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kettly1260

scifinder-route-mcp

by kettly1260
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scifinder-route-mcp

NAS-hosted MCP server for indexing and searching reaction-step-level synthesis routes from local SciFinder exports. It is designed to run long-term on Docker/NAS with a read-only inbox, durable SQLite queue fallback, optional external OCR/LLM/vector/parser/structure-recognition APIs, and an operational Admin Web UI for trusted LAN/VPN deployments.

GHCR visibility note: if anonymous pull fails, open GitHub → Packages → scifinder-route-mcp → Package settings → Change visibility → Public. The compose file is already configured for ghcr.io/kettly1260/scifinder-route-mcp:latest.

Quick Start With Prebuilt Image

The published Docker image targets both linux/amd64 and linux/arm64.

git clone https://github.com/kettly1260/scifinder-route-mcp.git
cd scifinder-route-mcp
cp .env.example .env
mkdir -p nas-data nas-inbox
docker compose -f docker-compose.image.yml up -d

Then open:

Admin Web UI: http://<nas-host>:8001/
MCP HTTP:     http://<nas-host>:8000/mcp
Legacy SSE:   http://<nas-host>:8000/sse

Put SciFinder exports into nas-inbox, then click Scan Inbox in the Admin Web UI or call the MCP scan_inbox tool. Supported import formats are .pdf, .rtf, .rdf, .html, .htm, .mhtml, .mht, .md, .markdown, and .txt. The image compose file uses image: only and does not build locally.

Do not expose the Admin Web UI directly to the public internet. Use a trusted LAN/VPN or a reverse proxy with TLS and authentication. The Python default Admin bind address is 127.0.0.1; the Docker compose profiles explicitly bind 0.0.0.0 for NAS access.

Related MCP server: scholar-toolkit-mcp

Local Build Deployment

docker compose up -d --build

Persistent paths:

./nas-data  -> /data
./nas-inbox -> /inbox (read-only in the container)
./nas-data/uploads -> /data/uploads (HTTP upload and sidecar staging)

Parsing is asynchronous in the NAS profile. Jobs are stored durably in SQLite; after a container restart, interrupted running jobs are re-queued. Poll get_parse_job_status or list_parse_jobs until completion.

Environment and Runtime Config

Copy .env.example to .env. Docker-level settings such as published ports, volumes, container network, and restart policy belong in .env/Compose only. The Admin Web UI never edits Docker files and never controls host Docker.

Hot application config is read from /data/config.yaml; copy config.example.yaml to ./nas-data/config.yaml if desired. Hot-reloadable sections include:

server.async_jobs, server.max_workers, server.storage_backend
queue.backend, queue.redis_url
security.allow_external_paths, security.token, security.users
ingest.scan_extensions, ingest.upload_extensions, ingest.upload_max_bytes,
ingest.reject_file_type_mismatch, ingest.extract_visual_evidence
integrations.*
extraction.llm_schema_version, extraction.llm_prompt_profile, extraction.llm_cost_limit_usd
thresholds.verification_confidence_threshold
retention.evidence_retention_days, retention.cache_retention_days
security.upload_av_scan_enabled, security.upload_av_engine,
security.upload_av_endpoint, security.upload_av_fail_closed

Use MCP tools get_config, update_config, validate_config, and reload_config, or use the Admin Web UI.

MCP Transport

Docker deployments default to adaptive MCP transport mode:

SCIFINDER_ROUTE_TRANSPORT=auto
SCIFINDER_ROUTE_MCP_PATH=/mcp
SCIFINDER_ROUTE_SSE_PATH=/sse

In auto mode, the same container and port expose both MCP endpoints:

http://<nas-host>:8000/mcp  Streamable HTTP for modern MCP clients
http://<nas-host>:8000/sse  Legacy SSE for older MCP clients

/mcp handles MCP JSON-RPC requests such as initialize, tools/list, and tools/call; GET /mcp behavior is provided by FastMCP according to the MCP Streamable HTTP transport. /sse is retained for older clients that have not moved to Streamable HTTP.

For debugging or strict compatibility, force a single transport explicitly:

SCIFINDER_ROUTE_TRANSPORT=http
SCIFINDER_ROUTE_MCP_PATH=/mcp

or:

SCIFINDER_ROUTE_TRANSPORT=sse
SCIFINDER_ROUTE_SSE_PATH=/sse

Admin Web UI

The Admin Web UI provides operational controls for:

- health/status cards and mounted storage diagnostics
- token-protected config changes
- queue status, recent jobs, failed-job retry
- HTTP upload endpoint for sidecar/client upload
- LLM endpoint/model/enable toggle, schema version, prompt profile, cost limit
- embedding endpoint/model, vector rebuild, vector index status and errors
- OCR endpoint/model, OCR backlog status
- document parser endpoint/model, parser fallback and endpoint health
- structure recognition endpoint/model health
- PostgreSQL URL/backend status with SQLite fallback
- DOI low-confidence queue count
- evaluation latest metrics
- SQLite backup, retention dry-run cleanup, NAS storage usage
- compound registry count and search via MCP

Secret fields in the UI are not prefilled. Leaving token, Redis URL, or PostgreSQL URL blank preserves the current value; entering a value replaces it. Docker-owned settings such as published ports, volume mounts, and container networks remain in .env/Compose.

MCP Tools

Implemented tools:

health_check
get_config
update_config
validate_config
reload_config
scan_inbox
register_document
upload_document
upload_document_content
get_parse_job_status
list_parse_jobs
retry_parse_job
retry_failed_jobs
search_reaction_steps
get_reaction_step
get_reaction_provenance
record_doi_verification
reparse_document
export_evaluation_set
compute_evaluation_metrics
get_evaluation_status
rebuild_vector_index
get_vector_index_status
semantic_search_reaction_steps
search_compounds
get_compound
merge_compounds
search_by_smiles
recognize_structure_image
backup_database
get_storage_usage
cleanup_evidence_cache
test_integration_endpoint
list_export_batches
get_export_batch
unlink_document_from_batch

Feature Matrix

Area

Status

Notes

Docker/NAS adaptive MCP service

Implemented

Default auto mode exposes /mcp Streamable HTTP and /sse legacy SSE on the same port.

Single-transport override

Implemented

Set SCIFINDER_ROUTE_TRANSPORT=http or sse to expose only one transport.

GHCR multi-arch image workflow

Implemented

linux/amd64, linux/arm64. GHCR package visibility may need manual public setting.

Read-only inbox scanning

Implemented

/inbox mounted read-only.

HTTP upload staging

Implemented

POST /api/upload writes to /data/uploads; hash dedupe supported.

Sidecar watcher

Implemented

scifinder-route-sidecar polling CLI uploads stable files.

Durable queue

Implemented

SQLite queue is default; restart recovery and retry tools. Redis is optional/degraded via config status, not required.

SQLite storage

Implemented

Source documents, jobs, reaction steps, provenance, DOI verification, vector rows, compounds, metrics.

PostgreSQL backend

Runnable degraded integration

SCIFINDER_ROUTE_BACKEND=postgres tests connectivity and reports status; SQLite remains active fallback unless a Postgres adapter is added for a deployment.

pgvector

Optional/degraded

SQLite stores embeddings as JSON and cosine-searches them; Postgres/pgvector reports endpoint/backend status.

PDF/HTML/MHTML/text parsing

Implemented

Built-in parser remains fallback.

External document parser

Implemented

/parse JSON adapter plus built-in MinerU and PaddleOCR-VL adapters; provider chains fall back unless disabled.

OCR worker

Implemented adapter

/ocr JSON adapter plus built-in MinerU and PaddleOCR-VL adapters for image-only PDFs/low-text docs; errors are job errors, not service crashes.

Rule extraction

Implemented

Candidate blocks and structured fields.

LLM JSON structuring

Implemented adapter

OpenAI-compatible /chat/completions; strict JSON; invalid responses fall back to rule fields with metadata error.

Embedding/vector index

Implemented adapter

OpenAI-compatible /embeddings; rebuild/status/semantic search tools.

Compound registry

Implemented

CAS/SMILES/InChIKey text extraction, alias registry, reaction roles; RDKit optional.

Image structure recognition

Implemented adapter

/recognize adapter creates low-confidence image candidates; does not overwrite text evidence.

Multi-user authorization

Implemented

viewer, operator, admin roles via SCIFINDER_ROUTE_USERS or config users. Legacy single token maps to admin.

Evaluation metrics

Implemented

JSONL gold-set metrics and latest metric status.

Backup/retention

Implemented

SQLite backup, storage usage, evidence/cache cleanup dry-run.

Endpoint health checks

Implemented

LLM, embedding, OCR, parser, structure recognition, Postgres.

External API Schemas

All external services are optional. If a service is not configured or fails, the server returns a degraded/skipped/error status instead of crashing the process.

Embedding endpoint: POST <endpoint>/embeddings

{"model":"bge-m3","input":["text"]}

Expected response can be OpenAI-like:

{"data":[{"embedding":[0.1,0.2]}]}

LLM endpoint: POST <endpoint>/chat/completions, OpenAI-compatible. The assistant content must be strict JSON with reaction-step fields.

OCR endpoint: POST <endpoint>/ocr

{"model":"mineru-layout","file_path":"/data/uploads/file.pdf"}

Expected response:

{"text":"OCR text", "confidence":0.85}

Document parser endpoint: POST <endpoint>/parse

{"model":"parser-name","file_path":"/data/uploads/file.pdf"}

Expected response:

{"file_type":"pdf","title":"...","doi":"10....","chunks":[{"text":"...","page_number":1,"parser_name":"external","parser_version":"1"}]}

Built-in document OCR/parser providers:

  • paddleocr_vl: submits the local file as multipart to an AI Studio PaddleOCR-VL job endpoint such as https://paddleocr.aistudio-app.com/api/v2/ocr/jobs, polls the job, and reads the provider result JSON.

  • mineru: submits the local file as multipart to <endpoint>/file_parse with return_md=true, then imports returned Markdown/text into parsed chunks.

Provider fallback chains can be configured with single-provider compatibility fields or ordered lists:

integrations:
  ai_providers:
    - id: paddleocr
      name: PaddleOCR AI Studio
      format: paddleocr_vl
      endpoint: https://paddleocr.aistudio-app.com/api/v2/ocr/jobs
      api_key: ${PADDLEOCR_TOKEN}
      enabled_models: [PaddleOCR-VL-1.6]
    - id: mineru
      name: MinerU
      format: mineru
      endpoint: https://mineru.example/api
      api_key: ${MINERU_TOKEN}
      enabled_models: [mineru]
  ocr_provider_ids: [paddleocr, mineru]
  document_parser_provider_ids: [mineru, paddleocr]
  document_parser_fallback: true

Structure recognition endpoint: POST <endpoint>/recognize

{"model":"decimer","image_path":"/data/evidence/page1.png"}

Expected response:

{"structures":[{"smiles":"CCO","confidence":0.7}]}

Sidecar Watcher

Create sidecar.yaml on a client machine:

watch_dir: /path/to/scifinder/exports
server_url: http://nas-host:8001
token: change-me
include_patterns:
  - "*.pdf"
  - "*.html"
settle_seconds: 3
upload_mode: http
poll_seconds: 2

Run:

scifinder-route-sidecar sidecar.yaml

The sidecar polls by default and does not require watchdog, making it suitable for Windows/macOS/Linux clients.

Authorization

Legacy single-token mode:

SCIFINDER_ROUTE_TOKEN=change-me

Multi-user token mode:

SCIFINDER_ROUTE_USERS=alice:viewer-token:viewer,bob:operator-token:operator,root:admin-token:admin

Roles:

viewer   search/read/status
operator scan/reparse/retry/vector/evaluation/integration tests
admin    config/backup/cleanup/secret operations

Development

python -m pytest -q

Optional Docker check:

docker compose build
docker compose -f docker-compose.image.yml config
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