brutzman / stoqs

STOQS (Spatial Temporal Oceanographic Query System) is a geospatial database software package designed to provide efficient access to in situ oceanographic measurement data.

Spatial Temporal Oceanographic Query System

STOQS is a geospatial database and web application designed to give oceanographers efficient integrated acccess to in situ measurement and ex situ sample data. See http://www.stoqs.org.

Getting started with a STOQS development system

First, install Vagrant and and VirtualBox — there are standard installers for Mac, Windows, and Linux. Then create an empty folder off your home directory such as Vagrants/stoqsvm, open a command prompt window, cd to that folder, and enter these commands:

curl "https://raw.githubusercontent.com/stoqs/stoqs/master/Vagrantfile" -o Vagrantfile
curl "https://raw.githubusercontent.com/stoqs/stoqs/master/provision.sh" -o provision.sh
vagrant up --provider virtualbox

The vagrant up command takes a few hours to provision and setup a complete CentOS 7 STOQS server that also includes all the data science tools bundled in packages such as Anaconda. All connections to this virtual machine are performed from the the directory you installed it in; you must cd to it (e.g. cd ~/Vagrants/stoqsvm) before logging in with the vagrant ssh -- -X command. After installation finishes log into your new virtual machine and test it:

vagrant ssh -- -X   # Wait for [vagrant@localhost ~]$ prompt
cd ~/dev/stoqsgit && source venv-stoqs/bin/activate
export DATABASE_URL=postgis://stoqsadm:[email protected]:5432/stoqs
./test.sh CHANGEME

In another terminal window start the development server (after a cd ~/Vagrants/stoqsvm):

vagrant ssh -- -X   # Wait for [vagrant@localhost ~]$ prompt
cd ~/dev/stoqsgit && source venv-stoqs/bin/activate
export DATABASE_URL=postgis://stoqsadm:[email protected]:5432/stoqs
stoqs/manage.py runserver 0.0.0.0:8000 --settings=config.settings.local

Visit your server's STOQS User Interface using your host computer's browser:

http://localhost:8000

More instructions are in the doc/instructions directory — see LOADING for how to load your own data and CONTRIBUTING for how to share your work. See example Jupyter Notebooks that demonstrate specific analyses and visualizations that cannot be accomplished in the STOQS User Interface. Visit the STOQS Wiki pages for updates and links to presentations. The stoqs-discuss list in Google Groups is also a good place to ask questions and engage in discussion with the STOQS user and developer communities.

Supported by the David and Lucile Packard Foundation, STOQS undergoes continual development to help support the mission of the Monterey Bay Aquarium Research Institute (MBARI). If you have your own server you will occasionally want to get new features with:

git pull
./setup.sh

If you use STOQS for your research please cite this publication:

McCann, M.; Schramm, R.; Cline, D.; Michisaki, R.; Harvey, J.; Ryan, J., "Using STOQS (The spatial temporal oceanographic query system) to manage, visualize, and understand AUV, glider, and mooring data," in Autonomous Underwater Vehicles (AUV), 2014 IEEE/OES, pp.1-10, 6-9 Oct. 2014 doi: 10.1109/AUV.2014.7054414