wiki:OpenClinica

Version 13 (modified by joshuadf, 10 years ago) (diff)

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OpenClinica Quick Install on Red Hat

This "quickstart" guide is a condensed version of the verbose instructions found in the OpenClinica download at install-docs/linux/install.txt. It should allow you to get Open`Clinica installed on a fully updated install of Red Hat Enterprise Linux 5 Update 3 (EL5.3) in a short amount of time.

Note: For Sun Java, you may need to add the channel "RHEL Supplementary (v. 5)" in the RHN web interface, or separately install and configure a JDK as described in the OpenClinica instructions. We prefer to use standard RHEL components when possible to take advantage of Red Hat's security/QA process. EL5.3's version of postgres is slightly older than in the OpenClinica recommendations, but Red Hat backports updates. We have not encountered any issues.

1. Download and install software.

1a. Install prequisite software on RHEL 5.3.

# install Java separately first because there are multiple options (Sun, IBM, BEA)
yum -y install java-1.6.0-sun-devel 
yum -y install postgresql-server tomcat5-admin-webapps 

rpm -q tomcat5 postgresql java-1.6.0-sun
# As of 2009 Mar 19
# tomcat5-5.5.23-0jpp.7.el5_2.1
# postgresql-8.1.11-1.el5_1.1
# java-1.6.0-sun-1.6.0.12-1jpp.3.el5

1b. Download and extract OpenClinica for Linux

First we'll set up links so that both Red Hat's default OS tools and OpenClinica install.txt instructions will work. In short the downloads will live in /usr/local/oc/ while the live webapp and data will be visible as /usr/local/tomcat/ but really live in /var/lib/tomcat5/ per Linux Standard Base (LSB).

mkdir /var/lib/tomcat5/openclinica.data
chown tomcat:tomcat /var/lib/tomcat5/openclinica.data
ln -s /var/lib/tomcat5/openclinica.data /usr/share/tomcat5
ln -s /usr/share/tomcat5 /usr/local/tomcat
mkdir /usr/local/oc

Next Register at OpenClinca.org and get OpenClinica 2.5.4 (02/17/2009), or browse for the latest version at the OpenClinica Downloads website.

Upload your OpenClinica-*.tar.gz download to /usr/local/oc/ on your EL5 host with a command like rsync -vaz OpenClinica-*.tar.gz $RHEL_HOST:/usr/local/oc/.

Now, on your EL5 host, decompress the download :

cd /usr/local/oc
tar zxvf OpenClinica-*.tar.gz 

2. Setup software

2a. PostgreSQL

Prepare a strong password to use for the db user and run the following:

/etc/init.d/postgresql start
chkconfig postgresql on
# change localhost access type to "md5" 
sed -i 's;127.0.0.1/32          ident sameuser;127.0.0.1/32          md5;' /var/lib/pgsql/data/pg_hba.conf
# switch to postgres user       
su - postgres
  createuser --no-superuser --no-createrole --no-createdb --pwprompt clinica
  # type a strong password and note it!
  createdb openclinica 
  psql -d openclinica -f /usr/local/oc/OpenClinica-*/config/database/PostgreSQL/*/install/create_database_*_tables_with_data.sql
exit
/etc/init.d/postgresql restart
# test the connection from localhost
psql --user clinica --host localhost openclinica

2b. Tomcat

By default, Tomcat is not configured for encrypted (HTTPS) requests. First uncomment the Connector port="8443" section in /etc/tomcat/server.xml to configure SSL. For more information, see http://tomcat.apache.org/tomcat-5.5-doc/ssl-howto.html

# create a keystore with a self-signed certificate for Tomcat
keytool -genkey -alias tomcat -keyalg RSA -dname "cn=Mark Jones, ou=JavaSoft, o=Sun, c=US" -storepass changeit -keypass changeit
mv /root/.keystore /usr/local/tomcat/


# small configuration, bugfixes, and workarounds 
cp /usr/local/oc/OpenClinica-*/config/libraries/postgresql-8.1-405.jdbc3.jar /usr/local/tomcat/common/lib/
# Bug: https://bugzilla.redhat.com/show_bug.cgi?id=217630
wget https://staff.washington.edu/joshuadf/java/naming-factory-dbcp.jar -O /var/lib/tomcat5/common/lib/naming-factory-dbcp.jar
# Open``Clinica is only compatible with Sun Java``Mail http://java.sun.com/products/javamail/
wget https://staff.washington.edu/joshuadf/java/mail.jar -O /usr/share/java/mail.jar
/usr/sbin/alternatives --install /usr/share/java/javamail.jar javamail /usr/share/java/mail.jar 4289
/usr/sbin/alternatives --set javamail /usr/share/java/mail.jar 


# set tomcat to start automatically on boot and start it now
chkconfig tomcat5 on
service tomcat5 start
# verify it is now running
netstat -anp |grep 8443
# tcp        0      0 :::8443                     :::*                        LISTEN      581/java            

2c. OpenClinica Deployment

# pre-deploy the WAR; we will edit some files before restarting Tomcat
cp /usr/local/oc/OpenClinica-*/distribution/OpenClinica.war /usr/local/tomcat/webapps 

Lastly, in /usr/local/tomcat/conf/Catalina/localhost/OpenClinica.xml change the JDBCRealm and SQLPostgres password lines for the "clinica" user to your db password and then run

# change OpenClinica settings
sed -i 's;smtpHost=mail.example.com;smtpHost=localhost;' /usr/local/tomcat/webapps/OpenClinica/properties/datainfo.properties
sed -i 's;adminEmail=.*;adminEmail=you@your.domain;' /usr/local/tomcat/webapps/OpenClinica/properties/datainfo.properties
/etc/init.d/tomcat5 restart

Now go to https://localhost:8443/OpenClinica/MainMenu (root/12345678) and enjoy! If you cannot log in, check the log files in /usr/local/tomcat/logs/ for details.