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mbari-org / SeafloorMappingDB

Make MBARI seafloor mapping datasets more accessible and useful
GNU General Public License v3.0
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Seafloor Mapping Database

Make MBARI seafloor mapping datasets more accessible and useful

Text from the proposal

MBARI has now conducted hundreds of Mapping AUV missions and several dozen low altitude survey ROV dives. Much of the resulting data have value to others in the MBARI community, but the survey data and data products are only accessible to those with both knowledge of where the data are stored, how they are organized, and how to run the software used to process the data in maps, images, and GIS objects. In order to make the Mapping AUV and LASS survey data more accessible, we propose to capture metadata such as geographic location and server storage paths in a relational database with a queryable web interface. The envisioned system will utilize the same approach and open-source software tools as the MBARI STOQS database for water-column data. This system can be developed without changing the current file-based structure on the SeafloorMapping share or impacting the work-flow for processing the sensor data. The data will remain as files on the SeafloorMapping share on Titan. Because the Titan server is web-accessible, metadata and data products can be mined for populating the database and viewed through the query interface.

Seafloor mapping database: A relational database with geographic capability, a geo-spatially enabled web query interface on Canyon Head, load scripts for mining data from the SeafloorMapping archive, and user interfaces for testing and manually adding data, will be built in Python with Django and PostgreSQL using the PostGIS extension. The entire software stack is free and open source.

Install a local development system using Docker

This software is placed in the open for the potential benefit of the wider MB-System community. The instructions here are tailored for its development and operation on internal MBARI servers.

First time

Install Docker and change directory to a location where you will clone this repository. Clone the repo and start the services with these commands:

# In your home directory or other preferred location copy the file locate database, e.g.:
mkdir -p ~/docker_smdb_vol/etc
scp smdb.shore.mbari.org:/opt/docker_smdb_vol/SeafloorMapping.db ~/docker_smdb_vol/etc
# cd to a development directory, e.g. ~/GitHub
git clone git@github.com:mbari-org/SeafloorMappingDB.git
cd SeafloorMappingDB
# Edit smdb/local.yml and replace "mccann" with full paths to your files
# Make the same edits in debug.yml if you intend to use VS Code
export SMDB_HOME=$(pwd)
export DOCKER_USER_ID=$(id -u)
export COMPOSE_FILE=$SMDB_HOME/debug.yml
# Mount `smb://titan.shore.mbari.org/SeafloorMapping` on your system
# Create smdb/.envs per https://docs.mbari.org/internal/smdb-docs/dev/
docker-compose up -d
docker-compose run --rm django python manage.py migrate
docker-compose run --rm django python manage.py createsuperuser

Then navigate to http://localhost:8000 to see the web application in local development mode. Sign In to the admin interface using the credentials you created in the last step above. You will then need to open an email in MailHog at http://localhost:8025 to click on the link and confirm the account registration. Click on Admin to administer the site.

Thereafter

cd ${SMDB_HOME}
export COMPOSE_FILE=$SMDB_HOME/smdb/local.yml
export DOCKER_USER_ID=$(id -u)
# Shut down the services
docker-compose down
# Bring back up
docker-compose up -d --build
# Monitor container logs (nice to always have running in its own window)
docker-compose logs -f

Load some sample data (5 Missions) with:

docker-compose run --rm django scripts/load.py -v --limit 5

Work on the code with VS Code

  1. Perform the First time steps above and then shut down the containers that use smdb/local.yml:
docker-compose -f $SMDB_HOME/smdb/local.yml down

Install VS Code and the Remote-Containers extension.

  1. Build the debug.yml configuration that VS Code uses and launch with the code command in a shell window following setting the environment variables:
export COMPOSE_FILE=$SMDB_HOME/debug.yml
export DOCKER_USER_ID=$(id -u)
docker-compose up -d --build
code

  1. From VS Code go to File -> Open and select your SMDB_HOME directory. The devcontainer.json file will be detected and you will be prompted to "Reopen in Container". Click the button and wait for the containers to build and run.

  2. Monitor the docker container logs in a terminal:

docker-compose logs -f
  1. The debug.yml "recipe" has the Django development server running at http://localhost:8001/, so to load and see some data there open a zsh terminal and execute at the ➜ /app git:(main) prompt:
cd smdb
scripts/load.py -v --limit 5
  1. Use the debug launch configurations to Run and Debug the server (at port 8000), execute load.py, or run an IPython shell giving access through Django to the database. For example, In the Debug panel click the play button next to the "manage.py shell_plus" item in the pick list at top. A "In [1]:" prompt should appear in the Terminal pane - test by printing all the Missions in the database:
    In [1]: Mission.objects.all()

You may set breakpoints and examine variables in VS Code while the Python code is executing. The other advantages of editing in VS Code is syntax highlighting, code completion, and automated formatting. Source code control is also a little nicer than using the command line for all the git commands. One caveat is that if you save a code change that crashes the django container (e.g. a syntax error in models.py) then you'll have to correct the error in another editor before you can bring back up the container in VS Code.

Deploy a production instance of smdb

  1. Clone the repository in a location on your production server with an account that can run docker, e.g.:
sudo -u docker_user -i
cd /opt
mkdir docker_smdb_vol && chown docker_user docker_smdb_vol
git clone git@github.com:mbari-org/SeafloorMappingDB.git
cd /opt/SeafloorMappingDB
export SMDB_HOME=$(pwd)

  1. Acquire certificate files, name them smdb.crt, and smdb.key and place them in ${SMDB_HOME}/smdb/compose/production/traefik

  2. Start the app and load some data:

sudo -u docker_user -i
cd /opt/SeafloorMappingDB
export DOCKER_USER_ID=$(id -u)
export SMDB_HOME=$(pwd)
export COMPOSE_FILE=$SMDB_HOME/smdb/production.yml
docker-compose up -d
docker-compose run --rm django python manage.py migrate
docker-compose run --rm django python manage.py createsuperuser
# Replace <uid> with return from 'id -u'
docker-compose run --rm -u <uid> -v /mbari/SeafloorMapping:/mbari/SeafloorMapping django scripts/load.py -v
  1. Navigate to https://smdb.shore.mbari.org (for example) to see the production web application.

Starting over - if you've run into problems

  1. To drop the database - do with caution:
docker-compose stop django
# Lookup the <dba> (POSTGRES_USER) value in file smdb/.envs/.production/.postgres
docker-compose exec postgres psql -U <dba> -d postgres
drop database smdb; \q
docker-compose down
  1. To remove the postgres data volumes - do with extreme caution:
# List your docker volumes
docker volume ls
# Select the volumes you want to remove and remove them, e.g.:
docker volume rm seafloormappingdb_local_postgres_data
docker volume rm seafloormappingdb_local_postgres_data_backups
docker volume rm smdb_local_postgres_data
docker volume rm smdb_local_postgres_data_backups
# You will need to recreate your admin account
git pull
docker-compose up -d --build
docker-compose run --rm django python manage.py migrate
docker-compose run --rm django python manage.py createsuperuser