Implements phase A of the DESIGN_clustering.md design: a Dirichlet-process
mixture of per-position categoricals over the first 32 header bytes (257-symbol
alphabet) that clusters the binary/ pile by file format, plus signature
extraction and promotion nomination. All base-Julia (a Lanczos loggamma keeps
the Dirichlet-multinomial marginal dependency-free).
- src/cluster.jl: header_symbols feature extraction, collapsed Gibbs sampler
(phase A), sequential CRP-predictive assignment (phase B core), signatures/
promotion, and ARI/V-measure calibration metrics.
- bin/cluster_calibrate.jl: grid-tunes hyperparameters against magic-collapsed
ground truth and cross-checks a model-free NCD (gzip) baseline.
- FS_CLUSTER_*/FS_PROMOTE_* config knobs; wire cluster.jl into the module.
- Tests for the three DESIGN §10 assertions plus the model primitives.
Calibrated defaults (n=32, alpha=1.0, beta=0.1) recover known formats at
ARI 0.77 (0.885 excl. tar); docx+zip and the ELF family merge correctly and the
NCD baseline agrees. DESIGN §11 records the results and three assumptions the
data corrected (tar/ELF header-zero merge, the cold-start seeding deadlock, and
the Bernoulli signature / Occam-penalized restart scoring).
Text files sorted by stage 3 now flow onto a new work queue and worker
pool that enrich them with natural language (Languages.jl LanguageDetector:
name, ISO 639-3 code, confidence) and programming language (github-linguist),
writing a .meta.json sidecar to data/text_done/ like the stage-2 known-file
pipeline.
github-linguist reads the git blob of a path inside a repo, so untracked
data/ files are copied to /tmp (outside any repo, name preserved for
extension heuristics) before detection. Programming-language lookup is
best-effort (startup warning if missing, degraded/null on failure);
natural-language failure yields a degraded sidecar, not a quarantine.
Factored exiftool's timeout-kill into shared run_with_timeout and the
durable sidecar-first commit into commit_enriched!, both reused by stage 4.
Recovery re-drives data/text/; graceful drain closes the text queue after
its stage-3 producers finish.
Address code-review findings on the metadata pipeline:
- finalize_known! now fsyncs the sidecar bytes before the rename and
fsyncs done/ after, so the "file in done/ implies sidecar present"
invariant holds across power loss, not just process crashes. The
docstring previously claimed an fsync the code never performed.
- run_exiftool's timeout escalates SIGTERM -> (2s grace) -> SIGKILL, so
an exiftool that ignores SIGTERM can't pin a worker forever on
wait(proc). Previously the timeout sent only SIGTERM.
- Add test/ (48 tests) covering the correctness-critical paths:
sanitize_filename, normalize_metadata, degraded build_metadata,
real exiftool extraction, finalize_known! end-to-end, recover_dir!.
Each uploaded file is scored by a fixed-structure neural net that labels it
known (resembling the training set) or unknown — novelty detection over the
first 16 + last 16 bytes (scaled to [0,1]), Dense(32->64->16->2), argmax.
- src/model.jl: shared architecture + byte->feature mapping (trainer + server)
- src/classify.jl: load committed artifact, classify a file at inference
- bin/train.jl: offline trainer, 1:1 blended negatives (random + grab-bag),
seeded 80/20 split, writes model/classifier.jld2
- worker: classify (annotate-only) and log classification=known|unknown
- config: FS_MODEL_PATH; server fails fast if the artifact is missing
- deps: Lux, JLD2, Optimisers, Zygote
REST endpoint (Oxygen.jl POST /upload, multipart) that spools uploaded
files to disk, enqueues lightweight references onto a bounded thread-safe
work queue, and hands off immediately (202 + job IDs; 503 when full). A
configurable pool of worker threads pulls jobs off the queue, logs the
received filename (placeholder for real processing), and moves files to
done/ on success or failed/ on error.
- Queue behind an enqueue!/dequeue!/close! seam for a future RabbitMQ swap
- Startup recovery: re-enqueues leftover files in spool/
- Graceful drain on SIGINT and SIGTERM (via atexit)
- Env-var config; filenames sanitized + UUID-prefixed on disk
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
