Fix provider switching, fresh install defaults, and health dashboard improvements by atomantic · Pull Request #33 · atomantic/PortOS

atomantic · 2026-02-27T18:56:47Z

Summary

Fix "Provider not found" when changing default AI provider — PUT /active was caught by the wildcard PUT /:id Express route, treating "active" as a provider ID and returning 404. Added explicit PUT /active route before the wildcard. (fixes changing default AI provider to LM Studio - error #32)
Fix CoS auto-starting on fresh installs — Sample state now sets alwaysOn: false so the Chief of Staff daemon doesn't immediately queue agent tasks on new machines without configured CLIs. Also cleared the sample pending task and removed placeholder example apps from data.sample/apps.json.
Health dashboard features — Config-driven metric cards with 50+ metrics across 8 categories, Apple Health clinical records (FHIR) import, and split Blood & Body into separate Age/Blood/Body/Eyes pages.
Apple Health ZIP upload — Upload the export ZIP directly instead of manually extracting export.xml.

Test plan

All 1206 server tests pass
Client builds successfully
Verify switching default AI provider no longer returns 404
Verify fresh install with data.sample/ copies correct defaults (no example apps, CoS not auto-starting)
Verify health dashboard loads with metric categories and clinical records

Only the root package-lock.json should be committed — client/, server/, and browser/ lock files are now gitignored to reduce merge noise.

Accept Apple Health export ZIP files directly — server extracts export.xml via streaming (unzipper) without loading the full archive into memory. Remove unused meatspace TSV import (endpoint, service, tests, validation, UI).

Replace hardcoded StepsCard/HeartRateCard/HrvCard with a generic MetricCard + registry of 50+ metrics across 8 collapsible categories. Adds available metrics discovery endpoint that samples across full history to catch sparse data (e.g. Withings body composition). Deep-linkable via useSearchParams. Move Alcohol/HRV correlation to Alcohol tab. Fix units to match Apple Health's actual stored format.

…w latest metric values Parse FHIR R4 JSON files from Apple Health ZIP exports to extract lab observations (CBC, metabolic panel, lipids, thyroid) with LOINC code mapping. Non-destructive merge preserves existing manual blood test entries. Also adds latest-value fallback for health metric cards and uses Apple Health body composition data in the overview when more recent than manual entries.

Each health domain now has its own dedicated tab and sidebar entry with distinct icons, improving navigation and reducing page bloat.

) PUT /active was caught by the wildcard PUT /:id route, treating "active" as a provider ID. Added explicit PUT /active route before the wildcard. Also added error handling to handleSetActive on the client side.

- Set alwaysOn: false in sample state.json so CoS doesn't immediately spawn agents on new machines without configured CLIs - Remove example pending task from sample TASKS.md - Remove placeholder example apps from sample apps.json, keep only PortOS

Copilot

Pull request overview

This PR fixes AI provider switching by correcting an Express route collision, improves fresh-install defaults to avoid unintended Chief-of-Staff activity, and significantly expands Apple Health/MeatSpace health dashboard capabilities (ZIP upload + many more metrics + new focused pages).

Changes:

Fix provider switching (PUT /providers/active) by adding an explicit route before the wildcard provider route.
Improve Apple Health ingestion: accept ZIP uploads, expand XML metric mappings, add available/latest metrics endpoints, and add clinical records (FHIR) import into blood-tests.json.
Refactor MeatSpace UI navigation by splitting “Blood & Body” into separate Age/Blood/Body/Eyes tabs and updating overview tile routing; adjust sample data defaults for fresh installs.

Reviewed changes

Copilot reviewed 41 out of 46 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
server/services/meatspaceImport.test.js	Removed TSV import tests (feature removal).
server/services/meatspaceImport.js	Removed TSV import service implementation.
server/services/meatspaceHealth.js	Adds helper to persist blood-tests data.
server/services/appleHealthXml.js	Expands XML→metric mapping and adds batch flushing to disk.
server/services/appleHealthQuery.js	Adds sum-metric aggregation set; adds available/latest metric discovery endpoints.
server/services/appleHealthClinical.test.js	Adds unit tests for clinical (FHIR) parsing/merge logic.
server/services/appleHealthClinical.js	Implements clinical records import + merge into blood-tests.json.
server/routes/providers.js	Adds explicit `PUT /active` route to prevent wildcard capture.
server/routes/meatspace.js	Removes TSV import endpoint wiring.
server/routes/appleHealth.js	Adds ZIP upload support, clinical record extraction, and new metric discovery endpoints.
server/package.json	Adds `unzipper` dependency for ZIP import.
server/lib/meatspaceValidation.js	Removes TSV import request schema.
package.json	Bumps version to 1.17.0.
package-lock.json	Updates lockfile version metadata for 1.17.0.
ecosystem.config.cjs	Raises PM2 memory restart thresholds to 2G.
data.sample/cos/state.json	Sets `alwaysOn: false` for safer fresh installs.
data.sample/apps.json	Removes placeholder/example apps from sample state.
data.sample/TASKS.md	Clears sample pending task to avoid agent spawning on first boot.
client/src/services/api.js	Adds health metrics available/latest API helpers; removes TSV import client call.
client/src/pages/MeatSpace.jsx	Adds new tabs (Age/Body/Eyes) to MeatSpace router view.
client/src/pages/AIProviders.jsx	Avoids unhandled rejection and only updates active provider on success.
client/src/components/meatspace/tabs/OverviewTab.jsx	Uses latest Apple Health body metrics when newer; fixes tile navigation targets.
client/src/components/meatspace/tabs/ImportTab.jsx	Removes TSV import UI; allows Apple Health ZIP upload with updated instructions.
client/src/components/meatspace/tabs/HealthTab.jsx	Replaces hardcoded cards with config-driven category sections + URL params.
client/src/components/meatspace/tabs/EyesTab.jsx	Adds dedicated Eyes page for prescriptions CRUD.
client/src/components/meatspace/tabs/BodyTab.jsx	Adds dedicated Body page (composition chart).
client/src/components/meatspace/tabs/BloodTab.jsx	Narrows Blood tab to blood tests only after page split.
client/src/components/meatspace/tabs/AlcoholTab.jsx	Adds HRV correlation chart alongside alcohol chart with synced range.
client/src/components/meatspace/tabs/AgeTab.jsx	Adds dedicated Age page for epigenetic results.
client/src/components/meatspace/healthMetrics.js	Adds metric registry/config (categories, units, formatting).
client/src/components/meatspace/constants.js	Splits tab definitions and extends blood reference ranges.
client/src/components/meatspace/StepsCard.jsx	Removed legacy hardcoded metric card.
client/src/components/meatspace/HrvCard.jsx	Removed legacy hardcoded metric card.
client/src/components/meatspace/HeartRateCard.jsx	Removed legacy hardcoded metric card.
client/src/components/meatspace/MetricCard.jsx	Adds generic metric card renderer for most metrics.
client/src/components/meatspace/HealthCategorySection.jsx	Adds collapsible/lazy-loaded metric category sections.
client/src/components/meatspace/BloodTestCard.jsx	Improves blood test categorization and labeling.
client/src/components/meatspace/AlcoholChart.jsx	Exposes view changes so correlation chart can stay in sync.
client/src/components/Layout.jsx	Adds sidebar entries for new MeatSpace sub-pages.
browser/package-lock.json	Removed subproject lockfile.
.gitignore	Ignores subdirectory lockfiles; root lockfile remains tracked.
.changelog/v1.17.x.md	Adds changelog entry for v1.17.x series.
.changelog/v1.15.x.md	Adds changelog entry for v1.15.x series.
.changelog/v1.14.x.md	Adds changelog entry for v1.14.x series.

Files not reviewed (1)

browser/package-lock.json: Language not supported

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Copilot · 2026-02-27T19:06:48Z

server/routes/appleHealth.js

+          } else if (entry.path.includes('clinical_records/') && entry.path.endsWith('.json')) {
+            // Buffer clinical record JSON files (~1-5KB each)
+            const chunks = [];
+            entry.on('data', (chunk) => chunks.push(chunk));
+            entry.on('end', () => clinicalJsons.push(Buffer.concat(chunks).toString('utf-8')));
+          } else {


Clinical record JSON files are fully buffered into memory (chunks → Buffer.concat → push into clinicalJsons). A large or malicious ZIP could contain very large JSON entries or huge counts and cause high memory usage/OOM. Consider enforcing per-entry and total byte limits, and/or streaming/processing records incrementally instead of storing all JSON strings at once.

Copilot · 2026-02-27T19:06:49Z

server/routes/appleHealth.js

+    await fs.unlink(filePath);
+    filePath = xmlPath;
+    console.log(`📋 Found ${clinicalJsons.length} clinical record files in ZIP`);
+  }
+
  const result = await importAppleHealthXml(filePath, io);
-  res.json(result);
+
+  // Import clinical records if any were found
+  let clinicalResult = null;
+  if (clinicalJsons.length > 0) {
+    clinicalResult = await importClinicalRecords(clinicalJsons, io);
+  }
+
+  res.json({ ...result, ...(clinicalResult && { clinical: clinicalResult }) });


Temp file cleanup is not guaranteed on failures: after extracting ZIP you unlink the uploaded ZIP, but the extracted xmlPath is only deleted inside importAppleHealthXml on success. If XML import throws, the temp XML can be left behind in the OS temp dir. Consider wrapping the import in a try/finally that removes xmlPath (and/or the uploaded file) on error as well.

Copilot · 2026-02-27T19:06:49Z

server/services/appleHealthQuery.js

+      // Use the last point's qty as the value
+      const lastPoint = points[points.length - 1];
+      const value = lastPoint.qty ?? lastPoint.Avg ?? lastPoint.value ?? null;
+      if (value != null) {
+        result[name] = { date: dateStr, value: Math.round(value * 100) / 100 };
+        remaining.delete(name);


getLatestMetricValues returns lastPoint.qty for a metric, but XML batch flushing can create multiple aggregated points per day for sum-metrics (e.g., step_count), so the last point may be only the last batch’s subtotal. For SUM_METRICS (and potentially sleep_analysis), compute the latest value by aggregating all points in the newest day file (sum/avg as appropriate) rather than taking the last point.

Copilot · 2026-02-27T19:06:49Z

server/services/appleHealthClinical.js

+  // Count what changed
+  const newDates = merged.tests.filter(t => !existingDates.has(t.date)).length;
+  const newValues = fhirData.totalParsed;
+
+  await ensureDir(PATHS.meatspace);
+  await writeFile(BLOOD_TESTS_FILE, JSON.stringify(merged, null, 2));
+
+  const summary = {
+    clinicalRecords: jsonStrings.length,
+    labsParsed: fhirData.totalParsed,
+    labsSkipped: fhirData.totalSkipped,
+    newDates,
+    totalDates: merged.tests.length
+  };


newValues is computed but never used (const newValues = fhirData.totalParsed;). Either include it in the returned summary or remove it to avoid dead code and keep the import summary consistent with what’s actually reported.

Copilot · 2026-02-27T19:06:49Z

server/services/appleHealthClinical.js

+  '1920-8': 'sgot_ast',
+  '1742-6': 'alt',
+  '4548-4': 'hba1c',
+  '17856-6': 'hba1c',
+  '33037-3': 'anion_gap',


LOINC_TO_KEY defines the key '4548-4' more than once. Duplicate keys are silently overwritten in object literals, which is easy to miss during future edits. Consider deduplicating to a single entry (or adding a comment if intentional).

Copilot · 2026-02-27T19:06:50Z

server/routes/meatspace.js


-// =============================================================================
-// IMPORT
-// =============================================================================
-
-/**
- * POST /api/meatspace/import/tsv
- * Import TSV spreadsheet (5MB limit handled by express.json middleware)
- */
-router.post('/import/tsv', asyncHandler(async (req, res) => {
-  const { content } = validateRequest(tsvImportSchema, req.body);
-  const stats = await importTSV(content);
-  if (stats.error) {
-    throw new ServerError(stats.error, { status: 400, code: 'IMPORT_FAILED' });
-  }
-  res.json(stats);
-}));

 export default router;


This PR removes the MeatSpace TSV import API/UI (endpoint and validation/service/test removal), which is a user-visible breaking change. The PR description/test plan don’t mention TSV import removal explicitly—please confirm it’s intended and update the PR description/test plan (or changelog/upgrade notes) accordingly so reviewers/users aren’t surprised.

Copilot · 2026-02-27T19:06:50Z

client/src/components/meatspace/tabs/EyesTab.jsx

+
+        {eyeExams.length === 0 ? (
+          <div className="bg-port-card border border-port-border rounded-xl p-6">
+            <p className="text-gray-500 text-sm">No eye exam data. Import your health spreadsheet or add exams manually.</p>


Copy references the removed “health spreadsheet” import (“Import your health spreadsheet…”), but TSV import was removed in this PR. Consider updating this empty-state message to point users at the currently supported import paths (Apple Health ZIP/XML, Health Auto Export JSON, or manual entry).

Suggested change

<p className="text-gray-500 text-sm">No eye exam data. Import your health spreadsheet or add exams manually.</p>

<p className="text-gray-500 text-sm">No eye exam data. Import from Apple Health (ZIP/XML), Health Auto Export (JSON), or add exams manually.</p>

Copilot · 2026-02-27T19:06:50Z

server/routes/appleHealth.js

+        .on('close', () => {
+          if (!foundXml) return settle(reject)(new ServerError('ZIP does not contain export.xml', { status: 400, code: 'BAD_REQUEST' }));
+          // Wait briefly for XML write stream to finish if close fires first
+          if (xmlWriteFinished) return settle(resolve)();
+          const check = setInterval(() => { if (xmlWriteFinished) { clearInterval(check); settle(resolve)(); } }, 50);
+          setTimeout(() => { clearInterval(check); settle(resolve)(); }, 5000);
+        })


ZIP extraction promise resolves after 5s even if export.xml hasn’t finished writing (setTimeout(... settle(resolve) ...)). That can cause importAppleHealthXml to parse a partially written XML file and produce corrupted/partial imports. Consider awaiting the XML write stream completion deterministically (e.g., using stream/promises.finished/pipeline) and rejecting on timeout instead of resolving, so the import only starts once the file is fully written.

atomantic added 7 commits February 26, 2026 22:47

fix: remove sub-directory package-lock files from git tracking

bbeab93

Only the root package-lock.json should be committed — client/, server/, and browser/ lock files are now gitignored to reduce merge noise.

feat: split Blood & Body into separate Age, Blood, Body, and Eyes pages

d317b78

Each health domain now has its own dedicated tab and sidebar entry with distinct icons, improving navigation and reducing page bloat.

fix: resolve "Provider not found" when changing default AI provider (#32

39e29e0

) PUT /active was caught by the wildcard PUT /:id route, treating "active" as a provider ID. Added explicit PUT /active route before the wildcard. Also added error handling to handleSetActive on the client side.

Copilot AI review requested due to automatic review settings February 27, 2026 18:56

Copilot started reviewing on behalf of atomantic February 27, 2026 18:57 View session

atomantic merged commit d7bcba3 into main Feb 27, 2026
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Copilot AI reviewed Feb 27, 2026

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Fix provider switching, fresh install defaults, and health dashboard improvements#33

Fix provider switching, fresh install defaults, and health dashboard improvements#33
atomantic merged 7 commits intomainfrom
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	<p className="text-gray-500 text-sm">No eye exam data. Import your health spreadsheet or add exams manually.</p>
	<p className="text-gray-500 text-sm">No eye exam data. Import from Apple Health (ZIP/XML), Health Auto Export (JSON), or add exams manually.</p>

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atomantic commented Feb 27, 2026 •

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