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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 | sudo bash

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

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.