OpenSpecimen HowTo Install

Tags: OpenSpecimen HowTo

See ​https://openspecimen.atlassian.net/wiki/display/CAT/Deployment+steps

• Have to make install.sh and catalina.sh executable.
• Have to amend apache config:
  • Amend loadmodule.conf to:

    ...
    # Tomcat - used for JBoss
    #LoadModule jk_module /usr/lib64/apache2/mod_jk.so
    
    # Proxy to divert to the JBoss Application Server
    LoadModule proxy_module                   /usr/lib64/apache2-prefork/mod_proxy.so
    LoadModule proxy_http_module               /usr/lib64/apache2-prefork/mod_proxy_http.so
    
    

  • Amend httpd.cong to

    ...
    # Proxy to provide access to the JBoss Application Server
     ProxyPass / http://localhost:8280/ timeout=180
     ProxyPassReverse / http://localhost:8280/
     ProxyTimeout 180
    
    # Use mod_jk to forward to JBoss - not used now, cos it broke
    # Include /local/apache2/etc/mod.d/mod_jk.conf
    ...
    

Notes from watching Nitesh upgrade our dev version

1. Our customisations are in the file /local/os_v20/app/plugin-dir/os-le-1.0.0.jar. This file can be copied between installations.
2. He copied the build zip file (linked in the page above) into the directory /local/os_v20/installable and unzipped it.
3. Give execute permission to the file install.sh script from within the unzipped directory.
4. He then ran the install.sh script from within the unzipped directory.
5. He ran the script using nohup so that the output for the installation is stored in the file nohup.out.
6. The full command was:

nohup ./install.sh -dhost localhost -dport 3306 -dname {db name} -duser {db user name} -dpass {db password name} -dtype mysql -ahome /local/{Open Specimen Directory}/app -ahost localhost -aport 8280 -adtype fresh -adatadir /local/{Open Specimen Directory}/app/os-data -aplugindir /local/{Open Specimen Directory}/app/plugin-dir &

7. Run cp /local/{Open Specimen Directory}/installable/os-le-1.0.0.jar /local/{Open Specimen Directory}/app/plugin-dir

7. Create the script run_open_specimen.sh:

#!/bin/bash

unset JAVA_TOOL_OPTIONS
export JAVA_ROOT=/usr/lib64/jvm/java
export JDK_HOME=/usr/lib64/jvm/java
export SDK_HOME=/usr/lib64/jvm/java
export JAVA_BINDIR=/usr/lib64/jvm/java/bin
export JRE_HOME=/usr/lib64/jvm/java/jre
JAVA_HOME=/opt/java
JRE_HOME=/opt/java/jre
OPEN_SPECIMEN_DIR=/local/{Open Specimen Directory}/app

export JAVA_TOOL_OPTIONS=-XX:CompressedClassSpaceSize=10m
export JAVA_OPTS="-Xmx2G -XX:-UseCompressedClassPointers"

$OPEN_SPECIMEN_DIR/bin/catalina.sh start >$OPEN_SPECIMEN_DIR/logs/tomcat-start.log  2>$OPEN_SPECIMEN_DIR/logs/tomcat-start.err &

8. Create the script stop_open_specimen.sh:

#!/bin/bash

unset JAVA_TOOL_OPTIONS
export JAVA_ROOT=/usr/lib64/jvm/java
export JDK_HOME=/usr/lib64/jvm/java
export SDK_HOME=/usr/lib64/jvm/java
export JAVA_BINDIR=/usr/lib64/jvm/java/bin
export JRE_HOME=/usr/lib64/jvm/java/jre
JAVA_HOME=/opt/java
JRE_HOME=/opt/java/jre
OPEN_SPECIMEN_DIR=/local/openSpecimen_v2_4/app

export JAVA_TOOL_OPTIONS=-XX:CompressedClassSpaceSize=10m
export JAVA_OPTS="-Xmx2G -XX:-UseCompressedClassPointers"

$OPEN_SPECIMEN_DIR/bin/catalina.sh stop

9. Give www-run account permission to run the scripts:

setfacl -m u:wwwrun:rx /local/{Open Specimen Directory}/run_open_specimen.sh
setfacl -m u:wwwrun:rx /local/{Open Specimen Directory}/stop_open_specimen.sh

10. Give www-run permission to write to the logs and work directories:

setfacl -R -m u:wwwrun:rwx /local/{Open Specimen Directory}/logs/
setfacl -R -m u:wwwrun:rwx /local/{Open Specimen Directory}/work/

11. Give www-run and yourself (go on, treat yourself) permission to run Tomcat:

    chmod 774 /local/{Open Specimen Directory}/app/bin/catalina.sh
    setfacl -m u:wwwrun:rx /local/{Open Specimen Directory}/app/bin/catalina.sh
    

12. Then run_open_specimen.sh as yourself. You need to do this to be able to unpack the WAR file. The site will not come up successfully because there is a bug or somesuch in the database upgrade scripts.

13. Nitesh changed one of the change sets because it fails if you don't. Hurray.
    1. The file is /local/{Open Specimen Directory}/app/webapps/openspecimen/WEB-INF/classes/db/2.0/schema.xml
    2. Change <changeSet author="vlonushte" id="FK on domain name of users table"> to <changeSet author="vlonushte" id="FK on domain name of users table" failOnError="false">

Error: Macro BackLinks(None) failed

'Environment' object has no attribute 'get_db_cnx'