Glider App

Web application for visualizing WHOI Spray autonomous underwater glider deployments. Built with Dash, Plotly, and Flask. Displays real-time and archived glider tracks, sensor profiles, and research publications.

Production site

The canonical production site is https://gliders.whoi.edu/. The Dash app is served at the site root behind Apache, while the legacy static /data/ tree is still served directly by Apache from /var/www/gliders.whoi.edu/data.

For host setup, Apache configuration, and deploy operations, see DEPLOYMENT.md. For the JSON-to-NetCDF ingest/cache layout, see DATA_SCHEMA.md.

Deployment

The app runs in Docker on racing at /opt/gliderapp.

Build and launch

ssh racing
cd /opt/gliderapp
git fetch && git pull
docker compose up --build --force-recreate -d

This builds a Python 3.12 image, installs dependencies, starts the Dash app with gunicorn on port 8050, runs the data-watcher ingest process, and starts the GoatCounter analytics service. The containers restart automatically unless explicitly stopped.

If the codebase changes, these are also the steps needed to deploy the code changes.

Apache serves https://gliders.whoi.edu/ publicly and proxies Dash requests to the gliderapp container on localhost port 8050.

Key details

• Port: 8050
• WSGI server: gunicorn
• Volumes: gliderapp mounts /srv/data at /app/data read-only and ./config at /app/config read-only. data-watcher mounts /srv/data/sync read-only and /srv/data/netcdf read-write so it can maintain the NetCDF cache. goatcounter stores analytics data in /srv/data/analytics.
• Environment: gliderapp and data-watcher load required production settings from prod.env

Configuration

Config files live in config/ and are mounted into the container at runtime. Changes take effect after restarting the container (docker compose up --force-recreate -d).

File	Purpose
config/homepage.html	Home page content (rendered as sanitized HTML)
config/datapage.html	Data page content (rendered as sanitized HTML)
config/people.yml	Team members — names, roles, emails, websites, and portrait image filenames
config/assets/people-imgs/	Portrait images referenced by people.yml
config/map_config.yml	Map region definitions (labels, enable flags, glider marker image)
config/publications.html	Publications list (generated by the bibtex module — see below)

Data and static plots

The app's data flow is documented in DATA_SCHEMA.md. In production, /srv/data/sync contains source *_web.json files, and data-watcher maintains generated NetCDF cache files in /srv/data/netcdf. The gliderapp container reads /srv/data read-only at /app/data.

Historical static pages, generated plot images, and directory indexes under https://gliders.whoi.edu/data/ are not served by Dash. Apache serves that legacy tree directly from /var/www/gliders.whoi.edu/data, and those files are updated by external processing outside this repo. Several app links intentionally point into that /data/ tree.

Environment variables

Production settings are committed in prod.env and loaded by gliderapp and data-watcher. Update prod.env when deployment defaults change.

Variable	Default	Description
PROD	1	Enables production Dash routing settings
DEBUG	0	Debug mode
SUBPATH	empty	External URL prefix used for Dash requests, nav links, and static HTML asset paths. Empty means the app is served at the site root.
PORTRAITS_DEFAULT	default.jpg	Fallback portrait image
PUBLICATIONS_HTML_PATH	config/publications.html	Path to publications HTML
HOME_HTML_PATH	config/homepage.html	Path to home page HTML
DATAPAGE_HTML_PATH	config/datapage.html	Path to data page HTML
DATA_DIR	/app/data/sync	Source *_web.json directory for data-watcher; defaults to ./data/sync for the app when unset
NETCDF_DIR	/app/data/netcdf	Generated NetCDF cache directory for data-watcher and the app
TRACKS_NETCDF	tracks.nc	Aggregate tracks-only NetCDF used for map loading
POLL_INTERVAL	300	Seconds between data-watcher source scans
ANALYTICS_ENDPOINT	https://analytics.gliders.whoi.edu	GoatCounter endpoint. Leave unset to disable analytics injection.

Local Development

Install dependencies, then run the app directly with Python:

python -m venv .venv
. .venv/bin/activate
pip install -r requirements.txt
PROD=0 DEBUG=1 python src/app.py

The app will be available at http://localhost:8050. By default, local runs look for source data in ./data/sync and NetCDF cache files in ./data/netcdf; set DATA_DIR and NETCDF_DIR if your local data lives elsewhere.

A fresh clone does not include local glider data. To exercise map/profile pages locally, point DATA_DIR and NETCDF_DIR at a copied or mounted data tree with the CSV metadata files and generated NetCDF cache described in DATA_SCHEMA.md.

BibTeX Module

The bibtex/ directory contains a pipeline for converting a BibTeX bibliography into formatted HTML for the publications page.

Prerequisites

• pandoc — install with sudo apt install pandoc pandoc-citeproc (Debian/Ubuntu)
• Python 3 environment with beautifulsoup4 and lxml

Usage

./bibtex/bib2html.sh bibtex/input/refs.bib

This generates bibtex/output/publications.html. To write directly to config:

./bibtex/bib2html.sh bibtex/input/refs.bib config/publications.html

What it does

1. pandoc converts the .bib file to HTML using the AGU citation style (american-geophysical-union.csl). The frontmatter.md file includes nocite: '@*' so all entries are rendered.
2. reformat.py post-processes the HTML:
   • Groups references under year headings (newest first)
   • Cleans up DOI links (https://doi.org/10.xxxx/yyy → doi: 10.xxxx/yyy)
   • Bolds author names listed in bibtex/input/bold_authors.txt
   • Strips <html>/<body> tags for embedding

Files

bibtex/
├── input/
│   ├── refs.bib              # Main bibliography
│   └── bold_authors.txt      # Authors to bold (one per line, e.g. "Todd, R. E.")
├── output/
│   └── publications.html     # Generated output
├── american-geophysical-union.csl  # Citation style
├── frontmatter.md            # Pandoc frontmatter
├── bib2html.sh               # Conversion script
└── reformat.py               # Post-processing script

Updating publications

1. Edit bibtex/input/refs.bib (add/remove BibTeX entries)
2. Run ./bibtex/bib2html.sh bibtex/input/refs.bib config/publications.html
3. Commit and deploy
   • docker compose up --force-recreate -d