CI failed on an unrelated PR when "seeds a package and hydrates it back
identically" passed vitest's default 5s timeout. The assertions were
fine; the suite is I/O bound and the runner was slow. Two changes.
migrate() ran every DDL statement through its own client.execute(), so
migration 1's ~30 statements each became a separate durable commit and
opening a store paid ~30 fsyncs. Batch each migration into one write
transaction instead: locally a fresh migration drops from ~8.2ms to
~5.0ms, and the gap widens as fsync gets more expensive. It also closes
a real hole -- a crash part-way could previously leave the schema
half-applied while schema_migrations recorded the migration as done,
because the statements and the bookkeeping insert were not atomic.
Then give the package a 30s testTimeout. These suites drive a real
file-backed SQLite database, so their wall time is set by the host
filesystem, not by our code. The 5s default is tuned for CPU-bound unit
tests and leaves no headroom on a contended runner.
Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
Everything the two shipped PRD phases deferred, minus what is called out below.
Storage (Phase 2)
@logicsrc/openontology gains a SQLite/Turso adapter. It hydrates the read
model at open, serves reads synchronously — a query evaluator that awaits per
triple pattern is unusable — and buffers mutations as SQL that flush() writes
in one transaction. Versioned idempotent migrations; indexes over subject,
predicate, entity-valued object, status, both time axes, aliases, and external
ids; FTS5 for label/alias search. The append-only status log is replayed on
open, so retractions, supersessions, and merge redirects survive a reopen.
REST + SSE + OpenAPI (Phase 2)
16 paths under /api/ontologies in logicsrc-web, described at
/api/ontologies/openapi and referencing the published JSON Schemas rather
than restating them. No token is read-only; a curator token can apply; an
agent token can propose and cannot apply. Idempotency-Key on mutations,
revision ETags, 409 on a stale base revision, and an SSE stream that emits
the same event objects as the JSON endpoint.
MCP (Phase 2)
OpenOntology and OpenPRD surfaces on the standards server: spec/manifest/
schema/queries and PRD spec/index as resources, 11 ontology tools and 6 PRD
tools, 7 prompts. Read-only by default; OPENONTOLOGY_MCP_WRITABLE=1 buys
proposals, never applies — the denial is the shared policy layer, not a
second rule that could drift.
Interoperability (Phase 3)
RDF/Turtle export and import of the reified profile, plus the plain triple
for asserted relationships so a consumer wanting only the accepted graph gets
one. SHACL for 5 of 7 constraint kinds; `unique` and `query` are reported as
unmapped in both the return value and the generated Turtle, because a shape
that quietly means something narrower is worse than no shape.
Source adapters (Phase 3)
CSV, JSON, YAML, NDJSON, Markdown, generic JSON HTTP, and GitHub. All produce
PROPOSED change-set operations with source, evidence selector, run id, and
confidence attached; fetch is injected so ingestion is offline and testable.
Each declares its capabilities, so "nothing was deleted upstream" is never
confused with "this adapter cannot see deletions" — none of the seven can.
TUI + explorer
Keyboard-first panels (types, entities, claims, sources, queries, change
sets, validation, audit) as plain strings that survive SSH and 60 columns;
status is a glyph and a word, never colour alone; the key bar wraps rather
than truncating. Wired as `logicsrc ontology tui`. A read-only web explorer
at /openontology/explore with entity and claim views showing status, both
clocks, confidence, sources, evidence, and append-only history — plus an
/openprd page for the companion standard.
Bugs found and fixed while testing
- the API built a new engine per request, so `explain` could never find a
resultId from a prior request; engines are now cached per role
- the TUI status bar called engine.validateOntologyPackage(), appending a
package.validated event on every repaint; it now uses the pure validator
Verification: 76 new tests (527 total across the monorepo, all passing); full
build green; the libSQL adapter is exercised against real files, the API
through its route handlers, and MCP over an in-memory transport.
Not included: PWA review/approval write flows (they need an auth story this
deployment does not have), OWL/RDFS mappings, SPARQL/Cypher/Datalog query
adapters, and Phase 4 governed actions. The compatibility matrix marks those
"planned", not "supported".
Refs: prd/0001-add-logicsrc-openontology-spec.md
Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
