monitor daemon.

>cd /path/to/fdtfiledaemon  >sh start_fdtfiledaemon.sh

10. In GNomEx, click on ‘Manage Dictionaries’. Create/edit these properties:

Property NameProperty Valuefdt_supportedYfdt_directory/path/to/fdt_stagefdt_directory_gnomexThe fdt staging dir. Only differs from fdt_directory when fdt server running on different machine than Orion (gnomex)fdt_client_codebaseThe URL to download fdtClient.jar. example: http:bioserver.hci.utah.edu/fdt (See step 6). fdt_server_nameThe machine (domain name) that the fdt server is running on. fdt_file_daemon_task_dirSet to /path/to/fdt_filedaemon/tasks fdt_userSet to the unix user account that has read/write access to the fdt_staging dir fdt_groupSet to the unix group that has read/write access to the fdt_staging directory and and gnomex data area

11. In GNomEx, go to Experiment downloads or Analysis Downloads. A button for ‘FDT Download’ should appear. Also, there should be an ‘FDT Upload’ link for uploading Analysis and Experiment data files.

12. When using the FDT Upload or Download, webstart will lauch the FDT GUI. In some browsers, you may need to download the .jnlp (the webstart file) first and then open it with Java. A small FDT GUI app will appear. From here you can select the local directory/file that you want to upload or download.

NOTE: To troubleshoot transfer problems, click on the menu Options -> Show Transfer Logs.

13. (Optional) To configure GNomEx to log FDT upload and download activity (for GNomEx upload/download usage charts), set up a shell script which will be executed when FDT performs a transfer:

a. Create a directory /path/to/fdtapplogger

       >mkdir /path/to/fdtapplogger

b. Copy the fdtapplogger files to your new fdtapplogger directory

       >cp /path/to/fdt_download/fdtapplogger/* /path/to/fdtapplogger/

c. Modify transfer_logger.sh, changing the -serverURL to match the server that is hosting GNomEx (example: https://server-abc.hci.utah.edu). NOTE: Don’t include /gnomex in the URL.

d. Make the fdt user account to owner and the fdt group the group. Give read and execute permissions to the script and jar.

>chown -R fdt_user_here:fdt_group_here /path/to/fdtapplogger/
>chmod -R 550 /path/to/fdtapplogger/

f. Restart the fdt server with the -appLogger argument

     >ps -ax | grep java     >kill 9999     >cd /path/to/fdt_home     >sh start_fdt.jar

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