diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..a3d1079
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,36 @@
+name: CI
+
+on:
+ pull_request:
+ push:
+ branches-ignore: [main]
+ workflow_dispatch:
+
+permissions:
+ contents: read
+
+concurrency:
+ group: ci-${{ github.ref }}
+ cancel-in-progress: true
+
+jobs:
+ test-and-build:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v6
+
+ - uses: actions/setup-node@v6
+ with:
+ node-version: 24
+ cache: npm
+
+ - run: npm ci
+ - run: npm test
+ - run: npm run build
+
+ - uses: actions/setup-python@v5
+ with:
+ python-version: "3.12"
+
+ - name: Check data build scripts compile
+ run: python3 -m py_compile scripts/*.py
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index e5df218..61c3568 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -3,9 +3,8 @@ name: Deploy to GitHub Pages
on:
push:
branches: [main]
- workflow_run:
- workflows: ["Refresh live environment"]
- types: [completed]
+ # The "Refresh live environment" workflow dispatches this workflow only when
+ # it committed a changed snapshot, so unchanged hourly runs do not redeploy.
workflow_dispatch:
permissions:
@@ -19,7 +18,6 @@ concurrency:
jobs:
build:
- if: github.event_name != 'workflow_run' || github.event.workflow_run.conclusion == 'success'
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
diff --git a/.github/workflows/live-temperature.yml b/.github/workflows/live-temperature.yml
index bd838a8..5a18577 100644
--- a/.github/workflows/live-temperature.yml
+++ b/.github/workflows/live-temperature.yml
@@ -9,6 +9,8 @@ on:
permissions:
contents: write
+ # Needed to dispatch the Pages deploy workflow when the snapshot changes.
+ actions: write
concurrency:
group: live-environment
@@ -28,13 +30,25 @@ jobs:
run: python3 scripts/build_live_temperature.py
- name: Commit snapshot if changed
+ id: commit
run: |
- if git diff --quiet -- src/data/liveTemperature.json; then
+ if git diff --quiet -- public/data/liveTemperature.json; then
echo "No change in liveTemperature.json"
+ echo "changed=false" >> "$GITHUB_OUTPUT"
exit 0
fi
git config user.name "github-actions[bot]"
git config user.email "github-actions[bot]@users.noreply.github.com"
- git add src/data/liveTemperature.json
+ git add public/data/liveTemperature.json
git commit -m "Refresh live environmental snapshot"
git push
+ echo "changed=true" >> "$GITHUB_OUTPUT"
+
+ # Pushes made with GITHUB_TOKEN do not fire `push` workflows, so the
+ # deploy is dispatched explicitly, and only when a new snapshot landed.
+ # Runs that found no change end here without rebuilding the site.
+ - name: Trigger Pages deploy
+ if: steps.commit.outputs.changed == 'true'
+ env:
+ GH_TOKEN: ${{ github.token }}
+ run: gh workflow run deploy.yml --ref main
diff --git a/.gitignore b/.gitignore
index e0b2635..1a0a533 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ docs/
*.local
.env
.env.*
+__pycache__/
diff --git a/CODEBASE_EVALUATION.md b/CODEBASE_EVALUATION.md
new file mode 100644
index 0000000..fa31959
--- /dev/null
+++ b/CODEBASE_EVALUATION.md
@@ -0,0 +1,175 @@
+# SHIELD Codebase Evaluation
+
+Date: 2026-09-07
+Scope: full read of `src/`, `scripts/`, `.github/workflows/`, `README.md`, the committed data bundles, a production build, and a headless render of the deployed dashboard route.
+
+## Summary
+
+SHIELD is a well scoped static dashboard. The architecture choice (build scripts produce JSON, React renders it, GitHub Pages hosts it) is the right one for this project, the README is unusually thorough, aggregation code is null-safe, and provenance links are carried all the way to the UI. The codebase is small enough to keep in one head.
+
+The problems cluster in three places:
+
+1. **Payload and render cost.** The site ships a single 19.9 MB JavaScript chunk and the dashboard mounts a hidden 30,000 row table on every load. Both are fixable without changing the architecture.
+2. **A survival data-loss bug.** Site-level replacement of field survival with per-bag survival silently drops 22 measured records that have no replacement, including all Sequim Bay heat-primed survival.
+3. **No safety net.** There are no tests, no lint, no CI on pull requests, and one build script only runs on one person's laptop.
+
+Everything below is ordered by impact. A prioritized roadmap is at the end.
+
+## Measurements
+
+| Measurement | Value |
+|---|---|
+| Production JS bundle (single chunk) | 19,916 kB raw, 670 kB gzip |
+| `growthObservations.json` | 19.9 MB raw, 422 kB gzip, 29,836 records |
+| Same growth data in compact columnar form | about 2.6 MB raw (7x smaller) |
+| DOM on dashboard first render | 30,665 `
`, 337,293 ``, 5.6 MB serialized HTML |
+| Commits in the last 50 | 50 of 50 are hourly bot snapshot commits |
+| Field survival records dropped with no replacement | 22 |
+| `npm audit` | 2 moderate (react-router) |
+| Test files, lint config, PR CI | none |
+
+## 1. Critical: performance
+
+### 1.1 One 20 MB chunk for every route
+
+All five JSON bundles are imported statically from `src/data/`, so Vite inlines them into the main chunk. Consequences:
+
+- The Research page and Site Map download and parse 20 MB of oyster volume rows they never use.
+- `liveTemperature.json` is in the same chunk. It changes hourly, so the chunk hash changes hourly and every returning visitor re-downloads the full 670 kB gzip bundle every hour. The cache is defeated by design.
+- The growth bundle is 87 percent redundant. Every record repeats `growth_mm: null`, `temperature_C: null`, `survival_percent: null`, `survival_source: "none"`, `growth_source: "measured-volume"`, `temperature_source: "none"`, `source_repo`, and a 90 character `source_url`. Those are constants per source file.
+
+Recommended fix, in order of leverage:
+
+1. Move the JSON bundles to `public/data/` and fetch them at runtime per route. The live snapshot then caches independently of the app code.
+2. Emit growth data in a columnar or per-source shape (constants once in `meta`, rows as arrays). Expect roughly 2.6 MB raw before gzip.
+3. Consider precomputing the per site, treatment, date aggregates the dashboard actually plots. The browser only needs raw rows for the data table and CSV export, and those could load on demand.
+4. As a minimum stopgap, add `build.rollupOptions.output.manualChunks` so vendor code, growth data, and the live snapshot are separate chunks.
+
+### 1.2 Hidden print appendix renders every filtered row
+
+`FieldReportExport.jsx` renders a `print-only` table containing every row in `data`. With default filters that is 30,648 rows and 337,000 cells mounted, diffed, and held in memory on every dashboard render, then hidden with `display: none`. This is the dominant cost of the dashboard route and it scales with the dataset.
+
+Fix: render the appendix only during printing (toggle a state flag in the `beforeprint` event, or build the print view in a dedicated route or `window.open` document), and cap or paginate the appendix. The CSV export already covers the full record dump.
+
+### 1.3 Smaller render costs
+
+- `DataTable.jsx` re-filters and re-sorts all rows on every keystroke with no debounce. Fine today, but it compounds with 1.2.
+- `getSiteGeographicSummaries` filters the whole array once per site. Trivial now, but it will matter if aggregation is not moved to build time.
+
+## 2. Critical: data correctness
+
+### 2.1 Site-level survival replacement drops measured data
+
+`mockShellfishData.js` nulls out `survival_percent` on every field row whose site appears in `survivalObservations.sites`. The intent is to avoid double counting per-bag rows. The replacement is coarser than the data:
+
+| Site | Field survival dropped | Per-bag replacement exists? |
+|---|---|---|
+| Sequim Bay, Heat primed, 3 dates (2025-05-28, 2025-10-06, 2026-05-31) | yes | No. Per-bag Sequim data is PolyIC only (Control vs Immune primed). Heat-primed survival at Sequim no longer appears anywhere in the dashboard. |
+| Sequim Bay, Control, 2025-05-28 | yes | No per-bag row on that date. |
+| Palix River/Willapa Bay, all 3 treatments, 6 dates 2024-06 to 2025-10 | yes | No. Per-bag Palix data is a single 2026-05-22 total. The 2024 to 2025 survival trajectory is gone from the time series. |
+
+None of the dropped dates overlap a per-bag date, so there was no double counting to prevent. Because `finalDateRowsWithValue` already picks the latest date per site and treatment, keeping the field rows would not have changed the final-survival cards either.
+
+Fix: replace at the granularity of (site, treatment, date), or better, (site, effort, date). Drop a field row only when a per-bag row exists for the same key.
+
+### 2.2 Pooled time series is confounded by site composition
+
+With "All Sites" selected, the growth time series averages whatever sites happened to be measured on each date. Site means differ by a factor of three (Palix about 57,600, Sequim about 33,400, Westcott about 21,600, Thorndyke about 19,200), and sites were sampled on different dates. The resulting line mostly tracks which site was sampled, not growth over time. Survival has the same issue. Plot one line per site (or per site and treatment) and let the user collapse them, or at least show the contributing sites in the tooltip.
+
+### 2.3 Growth and survival comparisons use different windows
+
+`getTreatmentComparisonData` and `getSiteComparisonData` use final-date rows for survival but pool every date for growth. A treatment measured more often, or only early, is penalized or inflated in the growth bar. Use the same final-assessment rule for both, or label the growth bars as "all assessments pooled".
+
+### 2.4 Mixed growth models under one axis
+
+`growth_metric` is `vol` for 16,236 Westcott rows and `Predicted_Volume_Poly` for 13,600 rows elsewhere. The dashboard averages them together as "Growth Volume". If the two models are not on the same scale this is a units error; if they are, say so in the caption and `meta`.
+
+### 2.5 Duplicate x-axis labels
+
+`getTimeSeriesData` groups by exact date but labels by `Month Year`. Nine months contain two to five distinct assessment dates (August 2024 has five), so the axis shows repeated labels and the tooltip reads "Period: Aug 2024" for several different points. Use the ISO date, or a day-level label.
+
+### 2.6 "Best-performing treatment" pools across sites
+
+The summary card ranks treatments by mean final survival pooled across all sites, but treatments differ per site (Immune primed exists at Thorndyke and Sequim only). Restrict the card to the current site filter or rank within site.
+
+### 2.7 Shipped but invisible data
+
+- 23 field rows carry `growth_mm` shell length that no chart, table column, or export shows.
+- The Thorndyke Bay survival anchors hard-coded in `build_real_observations.py` are superseded by `survivalObservations.json` and dropped at merge time, but still shipped.
+- `realObservations.json` still exports `Treated` handling in `TREATMENT_ORDER`, but `TreatmentComparisonChart` has no color for it. Latent, not live today.
+
+## 3. Data pipeline and reproducibility
+
+- `scripts/build_real_observations.py` reads from `/Users/sr320/Documents/GitHub/project-gigas-conditioning`. Nobody else and no CI job can regenerate `realObservations.json`. Point it at the raw GitHub URLs like the other scripts, or accept a path via environment variable.
+- It also needs `pandas` and `openpyxl` (for `read_excel`) while the README says only `pandas`. Add a `requirements.txt` or `pyproject.toml`.
+- `realObservations.json` derives its monthly temperatures from `archivalTemperatureData.json`, so regeneration order is archival, then real, then growth and survival. Nothing documents or enforces this. Add an `npm run build:data` that runs them in order.
+- `normal_treatment`, `date_fields`, `read_csv`, `site_slug`, `parse_date`, and `number` are copy-pasted between the growth and survival scripts. Extract a `scripts/shield_data.py` module. The treatment mapping in particular must stay identical across the two.
+- `datetime.utcnow()` is deprecated in Python 3.12 and emits warnings under `-W error`.
+- `urlopen` calls in the growth and survival scripts have no timeout and no retry.
+- The header comment in `mockShellfishData.js` points to `docs/DATA_FORMAT.md`, but `docs/` is in `.gitignore` so the schema document is not in the repo. Either un-ignore a `docs/` folder or fold the schema into the README.
+- No output validation. A one-line check that every record has the expected keys and that `treatments` contains only the controlled vocabulary would catch mapping regressions before they reach the site.
+
+## 4. CI, deployment, and repository hygiene
+
+- **History is dominated by snapshot commits.** All 50 most recent commits are "Refresh live environmental snapshot" from the bot, roughly 6 to 8 per day. Options: write the snapshot to an orphan `data` branch and fetch it at runtime, publish it as a workflow artifact consumed by the deploy job, or commit it to `public/` on the `gh-pages` deployment only. Any of these keep `main` history readable.
+- **Deploy runs hourly even when nothing changed.** `deploy.yml` triggers on `workflow_run` success, and the refresh job exits successfully whether or not it committed. Emit a job output such as `changed=true` and gate the deploy on it.
+- **No pull request CI.** Nothing builds, lints, or tests a branch before merge. Add a workflow that runs `npm ci && npm run build` on `pull_request`.
+- **No dependency automation.** Add Dependabot or Renovate.
+- **Audit findings.** `react-router-dom` 6.30.4 has two moderate advisories (open redirect via backslash in `Link`, SSR deserialization). The fixed range starts at 7.18, so this is a major upgrade rather than a patch. The app only uses `BrowserRouter`, `Routes`, `Route`, `Link`, `NavLink`, and `useSearchParams`, all unchanged in v7, so the upgrade is low risk.
+- **Major versions behind.** React 19, Recharts 3, react-leaflet 5, react-router 7, Vite 8. Not urgent; plan one upgrade pass.
+- `npm run deploy` is an alias for `npm run build` and does not deploy. Remove or rename it.
+
+## 5. Code quality and maintainability
+
+- **Naming.** `mockShellfishData.js` and the `mockShellfishData` export contain the real dataset. The README apologizes for this. Rename to `observations.js` and `observations`; it is a one-commit refactor with an IDE.
+- **Four copies of site constants.** Coordinates and colors for the same sites live in `SITE_LOCATIONS`, `SiteComparisonChart.SITE_COLORS`, `LiveTemperaturePanel.LIVE_SITE_LOCATIONS`, and `build_live_temperature.py SITES`. Keep one `sites.json` that both the app and the scripts read.
+- **Navigation.** The header offers Dashboard, Site Map, and an external Conditioning Atlas link. Live Data is reachable only through a "Beta" link under the archival chart, and Research only through the footer. Add both to the header nav.
+- **Stale copy.** The header disclaimer still describes "image-derived shell growth" and lists sites that no longer match the data. `DataTable` and `FieldReportExport` describe "field observation records" for what are mostly individual oyster rows.
+- **URL state is one-way.** `DashboardPage` reads `?site=` on load but never writes filter changes back, so a shared URL and the visible state diverge after the first click. Treatment, metric, and year are not in the URL at all.
+- **Search matches the string "null".** `DataTable` stringifies missing values before matching, so typing "nu" matches every row with a blank metric.
+- **`SiteMap` passes both `bounds` and `center` and `zoom`** to `MapContainer`; only `bounds` takes effect.
+- **One 1,739 line stylesheet.** Consider splitting by page or component, or at least adding a table of contents comment. Only one `!important`, which is good.
+- **OSEL score thresholds** live as constants inside a component. They are scientific parameters, so move them to a documented config and surface the thresholds in the UI legend.
+- **External font dependency.** `index.html` loads Inter from Google Fonts. For a research tool that is a privacy and offline consideration; self-host or fall back to system fonts.
+
+## 6. Testing
+
+There are none. The highest value targets are the pure functions in `mockShellfishData.js`: `finalDateRowsWithValue`, `summarizeValues`, `computeSummaryStats`, `getTimeSeriesData`, `getTreatmentComparisonData`, and the merge logic that produced bug 2.1. Add Vitest, write a fixture of about 20 rows, and assert the aggregates by hand. A second tier is a snapshot test that each committed JSON bundle matches its declared schema and controlled vocabularies.
+
+## 7. Accessibility
+
+Generally reasonable: semantic sections, `aria-label`s on control groups, `role="table"` on the ledger, labeled selects. Gaps:
+
+- Toggle buttons do not expose `aria-pressed`.
+- Charts have no text alternative. A short visually hidden summary or the data table link would cover it.
+- Two `` elements render on the dashboard (header and print title).
+- The `sort-button` headers do not expose `aria-sort`.
+
+## Prioritized roadmap
+
+**Quick wins (an afternoon)**, addressed on this branch
+
+1. Gate the print appendix behind a `beforeprint` flag. Removes 337,000 DOM nodes from every dashboard load. Done: the appendix mounts only while printing and is capped at 1,000 rows with a pointer to the CSV. Dashboard DOM went from 30,665 rows to 16.
+2. Fix survival replacement to key on (site, treatment, date). Restores 22 measured records. Done and verified against the merged dataset: Sequim Bay heat-primed survival and the Palix River 2024 to 2025 trajectory are back.
+3. Resolve the `npm audit` findings. Done by upgrading `react-router-dom` to 7.18.3; the audit is clean and all routes render.
+4. Add Live Data and Research to the header nav; refresh the disclaimer copy. Done.
+5. Label time series points by date, not month. Done; no duplicate labels remain.
+6. Skip the deploy when the snapshot did not change. Done: the refresh workflow now dispatches `deploy.yml` only after committing a changed snapshot, and the `workflow_run` trigger is removed from `deploy.yml`.
+
+**Medium (a few days)**, addressed on this branch
+
+7. Move data bundles to `public/data/` and fetch per route; split live snapshot from app code. Done: bundles are fetched through a small cached store in `src/data/resources.js`, routes are lazy-loaded, and the JavaScript entry chunk went from 19.9 MB to 197 kB (plus a 415 kB dashboard chunk and a 154 kB Leaflet chunk loaded only where needed). The live snapshot is a separate 33 kB file.
+8. Emit growth data in a compact shape. Done: a positional bundle format with lookups and constants, encoded by `scripts/shield_data.py` and decoded by `src/data/bundleFormat.js`. Growth data is 1.45 MB raw and 189 kB gzip, down from 19.9 MB and 422 kB. The committed data was re-encoded losslessly (round-trip verified).
+9. Per-site time series lines; same final-date rule for growth and survival. Done: the time series draws one line per site with per-site error bars and counts; treatment and site comparisons, the summary card, and the map summaries all use the latest assessment for growth as well as survival.
+10. Vitest and a pull request workflow. Done: 36 tests cover the bundle decoder, the merge rule, every aggregation function, and the schema and vocabularies of the committed bundles. `.github/workflows/ci.yml` runs tests and a build on pull requests and non-main branches.
+11. Shared Python helpers, `requirements.txt`, `npm run build:data`. Done: `scripts/shield_data.py` holds the treatment mapping, date parsing, fetch with retries, and the bundle encoder; the three observation scripts import it.
+12. Make `build_real_observations.py` reproducible from public URLs. Done: inputs are read from the public repository by default, or from a local checkout via `PGC_SOURCE`. All three observation scripts were run end to end against upstream on 2026-09-07. Survival matched the committed data exactly; growth differed by 0.1 on one value and the field bundle differed on seven Sequim and Palix rows because upstream has been updated since June. Those refreshed values were not committed here, so the change stays a pure refactor; run `npm run build:data` to take them.
+
+Also folded into this work because the module was rewritten anyway: `mockShellfishData.js` is replaced by `observations.js`, `resources.js`, and `siteMetadata.js` (part of item 16 below); `npm run deploy` was removed.
+
+**Larger (plan for)**
+
+13. Precompute aggregates at build time and load raw rows on demand.
+14. Move the hourly snapshot off `main` history.
+15. Dependency upgrade pass (React 19, Recharts 3, react-leaflet 5, react-router 7, Vite 8).
+16. Unify the remaining site constants (the Python live script and the live panel's environmental-only sites) into one shared file. The `mockShellfishData` rename is done.
diff --git a/README.md b/README.md
index f917f54..c241b55 100644
--- a/README.md
+++ b/README.md
@@ -10,8 +10,9 @@ so users can compare growth, survival, temperature, site conditions, source
coverage, and treatment outcomes in one browser-based view.
The app is built with React, Vite, Recharts, Leaflet, and React Router. It is
-deployed as a static single-page app, with data prepared ahead of time by build
-scripts rather than by a runtime application server.
+deployed as a static single-page app. Data is prepared ahead of time by build
+scripts into compact JSON bundles under `public/data/`, which the app fetches at
+runtime per route; there is no application server.
## Website
@@ -43,28 +44,42 @@ helps users:
## How It Works
-SHIELD has no browser-facing backend. The deployed site loads committed JSON
-bundles from `src/data/` and renders them entirely in the React app.
+SHIELD has no browser-facing backend. The deployed site fetches committed JSON
+bundles from `public/data/` when a route needs them (the dashboard and map load
+the observation bundles, the live-data page loads the live snapshot) and renders
+them entirely in the React app. Keeping data out of the JavaScript bundle means
+the Research page never downloads the growth dataset, and the hourly live
+snapshot caches independently of the application code.
The backend-like work happens before deployment:
-- `scripts/build_real_observations.py` reads RobertsLab observation files and
- writes `src/data/realObservations.json`.
+- `scripts/build_real_observations.py` reads RobertsLab field observation files
+ from the public `project-gigas-conditioning` repository (or a local checkout
+ via `PGC_SOURCE`) and writes `public/data/realObservations.json`.
- `scripts/build_growth_observations.py` downloads RobertsLab growth CSV
- outputs and writes `src/data/growthObservations.json`.
+ outputs and writes `public/data/growthObservations.json`.
- `scripts/build_survival_observations.py` downloads RobertsLab survival CSV
- outputs and writes `src/data/survivalObservations.json`.
+ outputs and writes `public/data/survivalObservations.json`.
- `scripts/buildArchivalTemperature.mjs` downloads high-frequency HOBO logger
CSVs, aggregates them to daily mean/min/max water temperature, and writes
- `src/data/archivalTemperatureData.json`.
+ `public/data/archivalTemperatureData.json`.
- `scripts/build_live_temperature.py` fetches recent public environmental
observations from nearby NOAA, USGS, and NANOOS-matched sources and writes
- `src/data/liveTemperature.json`.
+ `public/data/liveTemperature.json`.
+- `scripts/shield_data.py` holds the helpers the observation scripts share:
+ treatment normalization, date parsing, HTTP fetching with retries, and the
+ compact bundle encoder.
+- `npm run build:data` runs the four static builders in dependency order
+ (archival temperature first, because the field observations reuse its monthly
+ means).
+- `.github/workflows/ci.yml` runs the unit tests and a production build on
+ pull requests and non-main branches.
- `.github/workflows/live-temperature.yml` refreshes the live environmental
- snapshot hourly and commits it only when the JSON changes.
+ snapshot hourly, commits it only when the JSON changes, and dispatches the
+ deploy workflow only in that case.
- `.github/workflows/deploy.yml` builds the static app and deploys the `dist/`
- artifact to GitHub Pages after pushes to `main`, successful live-environment
- refreshes, or manual workflow dispatches.
+ artifact to GitHub Pages after pushes to `main` or workflow dispatches
+ (manual, or from a live-environment refresh that changed the snapshot).
This design keeps the public site simple to host on GitHub Pages while still
allowing scheduled server-side data refreshes for sources that cannot be fetched
@@ -72,30 +87,43 @@ directly from the browser because of CORS or credential constraints.
## Data
-The historical placeholder dataset has been replaced with real observation
-records. The `mockShellfishData` export name remains for component compatibility,
-but it now combines `src/data/realObservations.json`,
-`src/data/growthObservations.json`, and `src/data/survivalObservations.json`.
+All records are real observations. `src/data/observations.js` assembles the
+dashboard dataset from `public/data/realObservations.json`,
+`public/data/growthObservations.json`, and `public/data/survivalObservations.json`,
+and holds the null-safe aggregation functions; `src/data/resources.js` fetches
+and caches the bundles; `src/data/siteMetadata.js` holds site coordinates,
+colors, and controlled vocabularies.
Current committed data summary:
| Dataset | File | Description |
|---------|------|-------------|
-| Field observations | `src/data/realObservations.json` | 74 site x treatment x assessment-date records generated from RobertsLab outplant data and Thorndyke Bay 10K-Seed survival anchors |
-| Growth observations | `src/data/growthObservations.json` | 29,836 individual oyster predicted-volume records refreshed from Thorndyke Bay, Palix River/Willapa Bay, Sequim Bay thermal, Sequim Bay PolyIC, and Westcott growth CSV outputs |
-| Survival observations | `src/data/survivalObservations.json` | 738 per-bag percent-survival records from Thorndyke Bay, Palix River/Willapa Bay, Sequim Bay PolyIC, and Westcott survival CSV outputs (Sequim Bay PolyIC and Westcott per assessment date; Thorndyke Bay and Palix River/Willapa Bay total survival) |
-| Archival temperature | `src/data/archivalTemperatureData.json` | Daily water-temperature summaries aggregated from approximately 15-minute HOBO logger records |
-| Near-live environment | `src/data/liveTemperature.json` | Recent matched observations and source metadata for temperature, tide, wind, pressure, waves, streamflow where available, and chlorophyll source matches |
-| Site metadata | `src/data/mockShellfishData.js` | Site coordinates, regions, descriptions, colors, filter helpers, and chart aggregation helpers |
-
-The dashboard-facing observation array is assembled in `src/data/mockShellfishData.js`
+| Field observations | `public/data/realObservations.json` | 74 site x treatment x assessment-date records generated from RobertsLab outplant data and Thorndyke Bay 10K-Seed survival anchors |
+| Growth observations | `public/data/growthObservations.json` | 29,836 individual oyster predicted-volume records refreshed from Thorndyke Bay, Palix River/Willapa Bay, Sequim Bay thermal, Sequim Bay PolyIC, and Westcott growth CSV outputs |
+| Survival observations | `public/data/survivalObservations.json` | 738 per-bag percent-survival records from Thorndyke Bay, Palix River/Willapa Bay, Sequim Bay PolyIC, and Westcott survival CSV outputs (Sequim Bay PolyIC and Westcott per assessment date; Thorndyke Bay and Palix River/Willapa Bay total survival) |
+| Archival temperature | `public/data/archivalTemperatureData.json` | Daily water-temperature summaries aggregated from approximately 15-minute HOBO logger records |
+| Near-live environment | `public/data/liveTemperature.json` | Recent matched observations and source metadata for temperature, tide, wind, pressure, waves, streamflow where available, and chlorophyll source matches |
+| Site metadata | `src/data/siteMetadata.js` | Site coordinates, regions, descriptions, colors, and controlled vocabularies |
+
+### Bundle format
+
+The three observation bundles use a compact positional format so the growth
+dataset ships at about 1.5 MB instead of 20 MB. Each bundle carries `columns`
+(the field at each row position), `lookups` (columns stored as an index into a
+value list), `constants` (fields identical on every record), and `rows`.
+`year`, `month`, `quarter`, and `id` are derived on load. The encoder is
+`compact_bundle` in `scripts/shield_data.py` and the decoder is
+`src/data/bundleFormat.js`; `npm test` validates every committed bundle against
+the schema and vocabularies.
+
+The dashboard-facing observation array is assembled in `src/data/observations.js`
from field, growth, and survival observations. Field rows supply monthly
logger-temperature (and legacy shell-length growth) values; per-bag survival
rows carry percent survival; individual growth-volume rows carry predicted
-volume. Each record leaves metrics it does not measure as `null`, and the
-aggregated survival anchors formerly held in field rows are dropped where a
-per-bag survival dataset replaces them, avoiding double-counting. Field survival
-is retained for sites without a per-bag replacement. Aggregations and exports
+volume. Each record leaves metrics it does not measure as `null`. Aggregated field
+survival is dropped only where a per-bag survival row exists for the same site,
+treatment, and assessment date, avoiding double-counting; field survival is
+retained for every other site, treatment, and date. Aggregations and exports
are null-safe, so missing metrics show as unavailable rather than as zeroes.
### Sites
@@ -144,16 +172,18 @@ when reusing the dashboard or derived data products.
| OpenStreetMap contributors | Base map tiles and map attribution | `src/components/SiteMap.jsx`, `src/components/LiveTemperaturePanel.jsx` |
Direct public source URLs are stored in the generated JSON metadata where
-available, especially `src/data/archivalTemperatureData.json` and
-`src/data/liveTemperature.json`.
+available, especially `public/data/archivalTemperatureData.json` and
+`public/data/liveTemperature.json`.
## Features
- Interactive filters for site, treatment, metric, and study year
- Summary statistic cards for filtered records
-- Time-series chart for growth volume, temperature, or survival
+- Time-series chart for growth volume, temperature, or survival, one line per
+ site so sites sampled on different dates are never pooled
- Archival water-temperature chart from HOBO logger data
-- Treatment comparison and site comparison charts
+- Treatment comparison and site comparison charts, using the latest assessment
+ per site and treatment for both growth and survival
- Sortable, searchable, paginated data table
- Field report export for the current filter state
- Geographic site map with interactive markers
@@ -167,8 +197,9 @@ available, especially `src/data/archivalTemperatureData.json` and
- [Node.js](https://nodejs.org/) 18 or later
- npm, included with Node.js
-- Python 3. The growth refresh script uses only the standard library; `pandas`
- is needed only if regenerating `realObservations.json`.
+- Python 3.10 or later. The growth, survival, and live-environment scripts use
+ only the standard library. Regenerating `realObservations.json` needs the
+ packages in `requirements.txt` (`pip install -r requirements.txt`).
## Install Dependencies
@@ -202,6 +233,18 @@ npm run build
Output is written to `dist/`.
+Run the unit and bundle-validation tests:
+
+```bash
+npm test
+```
+
+Regenerate every static data bundle in dependency order:
+
+```bash
+npm run build:data
+```
+
Refresh the near-live environmental snapshot locally:
```bash
@@ -214,10 +257,12 @@ Regenerate the archival temperature bundle:
npm run build:temperature
```
-Regenerate real observations manually:
+Regenerate field observations manually (reads the public GitHub repository by
+default; set `PGC_SOURCE` to a local `project-gigas-conditioning` checkout to
+build offline):
```bash
-python3 scripts/build_real_observations.py
+npm run build:real
```
Regenerate growth observations manually:
@@ -297,9 +342,18 @@ The React Router basename is derived automatically from this setting.
shield-dashboard/
├── README.md
├── package.json
+├── requirements.txt
├── index.html
├── vite.config.js
+├── public/
+│ └── data/
+│ ├── archivalTemperatureData.json
+│ ├── growthObservations.json
+│ ├── liveTemperature.json
+│ ├── realObservations.json
+│ └── survivalObservations.json
├── scripts/
+│ ├── shield_data.py
│ ├── build_growth_observations.py
│ ├── build_survival_observations.py
│ ├── build_real_observations.py
@@ -310,12 +364,11 @@ shield-dashboard/
├── App.jsx
├── styles.css
├── data/
- │ ├── archivalTemperatureData.json
- │ ├── growthObservations.json
- │ ├── liveTemperature.json
- │ ├── mockShellfishData.js
- │ ├── realObservations.json
- │ └── survivalObservations.json
+ │ ├── bundleFormat.js
+ │ ├── observations.js
+ │ ├── resources.js
+ │ ├── siteMetadata.js
+ │ └── __tests__/
├── pages/
│ ├── DashboardPage.jsx
│ ├── LiveDataPage.jsx
@@ -323,6 +376,7 @@ shield-dashboard/
│ └── ResearchPage.jsx
└── components/
├── ArchivalTemperatureChart.jsx
+ ├── DataStatus.jsx
├── DataTable.jsx
├── FieldReportExport.jsx
├── Filters.jsx
@@ -342,11 +396,13 @@ shield-dashboard/
| `npm run dev` | Start the Vite development server |
| `npm run build` | Build the static app and create GitHub Pages SPA fallback files |
| `npm run preview` | Preview the production build locally |
-| `npm run deploy` | Alias for the production build |
-| `npm run build:growth` | Refresh `src/data/growthObservations.json` from RobertsLab growth CSV outputs |
-| `npm run build:survival` | Refresh `src/data/survivalObservations.json` from RobertsLab survival CSV outputs |
-| `npm run build:live-environment` | Refresh `src/data/liveTemperature.json` from public observing feeds |
-| `npm run build:temperature` | Regenerate `src/data/archivalTemperatureData.json` from source temperature CSVs |
+| `npm test` | Run the Vitest unit tests and validate the committed data bundles |
+| `npm run build:data` | Regenerate all static bundles in dependency order (temperature, field, growth, survival) |
+| `npm run build:real` | Refresh `public/data/realObservations.json` from RobertsLab field observation files |
+| `npm run build:growth` | Refresh `public/data/growthObservations.json` from RobertsLab growth CSV outputs |
+| `npm run build:survival` | Refresh `public/data/survivalObservations.json` from RobertsLab survival CSV outputs |
+| `npm run build:live-environment` | Refresh `public/data/liveTemperature.json` from public observing feeds |
+| `npm run build:temperature` | Regenerate `public/data/archivalTemperatureData.json` from source temperature CSVs |
## License
diff --git a/package-lock.json b/package-lock.json
index c79aa7d..413df20 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -12,12 +12,13 @@
"react": "^18.3.1",
"react-dom": "^18.3.1",
"react-leaflet": "^4.2.1",
- "react-router-dom": "^6.28.0",
+ "react-router-dom": "^7.18.3",
"recharts": "^2.15.0"
},
"devDependencies": {
"@vitejs/plugin-react": "^4.3.4",
- "vite": "^6.0.3"
+ "vite": "^6.0.3",
+ "vitest": "^5.0.0"
}
},
"node_modules/@babel/code-frame": {
@@ -814,15 +815,6 @@
"react-dom": "^18.0.0"
}
},
- "node_modules/@remix-run/router": {
- "version": "1.23.3",
- "resolved": "https://registry.npmjs.org/@remix-run/router/-/router-1.23.3.tgz",
- "integrity": "sha512-4An71tdz9X8+3sI4Qqqd2LWd9vS39J7sqd9EU4Scw7TJE/qB10Flv/UuqbPVgfQV9XoK8Np6jNquZitnZq5i+Q==",
- "license": "MIT",
- "engines": {
- "node": ">=14.0.0"
- }
- },
"node_modules/@rolldown/pluginutils": {
"version": "1.0.0-beta.27",
"resolved": "https://registry.npmjs.org/@rolldown/pluginutils/-/pluginutils-1.0.0-beta.27.tgz",
@@ -922,9 +914,6 @@
"arm"
],
"dev": true,
- "libc": [
- "glibc"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -939,9 +928,6 @@
"arm"
],
"dev": true,
- "libc": [
- "musl"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -956,9 +942,6 @@
"arm64"
],
"dev": true,
- "libc": [
- "glibc"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -973,9 +956,6 @@
"arm64"
],
"dev": true,
- "libc": [
- "musl"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -990,9 +970,6 @@
"loong64"
],
"dev": true,
- "libc": [
- "glibc"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -1007,9 +984,6 @@
"loong64"
],
"dev": true,
- "libc": [
- "musl"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -1024,9 +998,6 @@
"ppc64"
],
"dev": true,
- "libc": [
- "glibc"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -1041,9 +1012,6 @@
"ppc64"
],
"dev": true,
- "libc": [
- "musl"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -1058,9 +1026,6 @@
"riscv64"
],
"dev": true,
- "libc": [
- "glibc"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -1075,9 +1040,6 @@
"riscv64"
],
"dev": true,
- "libc": [
- "musl"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -1092,9 +1054,6 @@
"s390x"
],
"dev": true,
- "libc": [
- "glibc"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -1109,9 +1068,6 @@
"x64"
],
"dev": true,
- "libc": [
- "glibc"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -1126,9 +1082,6 @@
"x64"
],
"dev": true,
- "libc": [
- "musl"
- ],
"license": "MIT",
"optional": true,
"os": [
@@ -1264,6 +1217,17 @@
"@babel/types": "^7.28.2"
}
},
+ "node_modules/@types/chai": {
+ "version": "5.2.3",
+ "resolved": "https://registry.npmjs.org/@types/chai/-/chai-5.2.3.tgz",
+ "integrity": "sha512-Mw558oeA9fFbv65/y4mHtXDs9bPnFMZAL/jxdPFUpOHHIXX91mcgEHbS5Lahr+pwZFR8A7GQleRWeI6cGFC2UA==",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "@types/deep-eql": "*",
+ "assertion-error": "^2.0.1"
+ }
+ },
"node_modules/@types/d3-array": {
"version": "3.2.2",
"resolved": "https://registry.npmjs.org/@types/d3-array/-/d3-array-3.2.2.tgz",
@@ -1327,6 +1291,13 @@
"integrity": "sha512-Ps3T8E8dZDam6fUyNiMkekK3XUsaUEik+idO9/YjPtfj2qruF8tFBXS7XhtE4iIXBLxhmLjP3SXpLhVf21I9Lw==",
"license": "MIT"
},
+ "node_modules/@types/deep-eql": {
+ "version": "4.0.2",
+ "resolved": "https://registry.npmjs.org/@types/deep-eql/-/deep-eql-4.0.2.tgz",
+ "integrity": "sha512-c9h9dVVMigMPc4bwTvC5dxqtqJZwQPePsWjPlpSOnojbor6pGqdk541lfA7AqFQr5pB1BRdq0juY9db81BwyFw==",
+ "dev": true,
+ "license": "MIT"
+ },
"node_modules/@types/estree": {
"version": "1.0.9",
"resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.9.tgz",
@@ -1355,10 +1326,58 @@
"vite": "^4.2.0 || ^5.0.0 || ^6.0.0 || ^7.0.0"
}
},
+ "node_modules/@vitest/mocker": {
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/@vitest/mocker/-/mocker-5.0.0.tgz",
+ "integrity": "sha512-66PGTMIiVJP3t4a5yxU9qPtf7MdTBs8jmToMvy+HVflB3Yy13WJZTtPePdvU+wjRV02SKK5doLbSA6o9pwOmiA==",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "@jridgewell/trace-mapping": "0.3.31",
+ "@vitest/spy": "5.0.0",
+ "estree-walker": "^3.0.3",
+ "magic-string": "^1.2.3"
+ },
+ "funding": {
+ "url": "https://opencollective.com/vitest"
+ },
+ "peerDependencies": {
+ "msw": "^2.4.9",
+ "vite": "^6.0.0 || ^7.0.0 || ^8.0.0"
+ },
+ "peerDependenciesMeta": {
+ "msw": {
+ "optional": true
+ },
+ "vite": {
+ "optional": true
+ }
+ }
+ },
+ "node_modules/@vitest/spy": {
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/@vitest/spy/-/spy-5.0.0.tgz",
+ "integrity": "sha512-uy+luWBAPw9XfthoHi5AkfHUnuPYEESjl0p/r+meoBnU8bxg5GDQ3Ey8MjcJ6sqahkL4PFyrvfMJJBw7LbU06g==",
+ "dev": true,
+ "license": "MIT",
+ "funding": {
+ "url": "https://opencollective.com/vitest"
+ }
+ },
+ "node_modules/assertion-error": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/assertion-error/-/assertion-error-2.0.1.tgz",
+ "integrity": "sha512-Izi8RQcffqCeNVgFigKli1ssklIbpHnCYc6AknXGYoB6grJqyeby7jv12JUQgmTAnIDnbck1uxksT4dzN3PWBA==",
+ "dev": true,
+ "license": "MIT",
+ "engines": {
+ "node": ">=12"
+ }
+ },
"node_modules/baseline-browser-mapping": {
- "version": "2.10.34",
- "resolved": "https://registry.npmjs.org/baseline-browser-mapping/-/baseline-browser-mapping-2.10.34.tgz",
- "integrity": "sha512-IMDedajPifLnHNY0X9n8hKxRTQ6/eTHwr5bDo04WnuqxyKw6LYtQywCuuqPZwhl3aBXMvQpJov42GLCwRRdQzw==",
+ "version": "2.11.21",
+ "resolved": "https://registry.npmjs.org/baseline-browser-mapping/-/baseline-browser-mapping-2.11.21.tgz",
+ "integrity": "sha512-uh8vpY/1/YyFkunIDFH/12p7/7VdPKA1hejMVEbdkEaWnUz0Hesvx5EbiU6XxjyHZIOju+ZMbQJkRh+es3/spQ==",
"dev": true,
"license": "Apache-2.0",
"bin": {
@@ -1369,9 +1388,9 @@
}
},
"node_modules/browserslist": {
- "version": "4.28.2",
- "resolved": "https://registry.npmjs.org/browserslist/-/browserslist-4.28.2.tgz",
- "integrity": "sha512-48xSriZYYg+8qXna9kwqjIVzuQxi+KYWp2+5nCYnYKPTr0LvD89Jqk2Or5ogxz0NUMfIjhh2lIUX/LyX9B4oIg==",
+ "version": "4.28.9",
+ "resolved": "https://registry.npmjs.org/browserslist/-/browserslist-4.28.9.tgz",
+ "integrity": "sha512-EWazOblFYUvlGZcfGhPUPmYh3nikUxBVb+y9MJun5f3hBi812X+8MSQTujLBtgK3cf51fJWbWfOjyeO954d+Eg==",
"dev": true,
"funding": [
{
@@ -1389,11 +1408,11 @@
],
"license": "MIT",
"dependencies": {
- "baseline-browser-mapping": "^2.10.12",
- "caniuse-lite": "^1.0.30001782",
- "electron-to-chromium": "^1.5.328",
- "node-releases": "^2.0.36",
- "update-browserslist-db": "^1.2.3"
+ "baseline-browser-mapping": "^2.11.20",
+ "caniuse-lite": "^1.0.30001810",
+ "electron-to-chromium": "^1.5.420",
+ "node-releases": "^2.0.54",
+ "update-browserslist-db": "^1.3.2"
},
"bin": {
"browserslist": "cli.js"
@@ -1403,9 +1422,9 @@
}
},
"node_modules/caniuse-lite": {
- "version": "1.0.30001797",
- "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001797.tgz",
- "integrity": "sha512-l8xKG+gwAIExZGl9FrF7KUwuOmk6wbEPC9Xoy/RtnWv1XG0Q4LFlagaLpUv3Kiza3W/wm27zy0yWJEieYKAP6w==",
+ "version": "1.0.30001810",
+ "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001810.tgz",
+ "integrity": "sha512-TITQPUkaz+aVk5GL6NhOdwk1aEaNTSDPsGFWrTuhKGtjTF70jL/Oht2W4c6rXUe5fu7Ie19VIahAXHIIiWWNeg==",
"dev": true,
"funding": [
{
@@ -1423,6 +1442,16 @@
],
"license": "CC-BY-4.0"
},
+ "node_modules/chai": {
+ "version": "6.2.2",
+ "resolved": "https://registry.npmjs.org/chai/-/chai-6.2.2.tgz",
+ "integrity": "sha512-NUPRluOfOiTKBKvWPtSD4PhFvWCqOi0BGStNWs57X9js7XGTprSmFoz5F0tWhR4WPjNeR9jXqdC7/UpSJTnlRg==",
+ "dev": true,
+ "license": "MIT",
+ "engines": {
+ "node": ">=18"
+ }
+ },
"node_modules/clsx": {
"version": "2.1.1",
"resolved": "https://registry.npmjs.org/clsx/-/clsx-2.1.1.tgz",
@@ -1439,6 +1468,19 @@
"dev": true,
"license": "MIT"
},
+ "node_modules/cookie": {
+ "version": "1.1.1",
+ "resolved": "https://registry.npmjs.org/cookie/-/cookie-1.1.1.tgz",
+ "integrity": "sha512-ei8Aos7ja0weRpFzJnEA9UHJ/7XQmqglbRwnf2ATjcB9Wq874VKH9kfjjirM6UhU2/E5fFYadylyhFldcqSidQ==",
+ "license": "MIT",
+ "engines": {
+ "node": ">=18"
+ },
+ "funding": {
+ "type": "opencollective",
+ "url": "https://opencollective.com/express"
+ }
+ },
"node_modules/csstype": {
"version": "3.2.3",
"resolved": "https://registry.npmjs.org/csstype/-/csstype-3.2.3.tgz",
@@ -1601,12 +1643,19 @@
}
},
"node_modules/electron-to-chromium": {
- "version": "1.5.368",
- "resolved": "https://registry.npmjs.org/electron-to-chromium/-/electron-to-chromium-1.5.368.tgz",
- "integrity": "sha512-7RckJJK4uESJF9PxvfMWd3TGqIiieUTG4HxnKaKuIpGbcr+r2ZEB3g2gAhCP3Fqm42vJSzLfgab9eva/C4/XVw==",
+ "version": "1.5.422",
+ "resolved": "https://registry.npmjs.org/electron-to-chromium/-/electron-to-chromium-1.5.422.tgz",
+ "integrity": "sha512-UvA/32XqrLDdZSn7Jllo1AYNcWji/G0d5M0GTViE7KoGBiMunw3a34Sb2KO4ZZyrSEhqsxFoVhWWJshdyfKqJA==",
"dev": true,
"license": "ISC"
},
+ "node_modules/es-module-lexer": {
+ "version": "2.3.2",
+ "resolved": "https://registry.npmjs.org/es-module-lexer/-/es-module-lexer-2.3.2.tgz",
+ "integrity": "sha512-poHGpORABojJJucnV9KbOavETW8lBVnphkW77ER5/BQ5Fz7oXSoCNek7IH3vR5nRjdsEz926ibFYX8KtLQmdyw==",
+ "dev": true,
+ "license": "MIT"
+ },
"node_modules/esbuild": {
"version": "0.25.12",
"resolved": "https://registry.npmjs.org/esbuild/-/esbuild-0.25.12.tgz",
@@ -1659,12 +1708,32 @@
"node": ">=6"
}
},
+ "node_modules/estree-walker": {
+ "version": "3.0.3",
+ "resolved": "https://registry.npmjs.org/estree-walker/-/estree-walker-3.0.3.tgz",
+ "integrity": "sha512-7RUKfXgSMMkzt6ZuXmqapOurLGPPfgj6l9uRZ7lRGolvk0y2yocc35LdcxKC5PQZdn2DMqioAQ2NoWcrTKmm6g==",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "@types/estree": "^1.0.0"
+ }
+ },
"node_modules/eventemitter3": {
"version": "4.0.7",
"resolved": "https://registry.npmjs.org/eventemitter3/-/eventemitter3-4.0.7.tgz",
"integrity": "sha512-8guHBZCwKnFhYdHr2ysuRWErTwhoN2X8XELRlrRwpmfeY2jjuUN4taQMsULKUVo1K4DvZl+0pgfyoysHxvmvEw==",
"license": "MIT"
},
+ "node_modules/expect-type": {
+ "version": "1.4.0",
+ "resolved": "https://registry.npmjs.org/expect-type/-/expect-type-1.4.0.tgz",
+ "integrity": "sha512-KfYbmpRm0VbLjEvVa9yGwCi9GI34xvi7A/HXYWQO65CSD2u3MczUJSuwXKFIxlGsgBQizV9q5J9NHj4VG0n+pA==",
+ "dev": true,
+ "license": "Apache-2.0",
+ "engines": {
+ "node": ">=12.0.0"
+ }
+ },
"node_modules/fast-equals": {
"version": "5.4.0",
"resolved": "https://registry.npmjs.org/fast-equals/-/fast-equals-5.4.0.tgz",
@@ -1774,6 +1843,16 @@
"yallist": "^3.0.2"
}
},
+ "node_modules/magic-string": {
+ "version": "1.2.3",
+ "resolved": "https://registry.npmjs.org/magic-string/-/magic-string-1.2.3.tgz",
+ "integrity": "sha512-Bpb0W2TbLKOZ7vJnOUnVRGq3WL2p+ISV29M6hYPL1AFCpyKZpdr5ytiXoTSSxRVhg8YW7f65+6gbG8WG6PCa/g==",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "@jridgewell/sourcemap-codec": "^1.5.5"
+ }
+ },
"node_modules/ms": {
"version": "2.1.3",
"resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz",
@@ -1782,9 +1861,9 @@
"license": "MIT"
},
"node_modules/nanoid": {
- "version": "3.3.12",
- "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.12.tgz",
- "integrity": "sha512-ZB9RH/39qpq5Vu6Y+NmUaFhQR6pp+M2Xt76XBnEwDaGcVAqhlvxrl3B2bKS5D3NH3QR76v3aSrKaF/Kiy7lEtQ==",
+ "version": "3.3.18",
+ "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.18.tgz",
+ "integrity": "sha512-DTg4MJbGMWkfi6VZFdNt2/caMbQy4Ou+Op/hJQvGEWcnVfoA1QA+xzRKAzw9jD6+GVOOeYr/mIcuDSdug6F6+w==",
"dev": true,
"funding": [
{
@@ -1801,9 +1880,9 @@
}
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"license": "MIT",
"dependencies": {
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+ "cookie": "^1.0.1",
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},
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+ "node": ">=20.0.0"
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"license": "MIT",
"dependencies": {
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- "react-router": "6.30.4"
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+ "react": ">=18",
+ "react-dom": ">=18"
}
},
"node_modules/react-smooth": {
@@ -2087,6 +2199,19 @@
"semver": "bin/semver.js"
}
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+ "resolved": "https://registry.npmjs.org/set-cookie-parser/-/set-cookie-parser-2.7.2.tgz",
+ "integrity": "sha512-oeM1lpU/UvhTxw+g3cIfxXHyJRc/uidd3yK1P242gzHds0udQBYzs3y8j4gCCW+ZJ7ad0yctld8RYO+bdurlvw==",
+ "license": "MIT"
+ },
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+ "resolved": "https://registry.npmjs.org/siginfo/-/siginfo-2.0.0.tgz",
+ "integrity": "sha512-ybx0WO1/8bSBLEWXZvEd7gMW3Sn3JFlW3TvX1nREbDLRNQNaeNN8WK0meBwPdAaOI7TtRRRJn/Es1zhrrCHu7g==",
+ "dev": true,
+ "license": "ISC"
+ },
"node_modules/source-map-js": {
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"resolved": "https://registry.npmjs.org/source-map-js/-/source-map-js-1.2.1.tgz",
@@ -2097,12 +2222,46 @@
"node": ">=0.10.0"
}
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+ "dev": true,
+ "license": "MIT"
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"license": "MIT"
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+ "integrity": "sha512-9APumHG7r4yOk4X4WlkmE71aZcv1gvin1czO3OQ1U9iJcFA5Ja/ygyb0vPOVHTthFozUYs8CLoLUlM8grb2lTQ==",
+ "dev": true,
+ "license": "MIT",
+ "engines": {
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+ "version": "1.3.0",
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+ "dev": true,
+ "license": "MIT",
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+ }
+ },
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"version": "0.2.17",
"resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.17.tgz",
@@ -2138,23 +2297,10 @@
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- "license": "MIT",
- "engines": {
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- },
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+ "version": "1.3.2",
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"dev": true,
"funding": [
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@@ -2297,17 +2443,104 @@
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- "integrity": "sha512-QP88BAKvMam/3NxH6vj2o21R6MjxZUAd6nlwAS/pnGvN9IVLocLHxGYIzFhg6fUQ+5th6P4dv4eW9jX3DSIj7A==",
+ "node_modules/vitest": {
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/vitest/-/vitest-5.0.0.tgz",
+ "integrity": "sha512-gpsMNoRhMjMktVxPtstOH4/PJuPyovVaMDr4oDilXaGH1EcqM2OE96SoHT2VIQ6fTGtTjqmHDrEu2X9RQiXf8Q==",
"dev": true,
"license": "MIT",
+ "dependencies": {
+ "@types/chai": "^5.2.2",
+ "@vitest/mocker": "5.0.0",
+ "chai": "^6.2.2",
+ "es-module-lexer": "^2.3.2",
+ "expect-type": "^1.4.0",
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+ "obug": "^2.1.4",
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+ "tinyexec": "1.3.0",
+ "tinyglobby": "^0.2.17",
+ "why-is-node-running": "^2.3.0"
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+ "bin": {
+ "vitest": "vitest.mjs"
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"engines": {
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+ "node": "^22.12.0 || ^24.0.0 || >=26.0.0"
},
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+ "url": "https://opencollective.com/vitest"
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+ "@vitest/coverage-istanbul": "5.0.0",
+ "@vitest/coverage-v8": "5.0.0",
+ "@vitest/ui": "5.0.0",
+ "happy-dom": "*",
+ "jsdom": "*",
+ "vite": "^6.4.0 || ^7.0.0 || ^8.0.0"
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diff --git a/package.json b/package.json
index 889f4f6..75fcea5 100644
--- a/package.json
+++ b/package.json
@@ -5,24 +5,28 @@
"type": "module",
"scripts": {
"dev": "vite",
+ "test": "vitest run",
+ "test:watch": "vitest",
+ "build:real": "python3 scripts/build_real_observations.py",
"build:growth": "python3 scripts/build_growth_observations.py",
"build:survival": "python3 scripts/build_survival_observations.py",
"build:live-environment": "python3 scripts/build_live_temperature.py",
"build:temperature": "node scripts/buildArchivalTemperature.mjs",
+ "build:data": "npm run build:temperature && npm run build:real && npm run build:growth && npm run build:survival",
"build": "vite build && cp dist/index.html dist/404.html && touch dist/.nojekyll",
- "preview": "vite preview",
- "deploy": "npm run build"
+ "preview": "vite preview"
},
"dependencies": {
"leaflet": "^1.9.4",
"react": "^18.3.1",
"react-dom": "^18.3.1",
"react-leaflet": "^4.2.1",
- "react-router-dom": "^6.28.0",
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"recharts": "^2.15.0"
},
"devDependencies": {
"@vitejs/plugin-react": "^4.3.4",
- "vite": "^6.0.3"
+ "vite": "^6.0.3",
+ "vitest": "^5.0.0"
}
}
diff --git a/src/data/archivalTemperatureData.json b/public/data/archivalTemperatureData.json
similarity index 100%
rename from src/data/archivalTemperatureData.json
rename to public/data/archivalTemperatureData.json
diff --git a/public/data/growthObservations.json b/public/data/growthObservations.json
new file mode 100644
index 0000000..83e64a8
--- /dev/null
+++ b/public/data/growthObservations.json
@@ -0,0 +1,29954 @@
+{
+ "format": "shield-observations/1",
+ "meta": {
+ "generatedAt": "2026-08-26",
+ "source": "RobertsLab growth CSV outputs",
+ "studyTitle": "Crassostrea gigas individual oyster growth volume",
+ "sourceRows": {
+ "Thorndyke Bay": 1525,
+ "Palix River/Willapa Bay": 8739,
+ "Sequim Bay": 3336,
+ "Westcott": 16238
+ },
+ "recordCounts": {
+ "Thorndyke Bay": 1525,
+ "Palix River/Willapa Bay": 8739,
+ "Sequim Bay": 3336,
+ "Westcott": 16236
+ },
+ "growthMetric": "Predicted oyster volume from image-derived models",
+ "sourceUrls": [
+ "https://raw.githubusercontent.com/RobertsLab/10K-seed-Cgigas/main/output/baywater_growth.csv",
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv",
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/sequim_growth.csv",
+ "https://raw.githubusercontent.com/RobertsLab/polyIC-larvae/main/output/sequim_polyic_growth.csv",
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/westcott_growth.csv"
+ ],
+ "recordCount": 29836
+ },
+ "sites": [
+ "Palix River/Willapa Bay",
+ "Sequim Bay",
+ "Thorndyke Bay",
+ "Westcott"
+ ],
+ "treatments": [
+ "Control",
+ "Heat primed",
+ "Freshwater primed",
+ "Immune primed",
+ "Combined stress primed"
+ ],
+ "years": [
+ "2024",
+ "2025",
+ "2026"
+ ],
+ "columns": [
+ "date",
+ "site",
+ "treatment",
+ "raw_treatment",
+ "effort",
+ "tag",
+ "oyster_number",
+ "growth_volume",
+ "growth_metric",
+ "source_repo",
+ "source_url"
+ ],
+ "lookups": {
+ "site": [
+ "Palix River/Willapa Bay",
+ "Sequim Bay",
+ "Thorndyke Bay",
+ "Westcott"
+ ],
+ "treatment": [
+ "Control",
+ "Freshwater primed",
+ "Heat primed",
+ "Immune primed",
+ "Combined stress primed"
+ ],
+ "raw_treatment": [
+ "Control",
+ "Treated",
+ "Immune PolyIC",
+ "Temperature+Salinity",
+ "Salinity",
+ "Temperature"
+ ],
+ "effort": [
+ "weekly temperature",
+ "weekly fresh water",
+ "Temperature",
+ "PolyIC",
+ "Growth assay",
+ "Daily Temperature",
+ "Weekly Temperature"
+ ],
+ "growth_metric": [
+ "Predicted_Volume_Poly",
+ "vol"
+ ],
+ "source_repo": [
+ "RobertsLab/project-gigas-conditioning",
+ "RobertsLab/polyIC-larvae",
+ "RobertsLab/10K-seed-Cgigas"
+ ],
+ "source_url": [
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv",
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/sequim_growth.csv",
+ "https://raw.githubusercontent.com/RobertsLab/polyIC-larvae/main/output/sequim_polyic_growth.csv",
+ "https://raw.githubusercontent.com/RobertsLab/10K-seed-Cgigas/main/output/baywater_growth.csv",
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/westcott_growth.csv"
+ ]
+ },
+ "constants": {
+ "growth_mm": null,
+ "temperature_C": null,
+ "survival_percent": null,
+ "survival_source": "none",
+ "growth_source": "measured-volume",
+ "temperature_source": "none"
+ },
+ "rows": [
+["2024-06-24",0,0,0,0,"80","1",5763.3,0,0,0],
+["2024-06-24",0,0,0,0,"80","10",5986.7,0,0,0],
+["2024-06-24",0,0,0,0,"80","100",7070.7,0,0,0],
+["2024-06-24",0,0,0,0,"80","11",6207.9,0,0,0],
+["2024-06-24",0,0,0,0,"80","12",6170.0,0,0,0],
+["2024-06-24",0,0,0,0,"80","13",7804.5,0,0,0],
+["2024-06-24",0,0,0,0,"80","14",6664.2,0,0,0],
+["2024-06-24",0,0,0,0,"80","15",6435.0,0,0,0],
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+ ]
+}
diff --git a/src/data/liveTemperature.json b/public/data/liveTemperature.json
similarity index 100%
rename from src/data/liveTemperature.json
rename to public/data/liveTemperature.json
diff --git a/public/data/realObservations.json b/public/data/realObservations.json
new file mode 100644
index 0000000..2a04da5
--- /dev/null
+++ b/public/data/realObservations.json
@@ -0,0 +1,160 @@
+{
+ "format": "shield-observations/1",
+ "meta": {
+ "generatedAt": "2026-06-20",
+ "source": "RobertsLab/project-gigas-conditioning (+ 10K-Seed survival anchors)",
+ "studyTitle": "Crassostrea gigas stress-hardening outplant program",
+ "siteNotes": {
+ "Palix River/Willapa Bay": "Effort E (2023 POGS), weekly temperature + fresh water hardening; control/treated. Real survival (live/total) and image-derived shell length.",
+ "Sequim Bay": "Effort A (2 weeks daily 25°C thermal hardening), control/treated. Real survival from cumulative mortality; image-derived shell length.",
+ "Westcott": "Efforts B (daily) & D (weekly) thermal hardening, control/treated. Real survival (alive/initial per bag). Image growth not yet calibrated to mm.",
+ "Thorndyke Bay": "10K-Seed hardening (Control / 35C / FW / polyIC / FW+35C). Survival measured 2025-08-20 (n=150/bag); source repo RobertsLab/10K-seed-Cgigas. Growth not published numerically."
+ },
+ "treatmentMapping": {
+ "Control": "untreated control (any effort)",
+ "Heat primed": "temperature / thermal hardening (treated)",
+ "Freshwater primed": "fresh water / low-salinity hardening (treated)",
+ "Immune primed": "polyIC / immune challenge (Thorndyke Bay 10K-Seed)",
+ "Combined stress primed": "fresh water + temperature (Thorndyke Bay 10K-Seed)"
+ },
+ "recordCount": 74
+ },
+ "sites": [
+ "Palix River/Willapa Bay",
+ "Sequim Bay",
+ "Thorndyke Bay",
+ "Westcott"
+ ],
+ "treatments": [
+ "Control",
+ "Heat primed",
+ "Freshwater primed",
+ "Immune primed",
+ "Combined stress primed"
+ ],
+ "years": [
+ "2024",
+ "2025",
+ "2026"
+ ],
+ "columns": [
+ "date",
+ "site",
+ "treatment",
+ "effort",
+ "growth_mm",
+ "temperature_C",
+ "survival_percent",
+ "survival_source",
+ "growth_source"
+ ],
+ "lookups": {
+ "site": [
+ "Thorndyke Bay",
+ "Palix River/Willapa Bay",
+ "Sequim Bay",
+ "Westcott"
+ ],
+ "treatment": [
+ "Combined stress primed",
+ "Control",
+ "Freshwater primed",
+ "Heat primed",
+ "Immune primed"
+ ],
+ "effort": [
+ "10K-Seed (hardening)",
+ "Effort E — weekly fresh water; Effort E — weekly temperature",
+ "Effort E — weekly fresh water",
+ "Effort E — weekly temperature",
+ "Effort A — daily thermal",
+ "Effort B — daily thermal; Effort D — weekly thermal"
+ ],
+ "survival_source": [
+ "measured"
+ ],
+ "growth_source": [
+ "none",
+ "measured"
+ ]
+ },
+ "constants": {
+ "temperature_source": "logger-monthly-mean"
+ },
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+["2025-12-02",3,3,5,null,7.8,83.9,0,0]
+ ]
+}
diff --git a/public/data/survivalObservations.json b/public/data/survivalObservations.json
new file mode 100644
index 0000000..1079e3c
--- /dev/null
+++ b/public/data/survivalObservations.json
@@ -0,0 +1,857 @@
+{
+ "format": "shield-observations/1",
+ "meta": {
+ "generatedAt": "2026-08-26",
+ "source": "RobertsLab survival CSV outputs",
+ "studyTitle": "Crassostrea gigas outplant percent survival by bag",
+ "sourceRows": {
+ "Thorndyke Bay": 30,
+ "Palix River/Willapa Bay": 14,
+ "Sequim Bay": 24,
+ "Westcott": 672
+ },
+ "recordCounts": {
+ "Thorndyke Bay": 29,
+ "Palix River/Willapa Bay": 14,
+ "Sequim Bay": 24,
+ "Westcott": 671
+ },
+ "survivalMetric": "Percent survival per bag/replicate (0-100)",
+ "notes": "Westcott and Sequim Bay PolyIC have survival at each time point; Thorndyke Bay and Palix River/Willapa Bay report total (end-of-period) survival.",
+ "sourceUrls": [
+ "https://raw.githubusercontent.com/RobertsLab/10K-seed-Cgigas/main/output/baywater_survival.csv",
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_survival.csv",
+ "https://raw.githubusercontent.com/RobertsLab/polyIC-larvae/main/output/sequim_polyic_survival.csv",
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/westcott_survival.csv"
+ ],
+ "recordCount": 738
+ },
+ "sites": [
+ "Palix River/Willapa Bay",
+ "Sequim Bay",
+ "Thorndyke Bay",
+ "Westcott"
+ ],
+ "treatments": [
+ "Control",
+ "Heat primed",
+ "Freshwater primed",
+ "Immune primed",
+ "Combined stress primed"
+ ],
+ "years": [
+ "2024",
+ "2025",
+ "2026"
+ ],
+ "columns": [
+ "date",
+ "site",
+ "treatment",
+ "raw_treatment",
+ "effort",
+ "tag",
+ "survival_percent",
+ "survival_metric",
+ "source_repo",
+ "source_url"
+ ],
+ "lookups": {
+ "site": [
+ "Palix River/Willapa Bay",
+ "Sequim Bay",
+ "Thorndyke Bay",
+ "Westcott"
+ ],
+ "treatment": [
+ "Control",
+ "Freshwater primed",
+ "Heat primed",
+ "Immune primed",
+ "Combined stress primed"
+ ],
+ "raw_treatment": [
+ "Control",
+ "Treated",
+ "Immune PolyIC",
+ "Temperature+Salinity",
+ "Salinity",
+ "Temperature"
+ ],
+ "effort": [
+ "weekly temperature",
+ "weekly fresh water",
+ "PolyIC",
+ "Survival assay",
+ "Daily Temperature",
+ "Weekly Temperature"
+ ],
+ "survival_metric": [
+ "percent_survival",
+ "prop_survival",
+ "survival",
+ "proportion_remaining"
+ ],
+ "source_repo": [
+ "RobertsLab/project-gigas-conditioning",
+ "RobertsLab/polyIC-larvae",
+ "RobertsLab/10K-seed-Cgigas"
+ ],
+ "source_url": [
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_survival.csv",
+ "https://raw.githubusercontent.com/RobertsLab/polyIC-larvae/main/output/sequim_polyic_survival.csv",
+ "https://raw.githubusercontent.com/RobertsLab/10K-seed-Cgigas/main/output/baywater_survival.csv",
+ "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/westcott_survival.csv"
+ ]
+ },
+ "constants": {
+ "oyster_number": null,
+ "growth_mm": null,
+ "growth_volume": null,
+ "growth_metric": null,
+ "temperature_C": null,
+ "survival_source": "measured",
+ "growth_source": "none",
+ "temperature_source": "none"
+ },
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+["2024-08-29",3,2,1,4,"95",100.0,3,0,3],
+["2024-08-29",3,2,1,5,"96",100.0,3,0,3],
+["2024-09-03",3,2,1,5,"44",99.0,3,0,3],
+["2024-09-03",3,2,1,5,"56",72.3,3,0,3],
+["2024-09-03",3,2,1,5,"57",100.0,3,0,3],
+["2024-09-03",3,2,1,5,"61",100.0,3,0,3],
+["2024-09-03",3,2,1,4,"62",100.0,3,0,3],
+["2024-09-03",3,2,1,5,"65",100.0,3,0,3],
+["2024-09-03",3,2,1,4,"67",100.0,3,0,3],
+["2024-09-03",3,2,1,5,"71",99.0,3,0,3],
+["2024-09-03",3,2,1,4,"72",100.0,3,0,3],
+["2024-09-03",3,2,1,5,"74",100.0,3,0,3],
+["2024-09-03",3,2,1,5,"76",99.0,3,0,3],
+["2024-09-03",3,2,1,4,"77",100.0,3,0,3],
+["2024-09-03",3,2,1,5,"80",100.0,3,0,3],
+["2024-09-03",3,2,1,5,"93",99.0,3,0,3],
+["2024-09-03",3,2,1,4,"95",100.0,3,0,3],
+["2024-09-03",3,2,1,5,"96",100.0,3,0,3],
+["2024-09-12",3,2,1,5,"44",99.0,3,0,3],
+["2024-09-12",3,2,1,5,"56",70.2,3,0,3],
+["2024-09-12",3,2,1,5,"57",100.0,3,0,3],
+["2024-09-12",3,2,1,5,"61",100.0,3,0,3],
+["2024-09-12",3,2,1,4,"62",100.0,3,0,3],
+["2024-09-12",3,2,1,5,"65",100.0,3,0,3],
+["2024-09-12",3,2,1,4,"67",100.0,3,0,3],
+["2024-09-12",3,2,1,5,"71",99.0,3,0,3],
+["2024-09-12",3,2,1,4,"72",100.0,3,0,3],
+["2024-09-12",3,2,1,5,"74",100.0,3,0,3],
+["2024-09-12",3,2,1,5,"76",99.0,3,0,3],
+["2024-09-12",3,2,1,4,"77",100.0,3,0,3],
+["2024-09-12",3,2,1,5,"80",100.0,3,0,3],
+["2024-09-12",3,2,1,5,"93",96.9,3,0,3],
+["2024-09-12",3,2,1,4,"95",100.0,3,0,3],
+["2024-09-12",3,2,1,5,"96",100.0,3,0,3],
+["2024-12-17",3,2,1,5,"44",99.0,3,0,3],
+["2024-12-17",3,2,1,5,"56",67.0,3,0,3],
+["2024-12-17",3,2,1,5,"57",100.0,3,0,3],
+["2024-12-17",3,2,1,5,"61",100.0,3,0,3],
+["2024-12-17",3,2,1,4,"62",100.0,3,0,3],
+["2024-12-17",3,2,1,5,"65",100.0,3,0,3],
+["2024-12-17",3,2,1,4,"67",100.0,3,0,3],
+["2024-12-17",3,2,1,5,"71",99.0,3,0,3],
+["2024-12-17",3,2,1,4,"72",100.0,3,0,3],
+["2024-12-17",3,2,1,5,"74",100.0,3,0,3],
+["2024-12-17",3,2,1,5,"76",99.0,3,0,3],
+["2024-12-17",3,2,1,4,"77",100.0,3,0,3],
+["2024-12-17",3,2,1,5,"80",99.0,3,0,3],
+["2024-12-17",3,2,1,5,"93",95.9,3,0,3],
+["2024-12-17",3,2,1,4,"95",100.0,3,0,3],
+["2024-12-17",3,2,1,5,"96",100.0,3,0,3],
+["2025-05-13",3,2,1,5,"44",98.0,3,0,3],
+["2025-05-13",3,2,1,5,"56",62.8,3,0,3],
+["2025-05-13",3,2,1,5,"57",100.0,3,0,3],
+["2025-05-13",3,2,1,5,"61",100.0,3,0,3],
+["2025-05-13",3,2,1,4,"62",100.0,3,0,3],
+["2025-05-13",3,2,1,5,"65",100.0,3,0,3],
+["2025-05-13",3,2,1,4,"67",100.0,3,0,3],
+["2025-05-13",3,2,1,5,"71",99.0,3,0,3],
+["2025-05-13",3,2,1,4,"72",97.8,3,0,3],
+["2025-05-13",3,2,1,5,"74",99.0,3,0,3],
+["2025-05-13",3,2,1,5,"76",99.0,3,0,3],
+["2025-05-13",3,2,1,4,"77",96.0,3,0,3],
+["2025-05-13",3,2,1,5,"80",99.0,3,0,3],
+["2025-05-13",3,2,1,5,"93",93.9,3,0,3],
+["2025-05-13",3,2,1,4,"95",97.9,3,0,3],
+["2025-05-13",3,2,1,5,"96",98.0,3,0,3],
+["2025-05-29",3,2,1,5,"44",96.0,3,0,3],
+["2025-05-29",3,2,1,5,"56",62.8,3,0,3],
+["2025-05-29",3,2,1,5,"57",100.0,3,0,3],
+["2025-05-29",3,2,1,5,"61",98.0,3,0,3],
+["2025-05-29",3,2,1,4,"62",100.0,3,0,3],
+["2025-05-29",3,2,1,5,"65",100.0,3,0,3],
+["2025-05-29",3,2,1,4,"67",97.8,3,0,3],
+["2025-05-29",3,2,1,4,"72",95.7,3,0,3],
+["2025-05-29",3,2,1,5,"74",99.0,3,0,3],
+["2025-05-29",3,2,1,5,"76",99.0,3,0,3],
+["2025-05-29",3,2,1,4,"77",92.0,3,0,3],
+["2025-05-29",3,2,1,5,"80",99.0,3,0,3],
+["2025-05-29",3,2,1,5,"93",92.9,3,0,3],
+["2025-05-29",3,2,1,4,"95",97.9,3,0,3],
+["2025-05-29",3,2,1,5,"96",97.0,3,0,3],
+["2025-06-25",3,2,1,5,"44",92.1,3,0,3],
+["2025-06-25",3,2,1,5,"56",62.8,3,0,3],
+["2025-06-25",3,2,1,5,"57",99.0,3,0,3],
+["2025-06-25",3,2,1,5,"61",93.9,3,0,3],
+["2025-06-25",3,2,1,4,"62",98.0,3,0,3],
+["2025-06-25",3,2,1,5,"65",100.0,3,0,3],
+["2025-06-25",3,2,1,4,"67",97.8,3,0,3],
+["2025-06-25",3,2,1,5,"71",99.0,3,0,3],
+["2025-06-25",3,2,1,4,"72",95.7,3,0,3],
+["2025-06-25",3,2,1,5,"74",98.0,3,0,3],
+["2025-06-25",3,2,1,5,"76",99.0,3,0,3],
+["2025-06-25",3,2,1,4,"77",92.0,3,0,3],
+["2025-06-25",3,2,1,5,"80",99.0,3,0,3],
+["2025-06-25",3,2,1,5,"93",92.9,3,0,3],
+["2025-06-25",3,2,1,4,"95",97.9,3,0,3],
+["2025-06-25",3,2,1,5,"96",93.1,3,0,3],
+["2025-07-11",3,2,1,5,"44",87.1,3,0,3],
+["2025-07-11",3,2,1,5,"56",62.8,3,0,3],
+["2025-07-11",3,2,1,5,"57",97.9,3,0,3],
+["2025-07-11",3,2,1,5,"61",93.9,3,0,3],
+["2025-07-11",3,2,1,4,"62",96.0,3,0,3],
+["2025-07-11",3,2,1,5,"65",100.0,3,0,3],
+["2025-07-11",3,2,1,4,"67",95.7,3,0,3],
+["2025-07-11",3,2,1,5,"71",99.0,3,0,3],
+["2025-07-11",3,2,1,4,"72",95.7,3,0,3],
+["2025-07-11",3,2,1,5,"74",96.1,3,0,3],
+["2025-07-11",3,2,1,5,"76",98.1,3,0,3],
+["2025-07-11",3,2,1,4,"77",82.0,3,0,3],
+["2025-07-11",3,2,1,5,"80",99.0,3,0,3],
+["2025-07-11",3,2,1,5,"93",92.9,3,0,3],
+["2025-07-11",3,2,1,4,"95",97.9,3,0,3],
+["2025-07-11",3,2,1,5,"96",89.1,3,0,3],
+["2025-07-24",3,2,1,5,"44",81.2,3,0,3],
+["2025-07-24",3,2,1,5,"56",62.8,3,0,3],
+["2025-07-24",3,2,1,5,"57",94.8,3,0,3],
+["2025-07-24",3,2,1,5,"61",90.9,3,0,3],
+["2025-07-24",3,2,1,4,"62",96.0,3,0,3],
+["2025-07-24",3,2,1,5,"65",98.1,3,0,3],
+["2025-07-24",3,2,1,4,"67",89.1,3,0,3],
+["2025-07-24",3,2,1,5,"71",98.0,3,0,3],
+["2025-07-24",3,2,1,4,"72",95.7,3,0,3],
+["2025-07-24",3,2,1,5,"74",92.2,3,0,3],
+["2025-07-24",3,2,1,5,"76",94.2,3,0,3],
+["2025-07-24",3,2,1,4,"77",62.0,3,0,3],
+["2025-07-24",3,2,1,5,"80",98.0,3,0,3],
+["2025-07-24",3,2,1,5,"93",91.8,3,0,3],
+["2025-07-24",3,2,1,4,"95",97.9,3,0,3],
+["2025-07-24",3,2,1,5,"96",87.1,3,0,3],
+["2025-08-08",3,2,1,5,"44",75.2,3,0,3],
+["2025-08-08",3,2,1,5,"56",62.8,3,0,3],
+["2025-08-08",3,2,1,5,"57",93.8,3,0,3],
+["2025-08-08",3,2,1,5,"61",90.9,3,0,3],
+["2025-08-08",3,2,1,4,"62",96.0,3,0,3],
+["2025-08-08",3,2,1,5,"65",95.1,3,0,3],
+["2025-08-08",3,2,1,4,"67",84.8,3,0,3],
+["2025-08-08",3,2,1,5,"71",96.9,3,0,3],
+["2025-08-08",3,2,1,4,"72",95.7,3,0,3],
+["2025-08-08",3,2,1,5,"74",85.3,3,0,3],
+["2025-08-08",3,2,1,5,"76",91.3,3,0,3],
+["2025-08-08",3,2,1,4,"77",62.0,3,0,3],
+["2025-08-08",3,2,1,5,"80",98.0,3,0,3],
+["2025-08-08",3,2,1,5,"93",91.8,3,0,3],
+["2025-08-08",3,2,1,4,"95",89.6,3,0,3],
+["2025-08-08",3,2,1,5,"96",87.1,3,0,3],
+["2025-08-20",3,2,1,5,"44",71.3,3,0,3],
+["2025-08-20",3,2,1,5,"56",61.7,3,0,3],
+["2025-08-20",3,2,1,5,"57",93.8,3,0,3],
+["2025-08-20",3,2,1,5,"61",90.9,3,0,3],
+["2025-08-20",3,2,1,4,"62",96.0,3,0,3],
+["2025-08-20",3,2,1,5,"65",94.2,3,0,3],
+["2025-08-20",3,2,1,4,"67",84.8,3,0,3],
+["2025-08-20",3,2,1,5,"71",94.9,3,0,3],
+["2025-08-20",3,2,1,4,"72",95.7,3,0,3],
+["2025-08-20",3,2,1,5,"74",83.3,3,0,3],
+["2025-08-20",3,2,1,5,"76",91.3,3,0,3],
+["2025-08-20",3,2,1,4,"77",62.0,3,0,3],
+["2025-08-20",3,2,1,5,"80",98.0,3,0,3],
+["2025-08-20",3,2,1,5,"93",90.8,3,0,3],
+["2025-08-20",3,2,1,4,"95",81.2,3,0,3],
+["2025-08-20",3,2,1,5,"96",86.1,3,0,3],
+["2025-12-02",3,2,1,5,"44",66.3,3,0,3],
+["2025-12-02",3,2,1,5,"56",57.4,3,0,3],
+["2025-12-02",3,2,1,5,"57",93.8,3,0,3],
+["2025-12-02",3,2,1,5,"61",87.9,3,0,3],
+["2025-12-02",3,2,1,4,"62",96.0,3,0,3],
+["2025-12-02",3,2,1,5,"65",91.3,3,0,3],
+["2025-12-02",3,2,1,4,"67",84.8,3,0,3],
+["2025-12-02",3,2,1,5,"71",94.9,3,0,3],
+["2025-12-02",3,2,1,4,"72",95.7,3,0,3],
+["2025-12-02",3,2,1,5,"74",79.4,3,0,3],
+["2025-12-02",3,2,1,5,"76",91.3,3,0,3],
+["2025-12-02",3,2,1,4,"77",62.0,3,0,3],
+["2025-12-02",3,2,1,5,"80",94.9,3,0,3],
+["2025-12-02",3,2,1,5,"93",89.8,3,0,3],
+["2025-12-02",3,2,1,4,"95",58.3,3,0,3],
+["2025-12-02",3,2,1,5,"96",86.1,3,0,3]
+ ]
+}
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..08cc351
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,6 @@
+# Python dependencies for the data build scripts in scripts/.
+# build_growth_observations.py, build_survival_observations.py, and
+# build_live_temperature.py use only the standard library.
+# build_real_observations.py needs the packages below.
+pandas>=2.2
+openpyxl>=3.1
diff --git a/scripts/buildArchivalTemperature.mjs b/scripts/buildArchivalTemperature.mjs
index 461fdbe..c5d05d3 100644
--- a/scripts/buildArchivalTemperature.mjs
+++ b/scripts/buildArchivalTemperature.mjs
@@ -130,7 +130,7 @@ async function main() {
series,
};
- const outPath = join(__dirname, '..', 'src', 'data', 'archivalTemperatureData.json');
+ const outPath = join(__dirname, '..', 'public', 'data', 'archivalTemperatureData.json');
writeFileSync(outPath, JSON.stringify(bundle));
process.stderr.write(
`Wrote ${series.length} daily rows for ${siteNames.length} sites to ${outPath}\n`
diff --git a/scripts/build_growth_observations.py b/scripts/build_growth_observations.py
index 738a4fd..384c271 100644
--- a/scripts/build_growth_observations.py
+++ b/scripts/build_growth_observations.py
@@ -6,25 +6,30 @@
those rows as observation records so treatment/site means and error bars are
computed from the underlying measurements.
+Output: public/data/growthObservations.json in the compact bundle format
+described in shield_data.py.
+
Run: python3 scripts/build_growth_observations.py
"""
-import csv
-import json
-import math
import os
-import re
-from datetime import datetime
-from urllib.request import urlopen
+import sys
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
-HERE = os.path.dirname(os.path.abspath(__file__))
-REPO = os.path.abspath(os.path.join(HERE, ".."))
-OUT = os.path.join(REPO, "src", "data", "growthObservations.json")
+from shield_data import ( # noqa: E402
+ compact_bundle,
+ data_path,
+ normal_treatment,
+ number,
+ parse_date,
+ read_csv_url,
+ report,
+ utc_today,
+ write_bundle,
+)
+
+OUT = data_path("growthObservations.json")
-MONTHS = [
- "Jan", "Feb", "Mar", "Apr", "May", "Jun",
- "Jul", "Aug", "Sep", "Oct", "Nov", "Dec",
-]
SOURCES = [
{
"site": "Thorndyke Bay",
@@ -54,55 +59,22 @@
},
]
-
-def parse_date(value):
- text = str(value).strip()
- if "-" in text:
- return text[:10]
- return f"{text[0:4]}-{text[4:6]}-{text[6:8]}"
-
-
-def date_fields(dstr):
- dt = datetime.strptime(dstr, "%Y-%m-%d")
- return {
- "date": dstr,
- "year": str(dt.year),
- "month": MONTHS[dt.month - 1],
- "quarter": f"Q{(dt.month - 1) // 3 + 1}",
- }
-
-
-def read_csv(url):
- with urlopen(url) as response:
- text = response.read().decode("utf-8-sig")
- return list(csv.DictReader(text.splitlines()))
-
-
-def number(value):
- try:
- parsed = float(value)
- except (TypeError, ValueError):
- return None
- return parsed if math.isfinite(parsed) else None
-
-
-def normal_treatment(raw_treatment, experiment=""):
- treatment = str(raw_treatment).strip().lower()
- exp = str(experiment).strip().lower()
-
- if treatment == "control":
- return "Control"
- if "temperature+salinity" in treatment:
- return "Combined stress primed"
- if "immune" in treatment or "polyic" in treatment:
- return "Immune primed"
- if "salinity" in treatment or "fresh" in exp:
- return "Freshwater primed"
- if "temperature" in treatment or "temperature" in exp:
- return "Heat primed"
- if treatment == "treated":
- return "Treated"
- return str(raw_treatment).strip()
+COLUMNS = [
+ "date", "site", "treatment", "raw_treatment", "effort", "tag",
+ "oyster_number", "growth_volume", "growth_metric", "source_repo", "source_url",
+]
+LOOKUP_COLUMNS = [
+ "site", "treatment", "raw_treatment", "effort", "growth_metric",
+ "source_repo", "source_url",
+]
+CONSTANTS = {
+ "growth_mm": None,
+ "temperature_C": None,
+ "survival_percent": None,
+ "survival_source": "none",
+ "growth_source": "measured-volume",
+ "temperature_source": "none",
+}
def tag_for(row):
@@ -123,89 +95,54 @@ def volume_for(row):
return number(row.get("Predicted_Volume_Poly", row.get("vol")))
-def site_slug(site):
- return re.sub(r"[^A-Z0-9]+", "-", site.upper()).strip("-")
-
-
-records = []
-source_rows = {}
-record_counts = {}
-
-for source in SOURCES:
- rows = read_csv(source["url"])
- source_rows[source["site"]] = source_rows.get(source["site"], 0) + len(rows)
-
- for idx, row in enumerate(rows):
- volume = volume_for(row)
- if volume is None:
- continue
-
- dstr = parse_date(row["date"])
- experiment = row.get("experiment") or source.get("default_experiment") or ""
- treatment = normal_treatment(row.get("treatment"), experiment)
- tag = tag_for(row)
- oyster = oyster_for(row)
- fields = date_fields(dstr)
-
- records.append({
- "id": f"GROW-{site_slug(source['site'])}-{dstr}-{idx}",
- **fields,
- "site": source["site"],
- "treatment": treatment,
- "raw_treatment": row.get("treatment"),
- "effort": experiment or "Growth assay",
- "tag": tag,
- "oyster_number": oyster,
- "growth_mm": None,
- "growth_volume": round(volume, 1),
- "growth_metric": "Predicted_Volume_Poly" if "Predicted_Volume_Poly" in row else "vol",
- "temperature_C": None,
- "survival_percent": None,
- "survival_source": "none",
- "growth_source": "measured-volume",
- "temperature_source": "none",
- "source_repo": source["repo"],
- "source_url": source["url"],
- })
- record_counts[source["site"]] = record_counts.get(source["site"], 0) + 1
-
-records.sort(key=lambda r: (r["site"], r["treatment"], r["date"], str(r["tag"]), str(r["oyster_number"])))
-for i, record in enumerate(records):
- record["id"] = f"{record['id']}-{i}"
-
-sites = sorted({r["site"] for r in records})
-treatment_order = [
- "Control",
- "Heat primed",
- "Freshwater primed",
- "Immune primed",
- "Combined stress primed",
- "Treated",
-]
-treatments = [t for t in treatment_order if any(r["treatment"] == t for r in records)]
-years = sorted({r["year"] for r in records})
-
-bundle = {
- "meta": {
- "generatedAt": datetime.utcnow().strftime("%Y-%m-%d"),
+def build_records():
+ records = []
+ source_rows = {}
+ record_counts = {}
+
+ for source in SOURCES:
+ rows = read_csv_url(source["url"])
+ source_rows[source["site"]] = source_rows.get(source["site"], 0) + len(rows)
+
+ for row in rows:
+ volume = volume_for(row)
+ if volume is None:
+ continue
+
+ experiment = row.get("experiment") or source.get("default_experiment") or ""
+ records.append({
+ "date": parse_date(row["date"]),
+ "site": source["site"],
+ "treatment": normal_treatment(row.get("treatment"), experiment),
+ "raw_treatment": row.get("treatment"),
+ "effort": experiment or "Growth assay",
+ "tag": tag_for(row),
+ "oyster_number": oyster_for(row),
+ "growth_volume": round(volume, 1),
+ "growth_metric": "Predicted_Volume_Poly" if "Predicted_Volume_Poly" in row else "vol",
+ "source_repo": source["repo"],
+ "source_url": source["url"],
+ })
+ record_counts[source["site"]] = record_counts.get(source["site"], 0) + 1
+
+ records.sort(key=lambda r: (r["site"], r["treatment"], r["date"], str(r["tag"]), str(r["oyster_number"])))
+ return records, source_rows, record_counts
+
+
+def main():
+ records, source_rows, record_counts = build_records()
+ meta = {
+ "generatedAt": utc_today(),
"source": "RobertsLab growth CSV outputs",
"studyTitle": "Crassostrea gigas individual oyster growth volume",
- "recordCount": len(records),
"sourceRows": source_rows,
"recordCounts": record_counts,
"growthMetric": "Predicted oyster volume from image-derived models",
"sourceUrls": [source["url"] for source in SOURCES],
- },
- "sites": sites,
- "treatments": treatments,
- "years": years,
- "observations": records,
-}
+ }
+ write_bundle(OUT, compact_bundle(records, COLUMNS, LOOKUP_COLUMNS, CONSTANTS, meta))
+ report(records, OUT, "growth")
-with open(OUT, "w") as f:
- json.dump(bundle, f, indent=0)
-print(f"Wrote {len(records)} growth records to {OUT}")
-print("Sites:", sites)
-print("Treatments:", treatments)
-print("Years:", years)
+if __name__ == "__main__":
+ main()
diff --git a/scripts/build_live_temperature.py b/scripts/build_live_temperature.py
index bb3b12a..03dbc5d 100644
--- a/scripts/build_live_temperature.py
+++ b/scripts/build_live_temperature.py
@@ -7,7 +7,7 @@
do NOT send CORS headers, so a static GitHub Pages dashboard cannot fetch them
client-side. This script runs server-side (locally or in GitHub Actions), tries
an ordered list of candidate stations per site, and commits the first valid
-reading as `src/data/liveTemperature.json`. The Action re-runs on a schedule, so
+reading as `public/data/liveTemperature.json`. The Action re-runs on a schedule, so
the committed snapshot stays "near-live" (e.g. hourly) without any backend.
Sources (no API key required):
@@ -34,7 +34,7 @@
HERE = os.path.dirname(os.path.abspath(__file__))
REPO = os.path.abspath(os.path.join(HERE, ".."))
-OUT = os.path.join(REPO, "src", "data", "liveTemperature.json")
+OUT = os.path.join(REPO, "public", "data", "liveTemperature.json")
# Drop a reading if its timestamp is older than this many hours (stale sensor).
MAX_AGE_HOURS = 48
diff --git a/scripts/build_real_observations.py b/scripts/build_real_observations.py
index 8dafde5..948a33e 100644
--- a/scripts/build_real_observations.py
+++ b/scripts/build_real_observations.py
@@ -1,17 +1,22 @@
#!/usr/bin/env python3
"""
-Build real observation records for the Shellfish Farm Outplant Dashboard from
-the RobertsLab `project-gigas-conditioning` repo (+ Thorndyke Bay 10K-Seed survival
+Build SHIELD field observation records from the RobertsLab
+`project-gigas-conditioning` repository (plus Thorndyke Bay 10K-Seed survival
anchors quoted in the lab notebooks).
-Each output record is one site x treatment x assessment-date measurement with
-the dashboard schema. A metric is populated ONLY where it was actually measured;
-otherwise it is null (the dashboard aggregations are null-safe). Temperature is
-the real monthly mean from in-situ HOBO loggers (reused from
-src/data/archivalTemperatureData.json).
+Each output record is one site x treatment x assessment-date measurement. A
+metric is populated ONLY where it was actually measured; otherwise it is null
+(the dashboard aggregations are null-safe). Temperature is the real monthly
+mean from in-situ HOBO loggers, reused from public/data/archivalTemperatureData.json,
+so run scripts/buildArchivalTemperature.mjs first (or `npm run build:data`).
-Hybrid treatment mapping (per user choice): real groups are normalized onto the
-dashboard's treatment axis, and the original experiment is preserved in `effort`.
+Inputs are read from the public GitHub repository by default. Set the
+`PGC_SOURCE` environment variable to a local checkout path to build offline:
+
+ PGC_SOURCE=~/GitHub/project-gigas-conditioning python3 scripts/build_real_observations.py
+
+Hybrid treatment mapping: real groups are normalized onto the dashboard's
+treatment axis, and the original experiment is preserved in `effort`.
Control (any) -> Control
Temperature / thermal treated -> Heat primed
@@ -19,25 +24,85 @@
polyIC / immune -> Immune primed (Thorndyke Bay 10K-Seed only)
FW + temperature -> Combined stress primed (Thorndyke Bay 10K-Seed only)
-Run: python3 scripts/build_real_observations.py
+Requires pandas and openpyxl (see requirements.txt).
+
+Output: public/data/realObservations.json in the compact bundle format
+described in shield_data.py.
"""
+import io
import json
import os
+import sys
from collections import defaultdict
from datetime import datetime
import pandas as pd
-HERE = os.path.dirname(os.path.abspath(__file__))
-REPO = os.path.abspath(os.path.join(HERE, ".."))
-PGC = "/Users/sr320/Documents/GitHub/project-gigas-conditioning"
-OUT = os.path.join(REPO, "src", "data", "realObservations.json")
-ARCHIVAL = os.path.join(REPO, "src", "data", "archivalTemperatureData.json")
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+
+from shield_data import ( # noqa: E402
+ compact_bundle,
+ data_path,
+ fetch_bytes,
+ report,
+ utc_today,
+ write_bundle,
+)
+
+DEFAULT_SOURCE = "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main"
+SOURCE = os.environ.get("PGC_SOURCE", DEFAULT_SOURCE).rstrip("/")
+OUT = data_path("realObservations.json")
+ARCHIVAL = data_path("archivalTemperatureData.json")
MONTHS = ["Jan", "Feb", "Mar", "Apr", "May", "Jun",
"Jul", "Aug", "Sep", "Oct", "Nov", "Dec"]
+COLUMNS = [
+ "date", "site", "treatment", "effort", "growth_mm", "temperature_C",
+ "survival_percent", "survival_source", "growth_source",
+]
+LOOKUP_COLUMNS = ["site", "treatment", "effort", "survival_source", "growth_source"]
+CONSTANTS = {"temperature_source": "logger-monthly-mean"}
+
+
+# ---------------------------------------------------------------------------
+# Input access: remote by default, local checkout via PGC_SOURCE
+# ---------------------------------------------------------------------------
+def source_is_local():
+ return os.path.isdir(os.path.expanduser(SOURCE))
+
+
+def source_exists(relpath):
+ if source_is_local():
+ return os.path.exists(os.path.join(os.path.expanduser(SOURCE), relpath))
+ try:
+ fetch_bytes(f"{SOURCE}/{relpath}")
+ return True
+ except RuntimeError:
+ return False
+
+
+def source_handle(relpath):
+ """Binary file-like object for a repository-relative path."""
+ if source_is_local():
+ return open(os.path.join(os.path.expanduser(SOURCE), relpath), "rb")
+ print(f" fetching {relpath}", file=sys.stderr)
+ return io.BytesIO(fetch_bytes(f"{SOURCE}/{relpath}"))
+
+def read_csv(relpath):
+ with source_handle(relpath) as handle:
+ return pd.read_csv(handle)
+
+
+def read_excel(relpath):
+ with source_handle(relpath) as handle:
+ return pd.read_excel(handle)
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
def parse_ymd(v):
"""Accept '20240624', '2024-06-24', or a Timestamp -> date string YYYY-MM-DD."""
if isinstance(v, (pd.Timestamp, datetime)):
@@ -48,16 +113,6 @@ def parse_ymd(v):
return f"{s[0:4]}-{s[4:6]}-{s[6:8]}"
-def date_fields(dstr):
- dt = datetime.strptime(dstr, "%Y-%m-%d")
- return {
- "date": dstr,
- "year": str(dt.year),
- "month": MONTHS[dt.month - 1],
- "quarter": f"Q{(dt.month - 1) // 3 + 1}",
- }
-
-
def round1(x):
if x is None:
return None
@@ -69,22 +124,18 @@ def round1(x):
return round(float(x) * 10) / 10
-# ---------------------------------------------------------------------------
-# Real monthly mean temperature per site (from already-real logger archival)
-# ---------------------------------------------------------------------------
+# Real monthly mean temperature per site (from the logger archival bundle)
def monthly_temps():
- arch = json.load(open(ARCHIVAL))
- # site -> "YYYY-MM" -> [values]
+ with open(ARCHIVAL, encoding="utf-8") as handle:
+ arch = json.load(handle)
acc = defaultdict(lambda: defaultdict(list))
for row in arch["series"]:
ym = row["date"][:7]
for site in arch["sites"]:
if site in row and row[site] is not None:
acc[site][ym].append(row[site])
- out = {}
- for site, months in acc.items():
- out[site] = {ym: sum(v) / len(v) for ym, v in months.items()}
- return out
+ return {site: {ym: sum(v) / len(v) for ym, v in months.items()}
+ for site, months in acc.items()}
MONTHLY_TEMP = monthly_temps()
@@ -110,10 +161,8 @@ def temp_for(site, dstr):
def emit(site, treatment, effort, dstr, survival=None, growth=None,
survival_src="estimated", growth_src="estimated"):
- f = date_fields(dstr)
records.append({
- "id": f"{site[:2].upper()}-{treatment.split()[0][:4].upper()}-{dstr}",
- **f,
+ "date": dstr,
"site": site,
"treatment": treatment,
"effort": effort,
@@ -122,17 +171,16 @@ def emit(site, treatment, effort, dstr, survival=None, growth=None,
"survival_percent": round1(survival),
"survival_source": survival_src if survival is not None else "none",
"growth_source": growth_src if growth is not None else "none",
- "temperature_source": "logger-monthly-mean",
})
# ---------------------------------------------------------------------------
-# PALIX RIVER/WILLAPA BAY (Effort E: weekly temperature / weekly fresh water, control/treated)
+# PALIX RIVER/WILLAPA BAY (Effort E: weekly temperature / weekly fresh water)
# ---------------------------------------------------------------------------
def palix_river_willapa_bay():
- surv = pd.read_csv(os.path.join(PGC, "data/outplanting/GoosePoint/survival_GoosePoint.csv"))
- grow = pd.read_csv(os.path.join(PGC, "data/outplanting/GoosePoint/growth_GoosePoint.csv"))
- bags = pd.read_csv(os.path.join(PGC, "data/outplanting/GoosePoint/bag_list_GoosePoint.csv"))
+ surv = read_csv("data/outplanting/GoosePoint/survival_GoosePoint.csv")
+ grow = read_csv("data/outplanting/GoosePoint/growth_GoosePoint.csv")
+ bags = read_csv("data/outplanting/GoosePoint/bag_list_GoosePoint.csv")
def norm(group):
g = str(group).lower()
@@ -177,16 +225,18 @@ def norm(group):
emit("Palix River/Willapa Bay", trt, v.get("eff", "Effort E"), dstr,
survival=v.get("surv"), growth=v.get("grow"),
survival_src="measured", growth_src="measured")
- notes["Palix River/Willapa Bay"] = "Effort E (2023 POGS), weekly temperature + fresh water hardening; control/treated. Real survival (live/total) and image-derived shell length."
+ notes["Palix River/Willapa Bay"] = (
+ "Effort E (2023 POGS), weekly temperature + fresh water hardening; control/treated. "
+ "Real survival (live/total) and image-derived shell length.")
# ---------------------------------------------------------------------------
# SEQUIM (Effort A: daily thermal hardening, control/treated)
# ---------------------------------------------------------------------------
def sequim():
- surv = pd.read_csv(os.path.join(PGC, "data/outplanting/Sequim/survival_Sequim.csv"))
- size = pd.read_excel(os.path.join(PGC, "data/outplanting/Sequim/size_Sequim.xlsx"))
- bags = pd.read_csv(os.path.join(PGC, "data/outplanting/Sequim/bag_list_Sequim.csv"))
+ surv = read_csv("data/outplanting/Sequim/survival_Sequim.csv")
+ size = read_excel("data/outplanting/Sequim/size_Sequim.xlsx")
+ bags = read_csv("data/outplanting/Sequim/bag_list_Sequim.csv")
def norm(t):
return ("Heat primed" if str(t).strip().lower() == "treated" else "Control",
@@ -200,7 +250,7 @@ def norm(t):
# Per bag: baseline N0 = first alive + dead that visit; survival = (N0 - cum dead)/N0
rows = []
- for bag, g in surv.sort_values("dstr").groupby("bag"):
+ for _, g in surv.sort_values("dstr").groupby("bag"):
g = g.copy()
first = g.iloc[0]
n0 = (first["alive"] if pd.notna(first["alive"]) else 0) + first["dead"]
@@ -234,7 +284,9 @@ def norm(t):
emit("Sequim Bay", trt, v.get("eff", "Effort A"), dstr,
survival=v.get("surv"), growth=v.get("grow"),
survival_src="measured", growth_src="measured")
- notes["Sequim Bay"] = "Effort A (2 weeks daily 25°C thermal hardening), control/treated. Real survival from cumulative mortality; image-derived shell length."
+ notes["Sequim Bay"] = (
+ "Effort A (2 weeks daily 25°C thermal hardening), control/treated. "
+ "Real survival from cumulative mortality; image-derived shell length.")
# ---------------------------------------------------------------------------
@@ -246,11 +298,11 @@ def westcott():
("B_survival_12022025.xlsx", "Effort B — daily thermal"),
("D_survival_12022025.xlsx", "Effort D — weekly thermal"),
]:
- p = os.path.join(PGC, "data/survival/Westcott", eff_file)
- if not os.path.exists(p):
+ relpath = f"data/survival/Westcott/{eff_file}"
+ if not source_exists(relpath):
+ print(f" ! missing {relpath}; skipping", file=sys.stderr)
continue
- df = pd.read_excel(p)
- df = df.copy()
+ df = read_excel(relpath).copy()
df["eff_label"] = eff_label
frames.append(df)
if not frames:
@@ -264,7 +316,7 @@ def westcott():
# Per bag baseline = first alive_num; survival = alive_num / N0 * 100
rows = []
- for (bag, eff), g in surv.sort_values("dstr").groupby(["bag_num", "eff_label"]):
+ for (_, eff), g in surv.sort_values("dstr").groupby(["bag_num", "eff_label"]):
g = g.dropna(subset=["alive_num"])
if g.empty:
continue
@@ -272,7 +324,7 @@ def westcott():
if not n0:
continue
for _, r in g.iterrows():
- # cap at 100% — later counts can exceed the first due to recount noise
+ # cap at 100% since later counts can exceed the first due to recount noise
rows.append({"trt": r["trt"], "eff": eff, "dstr": r["dstr"],
"surv": min(100.0, r["alive_num"] / n0 * 100)})
sdf = pd.DataFrame(rows).groupby(["trt", "dstr"]).agg(
@@ -282,11 +334,13 @@ def westcott():
for _, r in sdf.sort_values(["dstr", "trt"]).iterrows():
emit("Westcott", r["trt"], r["eff"], r["dstr"],
survival=r["surv"], survival_src="measured")
- notes["Westcott"] = "Efforts B (daily) & D (weekly) thermal hardening, control/treated. Real survival (alive/initial per bag). Image growth not yet calibrated to mm."
+ notes["Westcott"] = (
+ "Efforts B (daily) & D (weekly) thermal hardening, control/treated. "
+ "Real survival (alive/initial per bag). Image growth not yet calibrated to mm.")
# ---------------------------------------------------------------------------
-# THORNDYKE BAY (10K-Seed, 5 treatments) — survival anchors quoted in lab notebooks
+# THORNDYKE BAY (10K-Seed, 5 treatments): survival anchors quoted in lab notebooks
# (raw data lives in RobertsLab/10K-seed-Cgigas, not in project-gigas-conditioning)
# ---------------------------------------------------------------------------
def thorndyke_bay():
@@ -301,31 +355,25 @@ def thorndyke_bay():
for trt, pct in anchor.items():
emit("Thorndyke Bay", trt, "10K-Seed (hardening)", "2025-08-20",
survival=pct, survival_src="measured")
- notes["Thorndyke Bay"] = "10K-Seed hardening (Control / 35C / FW / polyIC / FW+35C). Survival measured 2025-08-20 (n=150/bag); source repo RobertsLab/10K-seed-Cgigas. Growth not published numerically."
-
+ notes["Thorndyke Bay"] = (
+ "10K-Seed hardening (Control / 35C / FW / polyIC / FW+35C). Survival measured "
+ "2025-08-20 (n=150/bag); source repo RobertsLab/10K-seed-Cgigas. Growth not published numerically.")
-palix_river_willapa_bay()
-sequim()
-westcott()
-thorndyke_bay()
-records.sort(key=lambda r: (r["site"], r["treatment"], r["date"]))
-for i, r in enumerate(records):
- r["id"] = f"{r['id']}-{i}" # ensure uniqueness
+def main():
+ print(f"Reading project-gigas-conditioning inputs from {SOURCE}", file=sys.stderr)
+ palix_river_willapa_bay()
+ sequim()
+ westcott()
+ thorndyke_bay()
-sites = sorted({r["site"] for r in records})
-treatments_present = {r["treatment"] for r in records}
-TREATMENT_ORDER = ["Control", "Heat primed", "Freshwater primed",
- "Immune primed", "Combined stress primed"]
-treatments = [t for t in TREATMENT_ORDER if t in treatments_present]
-years = sorted({r["year"] for r in records})
+ records.sort(key=lambda r: (r["site"], r["treatment"], r["date"]))
-bundle = {
- "meta": {
- "generatedAt": datetime.utcnow().strftime("%Y-%m-%d"),
+ meta = {
+ "generatedAt": utc_today(),
"source": "RobertsLab/project-gigas-conditioning (+ 10K-Seed survival anchors)",
+ "inputSource": SOURCE,
"studyTitle": "Crassostrea gigas stress-hardening outplant program",
- "recordCount": len(records),
"siteNotes": notes,
"treatmentMapping": {
"Control": "untreated control (any effort)",
@@ -334,21 +382,17 @@ def thorndyke_bay():
"Immune primed": "polyIC / immune challenge (Thorndyke Bay 10K-Seed)",
"Combined stress primed": "fresh water + temperature (Thorndyke Bay 10K-Seed)",
},
- },
- "sites": sites,
- "treatments": treatments,
- "years": years,
- "observations": records,
-}
-
-json.dump(bundle, open(OUT, "w"), indent=0)
-print(f"Wrote {len(records)} records to {OUT}")
-print("Sites:", sites)
-print("Treatments:", treatments)
-print("Years:", years)
-for s in sites:
- srv = [r for r in records if r["site"] == s and r["survival_percent"] is not None]
- grw = [r for r in records if r["site"] == s and r["growth_mm"] is not None]
- print(f" {s:12} records={sum(1 for r in records if r['site']==s):3} "
- f"survival_pts={len(srv):3} growth_pts={len(grw):3} "
- f"dates={len(sorted({r['date'] for r in records if r['site']==s}))}")
+ }
+ write_bundle(OUT, compact_bundle(records, COLUMNS, LOOKUP_COLUMNS, CONSTANTS, meta))
+ report(records, OUT, "field observation")
+ sites = sorted({r["site"] for r in records})
+ for s in sites:
+ srv = [r for r in records if r["site"] == s and r["survival_percent"] is not None]
+ grw = [r for r in records if r["site"] == s and r["growth_mm"] is not None]
+ print(f" {s:24} records={sum(1 for r in records if r['site'] == s):3} "
+ f"survival_pts={len(srv):3} growth_pts={len(grw):3} "
+ f"dates={len({r['date'] for r in records if r['site'] == s})}")
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scripts/build_survival_observations.py b/scripts/build_survival_observations.py
index 9038653..215d7b9 100644
--- a/scripts/build_survival_observations.py
+++ b/scripts/build_survival_observations.py
@@ -7,32 +7,37 @@
treatment/site means and error bars are computed from the underlying replicates.
Survival files use the same treatment identifiers as the growth files:
- - Westcott reports survival at each assessment date (per-timepoint rows).
- - Thorndyke Bay and Palix River/Willapa Bay report a single total (end-of-period) survival per
- bag; those sites are stamped with their assessment date below.
+ - Westcott and Sequim Bay PolyIC report survival at each assessment date.
+ - Thorndyke Bay and Palix River/Willapa Bay report a single total
+ (end-of-period) survival per bag; those sites are stamped with their
+ assessment date below.
All source files carry survival as a 0-1 proportion, stored here as a 0-100
percent to match the rest of the dashboard.
+Output: public/data/survivalObservations.json in the compact bundle format
+described in shield_data.py.
+
Run: python3 scripts/build_survival_observations.py
"""
-import csv
-import json
-import math
import os
-import re
-from datetime import datetime
-from urllib.request import urlopen
-
-
-HERE = os.path.dirname(os.path.abspath(__file__))
-REPO = os.path.abspath(os.path.join(HERE, ".."))
-OUT = os.path.join(REPO, "src", "data", "survivalObservations.json")
+import sys
+
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+
+from shield_data import ( # noqa: E402
+ compact_bundle,
+ data_path,
+ normal_treatment,
+ number,
+ parse_date,
+ read_csv_url,
+ report,
+ utc_today,
+ write_bundle,
+)
-MONTHS = [
- "Jan", "Feb", "Mar", "Apr", "May", "Jun",
- "Jul", "Aug", "Sep", "Oct", "Nov", "Dec",
-]
+OUT = data_path("survivalObservations.json")
# Survival value column varies by source; checked in this order per row.
SURVIVAL_KEYS = (
@@ -71,66 +76,28 @@
},
]
-
-def parse_date(value):
- text = str(value).strip()
- if "-" in text:
- return text[:10]
- return f"{text[0:4]}-{text[4:6]}-{text[6:8]}"
-
-
-def date_fields(dstr):
- dt = datetime.strptime(dstr, "%Y-%m-%d")
- return {
- "date": dstr,
- "year": str(dt.year),
- "month": MONTHS[dt.month - 1],
- "quarter": f"Q{(dt.month - 1) // 3 + 1}",
- }
-
-
-def read_csv(url):
- with urlopen(url) as response:
- text = response.read().decode("utf-8-sig")
- return list(csv.DictReader(text.splitlines()))
-
-
-def number(value):
- try:
- parsed = float(value)
- except (TypeError, ValueError):
- return None
- return parsed if math.isfinite(parsed) else None
-
-
-def normal_treatment(raw_treatment, experiment=""):
- treatment = str(raw_treatment).strip().lower()
- exp = str(experiment).strip().lower()
-
- if treatment == "control":
- return "Control"
- if "temperature+salinity" in treatment:
- return "Combined stress primed"
- if "immune" in treatment or "polyic" in treatment:
- return "Immune primed"
- if "salinity" in treatment or "fresh" in exp:
- return "Freshwater primed"
- if "temperature" in treatment or "temperature" in exp:
- return "Heat primed"
- if treatment == "treated":
- return "Treated"
- return str(raw_treatment).strip()
+COLUMNS = [
+ "date", "site", "treatment", "raw_treatment", "effort", "tag",
+ "survival_percent", "survival_metric", "source_repo", "source_url",
+]
+LOOKUP_COLUMNS = [
+ "site", "treatment", "raw_treatment", "effort", "survival_metric",
+ "source_repo", "source_url",
+]
+CONSTANTS = {
+ "oyster_number": None,
+ "growth_mm": None,
+ "growth_volume": None,
+ "growth_metric": None,
+ "temperature_C": None,
+ "survival_source": "measured",
+ "growth_source": "none",
+ "temperature_source": "none",
+}
def tag_for(row):
- for key in (
- "purple.tag",
- "corrected_tag",
- "bag_tag_num",
- "outplant_tag",
- "tag",
- "bag",
- ):
+ for key in ("purple.tag", "corrected_tag", "bag_tag_num", "outplant_tag", "tag", "bag"):
if row.get(key):
return row[key]
return None
@@ -145,91 +112,54 @@ def survival_for(row):
return None, None
-def site_slug(site):
- return re.sub(r"[^A-Z0-9]+", "-", site.upper()).strip("-")
-
-
-records = []
-source_rows = {}
-record_counts = {}
-
-for source in SOURCES:
- rows = read_csv(source["url"])
- source_rows[source["site"]] = source_rows.get(source["site"], 0) + len(rows)
-
- for idx, row in enumerate(rows):
- survival, survival_key = survival_for(row)
- if survival is None:
- continue
-
- raw_date = row.get("date") or source.get("default_date")
- dstr = parse_date(raw_date)
- experiment = row.get("experiment") or source.get("default_experiment") or ""
- treatment = normal_treatment(row.get("treatment"), experiment)
- tag = tag_for(row)
- fields = date_fields(dstr)
-
- records.append({
- "id": f"SURV-{site_slug(source['site'])}-{dstr}-{idx}",
- **fields,
- "site": source["site"],
- "treatment": treatment,
- "raw_treatment": row.get("treatment"),
- "effort": experiment or "Survival assay",
- "tag": tag,
- "oyster_number": None,
- "growth_mm": None,
- "growth_volume": None,
- "growth_metric": None,
- "temperature_C": None,
- "survival_percent": survival,
- "survival_metric": survival_key,
- "survival_source": "measured",
- "growth_source": "none",
- "temperature_source": "none",
- "source_repo": source["repo"],
- "source_url": source["url"],
- })
- record_counts[source["site"]] = record_counts.get(source["site"], 0) + 1
-
-records.sort(key=lambda r: (r["site"], r["treatment"], r["date"], str(r["tag"])))
-for i, record in enumerate(records):
- record["id"] = f"{record['id']}-{i}"
-
-sites = sorted({r["site"] for r in records})
-treatment_order = [
- "Control",
- "Heat primed",
- "Freshwater primed",
- "Immune primed",
- "Combined stress primed",
- "Treated",
-]
-treatments = [t for t in treatment_order if any(r["treatment"] == t for r in records)]
-years = sorted({r["year"] for r in records})
-
-bundle = {
- "meta": {
- "generatedAt": datetime.utcnow().strftime("%Y-%m-%d"),
+def build_records():
+ records = []
+ source_rows = {}
+ record_counts = {}
+
+ for source in SOURCES:
+ rows = read_csv_url(source["url"])
+ source_rows[source["site"]] = source_rows.get(source["site"], 0) + len(rows)
+
+ for row in rows:
+ survival, survival_key = survival_for(row)
+ if survival is None:
+ continue
+
+ experiment = row.get("experiment") or source.get("default_experiment") or ""
+ records.append({
+ "date": parse_date(row.get("date") or source.get("default_date")),
+ "site": source["site"],
+ "treatment": normal_treatment(row.get("treatment"), experiment),
+ "raw_treatment": row.get("treatment"),
+ "effort": experiment or "Survival assay",
+ "tag": tag_for(row),
+ "survival_percent": survival,
+ "survival_metric": survival_key,
+ "source_repo": source["repo"],
+ "source_url": source["url"],
+ })
+ record_counts[source["site"]] = record_counts.get(source["site"], 0) + 1
+
+ records.sort(key=lambda r: (r["site"], r["treatment"], r["date"], str(r["tag"])))
+ return records, source_rows, record_counts
+
+
+def main():
+ records, source_rows, record_counts = build_records()
+ meta = {
+ "generatedAt": utc_today(),
"source": "RobertsLab survival CSV outputs",
"studyTitle": "Crassostrea gigas outplant percent survival by bag",
- "recordCount": len(records),
"sourceRows": source_rows,
"recordCounts": record_counts,
"survivalMetric": "Percent survival per bag/replicate (0-100)",
"notes": "Westcott and Sequim Bay PolyIC have survival at each time point; Thorndyke Bay and Palix River/Willapa Bay report total (end-of-period) survival.",
"sourceUrls": [source["url"] for source in SOURCES],
- },
- "sites": sites,
- "treatments": treatments,
- "years": years,
- "observations": records,
-}
+ }
+ write_bundle(OUT, compact_bundle(records, COLUMNS, LOOKUP_COLUMNS, CONSTANTS, meta))
+ report(records, OUT, "survival")
-with open(OUT, "w") as f:
- json.dump(bundle, f, indent=0)
-print(f"Wrote {len(records)} survival records to {OUT}")
-print("Sites:", sites)
-print("Treatments:", treatments)
-print("Years:", years)
+if __name__ == "__main__":
+ main()
diff --git a/scripts/shield_data.py b/scripts/shield_data.py
new file mode 100644
index 0000000..2bedb7a
--- /dev/null
+++ b/scripts/shield_data.py
@@ -0,0 +1,215 @@
+"""
+Shared helpers for the SHIELD data build scripts.
+
+Everything the growth, survival, and field-observation scripts have in common
+lives here so the treatment vocabulary, date handling, HTTP fetching, and the
+compact bundle format cannot drift between them.
+
+Compact bundle format (read by src/data/bundleFormat.js):
+
+ {
+ "format": "shield-observations/1",
+ "meta": {...},
+ "sites": [...], "treatments": [...], "years": [...],
+ "columns": ["date", "site", ...],
+ "lookups": {"site": ["Westcott", ...], ...},
+ "constants": {"growth_mm": null, ...},
+ "rows": [[...], ...]
+ }
+
+`columns` names the position of each value in a row. Columns listed in
+`lookups` store an index into that column's value list instead of the value.
+`constants` are fields identical on every record and are re-attached on load.
+`year`, `month`, `quarter`, and `id` are derived from `date` and row position on
+the client and are not stored.
+"""
+import csv
+import json
+import math
+import os
+import re
+import sys
+import time
+import urllib.request
+from datetime import datetime, timezone
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+REPO = os.path.abspath(os.path.join(HERE, ".."))
+DATA_DIR = os.path.join(REPO, "public", "data")
+
+BUNDLE_FORMAT = "shield-observations/1"
+
+MONTHS = [
+ "Jan", "Feb", "Mar", "Apr", "May", "Jun",
+ "Jul", "Aug", "Sep", "Oct", "Nov", "Dec",
+]
+
+# Dashboard treatment axis, in display order. Must match TREATMENT_ORDER in
+# src/data/observations.js.
+TREATMENT_ORDER = [
+ "Control",
+ "Heat primed",
+ "Freshwater primed",
+ "Immune primed",
+ "Combined stress primed",
+ "Treated",
+]
+
+HTTP_TIMEOUT = 60
+HTTP_RETRIES = 3
+USER_AGENT = "shield-dashboard-data-build"
+
+
+def data_path(filename):
+ """Absolute path of a bundle inside public/data/."""
+ return os.path.join(DATA_DIR, filename)
+
+
+def utc_today():
+ return datetime.now(timezone.utc).strftime("%Y-%m-%d")
+
+
+def fetch_bytes(url):
+ """GET a URL with a timeout and a few retries. Raises on final failure."""
+ last_error = None
+ for attempt in range(1, HTTP_RETRIES + 1):
+ try:
+ req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT})
+ with urllib.request.urlopen(req, timeout=HTTP_TIMEOUT) as response:
+ return response.read()
+ except Exception as error: # network or HTTP error; retry with backoff
+ last_error = error
+ if attempt < HTTP_RETRIES:
+ wait = 2 ** attempt
+ print(f" ! fetch failed ({error.__class__.__name__}), retrying in {wait}s: {url}",
+ file=sys.stderr)
+ time.sleep(wait)
+ raise RuntimeError(f"Failed to fetch {url}: {last_error}")
+
+
+def fetch_text(url):
+ return fetch_bytes(url).decode("utf-8-sig")
+
+
+def read_csv_url(url):
+ """Download a CSV and return a list of dict rows."""
+ return list(csv.DictReader(fetch_text(url).splitlines()))
+
+
+def parse_date(value):
+ """Accept '20240624' or '2024-06-24...' and return 'YYYY-MM-DD'."""
+ text = str(value).strip()
+ if "-" in text:
+ return text[:10]
+ return f"{text[0:4]}-{text[4:6]}-{text[6:8]}"
+
+
+def year_of(dstr):
+ datetime.strptime(dstr, "%Y-%m-%d") # validate
+ return dstr[:4]
+
+
+def number(value):
+ try:
+ parsed = float(value)
+ except (TypeError, ValueError):
+ return None
+ return parsed if math.isfinite(parsed) else None
+
+
+def normal_treatment(raw_treatment, experiment=""):
+ """Map a source treatment label (plus experiment hint) onto TREATMENT_ORDER."""
+ treatment = str(raw_treatment).strip().lower()
+ exp = str(experiment).strip().lower()
+
+ if treatment == "control":
+ return "Control"
+ if "temperature+salinity" in treatment:
+ return "Combined stress primed"
+ if "immune" in treatment or "polyic" in treatment:
+ return "Immune primed"
+ if "salinity" in treatment or "fresh" in exp:
+ return "Freshwater primed"
+ if "temperature" in treatment or "temperature" in exp:
+ return "Heat primed"
+ if treatment == "treated":
+ return "Treated"
+ return str(raw_treatment).strip()
+
+
+def site_slug(site):
+ return re.sub(r"[^A-Z0-9]+", "-", site.upper()).strip("-")
+
+
+def ordered_treatments(records):
+ present = {r["treatment"] for r in records}
+ return [t for t in TREATMENT_ORDER if t in present]
+
+
+def compact_bundle(records, columns, lookup_columns, constants, meta):
+ """Encode full records into the compact bundle shape."""
+ lookups = {c: [] for c in lookup_columns}
+ indexes = {c: {} for c in lookup_columns}
+ rows = []
+ for record in records:
+ row = []
+ for column in columns:
+ value = record.get(column)
+ if column in lookups and value is not None:
+ index = indexes[column]
+ if value not in index:
+ index[value] = len(lookups[column])
+ lookups[column].append(value)
+ value = index[value]
+ row.append(value)
+ rows.append(row)
+
+ return {
+ "format": BUNDLE_FORMAT,
+ "meta": {**meta, "recordCount": len(records)},
+ "sites": sorted({r["site"] for r in records}),
+ "treatments": ordered_treatments(records),
+ "years": sorted({year_of(r["date"]) for r in records}),
+ "columns": list(columns),
+ "lookups": lookups,
+ "constants": dict(constants),
+ "rows": rows,
+ }
+
+
+def write_bundle(path, bundle):
+ """Write a bundle with readable headers and one compact row per line."""
+ head = dict(bundle)
+ rows = head.pop("rows")
+ head_text = json.dumps(head, indent=2, ensure_ascii=False)
+ assert head_text.endswith("}")
+ body = ",\n".join(
+ json.dumps(row, ensure_ascii=False, separators=(",", ":")) for row in rows
+ )
+ text = head_text[:-1].rstrip() + ',\n "rows": [\n' + body + "\n ]\n}\n"
+ os.makedirs(os.path.dirname(path), exist_ok=True)
+ with open(path, "w", encoding="utf-8") as handle:
+ handle.write(text)
+
+
+def expand_bundle(bundle):
+ """Inverse of compact_bundle, without derived fields. Used for validation."""
+ columns = bundle["columns"]
+ lookups = bundle.get("lookups", {})
+ constants = bundle.get("constants", {})
+ records = []
+ for row in bundle["rows"]:
+ record = dict(constants)
+ for column, value in zip(columns, row):
+ if column in lookups and value is not None:
+ value = lookups[column][value]
+ record[column] = value
+ records.append(record)
+ return records
+
+
+def report(records, out_path, label):
+ print(f"Wrote {len(records)} {label} records to {out_path}")
+ print("Sites:", sorted({r['site'] for r in records}))
+ print("Treatments:", ordered_treatments(records))
+ print("Years:", sorted({year_of(r['date']) for r in records}))
diff --git a/src/App.jsx b/src/App.jsx
index 52a6c28..29c5c5c 100644
--- a/src/App.jsx
+++ b/src/App.jsx
@@ -1,40 +1,64 @@
+import { Suspense, lazy } from 'react';
import { BrowserRouter, Link, Routes, Route } from 'react-router-dom';
import Header from './components/Header';
-import DashboardPage from './pages/DashboardPage';
-import LiveDataPage from './pages/LiveDataPage';
-import MapPage from './pages/MapPage';
-import ResearchPage from './pages/ResearchPage';
-import { mockShellfishData } from './data/mockShellfishData';
+import DataStatus from './components/DataStatus';
+import { OBSERVATIONS_KEY, usePeekResource } from './data/resources';
+
+// Route-level code splitting: the map and live-data routes pull in Leaflet,
+// and the dashboard pulls in Recharts; none of that is needed on the others.
+const DashboardPage = lazy(() => import('./pages/DashboardPage'));
+const LiveDataPage = lazy(() => import('./pages/LiveDataPage'));
+const MapPage = lazy(() => import('./pages/MapPage'));
+const ResearchPage = lazy(() => import('./pages/ResearchPage'));
const basename = import.meta.env.BASE_URL.replace(/\/$/, '') || '/';
+function Footer() {
+ // Peek rather than load: the footer should not pull the observation
+ // bundles onto routes that do not otherwise need them.
+ const observations = usePeekResource(OBSERVATIONS_KEY);
+ const recordCount = observations.status === 'ready' ? observations.data.records.length : null;
+
+ return (
+
+
+ SHIELD · Shellfish Hardening and Integrated Environmental Longitudinal
+ Dashboard · Real field data from RobertsLab project-gigas-conditioning,
+ 10K-Seed, and polyIC-larvae outputs
+ {recordCount != null ? ` · ${recordCount.toLocaleString()} observation records` : ''}
+ {' '}· Research background ·{' '}
+
+ GitHub repository
+
+
+
+ );
+}
+
export default function App() {
return (
-
- } />
- } />
- } />
- } />
-
-
-
- SHIELD · Shellfish Hardening and Integrated Environmental
- Longitudinal Dashboard · Real field data — RobertsLab
- project-gigas-conditioning + Thorndyke Bay 10K-Seed ·{' '}
- {mockShellfishData.length.toLocaleString()} observation records ·{' '}
- Research background ·{' '}
-
- GitHub repository
-
-
-
+
+
+
+ }
+ >
+
+ } />
+ } />
+ } />
+ } />
+
+
+
);
diff --git a/src/components/ArchivalTemperatureChart.jsx b/src/components/ArchivalTemperatureChart.jsx
index 0df9c01..4abe5de 100644
--- a/src/components/ArchivalTemperatureChart.jsx
+++ b/src/components/ArchivalTemperatureChart.jsx
@@ -10,8 +10,9 @@ import {
ResponsiveContainer,
Legend,
} from 'recharts';
-import { SITE_LOCATIONS } from '../data/mockShellfishData';
-import archivalTemperature from '../data/archivalTemperatureData.json';
+import { siteColor } from '../data/siteMetadata';
+import { useArchivalTemperature } from '../data/resources';
+import DataStatus from './DataStatus';
function ArchivalTooltip({ active, payload, label }) {
if (!active || !payload?.length) return null;
@@ -46,7 +47,25 @@ function formatRange(start, end) {
}
export default function ArchivalTemperatureChart() {
- const { series, sites, meta, generatedAt } = archivalTemperature;
+ const archival = useArchivalTemperature();
+ if (archival.status !== 'ready') {
+ return (
+
+ Archival Water Temperature
+
+
+ );
+ }
+ return ;
+}
+
+function ArchivalTemperatureChartBody({ bundle }) {
+ const { series, sites, meta, generatedAt } = bundle;
const [activeSites, setActiveSites] = useState(() => new Set(sites));
const toggleSite = (site) => {
@@ -81,7 +100,7 @@ export default function ArchivalTemperatureChart() {
{sites.map((site) => {
const on = activeSites.has(site);
- const color = SITE_LOCATIONS[site]?.color ?? '#64748b';
+ const color = siteColor(site);
return (
+
+ Could not load {label}.{' '}
+ {error?.message ? {error.message} : null}
+
+ {retry ? (
+
+ Retry
+
+ ) : null}
+
+ );
+ }
+
+ return (
+
+ );
+}
diff --git a/src/components/FieldReportExport.jsx b/src/components/FieldReportExport.jsx
index 7368c09..0f5b490 100644
--- a/src/components/FieldReportExport.jsx
+++ b/src/components/FieldReportExport.jsx
@@ -1,4 +1,13 @@
-import { SITE_LOCATIONS } from '../data/mockShellfishData';
+import { useEffect, useState } from 'react';
+import { flushSync } from 'react-dom';
+import { SITE_LOCATIONS } from '../data/siteMetadata';
+
+/**
+ * Upper bound on rows rendered in the printed appendix. The full record set is
+ * available through the CSV download; the print view is a summary document and
+ * tens of thousands of rows would run to hundreds of pages.
+ */
+const MAX_PRINT_ROWS = 1000;
const REPORT_COLUMNS = [
{ key: 'date', label: 'Date' },
@@ -57,7 +66,7 @@ function buildCsv(data, filters, stats) {
['Date range', getDateRange(data)],
['Record count', data.length],
...getFilterSummary(filters).map(([label, value]) => [`Filter: ${label}`, value]),
- ['Mean growth volume', stats.meanGrowth ?? ''],
+ ['Final growth volume', stats.finalGrowth ?? ''],
['Mean temperature (deg C)', stats.meanTemp ?? ''],
['Final survival (%)', stats.finalSurvival ?? ''],
['Best-performing treatment', stats.bestTreatment],
@@ -84,6 +93,26 @@ export default function FieldReportExport({ filters, stats, data }) {
const generatedLabel = formatDate(Date.now());
const dateRange = getDateRange(data);
+ // The record appendix is mounted only while printing. Rendering it eagerly
+ // put every filtered row (30k+ by default) into the DOM on each dashboard
+ // load, hidden by CSS. `beforeprint` fires synchronously inside
+ // window.print() and on browser-initiated prints, so flushSync is needed to
+ // get the appendix committed before the print dialog snapshots the page.
+ const [isPrinting, setIsPrinting] = useState(false);
+ useEffect(() => {
+ const handleBeforePrint = () => flushSync(() => setIsPrinting(true));
+ const handleAfterPrint = () => setIsPrinting(false);
+ window.addEventListener('beforeprint', handleBeforePrint);
+ window.addEventListener('afterprint', handleAfterPrint);
+ return () => {
+ window.removeEventListener('beforeprint', handleBeforePrint);
+ window.removeEventListener('afterprint', handleAfterPrint);
+ };
+ }, []);
+
+ const printRows = isPrinting ? data.slice(0, MAX_PRINT_ROWS) : [];
+ const printTruncated = isPrinting && data.length > MAX_PRINT_ROWS;
+
const handleDownloadCsv = () => {
const csv = buildCsv(data, filters, stats);
const blob = new Blob([csv], { type: 'text/csv;charset=utf-8' });
@@ -180,27 +209,36 @@ export default function FieldReportExport({ filters, stats, data }) {
-
-
Filtered Observation Records
-
-
-
- {REPORT_COLUMNS.map((col) => (
- {col.label}
- ))}
-
-
-
- {data.map((row) => (
-
+ {isPrinting ? (
+
+
Filtered Observation Records
+ {printTruncated ? (
+
+ Showing the first {MAX_PRINT_ROWS.toLocaleString()} of{' '}
+ {data.length.toLocaleString()} records. Download the CSV for the
+ complete record set.
+
+ ) : null}
+
+
+
{REPORT_COLUMNS.map((col) => (
- {row[col.key] == null ? '-' : row[col.key]}
+ {col.label}
))}
- ))}
-
-
-
+
+
+ {printRows.map((row) => (
+
+ {REPORT_COLUMNS.map((col) => (
+ {row[col.key] == null ? '-' : row[col.key]}
+ ))}
+
+ ))}
+
+
+
+ ) : null}
);
}
diff --git a/src/components/Filters.jsx b/src/components/Filters.jsx
index 3c0b82e..4c40d10 100644
--- a/src/components/Filters.jsx
+++ b/src/components/Filters.jsx
@@ -1,6 +1,6 @@
-import { SITES, TREATMENTS, METRICS, YEARS } from '../data/mockShellfishData';
+import { METRICS } from '../data/siteMetadata';
-export default function Filters({ filters, onChange }) {
+export default function Filters({ filters, onChange, sites, treatments, years }) {
const handleChange = (field) => (e) => {
onChange({ ...filters, [field]: e.target.value });
};
@@ -13,7 +13,7 @@ export default function Filters({ filters, onChange }) {
Site
All Sites
- {SITES.map((s) => (
+ {sites.map((s) => (
{s}
@@ -25,7 +25,7 @@ export default function Filters({ filters, onChange }) {
Treatment
All Treatments
- {TREATMENTS.map((t) => (
+ {treatments.map((t) => (
{t}
@@ -48,7 +48,7 @@ export default function Filters({ filters, onChange }) {
Year
All Years
- {YEARS.map((y) => (
+ {years.map((y) => (
{y}
diff --git a/src/components/Header.jsx b/src/components/Header.jsx
index fe71d6d..362742b 100644
--- a/src/components/Header.jsx
+++ b/src/components/Header.jsx
@@ -42,19 +42,38 @@ export default function Header() {
>
Site Map
+
+ isActive ? 'nav-link active' : 'nav-link'
+ }
+ >
+ Live Data
+
+
+ isActive ? 'nav-link active' : 'nav-link'
+ }
+ >
+ Research
+
Conditioning Atlas
- Real field measurements: survival & image-derived shell growth
- from RobertsLab outplant assessments (Palix River/Willapa Bay, Sequim, Westcott)
- plus Thorndyke Bay 10K-Seed survival; temperature is the in-situ HOBO
- logger monthly mean. Metrics not measured at an assessment are blank.
+ Real field measurements from RobertsLab outplant assessments at
+ Thorndyke Bay, Sequim Bay, Palix River/Willapa Bay, and Westcott:
+ per-bag survival, image-derived oyster growth volume, and in-situ HOBO
+ logger monthly mean water temperature. Metrics not measured at an
+ assessment are blank.
diff --git a/src/components/LiveTemperaturePanel.jsx b/src/components/LiveTemperaturePanel.jsx
index 267485a..e72862f 100644
--- a/src/components/LiveTemperaturePanel.jsx
+++ b/src/components/LiveTemperaturePanel.jsx
@@ -1,6 +1,7 @@
-import liveTemperature from '../data/liveTemperature.json';
import { MapContainer, TileLayer, CircleMarker, Popup, Polyline } from 'react-leaflet';
import 'leaflet/dist/leaflet.css';
+import { useLiveTemperature } from '../data/resources';
+import DataStatus from './DataStatus';
const LIVE_SITE_LOCATIONS = {
'Thorndyke Bay': { lat: 47.808, lon: -122.738, color: '#2563eb' },
@@ -428,7 +429,25 @@ function LiveSourceLedger({ rows }) {
}
export default function LiveTemperaturePanel() {
- const { observations, description, generatedAt, maxAgeHours } = liveTemperature;
+ const live = useLiveTemperature();
+ if (live.status !== 'ready') {
+ return (
+
+ Live Environmental Snapshot
+
+
+ );
+ }
+ return ;
+}
+
+function LiveTemperaturePanelBody({ bundle }) {
+ const { observations, description, generatedAt, maxAgeHours } = bundle;
const sourceRows = getSourceRows(observations);
return (
diff --git a/src/components/SiteComparisonChart.jsx b/src/components/SiteComparisonChart.jsx
index a16dda3..06c28d4 100644
--- a/src/components/SiteComparisonChart.jsx
+++ b/src/components/SiteComparisonChart.jsx
@@ -10,22 +10,24 @@ import {
Cell,
ErrorBar,
} from 'recharts';
-
-const SITE_COLORS = {
- 'Thorndyke Bay': '#2563eb',
- 'Sequim Bay': '#0891b2',
- 'Palix River/Willapa Bay': '#d97706',
- Westcott: '#6366f1',
-};
+import { siteColor } from '../data/siteMetadata';
const VIEW_CONFIG = {
growth: {
- label: 'Growth Volume',
+ label: 'Final Growth Volume',
unit: 'predicted volume',
- caption: 'Average predicted oyster volume by site',
+ caption: 'Mean predicted oyster volume at the latest assessment by site',
+ },
+ survival: {
+ label: 'Final Survival',
+ unit: '%',
+ caption: 'Mean survival (%) at the latest assessment by site',
+ },
+ temperature: {
+ label: 'Mean Temperature',
+ unit: '°C',
+ caption: 'Average water temperature (°C) by site across the filtered period',
},
- survival: { label: 'Final Survival', unit: '%', caption: 'Mean end-of-period survival (%) by site' },
- temperature: { label: 'Mean Temperature', unit: '°C', caption: 'Average water temperature (°C) by site' },
};
export default function SiteComparisonChart({ growthData, survivalData, tempData }) {
@@ -62,6 +64,7 @@ export default function SiteComparisonChart({ growthData, survivalData, tempData
key={key}
type="button"
className={view === key ? 'toggle active' : 'toggle'}
+ aria-pressed={view === key}
onClick={() => setView(key)}
>
{VIEW_CONFIG[key].label}
@@ -117,7 +120,7 @@ export default function SiteComparisonChart({ growthData, survivalData, tempData
/>
)}
{data.map((entry) => (
- |
+ |
))}
diff --git a/src/components/SiteMap.jsx b/src/components/SiteMap.jsx
index 9e6583d..d7e692b 100644
--- a/src/components/SiteMap.jsx
+++ b/src/components/SiteMap.jsx
@@ -1,7 +1,6 @@
import { useMemo } from 'react';
import { Link } from 'react-router-dom';
import { MapContainer, TileLayer, CircleMarker, Popup } from 'react-leaflet';
-import { MAP_CENTER, MAP_ZOOM } from '../data/mockShellfishData';
import 'leaflet/dist/leaflet.css';
export default function SiteMap({ sites, selectedSite, onSelectSite }) {
@@ -19,8 +18,6 @@ export default function SiteMap({ sites, selectedSite, onSelectSite }) {
@@ -51,8 +48,8 @@ export default function SiteMap({ sites, selectedSite, onSelectSite }) {
{site.region}
-
Mean growth volume
- {site.meanGrowth?.toLocaleString() ?? '—'}
+ Final growth volume
+ {site.finalGrowth?.toLocaleString() ?? '—'}
Mean temp
diff --git a/src/components/SummaryCards.jsx b/src/components/SummaryCards.jsx
index 4b99a94..a1f9be2 100644
--- a/src/components/SummaryCards.jsx
+++ b/src/components/SummaryCards.jsx
@@ -1,12 +1,12 @@
export default function SummaryCards({ stats }) {
const cards = [
{
- label: 'Mean Growth Volume',
+ label: 'Final Growth Volume',
value:
- stats.meanGrowth != null
- ? stats.meanGrowth.toLocaleString()
+ stats.finalGrowth != null
+ ? stats.finalGrowth.toLocaleString()
: '—',
- detail: 'Predicted volume across filtered oysters',
+ detail: 'Mean predicted volume at the latest assessment per group',
},
{
label: 'Mean Temperature',
@@ -17,7 +17,7 @@ export default function SummaryCards({ stats }) {
label: 'Final Survival',
value:
stats.finalSurvival != null ? `${stats.finalSurvival}%` : '—',
- detail: 'Mean end-of-period survival by group',
+ detail: 'Mean survival at the latest assessment per group',
},
{
label: 'Best-performing Treatment',
diff --git a/src/components/TimeSeriesChart.jsx b/src/components/TimeSeriesChart.jsx
index 4069692..058d09c 100644
--- a/src/components/TimeSeriesChart.jsx
+++ b/src/components/TimeSeriesChart.jsx
@@ -10,6 +10,7 @@ import {
Legend,
ErrorBar,
} from 'recharts';
+import { siteColor } from '../data/siteMetadata';
const METRIC_LABELS = {
'Growth Volume': 'Predicted volume',
@@ -17,10 +18,37 @@ const METRIC_LABELS = {
Survival: 'Survival (%)',
};
+function SeriesTooltip({ active, payload, label, unit }) {
+ if (!active || !payload?.length) return null;
+ const point = payload[0]?.payload ?? {};
+
+ return (
+
+
Assessment: {label}
+ {payload
+ .filter((entry) => entry.value != null)
+ .map((entry) => {
+ const count = point[`${entry.dataKey}Count`];
+ return (
+
+
+ {entry.name}: {`${entry.value} ${unit}`.trim()}
+ {count != null ? (n={count}) : null}
+
+ );
+ })}
+
+ );
+}
+
export default function TimeSeriesChart({ data, metric }) {
const [showErrorBars, setShowErrorBars] = useState(false);
const yLabel = METRIC_LABELS[metric] ?? metric;
const unit = data.unit ?? '';
+ const sites = data.sites ?? [];
if (!data.series || data.series.length === 0) {
return (
@@ -32,7 +60,9 @@ export default function TimeSeriesChart({ data, metric }) {
}
const tickInterval = Math.max(1, Math.floor(data.series.length / 12));
- const canShowErrorBars = data.series.some((point) => point.error != null);
+ const canShowErrorBars = data.series.some((point) =>
+ sites.some((site) => point[`${site}Error`] != null)
+ );
return (
@@ -50,8 +80,9 @@ export default function TimeSeriesChart({ data, metric }) {
)}
- Mean {metric.toLowerCase()} across filtered cohorts at each field
- assessment{unit ? ` (${unit})` : ''}
+ Mean {metric.toLowerCase()} at each field assessment, one line per site
+ {unit ? ` (${unit})` : ''}. Sites are plotted separately because they were
+ sampled on different dates.
@@ -74,35 +105,31 @@ export default function TimeSeriesChart({ data, metric }) {
style: { fill: '#64748b', fontSize: 12 },
}}
/>
- [`${value} ${unit}`.trim(), metric]}
- labelFormatter={(label) => `Period: ${label}`}
- />
-
-
- {showErrorBars && canShowErrorBars && (
-
- )}
-
+ } />
+
+ {sites.map((site) => (
+
+ {showErrorBars && canShowErrorBars && (
+
+ )}
+
+ ))}
diff --git a/src/components/TreatmentComparisonChart.jsx b/src/components/TreatmentComparisonChart.jsx
index 0d5c126..912116d 100644
--- a/src/components/TreatmentComparisonChart.jsx
+++ b/src/components/TreatmentComparisonChart.jsx
@@ -10,24 +10,29 @@ import {
ResponsiveContainer,
ErrorBar,
} from 'recharts';
-import { TREATMENTS } from '../data/mockShellfishData';
+import { TREATMENT_COLORS, FALLBACK_COLOR } from '../data/siteMetadata';
-const TREATMENT_COLORS = {
- Control: '#64748b',
- 'Heat primed': '#dc2626',
- 'Freshwater primed': '#0891b2',
- 'Immune primed': '#7c3aed',
- 'Combined stress primed': '#059669',
+const VIEW_CONFIG = {
+ survival: {
+ label: 'Final Survival',
+ yLabel: 'Final survival (%)',
+ caption: 'Survival at the latest assessment by priming treatment within each site',
+ },
+ growth: {
+ label: 'Final Growth Volume',
+ yLabel: 'Final predicted volume',
+ caption:
+ 'Mean predicted oyster volume at the latest assessment by priming treatment within each site',
+ },
};
-export default function TreatmentComparisonChart({ survivalData, growthData }) {
+export default function TreatmentComparisonChart({ survivalData, growthData, treatments }) {
const [view, setView] = useState('survival');
const [showErrorBars, setShowErrorBars] = useState(false);
const data = view === 'survival' ? survivalData : growthData;
- const yLabel =
- view === 'survival' ? 'Final survival (%)' : 'Mean predicted volume';
+ const config = VIEW_CONFIG[view];
const canShowErrorBars = data?.some((row) =>
- TREATMENTS.some((treatment) => row[`${treatment}Error`] != null)
+ treatments.some((treatment) => row[`${treatment}Error`] != null)
);
if (!data || data.length === 0) {
@@ -45,20 +50,17 @@ export default function TreatmentComparisonChart({ survivalData, growthData }) {
Treatment Comparison by Site
- setView('survival')}
- >
- Final Survival
-
- setView('growth')}
- >
- Growth Volume
-
+ {Object.keys(VIEW_CONFIG).map((key) => (
+ setView(key)}
+ >
+ {VIEW_CONFIG[key].label}
+
+ ))}
{canShowErrorBars && (
@@ -72,11 +74,7 @@ export default function TreatmentComparisonChart({ survivalData, growthData }) {
)}
-
- {view === 'survival'
- ? 'End-of-period survival by priming treatment within each site'
- : 'Mean predicted oyster volume by priming treatment within each site'}
-
+ {config.caption}
@@ -88,7 +86,7 @@ export default function TreatmentComparisonChart({ survivalData, growthData }) {
- {TREATMENTS.map((t) => (
-
- {showErrorBars && canShowErrorBars && (
-
- )}
-
- ))}
+ {treatments.map((t) => {
+ const color = TREATMENT_COLORS[t] ?? FALLBACK_COLOR;
+ return (
+
+ {showErrorBars && canShowErrorBars && (
+
+ )}
+
+ );
+ })}
diff --git a/src/data/__tests__/bundleFormat.test.js b/src/data/__tests__/bundleFormat.test.js
new file mode 100644
index 0000000..88b171a
--- /dev/null
+++ b/src/data/__tests__/bundleFormat.test.js
@@ -0,0 +1,63 @@
+import { describe, expect, it } from 'vitest';
+import { BUNDLE_FORMAT, dateFields, hydrateBundle } from '../bundleFormat';
+import {
+ GROWTH_COLUMNS,
+ GROWTH_CONSTANTS,
+ GROWTH_LOOKUPS,
+ GROWTH_RECORDS,
+ encodeBundle,
+} from './fixtures';
+
+describe('dateFields', () => {
+ it('derives year, month, and quarter from an ISO date', () => {
+ expect(dateFields('2024-08-20')).toEqual({ year: '2024', month: 'Aug', quarter: 'Q3' });
+ expect(dateFields('2025-01-05')).toEqual({ year: '2025', month: 'Jan', quarter: 'Q1' });
+ expect(dateFields('2025-12-31')).toEqual({ year: '2025', month: 'Dec', quarter: 'Q4' });
+ });
+});
+
+describe('hydrateBundle', () => {
+ const bundle = encodeBundle(GROWTH_RECORDS, GROWTH_COLUMNS, GROWTH_LOOKUPS, GROWTH_CONSTANTS);
+
+ it('round-trips every stored column and re-attaches constants', () => {
+ const records = hydrateBundle(bundle, 'GROW');
+ expect(records).toHaveLength(GROWTH_RECORDS.length);
+ records.forEach((record, i) => {
+ for (const column of GROWTH_COLUMNS) {
+ expect(record[column]).toEqual(GROWTH_RECORDS[i][column] ?? null);
+ }
+ for (const [key, value] of Object.entries(GROWTH_CONSTANTS)) {
+ expect(record[key]).toEqual(value);
+ }
+ });
+ });
+
+ it('derives id, year, month, and quarter', () => {
+ const [first] = hydrateBundle(bundle, 'GROW');
+ expect(first.id).toBe('GROW-0');
+ expect(first.year).toBe('2024');
+ expect(first.month).toBe('Jun');
+ expect(first.quarter).toBe('Q2');
+ });
+
+ it('decodes null lookup values as null', () => {
+ const withNull = encodeBundle(
+ [{ date: '2024-01-01', site: 'Westcott', treatment: 'Control', effort: null }],
+ ['date', 'site', 'treatment', 'effort'],
+ ['site', 'treatment', 'effort'],
+ {}
+ );
+ expect(hydrateBundle(withNull, 'X')[0].effort).toBeNull();
+ });
+
+ it('accepts a legacy expanded bundle unchanged', () => {
+ const legacy = { observations: [{ id: 'a', date: '2024-01-01' }] };
+ expect(hydrateBundle(legacy, 'X')).toBe(legacy.observations);
+ });
+
+ it('rejects unknown formats', () => {
+ expect(() => hydrateBundle({ format: 'other/9', columns: [], rows: [] }, 'X')).toThrow(
+ BUNDLE_FORMAT
+ );
+ });
+});
diff --git a/src/data/__tests__/bundles.test.js b/src/data/__tests__/bundles.test.js
new file mode 100644
index 0000000..e74d698
--- /dev/null
+++ b/src/data/__tests__/bundles.test.js
@@ -0,0 +1,114 @@
+/**
+ * Validates the committed data bundles in public/data/ against the schema the
+ * app expects. Catches regressions in the build scripts before they reach the
+ * deployed site.
+ */
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
+import { describe, expect, it } from 'vitest';
+import { BUNDLE_FORMAT, hydrateBundle } from '../bundleFormat';
+import { assembleObservations } from '../observations';
+import { SITE_LOCATIONS, TREATMENT_ORDER } from '../siteMetadata';
+
+const DATA_DIR = join(process.cwd(), 'public', 'data');
+const load = (name) => JSON.parse(readFileSync(join(DATA_DIR, name), 'utf8'));
+
+const ISO_DATE = /^\d{4}-\d{2}-\d{2}$/;
+
+describe.each([
+ ['realObservations.json', 'FIELD'],
+ ['growthObservations.json', 'GROW'],
+ ['survivalObservations.json', 'SURV'],
+])('%s', (name, prefix) => {
+ const bundle = load(name);
+
+ it('declares the compact format with consistent columns and rows', () => {
+ expect(bundle.format).toBe(BUNDLE_FORMAT);
+ expect(bundle.columns).toContain('date');
+ expect(bundle.columns).toContain('site');
+ expect(bundle.columns).toContain('treatment');
+ for (const column of Object.keys(bundle.lookups)) {
+ expect(bundle.columns).toContain(column);
+ }
+ expect(bundle.rows).toHaveLength(bundle.meta.recordCount);
+ for (const row of bundle.rows) {
+ expect(row).toHaveLength(bundle.columns.length);
+ }
+ });
+
+ it('uses only known sites and treatments', () => {
+ for (const site of bundle.sites) expect(SITE_LOCATIONS).toHaveProperty(site);
+ for (const treatment of bundle.treatments) expect(TREATMENT_ORDER).toContain(treatment);
+ });
+
+ it('hydrates to records with valid dates and vocabularies', () => {
+ const records = hydrateBundle(bundle, prefix);
+ expect(records).toHaveLength(bundle.meta.recordCount);
+ const sites = new Set();
+ const treatments = new Set();
+ const years = new Set();
+ for (const record of records) {
+ expect(record.date).toMatch(ISO_DATE);
+ sites.add(record.site);
+ treatments.add(record.treatment);
+ years.add(record.year);
+ }
+ expect([...sites].sort()).toEqual([...bundle.sites].sort());
+ expect([...treatments].sort()).toEqual([...bundle.treatments].sort());
+ expect([...years].sort()).toEqual([...bundle.years].sort());
+ });
+});
+
+describe('assembled dataset', () => {
+ const dataset = assembleObservations({
+ field: load('realObservations.json'),
+ growth: load('growthObservations.json'),
+ survival: load('survivalObservations.json'),
+ });
+
+ it('carries every metric on at least one record', () => {
+ for (const key of ['growth_volume', 'temperature_C', 'survival_percent']) {
+ expect(dataset.records.some((r) => r[key] != null)).toBe(true);
+ }
+ });
+
+ it('never counts field survival where per-bag survival exists on the same key', () => {
+ const perBag = new Set(
+ dataset.records
+ .filter((r) => r.id.startsWith('SURV-'))
+ .map((r) => `${r.site}|${r.treatment}|${r.date}`)
+ );
+ const doubleCounted = dataset.records.filter(
+ (r) =>
+ r.id.startsWith('FIELD-') &&
+ r.survival_percent != null &&
+ perBag.has(`${r.site}|${r.treatment}|${r.date}`)
+ );
+ expect(doubleCounted).toEqual([]);
+ });
+});
+
+describe('archivalTemperatureData.json', () => {
+ const bundle = load('archivalTemperatureData.json');
+
+ it('has a date-sorted series covering the declared sites', () => {
+ const dates = bundle.series.map((row) => row.date);
+ expect([...dates].sort()).toEqual(dates);
+ for (const site of bundle.sites) {
+ expect(SITE_LOCATIONS).toHaveProperty(site);
+ expect(bundle.series.some((row) => row[site] != null)).toBe(true);
+ }
+ expect(bundle.meta.map((m) => m.site).sort()).toEqual([...bundle.sites].sort());
+ });
+});
+
+describe('liveTemperature.json', () => {
+ const bundle = load('liveTemperature.json');
+
+ it('has one observation per declared site', () => {
+ expect(bundle.observations.map((o) => o.site)).toEqual(bundle.sites);
+ for (const observation of bundle.observations) {
+ expect(observation).toHaveProperty('metrics');
+ }
+ });
+});
diff --git a/src/data/__tests__/fixtures.js b/src/data/__tests__/fixtures.js
new file mode 100644
index 0000000..dfd5735
--- /dev/null
+++ b/src/data/__tests__/fixtures.js
@@ -0,0 +1,104 @@
+/**
+ * Small hand-built dataset for the aggregation tests. Values are chosen so
+ * expected means and standard errors can be checked by hand.
+ *
+ * Two sites, two treatments, several dates. Field rows carry temperature and,
+ * for Sequim Bay, aggregated survival. Per-bag survival exists for Westcott on
+ * both dates and for Sequim Bay Control on the second date only.
+ */
+import { BUNDLE_FORMAT } from '../bundleFormat';
+
+/** Encode expanded records into the compact bundle format (mirrors shield_data.py). */
+export function encodeBundle(records, columns, lookupColumns, constants, meta = {}) {
+ const lookups = Object.fromEntries(lookupColumns.map((c) => [c, []]));
+ const rows = records.map((record) =>
+ columns.map((column) => {
+ let value = record[column] ?? null;
+ if (lookups[column] && value != null) {
+ let index = lookups[column].indexOf(value);
+ if (index < 0) {
+ lookups[column].push(value);
+ index = lookups[column].length - 1;
+ }
+ value = index;
+ }
+ return value;
+ })
+ );
+ const treatmentOrder = [
+ 'Control',
+ 'Heat primed',
+ 'Freshwater primed',
+ 'Immune primed',
+ 'Combined stress primed',
+ 'Treated',
+ ];
+ const present = new Set(records.map((r) => r.treatment));
+ return {
+ format: BUNDLE_FORMAT,
+ meta: { ...meta, recordCount: records.length },
+ sites: [...new Set(records.map((r) => r.site))].sort(),
+ treatments: treatmentOrder.filter((t) => present.has(t)),
+ years: [...new Set(records.map((r) => r.date.slice(0, 4)))].sort(),
+ columns,
+ lookups,
+ constants,
+ rows,
+ };
+}
+
+export const FIELD_RECORDS = [
+ // Sequim Bay: aggregated survival on two dates, both treatments
+ { date: '2025-05-28', site: 'Sequim Bay', treatment: 'Control', effort: 'Effort A', growth_mm: 74.5, temperature_C: 12.0, survival_percent: 95.1, survival_source: 'measured', growth_source: 'measured' },
+ { date: '2025-10-06', site: 'Sequim Bay', treatment: 'Control', effort: 'Effort A', growth_mm: 117.0, temperature_C: 14.0, survival_percent: 94.2, survival_source: 'measured', growth_source: 'measured' },
+ { date: '2025-05-28', site: 'Sequim Bay', treatment: 'Heat primed', effort: 'Effort A', growth_mm: 72.8, temperature_C: 12.0, survival_percent: 99.2, survival_source: 'measured', growth_source: 'measured' },
+ { date: '2025-10-06', site: 'Sequim Bay', treatment: 'Heat primed', effort: 'Effort A', growth_mm: 98.0, temperature_C: 14.0, survival_percent: 97.7, survival_source: 'measured', growth_source: 'measured' },
+ // Westcott: field rows carry temperature only (survival replaced per-bag)
+ { date: '2024-06-20', site: 'Westcott', treatment: 'Control', effort: 'Effort B', growth_mm: null, temperature_C: 10.0, survival_percent: 100.0, survival_source: 'measured', growth_source: 'none' },
+ { date: '2024-08-20', site: 'Westcott', treatment: 'Control', effort: 'Effort B', growth_mm: null, temperature_C: 16.0, survival_percent: 99.0, survival_source: 'measured', growth_source: 'none' },
+];
+
+export const FIELD_COLUMNS = ['date', 'site', 'treatment', 'effort', 'growth_mm', 'temperature_C', 'survival_percent', 'survival_source', 'growth_source'];
+export const FIELD_LOOKUPS = ['site', 'treatment', 'effort', 'survival_source', 'growth_source'];
+export const FIELD_CONSTANTS = { temperature_source: 'logger-monthly-mean' };
+
+export const GROWTH_RECORDS = [
+ // Westcott Control: two dates, two oysters each. Final date mean = 250.
+ { date: '2024-06-20', site: 'Westcott', treatment: 'Control', raw_treatment: 'Control', effort: 'Daily Temperature', tag: '1', oyster_number: null, growth_volume: 100, growth_metric: 'vol', source_repo: 'r', source_url: 'u1' },
+ { date: '2024-06-20', site: 'Westcott', treatment: 'Control', raw_treatment: 'Control', effort: 'Daily Temperature', tag: '1', oyster_number: null, growth_volume: 120, growth_metric: 'vol', source_repo: 'r', source_url: 'u1' },
+ { date: '2024-08-20', site: 'Westcott', treatment: 'Control', raw_treatment: 'Control', effort: 'Daily Temperature', tag: '1', oyster_number: null, growth_volume: 200, growth_metric: 'vol', source_repo: 'r', source_url: 'u1' },
+ { date: '2024-08-20', site: 'Westcott', treatment: 'Control', raw_treatment: 'Control', effort: 'Daily Temperature', tag: '1', oyster_number: null, growth_volume: 300, growth_metric: 'vol', source_repo: 'r', source_url: 'u1' },
+ // Westcott Heat primed: one date, mean 400.
+ { date: '2024-08-20', site: 'Westcott', treatment: 'Heat primed', raw_treatment: 'Treated', effort: 'Daily Temperature', tag: '2', oyster_number: null, growth_volume: 350, growth_metric: 'vol', source_repo: 'r', source_url: 'u1' },
+ { date: '2024-08-20', site: 'Westcott', treatment: 'Heat primed', raw_treatment: 'Treated', effort: 'Daily Temperature', tag: '2', oyster_number: null, growth_volume: 450, growth_metric: 'vol', source_repo: 'r', source_url: 'u1' },
+ // Sequim Bay Control on a date no other site was sampled: mean 1000.
+ { date: '2025-10-06', site: 'Sequim Bay', treatment: 'Control', raw_treatment: 'Control', effort: 'Temperature', tag: '9', oyster_number: '1', growth_volume: 900, growth_metric: 'Predicted_Volume_Poly', source_repo: 'r', source_url: 'u2' },
+ { date: '2025-10-06', site: 'Sequim Bay', treatment: 'Control', raw_treatment: 'Control', effort: 'Temperature', tag: '9', oyster_number: '2', growth_volume: 1100, growth_metric: 'Predicted_Volume_Poly', source_repo: 'r', source_url: 'u2' },
+];
+
+export const GROWTH_COLUMNS = ['date', 'site', 'treatment', 'raw_treatment', 'effort', 'tag', 'oyster_number', 'growth_volume', 'growth_metric', 'source_repo', 'source_url'];
+export const GROWTH_LOOKUPS = ['site', 'treatment', 'raw_treatment', 'effort', 'growth_metric', 'source_repo', 'source_url'];
+export const GROWTH_CONSTANTS = { growth_mm: null, temperature_C: null, survival_percent: null, survival_source: 'none', growth_source: 'measured-volume', temperature_source: 'none' };
+
+export const SURVIVAL_RECORDS = [
+ // Westcott Control per-bag survival on both field dates: replaces field rows.
+ { date: '2024-06-20', site: 'Westcott', treatment: 'Control', raw_treatment: 'Control', effort: 'Daily Temperature', tag: '1', survival_percent: 100, survival_metric: 'survival', source_repo: 'r', source_url: 'u3' },
+ { date: '2024-06-20', site: 'Westcott', treatment: 'Control', raw_treatment: 'Control', effort: 'Daily Temperature', tag: '2', survival_percent: 100, survival_metric: 'survival', source_repo: 'r', source_url: 'u3' },
+ { date: '2024-08-20', site: 'Westcott', treatment: 'Control', raw_treatment: 'Control', effort: 'Daily Temperature', tag: '1', survival_percent: 90, survival_metric: 'survival', source_repo: 'r', source_url: 'u3' },
+ { date: '2024-08-20', site: 'Westcott', treatment: 'Control', raw_treatment: 'Control', effort: 'Daily Temperature', tag: '2', survival_percent: 80, survival_metric: 'survival', source_repo: 'r', source_url: 'u3' },
+ // Sequim Bay Control per-bag on the second date only: replaces one field row.
+ { date: '2025-10-06', site: 'Sequim Bay', treatment: 'Control', raw_treatment: 'Control', effort: 'PolyIC', tag: 'A', survival_percent: 70, survival_metric: 'survival', source_repo: 'r', source_url: 'u4' },
+ { date: '2025-10-06', site: 'Sequim Bay', treatment: 'Control', raw_treatment: 'Control', effort: 'PolyIC', tag: 'B', survival_percent: 80, survival_metric: 'survival', source_repo: 'r', source_url: 'u4' },
+];
+
+export const SURVIVAL_COLUMNS = ['date', 'site', 'treatment', 'raw_treatment', 'effort', 'tag', 'survival_percent', 'survival_metric', 'source_repo', 'source_url'];
+export const SURVIVAL_LOOKUPS = ['site', 'treatment', 'raw_treatment', 'effort', 'survival_metric', 'source_repo', 'source_url'];
+export const SURVIVAL_CONSTANTS = { oyster_number: null, growth_mm: null, growth_volume: null, growth_metric: null, temperature_C: null, survival_source: 'measured', growth_source: 'none', temperature_source: 'none' };
+
+export function fixtureBundles() {
+ return {
+ field: encodeBundle(FIELD_RECORDS, FIELD_COLUMNS, FIELD_LOOKUPS, FIELD_CONSTANTS, { source: 'field' }),
+ growth: encodeBundle(GROWTH_RECORDS, GROWTH_COLUMNS, GROWTH_LOOKUPS, GROWTH_CONSTANTS, { source: 'growth' }),
+ survival: encodeBundle(SURVIVAL_RECORDS, SURVIVAL_COLUMNS, SURVIVAL_LOOKUPS, SURVIVAL_CONSTANTS, { source: 'survival' }),
+ };
+}
diff --git a/src/data/__tests__/observations.test.js b/src/data/__tests__/observations.test.js
new file mode 100644
index 0000000..8e71e08
--- /dev/null
+++ b/src/data/__tests__/observations.test.js
@@ -0,0 +1,205 @@
+import { describe, expect, it } from 'vitest';
+import {
+ assembleObservations,
+ computeSummaryStats,
+ filterData,
+ finalDateRowsWithValue,
+ getSiteComparisonData,
+ getSiteGeographicSummaries,
+ getTimeSeriesData,
+ getTreatmentComparisonData,
+ summarizeValues,
+} from '../observations';
+import { fixtureBundles } from './fixtures';
+
+const dataset = assembleObservations(fixtureBundles());
+const { records } = dataset;
+
+const fieldRows = records.filter((r) => r.id.startsWith('FIELD-'));
+const fieldRow = (site, treatment, date) =>
+ fieldRows.find((r) => r.site === site && r.treatment === treatment && r.date === date);
+
+describe('assembleObservations', () => {
+ it('concatenates field, growth, and survival records with generated ids', () => {
+ expect(records).toHaveLength(6 + 8 + 6);
+ expect(records.filter((r) => r.id.startsWith('GROW-'))).toHaveLength(8);
+ expect(records.filter((r) => r.id.startsWith('SURV-'))).toHaveLength(6);
+ });
+
+ it('drops field survival only where a per-bag row shares site, treatment, and date', () => {
+ // Westcott Control has per-bag rows on both dates: field survival removed.
+ expect(fieldRow('Westcott', 'Control', '2024-06-20').survival_percent).toBeNull();
+ expect(fieldRow('Westcott', 'Control', '2024-08-20').survival_percent).toBeNull();
+ expect(fieldRow('Westcott', 'Control', '2024-08-20').survival_source).toBe('none');
+
+ // Sequim Bay Control has per-bag rows on 2025-10-06 only.
+ expect(fieldRow('Sequim Bay', 'Control', '2025-10-06').survival_percent).toBeNull();
+ expect(fieldRow('Sequim Bay', 'Control', '2025-05-28').survival_percent).toBe(95.1);
+
+ // Sequim Bay Heat primed has no per-bag rows at all: fully retained.
+ expect(fieldRow('Sequim Bay', 'Heat primed', '2025-05-28').survival_percent).toBe(99.2);
+ expect(fieldRow('Sequim Bay', 'Heat primed', '2025-10-06').survival_percent).toBe(97.7);
+ });
+
+ it('keeps field temperature and nulls growth volume on field rows', () => {
+ const row = fieldRow('Westcott', 'Control', '2024-08-20');
+ expect(row.temperature_C).toBe(16);
+ expect(row.growth_volume).toBeNull();
+ expect(row.tag).toBeNull();
+ expect(row.oyster_number).toBeNull();
+ });
+
+ it('derives vocabularies in display order', () => {
+ expect(dataset.sites).toEqual(['Sequim Bay', 'Westcott']);
+ expect(dataset.treatments).toEqual(['Control', 'Heat primed']);
+ expect(dataset.years).toEqual(['2024', '2025']);
+ expect(dataset.meta.growth.source).toBe('growth');
+ });
+});
+
+describe('summarizeValues', () => {
+ it('returns mean, standard error, and count', () => {
+ const summary = summarizeValues([2, 4, 4, 4, 5, 5, 7, 9]);
+ expect(summary.mean).toBe(5);
+ expect(summary.count).toBe(8);
+ // sample sd = sqrt(32/7); se = sd / sqrt(8)
+ expect(summary.error).toBeCloseTo(Math.sqrt(32 / 7) / Math.sqrt(8), 10);
+ });
+
+ it('skips nulls and reports no error for a single value', () => {
+ expect(summarizeValues([null, 3, undefined, NaN])).toEqual({ mean: 3, error: null, count: 1 });
+ expect(summarizeValues([])).toEqual({ mean: null, error: null, count: 0 });
+ });
+});
+
+describe('finalDateRowsWithValue', () => {
+ it('keeps only rows on the latest date per site and treatment', () => {
+ const rows = finalDateRowsWithValue(records, 'growth_volume');
+ const keys = new Set(rows.map((r) => `${r.site}|${r.treatment}|${r.date}`));
+ expect(keys).toEqual(
+ new Set([
+ 'Westcott|Control|2024-08-20',
+ 'Westcott|Heat primed|2024-08-20',
+ 'Sequim Bay|Control|2025-10-06',
+ ])
+ );
+ expect(rows.every((r) => r.growth_volume != null)).toBe(true);
+ });
+});
+
+describe('filterData', () => {
+ it('filters by site, treatment, and year, treating "All" as no filter', () => {
+ const all = filterData(records, { site: 'All Sites', treatment: 'All Treatments', year: 'All Years' });
+ expect(all).toHaveLength(records.length);
+
+ const westcott2024 = filterData(records, { site: 'Westcott', treatment: 'All Treatments', year: '2024' });
+ expect(westcott2024.every((r) => r.site === 'Westcott' && r.year === '2024')).toBe(true);
+ expect(westcott2024).toHaveLength(2 + 6 + 4);
+
+ const heat = filterData(records, { site: 'All Sites', treatment: 'Heat primed', year: 'All Years' });
+ expect(heat.every((r) => r.treatment === 'Heat primed')).toBe(true);
+ });
+});
+
+describe('computeSummaryStats', () => {
+ it('uses the final assessment for growth and survival', () => {
+ const stats = computeSummaryStats(records);
+ // Final growth rows: Westcott Control 200,300; Westcott Heat 350,450; Sequim Control 900,1100.
+ expect(stats.finalGrowth).toBe(Math.round((200 + 300 + 350 + 450 + 900 + 1100) / 6));
+ // Final survival rows: Westcott Control per-bag 90,80 (2024-08-20);
+ // Sequim Control per-bag 70,80 (2025-10-06); Sequim Heat field 97.7 (2025-10-06).
+ expect(stats.finalSurvival).toBe(Math.round(((90 + 80 + 70 + 80 + 97.7) / 5) * 10) / 10);
+ expect(stats.bestTreatment).toBe('Heat primed');
+ // Westcott final per-bag mean 85 vs Sequim (70, 80, 97.7) mean 82.6
+ expect(stats.highestSurvivalSite).toBe('Westcott');
+ // Temperatures: 12,14,12,14,10,16
+ expect(stats.meanTemp).toBe(13);
+ });
+
+ it('returns placeholders for an empty selection', () => {
+ expect(computeSummaryStats([])).toEqual({
+ finalGrowth: null,
+ meanTemp: null,
+ finalSurvival: null,
+ bestTreatment: '—',
+ highestSurvivalSite: '—',
+ });
+ });
+});
+
+describe('getTimeSeriesData', () => {
+ it('produces one series per site with day-level labels in date order', () => {
+ const { series, sites, unit, metricKey } = getTimeSeriesData(records, 'Growth Volume');
+ expect(metricKey).toBe('growth_volume');
+ expect(unit).toBe('predicted volume');
+ expect(sites).toEqual(['Sequim Bay', 'Westcott']);
+ expect(series.map((p) => p.date)).toEqual(['2024-06-20', '2024-08-20', '2025-10-06']);
+ expect(series.map((p) => p.label)).toEqual(['Jun 20, 2024', 'Aug 20, 2024', 'Oct 6, 2025']);
+ });
+
+ it('does not pool sites sampled on different dates', () => {
+ const { series } = getTimeSeriesData(records, 'Growth Volume');
+ const aug = series.find((p) => p.date === '2024-08-20');
+ // Westcott only: (200+300+350+450)/4 = 325
+ expect(aug.Westcott).toBe(325);
+ expect(aug.WestcottCount).toBe(4);
+ expect(aug['Sequim Bay']).toBeUndefined();
+
+ const oct = series.find((p) => p.date === '2025-10-06');
+ expect(oct['Sequim Bay']).toBe(1000);
+ expect(oct.Westcott).toBeUndefined();
+ });
+
+ it('reports survival with retained field rows and per-bag rows together', () => {
+ const { series } = getTimeSeriesData(records, 'Survival');
+ const oct = series.find((p) => p.date === '2025-10-06');
+ // Sequim: per-bag Control 70, 80 plus field Heat primed 97.7
+ expect(oct['Sequim Bay']).toBe(Math.round(((70 + 80 + 97.7) / 3) * 10) / 10);
+ expect(oct['Sequim BayCount']).toBe(3);
+ });
+});
+
+describe('getTreatmentComparisonData', () => {
+ it('uses the final assessment for growth as well as survival', () => {
+ const growth = getTreatmentComparisonData(records, 'growth');
+ const westcott = growth.find((row) => row.site === 'Westcott');
+ expect(westcott.Control).toBe(250); // 200, 300 only; June rows excluded
+ expect(westcott.ControlCount).toBe(2);
+ expect(westcott['Heat primed']).toBe(400);
+
+ const survival = getTreatmentComparisonData(records, 'survival');
+ const sequim = survival.find((row) => row.site === 'Sequim Bay');
+ expect(sequim.Control).toBe(75);
+ expect(sequim.ControlError).toBe(5);
+ expect(sequim['Heat primed']).toBe(97.7);
+ expect(sequim['Heat primedError']).toBeNull();
+ });
+});
+
+describe('getSiteComparisonData', () => {
+ it('returns a row for every requested site, with nulls when unmeasured', () => {
+ const growth = getSiteComparisonData(records, 'growth', ['Sequim Bay', 'Westcott', 'Thorndyke Bay']);
+ expect(growth).toEqual([
+ { site: 'Sequim Bay', value: 1000, error: 100, count: 2 },
+ { site: 'Westcott', value: 325, error: expect.any(Number), count: 4 },
+ { site: 'Thorndyke Bay', value: null, error: null, count: 0 },
+ ]);
+ });
+
+ it('pools temperature across the filtered period', () => {
+ const temp = getSiteComparisonData(records, 'temperature', ['Westcott']);
+ expect(temp[0]).toEqual({ site: 'Westcott', value: 13, error: 3, count: 2 });
+ });
+});
+
+describe('getSiteGeographicSummaries', () => {
+ it('summarizes each site with final growth and survival plus metadata', () => {
+ const summaries = getSiteGeographicSummaries(records, dataset.sites);
+ const westcott = summaries.find((s) => s.site === 'Westcott');
+ expect(westcott.lat).toBeCloseTo(48.582);
+ expect(westcott.finalGrowth).toBe(325);
+ expect(westcott.finalSurvival).toBe(85);
+ expect(westcott.meanTemp).toBe(13);
+ expect(westcott.recordCount).toBe(2 + 6 + 4);
+ });
+});
diff --git a/src/data/bundleFormat.js b/src/data/bundleFormat.js
new file mode 100644
index 0000000..3bcd6c2
--- /dev/null
+++ b/src/data/bundleFormat.js
@@ -0,0 +1,61 @@
+/**
+ * Decoder for the compact observation bundles written by scripts/shield_data.py.
+ *
+ * A bundle stores rows as positional arrays. `columns` names each position,
+ * columns listed in `lookups` hold an index into that column's value list, and
+ * `constants` are fields identical on every record. `year`, `month`, `quarter`,
+ * and `id` are derived here rather than shipped.
+ */
+export const BUNDLE_FORMAT = 'shield-observations/1';
+
+const MONTHS = [
+ 'Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun',
+ 'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec',
+];
+
+/** `{ year, month, quarter }` for an ISO `YYYY-MM-DD` date string. */
+export function dateFields(date) {
+ const monthIndex = Number(date.slice(5, 7)) - 1;
+ return {
+ year: date.slice(0, 4),
+ month: MONTHS[monthIndex] ?? '',
+ quarter: `Q${Math.floor(monthIndex / 3) + 1}`,
+ };
+}
+
+/**
+ * Expand a compact bundle into full observation records.
+ *
+ * @param {object} bundle parsed JSON bundle
+ * @param {string} idPrefix prefix for generated record ids, e.g. `GROW`
+ * @returns {object[]} records
+ */
+export function hydrateBundle(bundle, idPrefix) {
+ if (Array.isArray(bundle.observations)) {
+ // Legacy expanded bundle; nothing to decode.
+ return bundle.observations;
+ }
+ if (bundle.format !== BUNDLE_FORMAT) {
+ throw new Error(
+ `Unsupported bundle format "${bundle.format}" (expected ${BUNDLE_FORMAT})`
+ );
+ }
+
+ const { columns, lookups = {}, constants = {}, rows } = bundle;
+ const decoders = columns.map((column) => {
+ const values = lookups[column];
+ return values
+ ? (value) => (value == null ? null : values[value])
+ : (value) => (value === undefined ? null : value);
+ });
+
+ return rows.map((row, index) => {
+ const record = { ...constants };
+ for (let j = 0; j < columns.length; j += 1) {
+ record[columns[j]] = decoders[j](row[j]);
+ }
+ Object.assign(record, dateFields(record.date));
+ record.id = `${idPrefix}-${index}`;
+ return record;
+ });
+}
diff --git a/src/data/growthObservations.json b/src/data/growthObservations.json
deleted file mode 100644
index 0f5e4ce..0000000
--- a/src/data/growthObservations.json
+++ /dev/null
@@ -1,686276 +0,0 @@
-{
-"meta": {
-"generatedAt": "2026-08-26",
-"source": "RobertsLab growth CSV outputs",
-"studyTitle": "Crassostrea gigas individual oyster growth volume",
-"recordCount": 29836,
-"sourceRows": {
-"Thorndyke Bay": 1525,
-"Palix River/Willapa Bay": 8739,
-"Sequim Bay": 3336,
-"Westcott": 16238
-},
-"recordCounts": {
-"Thorndyke Bay": 1525,
-"Palix River/Willapa Bay": 8739,
-"Sequim Bay": 3336,
-"Westcott": 16236
-},
-"growthMetric": "Predicted oyster volume from image-derived models",
-"sourceUrls": [
-"https://raw.githubusercontent.com/RobertsLab/10K-seed-Cgigas/main/output/baywater_growth.csv",
-"https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv",
-"https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/sequim_growth.csv",
-"https://raw.githubusercontent.com/RobertsLab/polyIC-larvae/main/output/sequim_polyic_growth.csv",
-"https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/westcott_growth.csv"
-]
-},
-"sites": [
-"Palix River/Willapa Bay",
-"Sequim Bay",
-"Thorndyke Bay",
-"Westcott"
-],
-"treatments": [
-"Control",
-"Heat primed",
-"Freshwater primed",
-"Immune primed",
-"Combined stress primed"
-],
-"years": [
-"2024",
-"2025",
-"2026"
-],
-"observations": [
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-0-0",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "1",
-"growth_mm": null,
-"growth_volume": 5763.3,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-9-1",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "10",
-"growth_mm": null,
-"growth_volume": 5986.7,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-99-2",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "100",
-"growth_mm": null,
-"growth_volume": 7070.7,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-10-3",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "11",
-"growth_mm": null,
-"growth_volume": 6207.9,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-11-4",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "12",
-"growth_mm": null,
-"growth_volume": 6170.0,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-12-5",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "13",
-"growth_mm": null,
-"growth_volume": 7804.5,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-13-6",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "14",
-"growth_mm": null,
-"growth_volume": 6664.2,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-14-7",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "15",
-"growth_mm": null,
-"growth_volume": 6435.0,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-15-8",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "16",
-"growth_mm": null,
-"growth_volume": 6589.0,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-16-9",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "17",
-"growth_mm": null,
-"growth_volume": 7365.9,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-17-10",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "18",
-"growth_mm": null,
-"growth_volume": 7230.8,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-18-11",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "19",
-"growth_mm": null,
-"growth_volume": 6992.3,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
-"source_url": "https://raw.githubusercontent.com/RobertsLab/project-gigas-conditioning/main/output/goosepoint_growth.csv"
-},
-{
-"id": "GROW-PALIX-RIVER-WILLAPA-BAY-2024-06-24-1-12",
-"date": "2024-06-24",
-"year": "2024",
-"month": "Jun",
-"quarter": "Q2",
-"site": "Palix River/Willapa Bay",
-"treatment": "Control",
-"raw_treatment": "Control",
-"effort": "weekly temperature",
-"tag": "80",
-"oyster_number": "2",
-"growth_mm": null,
-"growth_volume": 5601.1,
-"growth_metric": "Predicted_Volume_Poly",
-"temperature_C": null,
-"survival_percent": null,
-"survival_source": "none",
-"growth_source": "measured-volume",
-"temperature_source": "none",
-"source_repo": "RobertsLab/project-gigas-conditioning",
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