* feat(drug-reference): offline FDA drug labels, conditions, and remedies
Adds an offline medical-reference feature with three coupled layers:
- Drug Reference: full-text search over openFDA drug-label indications,
a detail page per label, and a side-by-side single-drug comparison view.
A two-phase background pipeline downloads the openFDA label parts to the
storage volume (resumable) and ingests them into the search table.
- Conditions ("When to use what"): a curated spine of first-aid situations
that maps each situation to matching OTC drugs, each linking back to its
Drug Reference detail page.
- Curated remedies: hand-authored natural and home-remedy entries drawn from
US-government public-domain sources (NCCIH, CDC, MedlinePlus, FDA), shown
with their source links and the same safety disclaimers as the rest of the
feature.
The drug-reference and conditions layers are intentionally coupled: the drug
detail page shows the situations a drug treats, and the conditions controller
reads the same drug_labels table.
Safety surfaces ship as written. The amber SafetyBanner ("informational only,
not medical advice, not an FDA endorsement, not a drug-interaction checker, in
an emergency call emergency services") renders on the condition pages and the
search page; the detail and comparison pages carry their own "not a cross-drug
interaction checker" callout; and every page carries the openFDA CC0 source
citation and no-FDA-affiliation footer.
Wiring on this branch:
- start/routes.ts: the /drug-reference and /conditions page GETs plus their
/api/* groups.
- commands/queue/work.ts: the drug-download and drug-ingest queues, both at
concurrency 1. The two drug queues get a per-queue stall override
(lockDuration 1_800_000, maxStalledCount 3) because each part is one long
stream; every other queue keeps the existing 300000 default.
- inertia/pages/home.tsx: Drug Reference and "When to use what" tiles. The
icon and display_order are a starting point, open to change.
- types/kv_store.ts: the two drugReference.* keys the pipeline reads and writes.
- package.json: yauzl and stream-json (plus their @types), used by the ingest
job to stream the label JSON out of the downloaded zips.
The app reads the conditions and remedy data from the compiled TS constants in
app/data/; the repo-root collections/*.json files are the browseable mirrors.
The natural-remedies standalone test reads collections/natural_remedies.json to
assert the two stay in sync, so that file is also a test fixture.
The four standalone tests pass (drug_interactions, drug_ingest_status,
conditions, natural_remedies). tsc reports no errors in the feature code.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* chore(drug-reference): drop a fork-internal comment reference
* fix(drug-reference): address review — defer FULLTEXT, fallback remedies prop, strip fork refs
- migration: wrap the FULLTEXT ALTER in this.defer so it runs after the
deferred createTable (was silently swallowed, index never created)
- controller: add remedies:[] to the index() error fallback (required prop)
- strip fork-internal issue/spec references from ported comments
- tsconfig: exclude tests/standalone (node --experimental-strip-types only)
- correct the varchar(768) byte-math comment; extend remedy-spine test
* fix(drug-reference): make the interaction comparison readable at five drugs
The comparison view laid its columns out on an equal-fraction CSS grid
(repeat(N, minmax(0, 1fr))), so each added drug shrank every column; at the
five-drug maximum the FDA interaction text was squeezed into unreadable slivers.
Lay the columns out with flex instead: full-width and stacked on phones, then
fixed-width columns that scroll sideways from the sm: breakpoint up, so they
never shrink below a readable width. Theme the columns with the same palette as
the rest of the page (they were on stock gray), and give the headers a fixed
min-height so columns line up when drug names wrap.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* feat(collections): route a 'dataset' tier resource to the drug pipeline
Add an optional `type` discriminator to SpecResource ('zim' | 'dataset',
absent == 'zim'), so the tier installer can carry a DB-ingested resource
alongside ZIM files. ZimService.downloadCategoryTier branches on it: a
'dataset' resource dispatches the existing FDA download+ingest pipeline
instead of RunDownloadJob, guarded against duplicate dispatch by the drug
ingest status. Every existing manifest entry has no `type` and keeps the
exact ZIM path.
Widen InstalledResource.resource_type to include 'dataset' and exclude
dataset rows from the ZIM/map catalog-update scan (datasets aren't
filename-versioned; their freshness path is separate). No dataset rows are
written yet: the InstalledResource 'dataset' row on ingest-ready, the
manifest entry, install-gating, and the downloads-aggregator integration
are follow-up commits.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* feat(drug-reference): rework into an opt-in medicine-standard tier dataset
Reshapes the offline FDA drug reference from a built-in feature into curated
content installed by selecting the Medicine / Standard tier, per maintainer
direction.
- install-state: the ingest writes an installed_resources 'dataset' row on
ready (version = the openFDA export_date), threaded installer to download to
ingest; the tier-status math and the home-tile gate read it. Manual ingests
write no row, so install-state stays tied to the curated path.
- manifest: declare the dataset in the medicine-standard tier (runtime fetches
the remote manifest, so this also needs to land upstream).
- install-gating: the drug-reference home tiles render only when installed.
- uninstall: DrugReferenceService.uninstall() stops the two drug queues, deletes
the on-disk parts, truncates drug_labels (schema kept), clears the KV markers,
and drops the install row. Best-effort, logged, scoped to drug data only.
- downloads: the download phase reports the canonical {percent, downloadedBytes,
totalBytes} shape as one drug-data card in the Active Downloads aggregator with
cancel/remove; the heavy ingest stays in the IngestStatus surface with an
Indexing handoff on the card.
- auto-update: a daily DrugAutoUpdateJob compares the manifest export_date and
re-downloads when newer, gated on installed + no active job.
typecheck clean; the drug standalone suites pass. Three points are flagged in
code for the maintainer: the InstalledResource 'dataset' approach, the tier
home, and the export_date string format.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* fix(downloads): keep the drug download card live across all parts
The Active Downloads card filtered to the deterministic jobId, but the
download's continuations run under auto-generated jobIds (only part 0 uses the
deterministic one). So the card tracked part 0 and then vanished while parts
2..N kept downloading. The queue is concurrency 1, so collapse to whichever
single part is in flight and report the deterministic jobId: one card tracks
aggregate progress through the whole download and cancel/remove still routes.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* feat(drug-reference): co-locate a persistent safety note with affirmative remedy guidance
Add RemedySafetyNote at the head of every natural-remedy section — the two on
Drug Reference and the one on "When to use what" — so the "informational only,
not medical advice, seek real medical care in an emergency" framing appears with
the guidance itself, not only in the page-top banner. Replaces the terse
per-section caveat with the same amber alert language as SafetyBanner.
Addresses the upstream #1040 review request that the disclaimer be unmistakable
and present wherever affirmative self-care guidance appears, not a one-time banner.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* fix(drug-reference): fold dataset freshness into the content-auto-update path
The drug dataset auto-updated on its own daily cron that ignored the
contentAutoUpdate.* master switch, so it would refresh even with content
auto-update turned off, and it didn't ride the content-update path the way
ZIMs and maps do.
Move the export_date freshness/apply orchestration onto
DrugReferenceService.attemptAutoUpdate(), add
ContentAutoUpdateService.attemptDrugDataset() gated on the same enabled +
window config, and have the hourly ContentAutoUpdateJob drive both. Retire
the standalone DrugAutoUpdateJob. The ZIM/map attempt() path is unchanged.
Addresses the upstream #1040 request to wire the openFDA export_date check
into the content updater so the dataset updates alongside ZIMs and maps.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* feat(drug-reference): strengthen the remedy note to consult a clinician before combining with meds
Widen the affirmative-remedy safety note from "talk to a clinician before use"
to explicitly cover using a remedy AND combining one with a medication the user
already takes — the interaction case is the higher-risk path for an off-grid
user self-treating.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* feat(drug-reference): gate affirmative remedy content behind an off-by-default flag
Add drugReference.remediesEnabled (default off), independent of the tier
install. When off, the server emits no remedy data at any boundary — the
drug-reference page prop, conditions show, and the /api/conditions/drugs
situation search — and the "Natural" filter is hidden, so installing the
medicine-standard tier lights up the verbatim FDA label search and the
condition-to-OTC matching but not the hand-authored self-care and herbal
sections. No user-facing toggle: it is flipped on after a clinician content-pass.
Implements the upstream #1040 split-by-risk request: the regulated label content
ships with the tier; the authored remedy guidance stays gated until sign-off.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: Jake Turner <52841588+jakeaturner@users.noreply.github.com>
* fix(rag): add proper .docx text extraction via mammoth
.docx files were classified as plain text and routed through raw-text
extraction (extractTXTText). Since .docx is a ZIP archive containing XML,
this produced garbage content in the Knowledge Base — XML tags and binary
noise instead of the actual document text.
Adds a dedicated 'docx' file type (split out of the generic 'text' bucket
in determineFileType) and a mammoth-based extractor that parses the
document XML properly.
* fix: clean up package-lock.json diff
* chore(deps): pin mammoth version
---------
Co-authored-by: John Cortright <jcortright@zscaler.com>
Co-authored-by: jakeaturner <jturner@cosmistack.com>
BullMQ instantiates a fresh ioredis client per Queue/Worker when handed a
plain {host, port} config object, and under sustained ZIM ingestion the
embed pipeline leaked ~1 client/sec until Redis maxclients was exhausted.
Pass a single shared ioredis instance (maxRetriesPerRequest: null, as
required by BullMQ) so all queues and workers reuse one client pool.
Workers still duplicate the connection once for their blocking client,
which is expected and bounded.
Closes#885
Correct package metadata and documentation accuracy:
- Set license to Apache-2.0 in package.json, admin/package.json and both
lockfiles (project has been Apache-2.0 since #197; metadata still said ISC)
- Replace the placeholder root package.json description with a real one
- Remove the dead README "Troubleshooting Guide" link (TROUBLESHOOTING.md
does not exist; FAQ.md already has its own entry)
- Fix README typos: "harware", "LLM's", "of of", "uses cases"
Carries forward the worthwhile fixes from #849 by @aqilaziz, minus the
version bump that conflicted with the current release line.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Replace literal string matching with ipaddr.js parsing
so equivalent encodings of 169.254.169.254
(::ffff:169.254.169.254, ::ffff:a9fe:a9fe,fully-expanded forms)
and fd00:ec2::254 are all rejected.
Add comprehensive benchmarking capability to measure server performance:
Backend:
- BenchmarkService with CPU, memory, disk, and AI benchmarks using sysbench
- Database migrations for benchmark_results and benchmark_settings tables
- REST API endpoints for running benchmarks and retrieving results
- CLI commands: benchmark:run, benchmark:results, benchmark:submit
- BullMQ job for async benchmark execution with SSE progress updates
- Synchronous mode option (?sync=true) for simpler local dev setup
Frontend:
- Benchmark settings page with circular gauges for scores
- NOMAD Score display with weighted composite calculation
- System Performance section (CPU, Memory, Disk Read/Write)
- AI Performance section (tokens/sec, time to first token)
- Hardware Information display
- Expandable Benchmark Details section
- Progress simulation during sync benchmark execution
Easy Setup Integration:
- Added System Benchmark to Additional Tools section
- Built-in capability pattern for non-Docker features
- Click-to-navigate behavior for built-in tools
Fixes:
- Docker log multiplexing issue (Tty: true) for proper output parsing
- Consolidated disk benchmarks into single container execution
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Jake Turner
caweis
just-jbc
jakeaturner
Henry Estela
Lorenzo Galassi
Chris Sherwood
dependabot[bot]
arn6694
orbisai0security