Revision as of 08:49, 28 May 2019

Introduction

This page contains a complete installation manual for ART-DECOR in production environments. This setup has been tested on CentOS 64 bits servers. It uses the somewhat older eXist-db 2.1 installer which will be updated in Q1 2015. It assumes you already have a user with sudo permissions. The installation process will assume you are are running scripts as a normal user (unless otherwise explicitly noted). It assumes you use yum as package installation manager. This script assumes you want to install:

the ART-DECOR installation script into: /opt/art-decor-linux/tooling
Apache tomcat at: /usr/share/tomcat
eXist-db at: /usr/local/exist_atp

Note: this installation page now downloads the trunk/developer version of installation scripts. This will be changed to stable when slightly more mature.

Download installation scripts

Here we setup a structure for installation scripts and packages, and then download the ART-DECOR installation scripts.

# setup the directory structure
sudo mkdir /opt/art-decor-linux;
cd /opt/art-decor-linux
sudo mkdir tooling
sudo mkdir tooling/backups
sudo mkdir tooling/packages
sudo mkdir tooling/packages_archives
sudo mkdir tooling/scripts_archives
sudo chown -R root:wheel /opt/art-decor-linux/
cd /opt/art-decor-linux/tooling
# get installation scripts from svn
sudo yum install svn
sudo svn checkout svn://svn.code.sf.net/p/artdecor/code-0/trunk/utilities/art_decor_installers/art-decor-linux/tooling/scripts scripts

This action should have downloaded the following files: (in /opt/art-decor-linux/tooling/scripts)

settings: a configuration file to store setting: java location and location for installation scripts
install_tomcat.sh: Tomcat installation script
install_exist.sh: eXist-db installer helper script

Install Sun java JDK

We want to use Sun/Oracle java JDK. First place the JDK rpm in /opt/art-decor-linux/tooling/packages

Visit: http://www.oracle.com/technetwork/java/javase/downloads/index.html

Download a JDK version, for instance: jdk-8u66-linux-x64.rpm (or a later version). One way to get the rpm to the server is to first download it to your desktop and then place it on the server with scp/winscp.

# Check the current version of java
java -version

Output might look somewhat like (this is the OpenJDK default version we don't want to use):

java version "1.6.0_24"
OpenJDK Runtime Environment (IcedTea6 1.11.11.90) (rhel-1.62.1.11.11.90.el6_4-x86_64)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

Upload the jdk to /opt/art-decor-linux/tooling/packages/

Start the java installation:

# sudo to a root shell
sudo su -l root
mkdir /usr/java; cd /usr/java
# install sun jdk (next to default installed openJDK)
chmod +x /opt/art-decor-linux/tooling/packages/jdk-*.rpm
rpm -Uvh /opt/art-decor-linux/tooling/packages/jdk-*.rpm
# check which version java the systeem now uses:
java -version

Output should look somewhat like:

java version "1.8.0_72"
Java(TM) SE Runtime Environment (build 1.8.0_72-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)

Check the java installation:

# if java -version does still report the OpenJDK version update java alternatives:
alternatives --install /usr/bin/java java /usr/java/latest/jre/bin/java 20000

# Check where java is installed?
ls /usr/java/

Output should look somewhat like:

default  jdk1.8.0_72  latest

Change the java version in scripts/settings

# exit the root shell
exit
# Change the java version in scripts/settings
cd /opt/art-decor-linux/tooling/scripts; sudo vi settings

In settings change the line with java_location to your current version: Example:

# set your java version here
# for centos
java_location=/usr/java/jdk1.8.0_72

To set the java location dynamically use: java_location=/usr/java/latest

Exit vi and save the file with: <esc> :wq

Amount of memory for your server

Check the amount of RAM memory on your server:

cat /proc/meminfo|grep MemTotal 
MemTotal:       24602824 kB

This output shows this server has 24GB total RAM memory.

Information pages at exist-db.org:

We would use the following setup:

amount of MB	used for
8192	Apache Tomcat
8192	eXist-db max mem = wrapper.java.maxmemory
2048	eXist-db cache (approx. 1/3 of exist-db max mem)
2048	eXist-db db-connection cacheSize (approx. 1/3 of exist-db max mem)
1024	eXist-db db-connection collectionCache (1/2 of db-connection cacheSize)

Apache Tomcat installation

Download Apache Tomcat

Download Apache Tomcat:

Select a version Tomcat that supports the installed Sun/Oracle java JDK version: http://tomcat.apache.org/whichversion.html
After choosing a version under 'Download', select the core, tar.gz binary distribution.
Place the Tomcat tar.gz in /opt/art-decor-linux/tooling/packages

Download and install ART-DECOR Orbeon web archive

Download the art-decor.war file from: http://sourceforge.net/projects/artdecor/files/Orbeon/art-decor.war/download

Place the art-decor.war in /opt/art-decor-linux/tooling/packages

Please note that since ART 1.6.0+ we use orbeon 4.7. The art-decor.war that we install here uses orbeon 4.7.

Install Tomcat and deploy ART-DECOR Orbeon web archive

Create a backup of the existing tomcat and art-decor.war configuration.

Run the Tomcat installer

Next we will run a script that does the following:

Install prerequisites: gcc gcc-c++ make
Caution: the installer script will remove any previous installation of Tomcat
Unpack Tomcat and move it to /usr/share/tomcat-<version>
Set up jsvc so that Tomcat can be run as a daemon
Set up permissions
Add an /etc/init.d/tomcat script to start Tomcat when the server starts
Set (java and tomcat) environment variables in /etc/profile.d/env.sh
Copy the ART-DECOR Orbeon web archive to tomcat and list it in the Tomcat config file

To perform these actions: run the Tomcat installer script:

# sudo to a root shell
sudo su -l root
cd /opt/art-decor-linux/tooling/scripts
# give the installer script executable permissions
chmod +x ./install_tomcat.sh   
# run the Tomcat installer script
./install_tomcat.sh
# exit the root shell
exit

If you get this error message: -bash: ./install_tomcat.sh: /bin/bash^M: bad interpreter: No such file or directory

# First open the file in vi
vi ./install_tomcat.sh
# convert to Unix line endings
:set fileformat=unix
# save the file
:wq
# next run the Tomcat installer script

Check that tomcat will start after server reboot (the Tomcat script should have handled this):

sudo chkconfig --list tomcat

Output should be similar to the following (for runlevel 3 to 5 tomcat should be listed as on)

tomcat          0:off   1:off   2:on    3:on    4:on    5:on    6:off

Configure the amount of memory for Tomcat

Next define the amount of memory that should be allocated to Tomcat:

See how much memory you need for Tomcat: Amount of memory for your server
Create a configuration file to set the jdk and amount of memory for Tomcat:

sudo vi /usr/share/tomcat/bin/setenv.sh

With the following content (change the jdk version and the amount of memory to your setup):

#!/bin/sh
#
# ENVARS for Tomcat environment
#
JRE_HOME=/usr/java/jdk1.8.0_92/jre

CATALINA_OPTS="-Xmx8192M -Xms8192M"
# EOF

Exit vi and save the file with: <esc> :wq

Set the proper permissions:

sudo chmod u+x /usr/share/tomcat/bin/setenv.sh
sudo chown tomcat:root /usr/share/tomcat/bin/setenv.sh

Extract ART-DECOR Orbeon web archive in Tomcat folder

We need to start Tomcat for a brief period to extract the ART-DECOR Orbeon web archive, so that we can change the configuration files for ART-DECOR Orbeon

Start Tomcat

sudo service tomcat start

Check that the ART-DECOR Orbeon war is extracted

ls /usr/share/tomcat/webapps/art-decor/

Output should show these folders:

META-INF  WEB-INF

Stop tomcat

sudo service tomcat stop

Check that Tomcat is stopped or kill it

sudo ps aux |grep tomcat

If it is still running you can kill the Tomcat process with:

sudo kill -15 <PID>

Edit ART-DECOR Orbeon configuration

Please note that since september 2015, we supply orbeon 4.7 in the ART-DECOR orbeon web archive. Some parts below are needed only for the older orbeon 3.9 installation and should be skipped for newer orbeon 4.7 installations.

Only for the older orbeon 3.9

Now we can edit the ART-DECOR Orbeon configuration files.

[only for the older orbeon 3.9] Change the location where orbeon saves its logfile.

This configation is done in the file: /usr/share/tomcat/webapps/art-decor/WEB-INF/resources/config/log4j.xml

The default setting is: ../logs/orbeon.log

We need to set the file location to a full path like: /usr/share/tomcat/logs/orbeon.log

sudo sed -i '/param/s/\(name="File"\svalue="\)\.\.\/logs\/orbeon\.log/\1\/usr\/share\/tomcat\/logs\/orbeon.log/g'  /usr/share/tomcat/webapps/art-decor/WEB-INF/resources/config/log4j.xml

Check that the path to orbeon.log is changed in the configuration file:

sudo grep orbeon.log  /usr/share/tomcat/webapps/art-decor/WEB-INF/resources/config/log4j.xml
        <param name="File" value="/usr/share/tomcat/logs/orbeon.log"/>
        <param name="File" value="/usr/share/tomcat/logs/orbeon.log"/>

[only for the older orbeon 3.9] Change the default Orbeon password

sudo vi /usr/share/tomcat/webapps/art-decor/WEB-INF/resources/config/properties-local.xml

Change the default password:

<!-- The password is already changed from the Orbeon default, it should be changed for each installation -->
   <property as="xs:string" name="oxf.xforms.password" value=".....”/>

For Orbeon 4 and Orbeon 2017.x

Change the variables that Tomcat passes to client browsers with links to ART-DECOR content (assumes we will use a HTTPS certificate later on):

sudo vi /usr/share/tomcat/webapps/art-decor/WEB-INF/resources/config/properties-local.xml

The original file contains lines like:

<property as="xs:anyURI" name="art.external.exist.url" value="http://localhost:8877/art"/>

Change each property that has external in it's name to point to the FQDN of your server:

<property as="xs:anyURI" name="art.external.exist.url" value="https://art-decor.org/art"/>

Exit vi and save the file with: <esc> :wq

Update the xforms structure in the eXist-db database

Through ART-DECOR user-interface (as a logged in dba-user), visit: Application -> Configuration -> Functions

Before running the upgrade it should show XForms 3.9

Click: Upgrade

After clicking the upgrade button it should show XForms: XForms updated (status): 16, Orbeon 4.7

(optional) If you want to change to default home page:

sudo vi /usr/share/tomcat/webapps/art-decor/WEB-INF/resources/page-flow.xml

Comment or uncomment the homepage you want to use: home or terminology-home. To use the default ART-DECOR homepage, leave as is:

  <!-- Welcome page, change to use a different homepage -->
   <page id="home" path-info="/home" view="http://localhost:8877/art/modules/get-form.xq?form=home"/>
<!--   <page id="home" path-info="/home" view="http://localhost:8877/art/modules/get-form.xq?form=terminology-home"/>-->

Start Tomcat

sudo service tomcat start

Output should be similar to the following:

Using CATALINA_BASE:   /usr/share/tomcat
Using CATALINA_HOME:   /usr/share/tomcat
Using CATALINA_TMPDIR: /usr/share/tomcat/temp
Using JRE_HOME:        /usr/java/jdk1.8.0_66/jre
Using CLASSPATH:       /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar

Check that the Tomcat process is running:

sudo ps aux|grep ^tomcat

Output should be similar to the following:

tomcat   23356 37.8  8.0 12114472 1972696 ?    Sl   00:31   0:28 /usr/java/jdk1.8.0_66/jre/bin/java -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xmx8192M -Xms8192M -Djava.endorsed.dirs=/usr/share/tomcat/endorsed -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.io.tmpdir=/usr/share/tomcat/temp org.apache.catalina.startup.Bootstrap start

Check that the Tomcat process is listening on port 8080:

sudo netstat -anp| grep :8

Output should be similar to the following:

tcp        0      0 ::ffff:127.0.0.1:8005       :::*                        LISTEN      14042/java
tcp        0      0 :::8009                     :::*                        LISTEN      14042/java
tcp        0      0 :::8080                     :::*                        LISTEN      14042/java

eXist-db installation

Install eXist-db from installer

The part will install the eXist-db database. First download the ART-DECOR eXist-db installer .jar from: http://sourceforge.net/projects/artdecor/files/eXist-db/

For ART 1.6.0+ download eXist-db-setup-2.2-rev0000.jar Before ART 1.6.0, we used the outdated eXist-db-setup-2.1-rev0000.jar which is listed here for historic reasons.

Place eXist-db-setup-2.2-rev0000.jar in /opt/art-decor-linux/tooling/packages

Start the installation:

cd /opt/art-decor-linux/tooling/scripts
# make the installation script executable:
sudo chmod +x ./install_exist.sh
# run the installation script:
sudo ./install_exist.sh

If you get this error message: sudo: unable to execute ./install_exist.sh: No such file or directory

# First open the file in vi
sudo vi ./install_exist.sh
# convert to Unix line endings
:set fileformat=unix
# save the file
:wq

Output will be similar to the following:

Starting exist-db installer. Press enter if settings are correct!
Select target path [/usr/local/exist_atp_22_20151030]
<to continue:><ENTER>

press 1 to continue, 2 to quit, 3 to redisplay
<to continue:>1<ENTER>
Set Data Directory
Please select a directory where eXist-db will keep its data files. On Windows, this should be outside the 'Program Files' directory. Please make sure eXist can write to the directory it is installed in.
Data dir:  [webapp/WEB-INF/data]
<to continue:><ENTER>

press 1 to continue, 2 to quit, 3 to redisplay
<to continue:>1<ENTER>
Set Admin Password and Configure Memory
Enter password:  []
<to continue: enter the exist-db admin password you want to use><ENTER>
Enter password:  []
<to continue: repeat the password><ENTER>
------------------------------------------

Maximum memory in mb: [1024]
<to continue: enter the amount of memory you want to use exist-db or accept the default><ENTER>

Cache memory in mb: [128]
<to continue: enter the amount of memory you want to use exist-db or accept the default><ENTER>

press 1 to continue, 2 to quit, 3 to redisplay
<to continue:>1<ENTER>
[ Starting to unpack ]
[ Processing package: Core (1/6) ]
[ Processing package: Sources (2/6) ]
[ Processing package: Apps (3/6) ]
[ Processing package: shared (4/6) ]
[ Processing package: dashboard (5/6) ]
[ Processing package: eXide (6/6) ]
[ Unpacking finished ]
[ Starting processing ]
Starting process Setting admin password ... (1/1)
--- Starting embedded database instance ---
Dec 16, 2014 10:11:13 PM org.expath.pkg.repo.util.Logger info
INFO: Create a new repository with storage: File system storage in /usr/local/exist_atp_22_20151030/webapp/WEB-INF/data/expathrepo
Setting admin user password...
--- Initialization complete. Shutdown embedded database instance ---
[ Console installation done ]

Note: The installation script installs eXist-db to: /usr/local/exist_atp_22_<date>

The installation script creates a symlink at /usr/local/exist_atp pointing to the actual installation path.

eXist-db post installation configuration

We need to check the following:

is the correct java linked from eXist-db
edit the memory settings for eXist-db

Link eXist-db to the correct java

# Check the current version of java
java -version

Output might look somewhat like (this is the Sun java JDK we want to use):

java version "1.8.0_60"
Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)

Check if the same JDK is used in the eXist-db configuration:

# is the correct java linked from eXist-db?
sudo vi /usr/local/exist_atp/tools/wrapper/conf/wrapper.conf

The file should contain a line like:

wrapper.java.command=/usr/lib/jvm/jdk1.8.0_60/jre/bin/java

Edit the memory settings for eXist-db

Still in wrapper.conf, edit the memory settings. Rationale is that the wrapper script determines the maximum amount of memory available for the eXist-db java instance, but is still set to 1024MB after installation.

Replace the old configuration with this one: (see Amount of memory for your server)

# Maximum Java Heap Size (in MB)
wrapper.java.maxmemory=8192

Still in wrapper.conf, edit the wrapper startup timeout. Rationale is that when you have the SNOMED CT terminology package installed, reindexing while starting the server can take 30 minutes and will otherwise time out. Add the following line at the end:

# set wrapper startup timeout to 50 minutes
wrapper.startup.timeout=60000

Exit vi and save the file with: <esc> :wq

Next edit eXist-settings.sh. By setting the java minimum amount of memory and maximum amount of memory to the same number, the garbage collector has to do less work.

sudo vi  /usr/local/exist_atp/bin/functions.d/eXist-settings.sh

At set_java_options, set Xms and Xmx to the same number as wrapper.java.maxmemory:

set_java_options() {
  if [ -z "${JAVA_OPTIONS}" ]; then
    JAVA_OPTIONS="-Xms8192m -Xmx8192m -Dfile.encoding=UTF-8";

Exit vi and save the file with: <esc> :wq

Next increase cacheSize up to approx. 1/3 of the main memory available to Java (we use 1/4)

sudo vi /usr/local/exist_atp/conf.xml

Set the cacheSize and collectionCache to the numbers in Amount of memory for your server:

<db-connection cacheSize="2048M" collectionCache="1024M" database="native"
      files="webapp/WEB-INF/data" pageSize="4096" nodesBuffer="1000"
      doc-ids="default">

Add eXist-db scheduler to make nightly backups

Still in conf.xml: add a eXist-db cron scheduler to make nightly backups. Insert this just above </scheduler>:

<!-- edit for ART-DECOR: do automated full backups, daily 03:23 to webapp/WEB-INF/data/export/ -->
<job type="system" class="org.exist.storage.ConsistencyCheckTask" cron-trigger="0 23 3 ? * *">
   <!-- the output directory. paths are relative to the data dir -->
   <parameter name="output" value="export"/>
   <parameter name="backup" value="yes"/>
   <parameter name="incremental" value="no"/>
   <parameter name="incremental-check" value="no"/>
</job>

Exit vi and save the file with: <esc> :wq

Check server startup settings

Do not start exist on server startup:

$ sudo chkconfig --list exist_atp

Our installation script has created a service script: /etc/init.d/exist_atp

We don't want to start eXist-db at server startup, since starting eXist-db (especially reindexing SNOMED CT) will prevent us from logging in with ssh while eXist-db is starting. Since we did not configure the exist_atp service to start at server startup the output should be similar to:

service exist supports chkconfig, but is not referenced in any runlevel (run 'chkconfig --add exist_atp')

All eXist-db config files outside the database are configured now.

Create a backup of an empty eXist-db

Create a backup of eXist-db before adding ART-DECOR packages. This helps speed up the installation process if you need to repeat it later, for instance if you want to restart with a clean database (of the installer has not changed in the meantime).

cd /opt/art-decor-linux/tooling/backups
# create a zipped tar archive
sudo tar zcvf exist_without_artdecor_$(date '+%Y%m%d%H%M').tgz /usr/local/exist_atp_22_$(date '+%Y%m%d')/

Starting eXist-db

Our installation script has created a service script: /etc/init.d/exist_atp

Start the eXist-db database with:

sudo service exist_atp start
Starting eXist Native XML Database...
Waiting for eXist Native XML Database.......
running: PID:32004

Check whether the server is running:

sudo service exist_atp status

Output should be similar to:

eXist-db Native XML Database is running: PID:32004, Wrapper:STARTED, Java:STARTED

Check that eXist-db is listening on ports 8877 (and 8477):

$ sudo netstat -anp|grep :8
tcp        0      0 :::8477    :::*      LISTEN      32004/java
tcp        0      0 :::8877    :::*      LISTEN      32004/java

eXist-db logging

The configuration file that determines where eXist-db output is logged to:

/usr/local/exist_atp/tools/wrapper/conf/log4j.xml

In our setup the eXist-db logging is located at:

/usr/local/exist_atp/webapp/WEB-INF/logs/exist.log

After starting output should be similar to:

2014-12-16 03:00:46,864 [WrapperListener_start_runner] INFO  (JettyStart.java [lifeCycleStarted]:417) - Jetty server started.
2014-12-16 03:00:46,865 [WrapperListener_start_runner] INFO  (JettyStart.java [run]:231) - -----------------------------------------------------
2014-12-16 03:00:46,865 [WrapperListener_start_runner] INFO  (JettyStart.java [run]:232) - Server has started on ports 8877 8477. Configured contexts:
2014-12-16 03:00:46,865 [WrapperListener_start_runner] INFO  (JettyStart.java [run]:241) - '/exist'
2014-12-16 03:00:46,865 [WrapperListener_start_runner] INFO  (JettyStart.java [run]:279) - -----------------------------------------------------

When you experience eXist-db startup problems, check the startup wrapper logging:

/usr/local/exist_atp/tools/wrapper/logs/wrapper.log

Install ART-DECOR software & data

All ART-DECOR software and data is installed using the eXist-db package manager. The default repository URL points to the eXist-db public repository, this needs to be changed to point to the public repository residing at repository.art-decor.org.

1.

Point your browser to: http://localhost:8877/apps/dashboard/index.html You should see the dashboard page:

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2.

Click on the ‘Not logged in’ and log in as admin with the password you entered during installation.

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3.

To change the default repository URL click on the ‘Collections’ icon to open the collections browser and locate the dashboard configuration at: /db/apps/dashboard

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4.

Double click on the file configuration.xml to open it in eXide.

To install the stable release (latest version):

Change the content of the repository element to:

https://repository.art-decor.org/stable2

Save the changes.

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Optionally: You can also download and install the packages from our repositories locally, although this is normally not a required step. You may find these XAR repositories at:

http://decor.nictiz.nl/apps/public-repo/retrieve.html (Stable release)
http://decor.nictiz.nl/apps/public-repo-dev/retrieve.html (Development release)

5.

Close the eXide editor window and click on the ‘Package Manager’ icon to open the package manager. In the default view all packages are shown, the ones that are already installed and all packages available in the repository. Selecting ‘installed’ shows the packages installed during the eXist-db installation:

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6.

Select ‘available’ to show the packages available in the repository. Hovering over a package will show the install icon:

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Clicking on the install icon will install the package in the database and remove it from this view.

7.

Install the application packages in the following order:

Advanced Requirements Tooling
This is the core application package.
DECOR core files
Contains Decor schema, xslt and other core resources.
DECOR services
Contains the modules for the Decor REST services.
ART-DECOR System Services
Contains resources related to ART-DECOR system services like ADANS (automatic notifier system) and ADRAM (release and release manager).
Terminology Applications
Contains the terminology applications and services.
XIS Test information system (optional)
Contains applications for testing of HL7 messages and messaging services.
OID Registry tools (optional)
Application for maintaining an OID registry, only install if you really need to maintain an OID registry.

8.

Install data packages (all optional). Click on ‘show details’ to view the Name (URI) part for all packages:

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There are several types of data packages available:

DECOR example files

Decor example project files and associated resources.

Terminology data packages

These packages have: Name (URI): http://art-decor.org/ns/terminology-data/<name>

Terminology data for use by the terminology explorers and ART terminology functions (terminology associations, creating value sets).

Terminology Data - SNOMED CT Data

Package for creating and maintaining SNOMED CT reference sets. Please note that the full terminology package SNOMED CT data is not supplied from our repository, due to licensing issues. We do supply an empty stub package Terminology Data - SNOMED CT version 14.1.1, but this essentially contains no SNOMED CT, but just serves as an example on how to host this content.

HL7 XML packages

These packages have: Name (URI): http://art-decor.org/ns/hl7/<name> These packages are named: HL7 - <name> XML packages for message validation and generation.

Other packages

Click on ‘show details’ to view a description of the content.

9.

Start Tomcat and point your browser to: http://localhost:8080/art-decor/home

10.

Start using the ART-DECOR web application and service. You can log in as admin with the password you provided during the eXist-db installation. Read the documentation online at: documentation

Load OIDIndex data

OIDIndex data is used to provide human readable names when OIDs are used. The data for OIDIndex must be loaded when, for instance, displaying the codeSystem name for a valueset derived from SNOMED CT. If the OIDIndex data is not loaded, only the SNOMED CT OID will show, and not the displayname for the SNOMED CT codeSystem.

The following process can be performed to load data into the OIDIndex:

Download the data for the OIDIndex:

Export the data file hl7org-oids.xml from repository at URL: https://bitbucket.org/art-decor/art-decor-backend/src/master/utilities/hl7-oid-registry/hl7org-oids-current.xml

Upload the data to the eXist-db database:

Open the eXist-db dashboard, log in as admin, Collections

Click to collection: /db/apps/tools/oids-data Upload resources: select the .xml file we downloaded from the repository.

Convert the data to a usable format:

Open the eXist-db dashboard, eXide

Open /db/apps/tools/oids/modules/create-oid-lookupfile.xquery

Eval

This xquery will create the file: /db/apps/tools/oids-data/hl7org-lookup.xml

Check wether the OIDIndex works:

https://<server>/decor/services/OIDIndex

Nginx installation

Not documented yet. Contact us if you are interested in the specifics.

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Revision as of 08:49, 28 May 2019

Contents

Introduction

Download installation scripts

Install Sun java JDK

Amount of memory for your server

Apache Tomcat installation

Download Apache Tomcat

Download and install ART-DECOR Orbeon web archive

Install Tomcat and deploy ART-DECOR Orbeon web archive

Run the Tomcat installer

Configure the amount of memory for Tomcat

Extract ART-DECOR Orbeon web archive in Tomcat folder

Edit ART-DECOR Orbeon configuration

Only for the older orbeon 3.9

For Orbeon 4 and Orbeon 2017.x

Start Tomcat

eXist-db installation

Install eXist-db from installer

eXist-db post installation configuration

Link eXist-db to the correct java

Edit the memory settings for eXist-db

Add eXist-db scheduler to make nightly backups

Check server startup settings

Create a backup of an empty eXist-db

Starting eXist-db

eXist-db logging

Install ART-DECOR software & data

Load OIDIndex data

Nginx installation

@@ Line 93: / Line 93: @@
 </syntaxhighlight>
 To set the java location dynamically use: java_location=/usr/java/latest
 Exit vi and save the file with: <esc> :wq

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Difference between revisions of "ART-DECOR installation on linux"

Revision as of 08:49, 28 May 2019

Contents

Introduction

Download installation scripts

Install Sun java JDK

Amount of memory for your server

Apache Tomcat installation

Download Apache Tomcat

Download and install ART-DECOR Orbeon web archive

Install Tomcat and deploy ART-DECOR Orbeon web archive

Run the Tomcat installer

Configure the amount of memory for Tomcat

Extract ART-DECOR Orbeon web archive in Tomcat folder

Edit ART-DECOR Orbeon configuration

Only for the older orbeon 3.9

For Orbeon 4 and Orbeon 2017.x

Start Tomcat

eXist-db installation

Install eXist-db from installer

eXist-db post installation configuration

Link eXist-db to the correct java

Edit the memory settings for eXist-db

Add eXist-db scheduler to make nightly backups

Check server startup settings

Create a backup of an empty eXist-db

Starting eXist-db

eXist-db logging

Install ART-DECOR software & data

Load OIDIndex data

Nginx installation