= 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.
3. `chmod 744 install.sh
6. 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`
1. Unzip the release `unzip openSpecimen_v2_4.zip`
1. `cd openSpecimen_v2_4`
2. Run install.sh
3. `sudo  -u wwwrun ./first_run_open_specimen.sh`
4. Check for process still running `ps -ef|grep cat`
5. If the process is still running, kill it using `sudo -u wwwrun kill {process id}`
6. `sudo  -u wwwrun ./run_open_specimen.sh`
7. Check it starts by running `tail -f app/logs/catalina.out`

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