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Note: on both servers we set selinux in permissive mode:

In /etc/sysconfig/selinux

SELINUX=permissive



Install the backend (transmart-core)

Install packages

First install all required packages with following commands:

sudo tee /etc/yum.repos.d/thehyve_internal.repo <<EOD

[thehyve_internal]

gpgcheck=0

baseurl=https://repo.thehyve.nl/content/repositories/releases

enabled=1

name=The Hyve Internal RPM releases

EOD

sudo yum localinstall \

https://yum.postgresql.org/9.6/redhat/rhel-6-x86_64/pgdg-redhat96-9.6-3.noarch.rpm

sudo yum install -y \

php55-cli-minimal   \

make                \

git                 \

java-1.8.0-openjdk  \

groovy              \

postgresql96 \

httpd               \

postgresql96-server


Configure apache

Make apache start on each bood

sudo systemctl enable httpd.service


Create virtual host for the application by creating /etc/httpd/conf.d/transmart.conf file with below content:

<VirtualHost *:80>

 Redirect permanent / https://<host>/

</VirtualHost>

<VirtualHost *:443>

 ## Vhost docroot

 DocumentRoot "/var/www/html"

 ## Directories, there should at least be a declaration for /var/www/html

 <Location "/">

 </Location>

 ## Logging

 ErrorLog "/etc/httpd/logs/transmart-revproxy-local_error.log"

 ServerSignature Off

 CustomLog "/etc/httpd/logs/transmart-revproxy-local_access.log" combined

 ## Proxy rules

 ProxyRequests Off

 ProxyPreserveHost Off

 ProxyPass / http://localhost:8080/

 ProxyPassReverse / http://localhost:8080/

</VirtualHost>


Start the apache server:

sudo systemctl start httpd.service


Create the database

Make sure database users could login with password. Make sure /var/lib/pgsql/9.6/data/pg_hba.conf file has below line:

host    all             all             127.0.0.1/32            md5


Initialize a database and start the server.

sudo /usr/pgsql-9.6/bin/postgresql96-setup initdb

sudo systemctl enable postgresql-9.6.service

sudo systemctl start postgresql-9.6.service


Clone schema from the github as postgres user:

sudo su postgres

cd /tmp

git clone --depth 1 https://github.com/thehyve/transmart-core.git

cd transmart-core/transmart-data/



Create environment variables file: Name it e.g. vars

PGHOST=

PGPORT=5432

PGDATABASE=transmart

PGUSER=postgres

PGPASSWORD=

PGSQL_BIN=/usr/bin/

TABLESPACES=/var/lib/pgsql/9.6/tablespaces/

export PGHOST PGPORT PGDATABASE PGUSER PGPASSWORD TABLESPACES PGSQL_BIN


Source the env. var. file:

source vars


And create the schema with:

make postgres


Generate configuration files:

TSUSER_HOME=/tmp/ make -C config install

Exit from postgres user.


Install transmart application

Create transmart user:

sudo useradd transmart


Move previously generated configuration files to his home folder:

sudo mv /tmp/.grails/ /home/transmart/

sudo chown -R transmart:transmart ~transmart/.grails


And change ~transmart/.grails/transmartConfig/Config.groovy


From:

def glowingBearRedirectUris = [

               org.transmartproject.app.transmartURL - ~/transmart\/?$/ + 'connections',

       ]

       // for dev, node reverse proxy runs on 8001

       glowingBearRedirectUris << 'http://localhost:8001/connections'

To:

def glowingBearRedirectUris = ['http://<IP>']


Add also cross origin setting to the configuration file:

grails.cors.enabled = true

grails.cors.allowedOrigins = http://<IP>


Download the latest transmart-core version with:


Create start_transmart.sh script with following content:

java -jar -server -Xms3000m -Xmx3000m -Djava.awt.headless=true -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -Dserver.port=8080 -Djava.security.egd=file:///dev/urandom transmart-server-17.1-SNAPSHOT.war

Make it executable:

chmod +x start_transmart.sh


Make transmart service


Create /etc/systemd/system/transmart.service

[Unit]

Description=TranSMART

After=network.target

[Service]

Type=simple

User=transmart

WorkingDirectory=/home/transmart

ExecStart=/home/transmart/start_transmart.sh

Restart=on-abort

[Install]

WantedBy=multi-user.target


Start with:

systemctl enable transmart.service

systemctl start transmart.service


Enable https (did not make it work)

Follow https://wiki.thehyve.nl/display/CMIshared/How+to+configure+Mica+Apache+HTTPS+on+CentOS


Install frontend (glowing bear)

Create glowingbear user and get recent glowing bear application:

sudo useradd glowingbear

sudo su glowingbear

cd ~

chmod o+x .

curl  https://ci.ctmmtrait.nl/browse/TM-GBFRONT/latest/artifact/shared/glowing-bear.tar/TM-GBFRONT-JOB1-0.0.1-SNAPSHOT.tar -O

tar -xvf TM-GBFRONT-JOB1-0.0.1-SNAPSHOT.tar

Make sure other linux users would be able read the folder content:

chmod -R 644 TM-GBFRONT-JOB1-0.0.1-SNAPSHOT

find TM-GBFRONT-JOB1-0.0.1-SNAPSHOT -type d -exec chmod o+x {} +


Change configurations in TM-GBFRONT-JOB1-0.0.1-SNAPSHOT/app/config/config.prod.json to:

"api-url": "http://...",

"app-url": "http://...",


Install apache


sudo yum install -y httpd

sudo systemctl enable httpd.service




Create /etc/httpd/conf.d/glowingbear.conf with folowing content:

<VirtualHost *:80>

 ## Vhost docroot

 DocumentRoot "/home/glowingbear/TM-GBFRONT-JOB1-0.0.1-SNAPSHOT"

 <Directory "/home/glowingbear/TM-GBFRONT-JOB1-0.0.1-SNAPSHOT">

   Options Indexes FollowSymLinks MultiViews

   AllowOverride None

   Require all granted

 </Directory>

 ## Logging

 ErrorLog "/etc/httpd/logs/gb_error.log"

 ServerSignature Off

 CustomLog "/etc/httpd/logs/gb_access.log" combined

 ## Rewrite rules

 RewriteEngine On

 #If an existing asset or directory is requested go to it as it is

 RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} -f [OR]

 RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} -d

 RewriteRule ^ - [L]

 #If the requested resource doesn't exist, use index.html

 RewriteRule ^ /index.html

</VirtualHost>


And start the service:

sudo systemctl start httpd.service


Check that application works.


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