OPENCLINICA INSTALLATION GUIDE -------------------------------------------------------------- Updated: March 24, 2005 This installation guide assumes that OpenClinica will be installed on a Linux-based server running Redhat ES 3.x or compatible. Please contact contact@akazaresearch.com for services to assist with on-site or remote installation, validation and QA testing of OpenClinica to assure complete deployment. Note: means logging into your Linux-based Server and running the commands that follow. About OpenClinica ------------------------------------------------------ Professional Open Source Solutions for the Clinical Research Enterprise OpenClinica is a software platform for protocol configuration, design of Case Report Forms (CRFs), and electronic data capture, retrieval, and management. It is extensible, modular, standards-based, and open source. More about OpenClincia: http://www.OpenClinica.org Installation Summary -------------------------------------------------------------- OpenClinica runs and depends on three external applications. Although many Linux systems already have these applications installed or can easily be installed, OpenClinica has been testing only on the vanilla packages provided by their respective websites. Although compatible with the pacakges supplied by your distribution, this manual does not assume distribution specific installions of required applications 1) Install Java J2SDK 1.4.2x 2) Install Tomcat 5.0.x 3) Install PostgreSQL 8.0.x 4) Install OpenClinica Application 5) Install OpenClinica Libraries Install Java J2SDK 1.4.2x -------------------------------------------------------------- This step might not required since many systems have Java SDK installed. If there are any issues with applications or only have Java JRE please do the following steps. This will archive your previous installation and install the new version in its proper location. If you want to download from website please go to: http://java.sun.com/j2se/1.4.2/download.html Click on link "Download J2SE SDK for Other Platforms" and Read License. If you agree with the license continue. Under the Linux section click on link labeled "self-extracting file" After you download it run the following commands: sh j2sdk-1_4_2_07-linux-i586.bin; su mv j2sdk1.4.2_07 /usr/share/ cd /usr/share/ mv java java.old ln -s j2sdk1.4.2_07 java If Java was not previously installed you will need to set JAVA_HOME environment variable with the following command: echo "export JAVA_HOME=/usr/share/java" >> /etc/profile; Install Apache Tomcat 5.0 -------------------------------------------------------------- We will download the binary files of Tomcat extract the file. We will then create a user called tomcat. root will put it in a system directory and set the environment variable pointing to install directory. su - root; adduser tomcat; su - tomcat; cd; wget http://www.apache.org/dist/jakarta/tomcat-5/v5.0.28/bin/jakarta-tomcat-5.0.28.tar.gz tar -zxvf jakarta-tomcat-5.0.28.tar.gz exit; mv jakarta-tomcat /usr/share/; cd /usr/share; ln -s jakarta-tomcat tomcat su - root; echo "export CATALINA_HOME=/usr/share/tomcat" >> /etc/profile; PostgreSQL 8.0.1 -------------------------------------------------------------- For more information about installation please check the file called INSTALL after extracting the tar file. This is essentially the same set of scripts for modified to take the OpenClinica into account. This installion assumes that the development libraries are properly installed, including gcc and make. Go to http://www.postgresql.org/ftp/v8.0.1/ and select "postgresql-8.0.1.tar.bz2". You will be presented with mirrors. Select one in your country and it will download. tar -jxvf postgresql-8.0.1.tar.bz2 cd postgresql ./configure gmake su gmake install adduser postgres mkdir /usr/local/pgsql/data chown postgres /usr/local/pgsql/data echo "export PGDATA=/usr/local/pgsql/data" >> /etc/profile; su - postgres /usr/local/pgsql/bin/initdb -D /usr/local/pgsql/data /usr/local/pgsql/bin/postmaster -D /usr/local/pgsql/data >logfile 2>&1 & Install OpenClinica Application --------------------------------- Create a user account and download OpenClinica from http://www.openclinica.org/entities/entity_details.php?eid=48 tar -xvf OpenClinica-0.9.0.tar cd OpenClinica ant install su - root su - postgres /usr/local/pgsql/bin/createdb openclinica /usr/local/pgsql/bin/psql -d openclinica -f database/PostgreSQL/schema_0.9.0.sql Please apply all patches /usr/local/pgsql/bin/psql -d openclinica -f database/PostgreSQL/schema_patch_0.9.0.sql After the schema has been updated, import the data: /usr/local/pgsql/bin/psql -d openclinica -f database/PostgreSQL/baseline_data_0.9.0.sql Configuration Files ------------------- There are two configurations files that need Edit $TOMCAT_HOME/webapps/OpenClinica/properties/datainfo.properties and change localhost if needed. Edit $TOMCAT_HOME/conf/Catalina/localhost/OpenClinica.xml to fit your enviroment Configure HTTPS --------------------------------- First generate an SSL Certificate. Please go to the Apache website for longer explanation: http://jakarta.apache.org/tomcat/tomcat-5.0-doc/ssl-howto.html For summary run the following commands: $JAVA_HOME/bin/keytool -genkey -alias tomcat -keyalg RSA and specify the password. The default Tomcat password is "changeit". Please use another password. In $TOMCAT_HOME/conf/server.xml comment out the Connector whose port is 8080. Like the example below: Then enable the Connector whose port is 8443. And be sure to specify the password. The Connector should look like this: For Tomcat to run in port 443 (https) Tomcat will need to run as root or a rerouting must enabled at the firewall level. We discourage running Tomcat as root so the following explains how to setup iptables to redirect traffic from port 8443 to 443. When redirecting port, localhost will still need to access in port 8443 and external users will see it in port 443. First login as root and run the following command in your shell: iptables -t nat -A PREROUTING -p tcp --dport 443 -j REDIRECT --to-port 8443 Then save the iptables configuration, so it can be loaded at system boot. iptables-save > /etc/sysconfig/iptables Verify System Environment -------------------------------------------------------------- The following set of tasks must be conducted to ensure the system is correctly setup and integrated for user testing. 1. First ensure that Tomcat is running and properly configured in Linux Login as root and type "su - tomcat" to login as tomcat Type ps aux | grep tomcat and see if its running Type env | grep CATALINA_HOME and make sure that its set 2. If you using PostgreSQL in Linux Login as postgres and type "su - postgres" to login as postgres Type env | grep PGDATA and make sure that its set. Next, type "/usr/local/psql -U clinica -W" 3. To install OpenClinica Extract the OpenClinica-VERSION-.tar file into any directory that you have permission in. Enter the new created OpenClinica directory and type: ant deploy Restart tomcat, if possible, and make sure that a directory called OpenClinica exists in the webapps directory. If so, you've had a successful deploy 4. Test in browser. On the server, if browser is installed, type https://:8443/OpenClinica If it loads the OpenClinica page, then installation is OK. Next load the https://:8443/OpenClinica on a remote machine that can access the server. 5. Login. Login with the username "root" and the password "12345678". Please change as soon as you log in. root will be assigned a default project called "default". Create an admin login for youself and remove the default root user and other "demo" accounts. Validation and Testing ------------------------------ Please contact contact@akazaresearch.com for services to assist with on-site or remote installation, validation and QA testing of OpenClinica to assure complete deployment. Developer and Contact Information ------------------------------------------------------ Akaza Research, based in Cambridge, MA, provides open informatics solutions that address the needs of academic and non-profit institutions engaged in clinical, healthcare and biomedical research. Akaza utilizes internally- and community-developed open source software and open standards to provide professional services and consulting. These open solutions enable Akaza's academic customers to effectively address the challenges of data management, compliance, and interoperability in the modern clinical and healthcare research environment. Akaza Research One Kendall Square Bldg. 400, 4th Floor Cambridge, MA 02139 phone: 617.621.8585 fax: 617.621.0065 email: contact@akazaresearch.com For more about Akaza's products and initiatives see: http://www.akazaresearch.com