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>
Implements OpenPRD 0001 through Phase 0 (specification, schemas, example,
docs surface) and Phase 1 (local engine, CLI, conformance tests).
Schemas (17 contracts, JSON Schema Draft 2020-12, additionalProperties:false)
manifest, namespace, entity-type, property, relationship-type, constraint,
query, action, entity, claim, source, evidence, changeset, review, approval,
event, package — registered in @logicsrc/validators and exported from
@logicsrc/schemas under https://logicsrc.com/schemas/openontology/.
@logicsrc/openontology
- canonical JSON + sha256 package digests; YAML, JSON, NDJSON, and inline
authoring all compile to the same bytes, so digests are authoring-agnostic
- id profile: compact / IRI / urn with one canonicalization rule, prefix
bound by a Namespace object so IRIs reverse unambiguously
- validation: schema, graph (domain/range, datatypes, dangling refs),
provenance (source-or-firstParty, agent runId, derivation inputs), policy
(excerpt limits, licensing, visibility, staleness) and declared
constraints; four severities, stable codes, text/json/yaml/markdown
- portable triple-pattern query AST: multi-hop, 14 operators, asOf and
recordedAsOf, per-status filtering, distinct/order/limit, explanation
mode, and enforced depth/binding/row limits
- append-only store: claims are immutable; dispute/retract/supersede append
status transitions and the effective status is the latest one
- change sets: 9 operations, atomic pre-flight, conflict detection on stale
base revisions, semantic diff with duplicate-identity warnings and
affected-query deltas, per-operation reviewer decisions
- policy: agents propose but can never apply — the denial keys on actor
type, so every scope plus high confidence plus --yolo still cannot apply;
merges need approval, bulk retractions need two, undeclared action side
effects are denied
- JSON-LD 1.1 export/import with PROV-O aliases and lossy-field reporting
- pluggable signature envelope with a jws-ed25519 reference profile and a
fail-closed trust policy
CLI: logicsrc ontology init|validate|lint|build|inspect, entity, claim, query,
changeset, import, export, audit. Reads take --format, writes default to a
proposal, exit codes are stable for CI.
Example: examples/openontology/ethereum-ecosystem — 12 entity types, 17
relationship types, 63 entities, 169 claims, 25 sources, 31 evidence records,
5 saved queries, every claim lifecycle state, and a pending merge proposal.
All data is fictional; the directory is removable without affecting any core
test.
Docs: docs/openontology{,-governance,-interoperability}.md, a real
/openontology route, homepage + nav + sitemap entries, and a root README
section.
Verification: 112 new tests; full monorepo build and every workspace test
pass; conformance bundle (18 valid + 13 invalid fixtures) runs against the
published schemas alone; Node.js 25 and Bun 1.3 produce byte-identical
digests, revisions, event trails, and query results.
Not included (later PRD phases): MCP resources, REST/SSE, Turso adapter, TUI
and PWA surfaces, RDF/SHACL mappings, source adapters, governed actions.
Refs: prd/0001-add-logicsrc-openontology-spec.md
Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
