Physioshark Data

http://data.physioshark.org/ · thirteen seasons of Physioshark shark-nursery surveys in Mo'orea, French Polynesia, joined with weather, ocean, tide, climate and sun/moon data, and turned into charts, findings and profiles.

Led by Dr Jodie Rummer (RummerLab, James Cook University) in collaboration with CRIOBE. Built with SvelteKit, Drizzle and SQLite.

What's in it

Section	Pages
Explore	Overview, season report cards, nursery map and profiles, every tagged shark, auto-generated findings
Biology	Body size & condition, newborns and birth timing, growth, recaptures & site fidelity, adult blacktips, physiology & lab
Environment	What drives catches, ocean & heat stress (SST, DHW, ENSO, waves), weather, tides, moon, time of day, human pressure
Fieldwork	Sampling effort, crew leaderboards, water quality and in-situ logger temperatures, searchable field notes
About	Methods, data sources, publications, data-quality report

More than 130 server-rendered SVG charts and maps (several repeat per season, nursery or shark), with hover tooltips, legends and data tables, in light and dark themes.

The data (read this first)

• The spreadsheets are the source of truth and are never edited by this app.
• They are never committed to this public repository, and never baked into the Docker image. data/ and *.xlsx are git- and docker-ignored. On the server they are mounted read-only into the container.
• Raw temperature logger exports (HOBO and EnvLogger .csv files) can sit anywhere under data/, e.g. data/Temperature loggers/. They are read the same way: never edited, never committed.
• The app imports them into a derived SQLite cache on startup and re-imports automatically (within a minute) whenever a workbook is added or changed. Drop in next season's Physioshark_Shark Log 2026-2027.xlsx and the site updates.
• Anything odd the importer notices (unit conversions, impossible measurements, out-of-season dates, tag conflicts, unknown sites) is listed on the Data quality page for the lab to fix in the source sheets.
• Environmental data are public and live in external/ (Open-Meteo ERA5 weather and waves, NOAA OISST, NOAA Coral Reef Watch via PacIOOS, UHSLC Papeete tide gauge, NOAA CPC ENSO indices, NOAA IBTrACS cyclone tracks, French Polynesia school holidays). scripts/fetch-external.mjs refreshes them; a weekly workflow commits updates and publishes a new image.
• Tests, CI and the container smoke test use synthetic workbooks in samples/fixture/ (pnpm fixture regenerates them).

Run locally

Requires Node 26 and pnpm (pinned in package.json#packageManager).

pnpm install

Put the Physioshark .xlsx workbooks in ./data (any sub-folders are fine), then:

pnpm dev

Without ./data, point at the synthetic fixture:

DATA_DIR=samples/fixture pnpm dev

Variable	Default	Meaning
DATA_DIR	./data	Folder with the workbooks (read-only)
DATABASE_PATH	./cache/physioshark.sqlite	Derived SQLite cache (safe to delete)
EXTERNAL_DIR	./external	Environmental snapshots
ORIGIN	–	Public URL when the proxy sends no protocol

Deploy (Docker / GHCR)

Images are published to ghcr.io/rummerlab/data-stats (linux/amd64 + linux/arm64) on every v* tag, nightly dependency release and weekly data refresh.

cp .env.example .env

docker compose -f docker-compose.ghcr.yml pull && docker compose -f docker-compose.ghcr.yml up -d

The compose file mounts ${DATA_PATH:-./data} read-only at /data and keeps the derived database in a cache volume. See docs/DEPLOY.md for data.physioshark.org (reverse proxy / Cloudflare Tunnel, updating the spreadsheets).

Development

pnpm check && pnpm lint && pnpm test

pnpm build && pnpm test:e2e

Opt-in check against the real spreadsheets (prints counts; never writes to them):

REAL_DATA_DIR=data pnpm vitest run src/lib/server/import/realData.test.ts

Read AGENTS.md before changing the importer, charts or release process. Ideas, epics and data questions are tracked as GitHub issues.

Credits

Survey data © the Physioshark project. Environmental data: Open-Meteo (CC BY 4.0, ERA5 © Copernicus/ECMWF), NOAA OISST v2.1, NOAA Coral Reef Watch (via PacIOOS), University of Hawaii Sea Level Center, NOAA Climate Prediction Center, NOAA IBTrACS. School calendars: Gouvernement de la Polynésie française (2013–2017 orders) and Ministère de l'Éducation nationale, « Le calendrier scolaire » (Licence Ouverte 2.0). Coastline and street map tiles © OpenStreetMap contributors (ODbL). Satellite imagery © Esri, Maxar, Earthstar Geographics.