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README.md

Spatial Temporal Oceanographic Query System

Build Status Coverage Status Requirements Status Code Health DOI

STOQS is a geospatial database and web application designed to give oceanographers efficient integrated access 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. (You will also need X Windows System sofware on your computer.) 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 plugin install vagrant-vbguest
vagrant up --provider virtualbox

The vagrant up command takes an hour or so to provision and setup a complete CentOS 7 STOQS Virtual Machine that also includes MB-System, InstantReality, and all the Python data science tools bundled in packages such as Anaconda. You will be prompted for your admin password for configuring a shared folder from the VM. All connections to this VM 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 VM and test it:

vagrant ssh -- -X   # Wait for [vagrant@localhost ~]$ prompt
cd /vagrant/dev/stoqsgit && source venv-stoqs/bin/activate
export DATABASE_URL=postgis://stoqsadm:CHANGEME@127.0.0.1:5438/stoqs
./test.sh CHANGEME load noextraload

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

vagrant ssh -- -X   # Wait for [vagrant@localhost ~]$ prompt
cd /vagrant/dev/stoqsgit && source venv-stoqs/bin/activate
export DATABASE_URL=postgis://stoqsadm:CHANGEME@127.0.0.1:5438/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:8008

More instructions are in the doc/instructions directory — see LOADING for specifics on loading your own data. For example, you may create your own database of an archived MBARI campaign:

cd stoqs
ln -s mbari_campaigns.py campaigns.py
loaders/load.py --db stoqs_cce2015

You are encouraged to contribute to the STOQS project! Please see CONTRIBUTING for how to share your work. Also, see example Jupyter Notebooks that demonstrate specific analyses and visualizations that go beyond the capabilities of 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 Institue. If you have your own server you will occasionally want to get new features with:

git pull
./setup.sh

Production Deployment with Docker

First, install Docker and docker-compose on your system. Then clone the repository; in the docker directory copy the template.env file to .env and edit it for your specific installation, then execute docker-compose up:

git clone https://github.com/stoqs/stoqs.git stoqsgit
cd stoqsgit/docker
cp template.env .env
chmod 600 .env      # Edit .env to customize (Ensure that STOQS_HOME is set to the full path of stoqsgit)
docker-compose build
docker-compose up

The docker-compose build and docker-compose up commands should each take about 15 minutes. The first time the latter is executed a default database is created and tests are executed. Once you see ... [emperor] vassal /etc/uwsgi/django-uwsgi.ini is ready to accept requests you can visit the site at https://localhost — it uses a self-signed certificate, so your browser will complain. (The nginx service also delivers the same app at http://localhost:8000 without the cerificate issue.)

The default settings in template.env will run a production nginx/uwsgi/stoqs server configured for https://localhost. To configure a server for intranet or public serving of your data follow the instructions provided in the comments for the settings in your .env file. After editing your .env file you will need to rebuild your stoqs image and restart the Docker services, this time with the -d option to run the containers in the background:

docker-compose build stoqs
docker-compose up -d

See https://docs.docker.com/compose/production/ for more information about running in production.

To load some existing MBARI campaign data edit your .env file to uncomment the line:

CAMPAIGNS_MODULE=stoqs/mbari_campaigns.py

and restart the stoqs service, then from the docker directory execute the load script for a campaign, e.g.:

docker-compose exec stoqs stoqs/loaders/load.py --db stoqs_simz_aug2013

In another window monitor its output:

docker-compose exec stoqs tail -f /srv/stoqs/loaders/MolecularEcology/loadSIMZ_aug2013.out
# Or (The stoqs code is bound as a volume in the container from the GitHub cloned location)
tail -f $STOQS_HOME/stoqs/loaders/MolecularEcology/loadSIMZ_aug2013.out

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

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