products.yml

# Products shown on calcofi.io. One card per product; `section` controls
# placement. Cards are named for the thing itself — the repo or app name used
# everywhere else (db-viz-hex, not "Integrated App") — so a card, its source,
# its status page and its usage report are obviously the same product. Student
# contributions keep human-friendly titles.
#
# Canonical app URLs follow uptime/.upptimerc.yml (https://app.calcofi.io/<app>/).
#
# status:       active (default, no badge) | interim | superseded | archived
# superseded_by: key of the replacing product (renders "superseded by <link>")
# extra_links:  [{label, url}] — extra deep links in the card's link row
# shots:        themed — the product honours ?theme= and has images/<key>_{dark,light}.png
#               (img: then just names the dark one as a fallback)
#               (scripts/shots.py); the card swaps them with the site's theme toggle
# credits:      {org, year, team[]} — shown on student contributions
# group:        an eyebrow group inside a section (Explore's `across` / `one`), from sections[].groups
# lenses:       the spatial grains an Explore app shows the data at — ids from sections[explore].lenses
#               (stations · hexagons · cruises · regions · sections · contours); drawn as suffix
#               icons after the card's title and on a dataset page's Access > Explore row
# dataset_url_realm: bio | env — the deep link only selects a dataset of this realm; a dataset of
#               the other realm gets the plain app link (db-viz-hex's ?datasets= is taxa-only)
# dataset_url_env: a second template for the env realm where the app opens on an environmental
#               dataset by a different parameter (db-viz-hex's ?env= selects the dataset's leading
#               variable and turns Compare on); with it set, dataset_url_realm governs dataset_url only
# datasets:     the dataset_keys this product covers — a list, or `all` (every dataset in the
#               release record). Validated at build against _data/datasets.json's datasets[] and
#               holdings[]: an unknown key FAILS the build (plan D-2). It is also the reverse index
#               behind each dataset page's Access > Explore rows, so this is the ONE place a
#               product-to-dataset link is written.

sections:
  - id: datasets
    emoji: "🗂"
    title: Datasets
    blurb: >-
      Find what has been collected. One record per dataset — coverage, every endpoint it can be
      reached through, its licence and how to cite it — by category, with the holdings CalCOFI has
      but has not ingested yet.
  - id: explore
    emoji: "🔭"
    featured: true
    title: Explore
    # the lenses, with the brand glyph each is drawn as (brand/v2/icons/, lens-*)
    lenses:
      - { id: stations, title: Stations, blurb: one value per station, the CalCOFI grid as points }
      - { id: hexagons, title: Hexagons, blurb: H3 hexagons, aggregated at a chosen resolution }
      - { id: cruises, title: Cruises, blurb: one cruise at a time, along its track }
      - { id: regions, title: Regions, blurb: pooled over a boundary or a region }
      - { id: sections, title: Sections, blurb: a vertical section along a CalCOFI line }
      - { id: contours, title: Contours, blurb: interpolated maps of one variable }
    groups:
      - id: across
        title: Across datasets
        blurb: >-
          The Explorer brings the spatial grains together as lenses in one app; the others each go
          deep on one grain — station, hexagon, cruise, or contour.
      - id: one
        title: One dataset
        blurb: >-
          Apps focused on a single dataset or data source.
    blurb: >-
      Explore CalCOFI data in the browser — across every ingested dataset, or deep on one.
  - id: access
    emoji: "☁️"
    title: Access
    blurb: >-
      The ways to get the data: standards-based services, public cloud storage, browser SQL, and
      the R and Python packages that read a release directly.
  - id: build
    emoji: "🛠"
    title: Build
    blurb: >-
      The pipeline behind every release and the documentation tying it together — the ingest
      workflows, the database tooling, the schema browser and the technical docs.
  - id: students
    emoji: "🎓"
    title: Students
    blurb: >-
      Capstone and fellowship projects by university students partnering with CalCOFI.

products:

  # ── explore · across datasets ────────────────────────────────────────────

  - key: explore
    title: CalCOFI Explorer
    uptime: explore
    usage: explore
    section: explore
    group: across
    lenses: [stations, hexagons, cruises, regions, sections]
    datasets: all
    live_url: https://calcofi.io/explore/
    # dataset_url: the deep link a dataset page builds for this product — {key} is the dataset_key.
    # This is the ONE place a product-to-dataset link is written (UI plan Decision 10); a product
    # with no template gets a row that says it opens the app, not the dataset.
    dataset_url: https://calcofi.io/explore/?datasets={key}
    source_url: https://github.com/CalCOFI/explore
    img: images/explore_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    extra_links:
      - label: Hexagons
        url: https://calcofi.io/explore/?lens=hex&res=5
      - label: Sections
        url: https://calcofi.io/explore/?lens=section&var=temperature&line=90
    description: >-
      One app, five lenses — stations, hexagons, cruises, regions and sections — for one
      organism or one ocean variable at a time over the frozen release. The queries run in your
      browser (no server), every view is a URL you can share, every download carries its SQL, and
      feedback comes with an annotated screenshot.
    tech: [DuckDB-WASM, TypeScript, MapLibre, deck.gl, Plotly]

  - key: db-viz-station
    title: Station Explorer
    uptime: db-viz-station
    usage: db-viz-station
    section: explore
    group: across
    lenses: [stations]
    datasets: all
    live_url: https://app.calcofi.io/station/
    dataset_url: https://app.calcofi.io/station/?dataset={key}
    source_url: https://github.com/CalCOFI/db-viz-station
    img: images/db-viz-station_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Discover what's measured at each CalCOFI station — station × dataset
      coverage (time, depth, observations, surveys) built from the integrated
      release database, with variable search and dataset crosswalk. Continues
      the 2026 UCSB student capstone.
    tech: [DuckDB, JavaScript, MapLibre]

  - key: db-viz-hex
    title: Hexagon Explorer
    uptime: db-viz-hex
    usage: db-viz-hex
    section: explore
    group: across
    lenses: [hexagons]
    datasets: all
    live_url: https://app.calcofi.io/hex/
    dataset_url: https://app.calcofi.io/hex/?datasets={key}
    # ?datasets= drives the TAXA-dataset group only (the environmental variable is chosen
    # separately), so it deep-links a biological dataset; an environmental one deep-links
    # through ?env=, which opens with Compare on and the dataset's leading variable selected
    # (db-viz-hex since 2026-09-07) — so every dataset page now says "opens on this dataset"
    dataset_url_realm: bio
    dataset_url_env: https://app.calcofi.io/hex/?env={key}
    source_url: https://github.com/CalCOFI/db-viz-hex
    img: images/db-viz-hex_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Explore decades of fish larvae and oceanographic bottle data together —
      filter by taxa, depth and season over dynamic hexagon maps, time series
      and depth profiles.
    tech: [R, Shiny, DuckDB, H3, MapLibre]

  - key: db-viz-cruise
    title: Cruise Explorer
    uptime: db-viz-cruise
    usage: db-viz-cruise
    section: explore
    group: across
    lenses: [cruises]
    datasets: all
    live_url: https://app.calcofi.io/cruise/
    dataset_url: https://app.calcofi.io/cruise/?datasets={key}
    source_url: https://github.com/CalCOFI/apps/tree/main/db-viz-cruise
    img: images/db-viz-cruise_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Cross-dataset observation explorer — compare coverage across cruises,
      datasets and depths, with shareable deep-link URLs.
    tech: [R, Shiny, DuckDB]

  - key: oceano
    title: Contour Explorer
    uptime: oceano
    usage: oceano
    section: explore
    group: across
    lenses: [contours]
    datasets: [calcofi_bottle]
    status: superseded
    superseded_by: db-viz-hex
    live_url: https://app.calcofi.io/contour/
    source_url: https://github.com/CalCOFI/apps/tree/main/oceano
    img: images/oceano.png
    description: >-
      Visualize and download CalCOFI oceanographic data in map, time-series
      and depth-profile views.

# ── explore · one dataset ────────────────────────────────────────────────────
  
  - key: ctd-transects
    title: CTD Transects
    uptime: ctd-transects
    usage: ctd-transects
    section: explore
    group: one
    lenses: [sections]
    datasets: [calcofi_ctd-cast]
    live_url: https://calcofi.io/ctd-transects/
    source_url: https://github.com/CalCOFI/ctd-transects
    img: images/ctd-transects_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Cross-shelf temperature, salinity, oxygen, density and fluorescence
      sections along every CalCOFI line, for every cruise since 1993 — drawn
      nearshore to offshore with no station picking, and mapped so you can see
      where each transect is. Opens on the anomaly against each station's
      day-of-year climatology (warmer or colder than usual, and by how much),
      with the measured value one click away. Flags each cruise's processing
      stage, and shows the uncorrected sensor series on cruises whose bottle
      merge has not run.
    tech: [DuckDB, Plotly, JavaScript]

  - key: ctd-viz
    title: CTD Explorer
    uptime: ctd-viz
    usage: ctd-viz
    section: explore
    group: one
    lenses: [stations, contours]
    datasets: [calcofi_ctd-cast]
    live_url: https://app.calcofi.io/ctd/
    source_url: https://github.com/CalCOFI/apps/tree/main/ctd-viz
    img: images/ctd-viz_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Visualize CTD casts — temperature, salinity, oxygen and more — by
      cruise, station and depth, from individual profiles to whole-grid maps.
    tech: [R, Shiny, DuckDB, MapLibre]

  - key: pollutants
    title: Pollutants Explorer
    uptime: pollutants
    usage: pollutants
    section: explore
    group: one
    live_url: https://app.calcofi.io/pollutants/
    source_url: https://github.com/CalCOFI/pollutants-app
    img: images/pollutants_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Map pollutants in the Southern California Bight from the Regional
      Monitoring Program via SCCWRP.

  # ── access (services, then the browser SQL and the two packages) ─────────
  - key: erddap
    title: erddap
    uptime: erddap
    usage: erddap
    section: access
    datasets: all
    live_url: https://erddap.calcofi.io/
    source_url: https://github.com/CalCOFI/erddap
    img: images/erddap_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      CalCOFI datasets served through NOAA's ERDDAP — subset and download in
      CSV, NetCDF, JSON and more, or connect from analysis tools.

  - key: storage
    title: storage
    uptime: storage
    usage: storage
    section: access
    datasets: all
    live_url: https://storage.calcofi.io/
    source_url: https://github.com/CalCOFI/server
    img: images/storage_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Browse the public CalCOFI cloud buckets over HTTPS — versioned database
      releases, source files and project outputs, with folder listings that
      the raw storage host does not provide.
    extra_links:
      - { label: netcdf, url: "https://storage.calcofi.io/calcofi-files-public/netcdf/" }

  # ── access / build interleaved: calcofi4r, calcofi4py, db-query are Access ─
  - key: calcofi4r
    title: calcofi4r
    uptime: calcofi4r
    usage: calcofi4r
    section: access
    datasets: all
    live_url: https://calcofi.io/calcofi4r/
    source_url: https://github.com/CalCOFI/calcofi4r
    img: images/calcofi4r_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      R package of helper functions to read, analyze and visualize CalCOFI
      data — connects directly to versioned database releases.
    tech: [R]

  - key: calcofi4db
    title: calcofi4db
    uptime: calcofi4db
    usage: calcofi4db
    section: build
    datasets: all
    live_url: https://calcofi.io/calcofi4db/
    source_url: https://github.com/CalCOFI/calcofi4db
    img: images/calcofi4db_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      R package of database tools for ingest workflows — cloud storage,
      Parquet conversion, DuckDB management and frozen releases.
    tech: [R]

  - key: calcofi4py
    title: calcofi4py
    uptime: calcofi4py
    usage: calcofi4py
    section: access
    datasets: all
    live_url: https://calcofi.io/calcofi4py/
    source_url: https://github.com/CalCOFI/calcofi4py
    img: images/calcofi4py_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Python package mirroring calcofi4r — query the versioned database
      releases with DuckDB and the CTD team's PostgreSQL working database,
      credentials-free via .pgpass.
    tech: [Python]

  - key: db-query
    title: db-query
    uptime: db-query
    usage: db-query
    section: access
    datasets: all
    live_url: https://calcofi.io/db-query/
    source_url: https://github.com/CalCOFI/db-query
    img: images/db-query_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Run SQL on the CalCOFI database right in your browser — DuckDB-WASM
      reads the released Parquet files directly; no server, no credentials.
    tech: [SQL, DuckDB-WASM]

  - key: db-schema
    title: db-schema
    uptime: db-schema
    usage: db-schema
    section: build
    datasets: all
    live_url: https://calcofi.io/db-schema/
    source_url: https://github.com/CalCOFI/db-schema
    img: images/db-schema_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Browse tables, columns, datasets and entity-relationship diagrams of
      each versioned database release.

  - key: workflows
    title: workflows
    uptime: workflows
    usage: workflows
    section: build
    datasets: all
    live_url: https://calcofi.io/workflows/
    source_url: https://github.com/CalCOFI/workflows
    img: images/workflows_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Reproducible Quarto notebooks that ingest each dataset into the
      versioned database — the pipeline behind every release.
    tech: [R, Quarto, DuckDB, Parquet]

  - key: docs
    title: docs
    uptime: docs
    usage: docs
    section: build
    datasets: all
    live_url: https://calcofi.io/docs/
    source_url: https://github.com/CalCOFI/docs
    img: images/docs_dark.png   # fallback; the card shows the _dark/_light pair
    shots: themed
    description: >-
      Technical documentation of the data ecosystem — data access, database,
      API, apps, maps and reports.

  # ── students (sorted by year desc, then title) ───────────────────────────
  - key: ucla-monitoring-map
    title: CA Ocean & Coastal Monitoring Map
    uptime: ucla-monitoring-map
    usage: ucla-monitoring-map
    section: students
    lenses: [hexagons]
    live_url: https://calcofi.io/2026-ucla-cal-ocean-coastal-monitoring-map/
    source_url: https://github.com/CalCOFI/2026-ucla-cal-ocean-coastal-monitoring-map
    img: images/ucla-coastal-monitoring-map.png
    description: >-
      Statewide inventory of California ocean and coastal monitoring programs
      within 12 nmi of the coast — hex-grid coverage at 1/3/5 km, survey
      transects, discharger stations, bathymetry, monitoring gaps, wind energy
      areas, and marine protected areas.
    credits:
      org: UCLA Capstone
      year: 2026
      team: Betty Huang

  - key: ucsb-larvae-dashboard
    title: Larvae Dashboard
    uptime: ucsb-larvae-dashboard
    usage: ucsb-larvae-dashboard
    section: students
    datasets: [swfsc_ichthyo]
    status: archived   # GitHub repo archived 2026-07-29; the site keeps serving
    live_url: https://app.calcofi.io/2026-ucsb-larvae-dashboard/
    source_url: https://github.com/CalCOFI/2026-ucsb-larvae-dashboard
    img: images/ucsb-larvae-dashboard.png
    description: >-
      Explore CalCOFI fish-larvae (ichthyoplankton) abundance over time and
      space — filter by species or habitat across seasons and decades, with
      trend, correlation, stability and spatial views plus CSV/PDF export.
    credits:
      org: UCSB Data Science Capstone
      year: 2026
      team: [Joy Chang, Abhijit Brahme, A. Senthil, Chengcheng Fang, Kaeya Mehta, Shenyi Jiang]

  - key: ucsb-station-portal
    title: Station Data Portal
    uptime: ucsb-station-portal
    usage: ucsb-station-portal
    section: students
    lenses: [stations]
    datasets: [cce-lter_euphausiids, cce-lter_zoodb]
    status: archived
    superseded_by: db-viz-station
    live_url: https://calcofi.io/2026-ucsb-station-data-portal/
    source_url: https://github.com/CalCOFI/2026-ucsb-station-data-portal
    img: images/ucsb-station-portal.png
    description: >-
      Map-based discovery of what is measured at each of 115 CalCOFI stations,
      with live variable search and auto-generated ERDDAP, Euphausiid and
      ZooDB queries.
    credits:
      org: UCSB Data Science Capstone
      year: 2026
      team: [Nicole Xu, Aashish Krishnan, Qiongwen (Lucy) Cao]

  - key: marmam
    title: Marine Mammal App
    uptime: marmam
    usage: marmam
    section: students
    status: archived   # GitHub repo archived 2026-07-29; the site keeps serving
    live_url: https://app.calcofi.io/marmam/
    source_url: https://github.com/CalCOFI/marmam-app
    img: images/marmam-app.png
    description: >-
      Marine mammal eDNA detections and visual sightings visualized against
      oceanographic conditions on the CalCOFI grid.
    credits:
      org: UCSB Data Science Capstone
      year: 2025

  - key: calcofi-75th-timeline
    title: 75th Anniversary Timeline
    section: students
    live_url: https://cdn.knightlab.com/libs/timeline3/latest/embed/index.html?source=12x10Qrf0UAyUT2BQ_TA3wTDgQJHYqov0fEQV42VtByU&font=Default&lang=en
    source_url: https://docs.google.com/spreadsheets/d/12x10Qrf0UAyUT2BQ_TA3wTDgQJHYqov0fEQV42VtByU/edit?usp=sharing
    img: images/calcofi-75th-timeline.png
    description: >-
      An interactive TimelineJS journey through 75 years of CalCOFI milestones
      — from the 1949 founding after the sardine collapse to the NORPAC
      expedition, the 1957–58 El Niño, CTD sampling, and the first all-female
      research cruise.
    credits:
      org: CalCOFI–CA Sea Grant Data Storytelling Internship
      year: 2024
      team: Anneliese (Annie) Adams

  - key: hypoxia-story
    title: Hypoxia Story
    uptime: hypoxia-story
    usage: hypoxia-story
    section: students
    datasets: [calcofi_bottle]
    status: archived   # GitHub repo archived 2026-07-29; the site keeps serving
    live_url: https://calcofi.io/hypoxia-story/
    source_url: https://github.com/CalCOFI/hypoxia-story
    img: images/hypoxia.png
    description: >-
      A scrollable story of hypoxia in the California Current Ecosystem and
      its changing oxygen levels over the past 71 years.
    credits:
      org: CalCOFI–CA Sea Grant Data Storytelling Internship
      year: 2024
      team: [Mallika Gupta, Anneliese (Annie) Adams]

  - key: offshore-wind-monitoring
    title: Offshore Wind Monitoring
    section: students
    live_url: https://elizathomas.shinyapps.io/california_ofw_monitoring/
    img: images/offshore-wind-monitoring.png
    description: >-
      An interactive map for planning ocean monitoring around California's
      floating offshore wind areas — toggle Essential Ocean Variables and
      long-term monitoring programs to reveal gaps in baseline datasets.
    credits:
      org: SIO Masters Capstone
      year: 2024
      team: Eliza Thomas

  - key: saferseafood
    title: SaferSeafood App
    uptime: saferseafood
    usage: saferseafood
    section: students
    status: archived   # GitHub repo archived 2026-07-29; the site keeps serving
    live_url: https://app.calcofi.io/SaferSeafood/
    source_url: https://github.com/CalCOFI/SaferSeafood
    img: images/saferseafood.png
    description: >-
      Personalized fish-consumption advisories for Southern California
      anglers — DDT levels predicted by species and catch location.
    credits:
      org: UCSB Bren MEDS Capstone
      year: 2024

  - key: capstone
    title: Capstone App
    uptime: capstone
    usage: capstone
    section: students
    datasets: [calcofi_bottle]
    status: archived
    live_url: https://app.calcofi.io/capstone/
    source_url: https://github.com/PK0207/CalCOFI22
    img: images/capstone.png
    description: >-
      Spatial and temporal visualization of the CalCOFI bottle dataset — the
      first student capstone built on the database.
    credits:
      org: UCSB CCDSP Fellowship
      year: 2022