Configuration of the MDM

How to configure the Medical Data Management

The configuration of the Medical Data Manager is done by the MDM configuration software. This software needs a site definition file and a configuration file. The site defintion is used by yaim to configure most of the gLite components. The configuration file is specific to the MDM. It defines many parameters such as the administrator of the MDM and the size of the DPM buffer.

Create the site definition for yaim

If you have already a site definition from a similar site, you should use it. We provided a site definition that can be used for the biomed VO site. You can download it form this url.
To adapt the site definition to your site, there are some parameters to modify. The file provides examples for these parameters.

Create a user account for the server administrator

Create a new account under which the server will operate

  adduser mdm

Copy the certificates of the operating user (usercert.pem and userkey.pem) in the .globus subdirectory of the user home dir (typically /home/mdm/.globus).

Create the configuration file for the Medical Data Manager

The configuration file of the MDM is a small file with a few parameters. An example of the configuration file is the /opt/glite/etc/mdm/installation.conf. You can download a fresh file from here. Most of them have default value but you should fill in the missing ones:

  • The main parameter is the file_site_definition. It is the pathname of the site definition file that will be used by yaim.
  • Set install_dicom_server_conquest to 1 if you have not DICOM server installed and you want to use the default Conquest server.
  • Set can_erase_mysql_database for a fresh installation.
  • Set the login of the operating user in the admin field. The user DN (extracted from the user certificate) should also be given as admin_certificate.
  • update the remaining values as needed for your local configuration.

Certificate

The certificate of the server must be installed in the /etc/grid-security/ directory. The name of the certificate must be hostcert.pem and the associated right must be -r–r–r–. The name of the key must be hostkey.pem and the associated right must be -r——–. You can't generate this certificate. It must be given by a certification authority, see the documentation about certificate.
The certificate of the operating user must be stored in her/his ~/.globus repository.

Network Time Protocol (NTP) daemon

Some commands of the MDM server needs an accurate date and time. You should install and configure the NTP daemon. A default configuration file for NTP is provided in /etc/ntp.conf after system installation. If you are satisfied with it, you can simply start the service:

  /etc/rc.d/init.d/ntpd start
  chkconfig --level 345 ntpd on

The NTP daemon will provide an accurate hour, but it will not work for big deviation. You should check the local time and set it to the right value with the 'date' command.

Start the configuration process

To start the configuration process, use the glite-mdm-configuration command. You must be root. If the configuration file is /opt/glite/etc/mdm/installation.conf:
/opt/glite/bin/glite-mdm-configuration /opt/glite/etc/mdm/installation.conf

The command will display information about the progress of the configuration. It can take half an hour to do all the configuration.
At some step of the installation process, a directory will be create in the DPM server. This directory will have the admin credential. This step need a proxy with the administrator credential. To create the administrator proxy, you will be prompt to enter the passphrase of the administrator certificate. This passphrase will not be store on any file. If an error occurs, you should check your certificate permission in the ~/.globus directory.

Register and retrieve a DICOM picture

The administrator need some environment variables to use the MDM commands. We suggest to add in his .bashrc : export PATH=$PATH:/opt/MDM/bin/ and source /etc/MedicalDataManager.conf

You should use glite-mdm-register and glite-mdm-get to register and retrieve a DICOM picture.

Adding new MDM users

To add new users, follow this link.