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Installing OC 3.14 in Ubuntu Server 18.10

I have just gone through installing OpenClinica 3.14 on Ubuntu server 16.10 and thought people here might make use of my notes (and/or offer suggestions for improvement). This successfully works in a VMWare virtual machine assigned with 2 Gig RAM.

# WARNING: be VERY careful with versions of supporting apps. # Openclinica 3.14 # JDK 1.8 # PostgreSQL 9.5 # Tomcat 7 # Update ubuntu software sudo apt-get update sudo apt-get dist-upgrade # Update ubuntu root password sudo passwd root # install unzip sudo apt-get install unzip ########## # Install Java # https://askubuntu.com/questions/761127/how-do-i-install-openjdk-7-on-ubuntu-16-04-or-higher #NOT MOST RECENT VERSION sudo apt-get install default-jre # Cheating with debian package installer sudo apt-get install dpkg # Create file: /etc/apt/preferences.d/debian sudo pico /etc/apt/preferences.d/debian # with contents as per # https://askubuntu.com/questions/761127/how-do-i-install-openjdk-7-on-ubuntu-16-04-or-higher ## ----------- follow text is contents of file Package: * Pin: release o=Debian,n=experimental Pin-Priority: -1 Package: * Pin: release o=Debian,n=sid Pin-Priority: -1 Package: openjdk-7-jdk Pin: release o=Debian,n=experimental Pin-Priority: 500 Package: openjdk-7-jre Pin: release o=Debian,n=experimental Pin-Priority: 500 Package: openjdk-7-jre-headless Pin: release o=Debian,n=experimental Pin-Priority: 500 Package: libjpeg62-turbo Pin: release o=Debian,n=sid Pin-Priority: 500 ## ----------- end text (exclude this line) sudo apt install debian-archive-keyring sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 8B48AD6246925553 sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 7638D0442B90D010 sudo add-apt-repository 'deb http://httpredir.debian.org/debian experimental main' sudo add-apt-repository 'deb http://httpredir.debian.org/debian sid main' sudo apt update # sudo apt install openjdk-7-jdk sudo apt install openjdk-8-jdk # test what version is active java -version # 1.8 should be the default, but sometimes for some reason, v11 gets installed update-java-alternatives --list sudo update-java-alternatives -s java-1.8.0-openjdk-amd64 # test version java -version ########## # TOMCAT # Install tomcat sudo add-apt-repository 'deb http://us.archive.ubuntu.com/ubuntu/ xenial main' sudo add-apt-repository 'deb http://us.archive.ubuntu.com/ubuntu/ xenial universe' sudo apt-get update sudo apt-get install tomcat7 sudo apt-get install tomcat7-admin sudo apt-get install tomcat7-docs # optional: apt-get install tomcat7-examples sudo pico /var/lib/tomcat7/conf/tomcat-users.xml # EDIT in tomcat user into the above file ## ----------- follow text inserted into xml under <tomcat-users> <role rolename="manager-gui"/> <role rolename="admin-gui"/> <user username="username" password="XXXX" roles="manager-gui,admin-gui"/> ## ----------- end text (exclude this line) systemctl restart tomcat7 # Tomcat cmd control systemctl start tomcat7 systemctl stop tomcat7 systemctl restart tomcat7 # Tomcat test (Change to your IP) # web browser http://172.23.75.64:8080/ # tomcat index.html in /var/lib/tomcat8/webapps/ROOT cd ~ sudo ln -s /var/lib/tomcat7/webapps/ROOT web sudo ln -s /var/lib/tomcat7/logs logs # Permissions ## probably not necessary as tomcat7 is created automatically: adduser tomcat # chown -R tomcat /var/lib/tomcat7/* chown -R tomcat7 /var/lib/tomcat7/* ########## # POSTGRESS sudo apt-get install postgresql-9.5 sudo apt-get install postgresql-client-9.5 # Change user account to postgress // use exit or logout sudo -i -u postgres # CREATE ROLE psql -U postgres -c "CREATE ROLE clinica LOGIN ENCRYPTED PASSWORD 'clinica' SUPERUSER NOINHERIT NOCREATEDB NOCREATEROLE" # CREATE DATABASE psql -U postgres -c "CREATE DATABASE openclinica WITH ENCODING='UTF8' OWNER=clinica" # CHANGE PASSWORD psql -U postgres ALTER USER clinica WITH PASSWORD 'XXXX'; \q exit ########## # OPENCLINICA su mkdir -p ~/tmp cd ~/tmp # can't download OpenClinica directly because they place login auth on the page # grab the software and place elsewhere that is web accessible # or use vmware tools to connect to a shared folder curl -O http://your.domain.com/tmp/OpenClinica-3.14.zip unzip OpenClinica-3.14.zip cd ~/tmp/OpenClinica-3.14/distribution unzip OpenClinica.war -d OpenClinica # create new web app : copy war file and the folder cp -rf OpenClinica* /var/lib/tomcat7/webapps mkdir /var/lib/tomcat7/OpenClinica.data/ mkdir /var/lib/tomcat7/OpenClinica.attached/ chown -R tomcat7 /var/lib/tomcat7/* chown -R tomcat7 /usr/share/tomcat7 # For first install pico /var/lib/tomcat7/webapps/OpenClinica/WEB-INF/classes/datainfo.properties # For subsequent alterations pico /usr/share/tomcat7/openclinica.config/datainfo.properties # dbType=postgres # dbUser=clinica # dbPass=XXXX # db=openclinica # dbPort=5432 # dbHost=localhost # # filePath=/var/lib/tomcat7/OpenClinica.data/ # # attached=/var/lib/tomcat7/OpenClinica.attached/ # # [email protected] # # mailHost=smtp.your.domain.com # mailPort=25 # mailProtocol=smtp # mailUsername= # mailPassword= # mailSmtpAuth=false # mailSmtpStarttls.enable=false # mailSmtpsAuth=false # mailSmtpsStarttls.enable=false # mailSmtpConnectionTimeout=100 # [email protected] # # sysURL=http://localhost:8080/OpenClinica/MainMenu cp /var/lib/tomcat7/webapps/OpenClinica/WEB-INF/classes/datainfo.properties ~/ # Start OpenClinica (Change to your IP) http://172.23.74.227:8080/manager/html # If errors then investigate logs because the error on the web page is exceedingly uninformative # Likely: folder permissions, postgres login issue # OPENCLINICA! (Change to your IP) http://172.23.74.227:8080/OpenClinica # Log in as username: root password: 12345678 # Tasks > Users > Create New User # Create a technical administrator account ########## # LOGS [useful when things go wrong] # /var/log/tomcat7 cd /var/lib/tomcat7/logs less -S /var/lib/tomcat7/logs/localhost. ########## # WEB PAGE [optional] # Change the ugly tomcat page with this slightly less ugly page pico /var/lib/tomcat7/webapps/ROOT/index.html ## ----------- Replace existing text with text below <?xml version="1.0" encoding="ISO-8859-1"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>OpenClinica Community Edition</title> </head> <style TYPE="text/css"> H1 {font-family: Calibri, sans-serif; font-weight: bold; font-size: 1.2em} body {font-family:calibri, arial, sans-serif; font-size:1em;} </style> <body> <p><a href="/OpenClinica" target=_blank><h1>OpenClinica Community Edition</h1></a></p> <ul><li><a href="https://forums.openclinica.com/" target=_blank>Community forums</a></li> <li><a href="https://docs.openclinica.com/3.1/technical-documents" target=_blank>Tech doc</a></li> <li><a href="http://docs.openclinica.com/downloads" target=_blank>Downloads</a></li> </ul> <h1>Tomcat:</h1> <ul><li><a href="docs/" target=_blank>Documentation</a></li> <li><a href="examples/" target=_blank>Examples</a></li> <li><a href="manager/html" target=_blank>Manager webapp</a></li> <li><a href="host-manager/html" target=_blank>Host-manager webapp</a></li> </ul> </body> </html> ## ----------- end text (exclude this line)

Comments

  • elecboyelecboy Posts: 1
    Hi @simonforsyth


    I almost finish the installation but I am having problems with the Starting OC, can you help me? Thanks!
  • Hi @elecboy - most problems are wrong version of the support software (tomcat / postgress), permissions / ownership of tomcat or openclinica folders, or settings in the datainfo.properties file. Check the PHP log files for clues.

    Unfortunately, I am away from my office and dev servers for a while, so that is the limit of my help at the moment.

    Last bit of help: I can't recommend a system that relies on outdated and unsupportd modules that have potential security issues. Particularly if you are storing confidential data.
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