1516684bbb
Enable roadmap R-A (GROBID reference extraction) end-to-end and run it against local Jetson infra instead of a Mac/Rosetta emulation. Backfill: - Add scripts/ra_grobid_backfill.py: references-only, idempotent citation backfill (dry-run default). Deliberately not ingest_paper(source_path=pdf), which re-OCRs and replaces the DQ-3-clean .txt chunks; this touches only the citations table (ON CONFLICT DO NOTHING). 7 tests. - Make extract_references timeout configurable (large theses exceed the 60s default, especially against a slower GROBID). Jetson infra: - Bump grobid/grobid 0.8.2 -> 0.9.0-crf. The -crf tag is the only GROBID variant published as an arm64 multi-arch manifest; every 0.8.x tag and the full deep-learning image are amd64-only, which is why GROBID never ran on the aarch64 Jetson. Enable the 4g memory cap + init/ulimits per GROBID docs. - Add docs/infra/grobid-jetson.md runbook: arm64 image rationale, the two host prerequisites (docker-group membership + the Compose v2 CLI plugin, both missing on the Jetson), service-scoped deploy, and the GET /api/isalive check. Verified live 2026-06-17: native arm64 pull, isalive=true, end-to-end extract_references on lutz-2024-thesis.pdf = 116 refs (101 with DOI/arXiv). docs(audit): mark R-A core done (citing coverage 27/29 -> 29/29; edges 920 -> 1022). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
58 lines
2.1 KiB
YAML
58 lines
2.1 KiB
YAML
# Paper knowledge base: Provenance + Citation graph + Semantic search
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# A single Postgres instance (pgvector) covers all three layers.
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# GROBID parses references / structure from PDFs without an arXiv source.
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#
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# Quick start:
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# docker compose up -d
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# psql "${DATABASE_URL}" # see .env.example for default value
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services:
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db:
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image: pgvector/pgvector:pg17 # official pgvector image
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container_name: papers-db
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environment:
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POSTGRES_DB: papers
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POSTGRES_USER: researcher
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POSTGRES_PASSWORD: change_me # change before production use
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ports:
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- "5432:5432"
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volumes:
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- pgdata:/var/lib/postgresql/data
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# schema.sql is executed automatically on first start:
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- ./schema.sql:/docker-entrypoint-initdb.d/01-schema.sql:ro
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healthcheck:
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test: ["CMD-SHELL", "pg_isready -U researcher -d papers"]
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interval: 10s
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timeout: 5s
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retries: 5
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restart: unless-stopped
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grobid:
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# CRF-only image: sufficient for reference extraction (/api/processReferences)
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# and ~500MB vs ~10GB for the full deep-learning variant.
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#
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# The `-crf` tag is also the ONLY GROBID variant published as a multi-arch
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# manifest that includes linux/arm64 — the full image (grobid/grobid:0.9.0)
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# and every 0.8.x tag are amd64-only. So this is what lets GROBID run
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# *natively* on the aarch64 Jetson (no slow/RAM-heavy qemu emulation). arm64
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# builds start at 0.9.0-crf; there is no arm64 0.8.x.
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# Deploy + docker-permission fix: docs/infra/grobid-jetson.md
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image: grobid/grobid:0.9.0-crf
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container_name: papers-grobid
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ports:
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- "8070:8070"
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init: true # reap zombie children (GROBID docs recommend --init)
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ulimits:
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core: 0 # disable core dumps (GROBID docs: --ulimit core=0)
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restart: unless-stopped
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# GROBID is RAM-hungry; cap usage on the constrained Jetson (Orin Nano, 8GB
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# RAM shared with Postgres). 3GB suffices for references; 4g leaves headroom.
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# Honored by `docker compose up` under Compose v2 (no swarm needed).
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deploy:
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resources:
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limits:
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memory: 4g
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volumes:
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pgdata:
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