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. cd into the newly unzipped folder.
4. `chmod 744 install.sh
5. Run:

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

UPDATE WORKFLOW table to correct format

Run the command:

update os_cp_workflows set workflows = '[{"name":"registerParticipant","view":"plugin-ui-resources/le/collect-specimens.html","ctrl":"leRegAndCollectSpecimensCtrl","data":{"boxOpts":{"dimension":{"rows":8,"columns":12},"compact":false}}}]';

New Process

1. cd /local
2. Unzip the release unzip openSpecimen_v2_4.zip
3. cd openSpecimen_v2_4
4. Run install.sh
5. sudo -u wwwrun ./first_run_open_specimen.sh
6. Check for process still running ps -ef|grep cat
7. If the process is still running, kill it using sudo -u wwwrun kill {process id}
8. sudo -u wwwrun ./run_open_specimen.sh
9. Check it starts by running tail -f app/logs/catalina.out

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