Install & Configure DSpace6 for SARA using bwCloud

Intro

This manual provides a step-by-step setup for a fully configured instance of DSpace6 server. The final instance can be used as institutional repository to receive automated deposits from SARA Service via swordv2.

Further reading: https://wiki.duraspace.org/display/DSDOC6x/DSpace+6.x+Documentation

About SARA: https://sara-service.org

In case of questions please contact:

Stefan Kombrink, Ulm University, Germany / e-mail: stefan.kombrink[at]uni-ulm.de
Volodymyr Kushnarenko, Ulm University, Germany / e-mail: volodymyr.kushnarenko[at]uni-ulm.de
Franziska Rapp, Ulm University, Germany / e-mail: franziska.rapp[at]uni-ulm.de

Setup

Connect to the machine using your credentials (ssh, putty)

Please use the credentials handed out to you, e.g.

Linux/MacOS:

ssh ubuntu@vm-XXX-XXX.bwcloud.uni-ulm.de

Windows: Download putty and install it

Get Resources

git clone https://github.com/sara-service/workshop.git

Installation

sudo apt-get update && sudo apt-get -y upgrade
sudo apt-get -y install openjdk-8-jdk maven ant postgresql postgresql-contrib curl wget haveged ruby-compass ruby-sass
sudo apt-get remove -y openjdk-11-jre-headless # do NOT install java 11

Postgres

sudo systemctl start postgresql
sudo groupadd dspace
sudo useradd -m -g dspace dspace
sudo -u postgres createuser --no-superuser dspace
sudo -u postgres psql -c "ALTER USER dspace WITH PASSWORD 'dspace';"
sudo -u postgres createdb --owner=dspace --encoding=UNICODE dspace
sudo -u postgres psql dspace -c "CREATE EXTENSION pgcrypto;"

Tomcat

wget http://archive.apache.org/dist/tomcat/tomcat-8/v8.5.32/bin/apache-tomcat-8.5.32.tar.gz -O /tmp/tomcat.tgz
sudo mkdir /opt/tomcat
sudo tar xzvf /tmp/tomcat.tgz -C /opt/tomcat --strip-components=1
sudo cp ~/workshop/DSpace/config/tomcat/tomcat.service /etc/systemd/system/tomcat.service
sudo cp ~/workshop/DSpace/config/tomcat/server.xml /opt/tomcat/conf/server.xml
sudo chown -R dspace.dspace /opt/tomcat
sudo systemctl daemon-reload
sudo systemctl start tomcat

Now you should be able to find your tomcat running under http://vm-XXX-XXX.bwcloud.uni-ulm.de:8080

DSpace

# install mirage2 deps locally
sudo -H -u dspace sh -c 'wget -qO- https://raw.githubusercontent.com/creationix/nvm/v0.34.0/install.sh | bash'
sudo -H -u dspace bash -c 'export NVM_DIR="$HOME/.nvm" && source "$NVM_DIR/nvm.sh" && nvm install v8'
sudo -H -u dspace bash -c 'export NVM_DIR="$HOME/.nvm" && source "$NVM_DIR/nvm.sh" && npm install -g bower grunt grunt-cli'

wget https://github.com/DSpace/DSpace/releases/download/dspace-6.3/dspace-6.3-src-release.tar.gz -O /tmp/dspace-src.tgz
mkdir -p /tmp/dspace-src
tar -xzvf /tmp/dspace-src.tgz -C /tmp/dspace-src --strip-components=1
sudo chown -R dspace:dspace /tmp/dspace-src

sudo mkdir /dspace
sudo chown dspace /dspace
sudo chgrp dspace /dspace

# NOTE needs sudo interactive or else build fails for Mirage2(xmlui)
sudo -H -u dspace bash -c 'export GEM_HOME=/var/lib/gems/2.5.0 && export GEM_PATH=/var/lib/gems/2.5.0 && export NVM_DIR="$HOME/.nvm" && source "$NVM_DIR/nvm.sh" && cd /tmp/dspace-src && mvn -e clean package -Dmirage2.on=true -Dmirage2.deps.included=false'
sudo -H -u dspace -- sh -c 'cd /tmp/dspace-src/dspace/target/dspace-installer; ant fresh_install'

ADMIN_EMAIL="dspace-admin@notexisting.com" # will be needed later again...
# Create dspace admin
sudo -u dspace /dspace/bin/dspace create-administrator -e $ADMIN_EMAIL -f "Super" -l "User" -p "iamthebest" -c en

Apply presets

# Enable Mirage2 Themes
cat ~/workshop/DSpace/config/xmlui.xconf             | sudo -u dspace sh -c 'cat > /dspace/config/xmlui.xconf'
# Apply customized item submission form
cat ~/workshop/DSpace/config/item-submission.xml     | sudo -u dspace sh -c 'cat > /dspace/config/item-submission.xml'
cat ~/workshop/DSpace/config/input-forms.xml         | sudo -u dspace sh -c 'cat > /dspace/config/input-forms.xml'
# Custom item view
cat ~/workshop/DSpace/config/xmlui/item-view.xsl     | sudo -u dspace sh -c 'cat > /dspace/webapps/xmlui/themes/Mirage2/xsl/aspect/artifactbrowser/item-view.xsl'
# Custom messages
cat ~/workshop/DSpace/config/xmlui/messages.xml      | sudo -u dspace sh -c 'cat > /dspace/webapps/xmlui/i18n/messages.xml'
cat ~/workshop/DSpace/config/xmlui/messages_de.xml   | sudo -u dspace sh -c 'cat > /dspace/webapps/xmlui/i18n/messages_de.xml'
# Custom landing page
cat ~/workshop/DSpace/config/xmlui/news-xmlui.xml    | sudo -u dspace sh -c 'cat > /dspace/config/news-xmlui.xml'
# Custom thumbnails
cat ~/workshop/DSpace/config/xmlui/Logo_SARA_RGB.png | sudo -u dspace sh -c 'cat > /dspace/webapps/xmlui/themes/Mirage2/images/Logo_SARA_RGB.png'
# Custom icons
cat ~/workshop/DSpace/config/xmlui/arrow.png         | sudo -u dspace sh -c 'cat > /dspace/webapps/xmlui/themes/Mirage2/images/arrow.png'
# Copy email templates
sudo cp ~/workshop/DSpace/config/emails/* /dspace/config/emails/
sudo chown -R dspace /dspace/config/emails
sudo chgrp -R dspace /dspace/config/emails
# Apply custom local configurations
cat ~/workshop/DSpace/config/local.cfg | sed 's/devel-dspace.sara-service.org/'$(hostname)'/g' | sudo -u dspace tee /dspace/config/local.cfg
# Apply default deposit license
cat ~/workshop/DSpace/config/default.license | sudo -u dspace tee /dspace/config/default.license

# Copy all webapps from dspace to tomcat
sudo rsync -a -v -z --delete --force /dspace/webapps/ /opt/tomcat/webapps

sudo systemctl restart tomcat
sudo systemctl enable postgresql
sudo systemctl enable tomcat

Test your instance

hostname # this is your DSpace hostname!

Open the start page of your DSpace server: http://vm-XXX-XXX.bwcloud.uni-ulm.de:8080/xmlui You should be able to login with your admin account.

Configuration

Create an initial configuration

First we will create a sample bibliography:

sudo -u dspace /dspace/bin/dspace structure-builder -f ~/workshop/DSpace/config/DSpace_Import_Structure.xml -o /tmp/DSpace_Export_Structure.xml -e "$ADMIN_EMAIL"

Now we will create a service user dedicated to SARA. This user restrains the collections a SARA user will have access to! You can even use a non-existing email address here since you are admin.

sudo /dspace/bin/dspace user --add --email project-sara@uni-konstanz.de --password SaraTest --givenname SARA --surname ServiceUser

...and two demo users

sudo /dspace/bin/dspace user --add --email demo-user@sara-service.org --password SaraTest --givenname Demo --surname User
sudo /dspace/bin/dspace user --add --email demo-user-noaccess@sara-service.org --password SaraTest --givenname Demo --surname Loser

After that, we need to create groups and configure permissions. You will need to login with $ADMIN_EMAIL using the DSpace UI:

create a group called SARA User and add project-sara@uni-konstanz.de
create a group called DSpace User and add demo-user@sara-service.org
for the two Research Data collections allow submissions for both DSpace User and SARA User
for Faculty of Education -> Publication do nothing
for Faculty of Science and Technology -> Publication collection allow submissions for SARA User group only

Validate Swordv2 functionality (HTTP)

Now we check whether the Sword Interface is configured properly and a valid ServiceDocument is being delivered. We distinguish three cases:

USER1 is registered and has access to at least one collection
USER2 is registered but has no access to any collection
USER3 is not registered at all

DSPACE_SERVER="$(hostname):8080"

SARA_USER="project-sara@uni-konstanz.de"
SARA_PWD="SaraTest"
USER1="demo-user@sara-service.org" # set existing SARA User
USER2="demo-user-noaccess@sara-service.org" # set existing user without any permissions
USER3="daniel.duesentrieb@entenhausen.de" # set nonexisting user

curl -H "on-behalf-of: $USER1" -i $DSPACE_SERVER/swordv2/servicedocument --user "$SARA_USER:$SARA_PWD"  # => downloads TermsOfServices for all available collections
curl -H "on-behalf-of: $USER2" -i $DSPACE_SERVER/swordv2/servicedocument --user "$SARA_USER:$SARA_PWD"  # => downloads empty service document
curl -H "on-behalf-of: $USER3" -i $DSPACE_SERVER/swordv2/servicedocument --user "$SARA_USER:$SARA_PWD"  # => HTML Error Status 403: Forbidden

Install apache httpd

sudo apt-get -y install apache2
sudo a2enmod ssl proxy proxy_http proxy_ajp
sudo systemctl restart apache2

Now you will see the standard apache index page: http://vm-XXX-XXX.bwcloud.uni-ulm.de

Install letsencrypt, create and configure SSL cert

sudo apt -y install python3-certbot-apache
sudo systemctl stop apache2
sudo letsencrypt --authenticator standalone --installer apache --domains $(hostname)

Choose secure redirect . Now you should be able to access via https only: http://vm-XXX-XXX.bwcloud.uni-ulm.de

Configure apache httpd

First stop tomcat:

sudo systemctl stop tomcat

Then append the following section to your virtual server config under /etc/apache2/sites-enabled/000-default-le-ssl.conf :

sudo vim /etc/apache2/sites-enabled/000-default-le-ssl.conf

        ProxyPass /xmlui ajp://localhost:8009/xmlui
        ProxyPassReverse /xmlui ajp://localhost:8009/xmlui

        ProxyPass /oai ajp://localhost:8009/oai
        ProxyPassReverse /oai ajp://localhost:8009/oai
        ProxyPass /rest ajp://localhost:8009/rest
        ProxyPassReverse /rest ajp://localhost:8009/rest
        ProxyPass /solr ajp://localhost:8009/solr
        ProxyPassReverse /solr ajp://localhost:8009/solr
        ProxyPass /swordv2 ajp://localhost:8009/swordv2

        ProxyPass / ajp://localhost:8009/xmlui
        ProxyPassReverse / ajp://localhost:8009/xmlui

Restart apache:

sudo systemctl restart apache2

Update DSpace local.cfg

Now you need to remove the local port 8080 and the http in the dspace config:

sudo sed -i 's#dspace.baseUrl = http://${dspace.hostname}:8080#dspace.baseUrl = https://${dspace.hostname}#' /dspace/config/local.cfg
sudo service tomcat restart

Validate Swordv2 functionality (HTTPS)

Experience shows that many things can break while setting up apache+SSL hence we will repeat the previous checks.

DSPACE_SERVER="https://$(hostname)"

SARA_USER="project-sara@uni-konstanz.de"
SARA_PWD="SaraTest"
USER1="demo-user@uni-ulm.de" # set existing SARA User
USER2="demo-user-noaccess@sara-service.org" # set existing user without any permissions
USER3="daniel.duesentrieb@uni-entenhausen.de" # set nonexisting user

curl -H "on-behalf-of: $USER1" -i $DSPACE_SERVER/swordv2/servicedocument --user "$SARA_USER:$SARA_PWD"  # => downloads TermsOfServices for all available collections
curl -H "on-behalf-of: $USER2" -i $DSPACE_SERVER/swordv2/servicedocument --user "$SARA_USER:$SARA_PWD"  # => downloads empty service document
curl -H "on-behalf-of: $USER3" -i $DSPACE_SERVER/swordv2/servicedocument --user "$SARA_USER:$SARA_PWD"  # => HTML Error Status 403: Forbidden

Congratulations, you are done!

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DSpace4SARA-HOWTO.md

DSpace4SARA-HOWTO.md

Install & Configure DSpace6 for SARA using bwCloud

Intro

Setup

Connect to the machine using your credentials (ssh, putty)

Get Resources

Installation

Postgres

Tomcat

DSpace

Apply presets

Test your instance

Configuration

Create an initial configuration

Validate Swordv2 functionality (HTTP)

Install apache httpd

Install letsencrypt, create and configure SSL cert

Configure apache httpd

Update DSpace local.cfg

Validate Swordv2 functionality (HTTPS)

Files

DSpace4SARA-HOWTO.md

Latest commit

History

DSpace4SARA-HOWTO.md

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Install & Configure DSpace6 for SARA using bwCloud

Intro

Setup

Connect to the machine using your credentials (ssh, putty)

Get Resources

Installation

Postgres

Tomcat

DSpace

Apply presets

Test your instance

Configuration

Create an initial configuration

Validate Swordv2 functionality (HTTP)

Install apache httpd

Install letsencrypt, create and configure SSL cert

Configure apache httpd

Update DSpace local.cfg

Validate Swordv2 functionality (HTTPS)