Chef setup for biodiversity portal
A sample chef repository to install and configure biodiv the generic biodiversity informatics platform. The platform serves the need for sourcing and aggregating biodiversity information and providing the information in the public domain. It provide open access to all biodoiversity information under the creative commons license with clear attribution to the contributor. The platform can be used for a country, region or group. There are currently three portals running on the codebase:
The biodiv platform has an well-integrated set of modules required for biodiversity information:
- An observation module for citizen science and to crowd source biodiversity information
- A species pages module with one page for every species conforming to the TDWG standards of the Species Profile Model (SPM)
- A fully featured web-GIS module
- A document module for documents and reports
- A discussion forum
Requirements
Hardware
Quad core processor. (Tested on Intel(R) Xeon(R) CPU E3110 @ 3.00GHz)
RAM at least 4GB
HDD at least 160 GB
Platforms
- Ubuntu 14.04 LTS (64 bit recommended)
Tested on:
- Ubuntu 14.04 LTS (64 bit)
Sudo privilege
You will need sudo privilege to install packages and biodiversity portal.
Packages
Install in the following order
curl
sudo apt-get install curl
git
sudo apt-get install git
chef develepment kit
wget http://opscode-omnibus-packages.s3.amazonaws.com/ubuntu/12.04/x86_64/chefdk_0.3.0-1_amd64.deb
sudo dpkg -i chefdk_0.3.0-1_amd64.deb
chef
sudo curl -L https://www.opscode.com/chef/install.sh > /tmp/install.sh ; sudo bash /tmp/install.sh -v 11.16.2
Usage
Clone this repository
git clone https://github.com/strandls/chef-biodiv.git
Change to the clone repository cd chef-biodiv
Edit biodiv.json to change
- server name
- app data dir
- solr data dir
- geoserver data dir
Install chef cookbooks
/opt/chefdk/bin/berks vendor cookbooks/
Setup biodoiversity portal
sudo chef-solo -c solo.rb -j biodiv.json
Update installation
Update cookbooks
Change to the directory where you cloned this repository
cd <repository directory>
Update the cookbooks
/opt/chefdk/bin/berks update
rm -rf cookbooks
/opt/chefdk/bin/berks vendor cookbooks/
Update biodiv installation
sudo chef-solo -c solo.rb -j biodiv.json
Verifying the installation
The services will take a while to startup after install. Wait for about 5 minutes before you begin verification.
Check solr
Visit
localhost:8080/solr
It should see solr interface.
Check geoserver
Visit
localhost:8080/geoserver
It should see geoserver interface.
Check biodiversity taxonomic nameparser
Run the following command
sudo ps -aef | grep parserver
You should see output like so
namepar+ 10996 1 0 18:52 ? 00:00:00 /usr/bin/ruby2.0 /usr/local/bin/parserver
Check biodiversity portal
Visit
localhost:8080/biodiv
You should see the biodiv homepage.
Check biodiversity portal access through nginx
Visit
http://[server name set in biodiv.json]/
You should see the biodiv homepage.
You can login as the admin user using username: admin and password: admin.
Additionally you could register a new user to check email notifications work.
Compiling biodiv war without chef
sudo su
cd /usr/local/src/biodiv-wikwio
export JAVA_HOME=/usr/lib/jvm/default-java
export BIODIV_CONFIG_LOCATION=biodiv-additional-config.groovy
/usr/local/grails-2.3.9/bin/grails --stacktrace upgrade
/usr/local/grails-2.3.9/bin/grails --stacktrace -Dgrails.env=kk war
JBOSS jar manual download
wget --no-check-certificate https://repository.jboss.com/nexus/content/repositories/root_repository/maven2/org/mobicents/external/freetts/cmu_us_kal/1.2.2/cmu_us_kal-1.2.2.jar