OKFgraph

Ladybug-backed knowledge graph with ONNX-optimized Jina v5 embeddings, multimodal image ingestion, delta-aware incremental imports, and schema migration.

Architecture: architecture.md v5.9 — all 16 gaps CLOSED.

OKFgraph is a Python library and CLI tool for building, querying, and managing knowledge graphs from Markdown/OKF documents. It combines graph traversal, hybrid semantic search, chunk-level retrieval, and — in v5.1 — delta detection with safe purge of deleted concepts into a single SQLite-backed system.

Features

Category	Features
Embeddings	ONNX-optimized Jina v5 text model, SentenceTransformer omni model (lazy-loaded), Matryoshka truncation (32–1024 dims, default 512), numpy-only post-processing (no torch)
Search	Hybrid RRF fusion (vector + FTS), graph traversal, chunk-level search with RRF, graph-aware reranking (hub scores), context expansion, direct lookup, image search via unified index
Storage	LadybugDB — graph + vector + full-text search in a single SQLite file
Images	Three ingestion modes (`text` / `optional` / `omni`), unified vector space for text + image, content-hash dedup, `okf-asset://` protocol
Import/Export	OKF Markdown round-trip, batch import with single-transaction upsert, delta detection (SHA-256 hash skip), purge deleted concepts (`--purge`), filtered bulk export with graph enrichment (See Also + Cited By), auto-generated index.md files
PDF Ingestion	`okfgraph.ingest` sub-module — pdf_oxide fast path + ONNX/Rapid heavy passes (RapidLaTeXOCR, RapidOCR, RapidLayout, RapidTable), four routing modes (NEVER/AUTO/SURGICAL/ALWAYS), Paddle-free
CLI	14 commands + interactive REPL, `--mode` for image ingestion, `--device cuda` with auto-fallback, chunking flags (`--chunk-overlap`, `--no-chunking`), `--purge` for stale concept cleanup
LLM Tools	16 OpenAI-compatible tool definitions for agent integration (search, traverse, chunks, graph enrichment, path finding, export, ingest_md, ingest_thoughts, ingest_pdf)
MCP Server	Model Context Protocol server (`okf-mcp`) — stdio transport, lifespan-managed router, 16 tools with read/write annotations, compatible with Claude Desktop, Cursor, Continue

Quick Start

Installation

pip install ladybug pydantic python-frontmatter pyyaml optimum[onnxruntime] transformers torch sentence-transformers Pillow

Programmatic Usage

fromokfgraphimportOKFRouter, ConceptModel# Initialize the routerrouter=OKFRouter(
db_path="okfgraph.db",
bundle_root="./my-knowledge-base",
embedding_dim=512, # Matryoshka: 32, 64, 128, 256, 512, 768, 1024device="cuda", # or "cpu" — defaults to CUDA when onnxruntime-gpu is available
)
# Import an OKF bundleids=router.import_bundle(mode="optional")
print(f"Imported {len(ids)} concepts")
# Hybrid searchresults=router.search_hybrid("machine learning basics", limit=5)
forrinresults:
print(f" [{r['relevance_score']:.3f}] {r['title']} ({r['type']})")
# Chunk-level search (RRF-fused vector + FTS)chunks=router.search_chunks("neural network architecture", limit=5)
forcinchunks:
print(f" [{c['rrf_score']:.3f}] {c['parent_title']} §{c['chunk_index']}")
# Search with graph contextenriched=router.search_with_context("graph neural networks", limit=3)
forrinenriched:
chunk=r["chunk"]
print(f" [{chunk['rrf_score']:.3f}] {chunk['parent_title']}")
print(f" ← linked by: {len(r['incoming_links'])} docs")
# Hub-score rerankingranked=router.search_chunks_with_hub_score("fundamentals", limit=10)
forrinranked:
print(f" [{r['final_score']:.3f}] hub={r['hub_score']:.2f}{r['parent_title']}")
# Reconstruct document from chunksoriginal=router.reconstruct_document("concepts/intro")
# Image search (text → image via unified index)images=router.search_images_with_text("diagram of a neural network", limit=10)
forimginimages:
print(f" [{img['relevance_score']:.3f}] {img['file_name']}")
# Graph traversalnodes=router.traverse("concepts", relationship="CONTAINS", direction="OUTGOING", depth=2)

CLI Usage

# Initialize database
okf init --bundle ./my-knowledge-base --dim 512
# Import a single file
okf import ./concepts/intro.md --mode optional
# Import an entire bundle
okf import --all --mode omni --allow-remote-images
# Import with delta detection + purge deleted concepts
okf import --all --purge
# Hybrid search
okf search "graph neural networks" --type section --limit 5
# Hybrid search with matched chunks
okf search "machine learning" --chunks
# Chunk-level search
okf search-chunks "neural network architecture"# Search with graph context
okf context "graph neural networks"# Hub-score reranking
okf hub-search "fundamentals"# Find path between concepts
okf path concepts/intro concepts/advanced
# List chunks for a concept
okf chunks concepts/intro
# Reconstruct document from chunks
okf reconstruct concepts/intro
# Image search
okf search-images "network architecture diagram"# List directory
okf list concepts
# Interactive shell
okf shell

MCP Server

OKFgraph includes a Model Context Protocol server that exposes all 16 tools over stdio transport. Compatible with Claude Desktop, Cursor, Continue, and any MCP client.

# Start MCP server (stdio transport)
okf-mcp --db-path ./okfgraph.db
# With GPU acceleration
okf-mcp --db-path ./okfgraph.db --device cuda
# With custom embedding dimension
okf-mcp --db-path ./okfgraph.db --embedding-dim 512

Claude Desktop config (claude_desktop_config.json):

{
"mcpServers": {
"okfgraph": {
"command": "python",
"args": ["-m", "okfgraph.mcp_server", "--db-path", "/path/to/okfgraph.db"]
}
}
}

Programmatic usage:

fromokfgraph.mcp_serverimportcreate_mcp_servermcp=create_mcp_server(
db_path="./okfgraph.db",
bundle_root="./my-knowledge-base",
device="cpu",
embedding_dim=1024,
)
mcp.run(transport="stdio")

Architecture

Embedding Engine

OKFgraph uses a dual-model approach with a unified vector space:

Model	Role	Framework	Loaded
`jina-embeddings-v5-text-small-retrieval`	Text embeddings for concepts	ONNX Runtime (`optimum`)	Always
`jina-embeddings-v5-omni-small-retrieval`	Image embeddings (vision tower)	SentenceTransformer	Lazy (first use)

Both models output vectors in the same Matryoshka space, so text and image embeddings are directly comparable in the image_omni_idx index.

Image Ingestion Modes

Mode	Image with alt-text	Image without alt-text	Omni model loaded?
`text`	Embed alt-text (lightweight)	Embed `filename + image-number`	Never
`optional`	Embed alt-text (lightweight)	Embed image bytes (rich)	Only for images without alt-text
`omni`	Embed image bytes (rich)	Embed image bytes (rich)	Always (if bytes available)

When omni is requested but raw bytes are unavailable (e.g. remote URLs not fetched), the system degrades gracefully to the text path.

Database Schema

Concept ImageAsset Directory BrokenLink Chunk FileHash
├── id ├── id ├── id ├── id ├── id ├── path (PK)
├── type ├── file_name └── (empty) ├── source_id ├── parent_doc_id ├── hash
├── title ├── mime_type ├── target_id ├── chunk_index ├── concept_id
├── body ├── alt_text └── timestamp ├── chunk_text
├── embedding ├── caption ├── block_type
└── extra ├── embed_route ├── start_offset
├── content_hash ├── end_offset
├── data (BLOB) └── embedding
└── embedding
CONTAINS: Directory → Directory / Concept
LINKS_TO: Concept → Concept
INCLUDES_ASSET: Concept → ImageAsset
PART_OF: Concept → Chunk

Chunking & Graph Retrieval

OKFgraph v5.0 adds document chunking with graph-aware retrieval:

Feature	Description
Mordant chunker	Rust-based Markdown parser that splits documents into semantic blocks (paragraphs, headings, code blocks, lists, tables, blockquotes)
Heading context injection	Paragraph chunks get parent heading prepended to embedding payloads without mutating stored text
Structural boundaries	Headings, code blocks, lists, tables, blockquotes, and diagrams enforce hard boundaries — no overlap tails bleed across them
RRF-fused chunk search	Vector + FTS fusion at chunk granularity with per-doc limits and graph filters
Hub-score reranking	Chunks from authoritative documents (high incoming link count) rank higher
Graph context expansion	Search results enriched with incoming/outgoing links, directory ancestry, and sibling concepts
Path finding	BFS shortest path between any two concepts in the knowledge graph
Document reconstruction	~98% fidelity round-trip from chunks back to original Markdown
Hybrid search with chunks	`search_hybrid(query, include_chunks=True)` attaches matched chunks to concept results

PDF Ingestion Engine (`okfgraph.ingest`)

The okfgraph.ingest sub-module provides a Paddle-free PDF → Markdown conversion pipeline using the RapidAI family of ONNX models. Four routing modes control when ONNX models are invoked:

Mode	Behaviour
NEVER	Fast path only (pdf_oxide). No ONNX models loaded.
AUTO	Heuristics per page → full ONNX pipeline only on flagged pages.
SURGICAL	Formula crops via RapidLaTeXOCR; full pipeline only for scans.
ALWAYS	Every page through the full ONNX layout + OCR pipeline.

Key features:

Zero hard dependencies — all RapidAI imports are guarded; the module loads cleanly without them
Lazy loading — born-digital PDFs never pay for OCR/layout/table models
Graceful degradation — if a model fails to load, the pipeline falls back to the fast path
Device → ort_providers coercion — device="cuda" auto-resolves to ["CUDAExecutionProvider", "CPUExecutionProvider"] (accepts "gpu" as alias)
Output contract — single .md with inline/display LaTeX, fenced code, GFM tables, and okf-asset:// links

Key Design Decisions

Last-token pooling (not mean pooling) — required by Jina v5's training protocol
Delete-then-create upserts — LadybugDB vector indexes block SET on indexed properties
Sequential encoding — padded batch tokenization wastes attention compute with variable-length documents
Content-hash dedup — unchanged images are not re-embedded on re-import
okf-asset:// protocol — markdown references use UUID-based URIs instead of inline Base64

API Reference

`OKFRouter`

Method	Description
`__init__(db_path, bundle_root, model_id, omni_model_id, embedding_dim, cache_dir, device, allow_remote_images)`	Initialize router
`import_from_okf(file_path, mode)`	Import a single OKF file
`import_bundle(bundle_path, batch_size, mode, purge_deleted)`	Import entire bundle with batch encoding and delta detection
`export_to_okf(concept_id, output_path)`	Export a single concept to OKF markdown
`export_bundle(output_dir, directory_id, concept_type, tags)`	Export filtered bundle with graph enrichment
`search_hybrid(query, concept_type, tags, parent_id, exclude_reserved, limit)`	Hybrid RRF search
`search_images_with_text(text_query, use_text_model, limit)`	Text→image search via unified index
`traverse(start_id, relationship, direction, depth, node_type)`	Graph traversal
`list_directory(directory_id)`	List children of a directory
`get_by_id(concept_id)`	Fetch full concept by ID
`list_images(concept_id)`	List image assets attached to a concept
`get_image_data(asset_id)`	Fetch image asset with raw bytes
`list_broken_links()`	List orphaned links
`repair_links()`	Repair broken links
`model_info(model_id, cache_dir)`	Inspect model cache status (class method)
`search_chunks(query, concept_type, tags, parent_id, limit, max_chunks_per_doc)`	RRF-fused chunk search
`search_with_context(query, limit, context_hops)`	Chunk search + graph neighborhood expansion
`search_chunks_with_hub_score(query, limit, hub_weight)`	Chunk search reranked by hub score
`get_chunks(concept_id)`	List all chunks for a concept
`reconstruct_document(document_id)`	Reconstruct original Markdown from chunks
`find_path(start_id, end_id, max_length)`	BFS shortest path between concepts
`expand_with_graph_context(chunk_ids)`	Discover related concepts via graph edges
`rerank_with_hub_score(chunk_results)`	Adjust chunk scores by parent hub score
`ingest_pdf(pdf_path, auto_import, output_dir, ...)`	Programmatic PDF ingestion (Gap #5b)
`_purge_concept(concept_id)`	Safe cascading delete (concept, chunks, links, orphaned assets)
`_changed_files(source_files)`	Delta detection — returns `(changed, deleted)` tuple
`_file_hash(path)`	Compute SHA-256 hex digest of a file

`IngestMode`

fromokfgraph.imagesimportIngestModeIngestMode.TEXT# alt-text / filename fallback (no omni)IngestMode.OPTIONAL# omni only for images lacking alt-textIngestMode.OMNI# every image via omni model

Aliases: text-only, alt → TEXT; hybrid, auto → OPTIONAL; full, multimodal → OMNI.

`ConceptModel`

classConceptModel(BaseModel):
id: strtype: strtitle: Optional[str] =Nonedescription: Optional[str] =Noneresource: Optional[str] =Nonetags: List[str] =Field(default_factory=list)
timestamp: Optional[datetime] =Nonebody: str=""embedding: Optional[List[float]] =None# extra frontmatter keys captured via model_config.extra = "allow"

CLI Reference

Command	Description
`okf init`	Initialize database and schema
`okf model-info`	Show model cache status
`okf import <files>`	Import one or more OKF files
`okf import --all`	Import entire bundle recursively
`okf search <query>`	Hybrid search (with `--chunks` for matched chunks)
`okf search-images <query>`	Find images via unified vector index
`okf search-chunks <query>`	Chunk-level RRF-fused search
`okf context <query>`	Search with graph neighborhood expansion
`okf hub-search <query>`	Chunk search reranked by hub score
`okf traverse <id>`	Graph traversal
`okf list [dir]`	List directory contents
`okf get <id>`	Fetch full concept
`okf export --all`	Export entire bundle
`okf path <id1> <id2>`	Find shortest path between concepts
`okf siblings <id>`	List sibling concepts in same directory
`okf ancestry <id>`	Show directory hierarchy for a concept
`okf chunks <id>`	List chunks for a concept
`okf reconstruct <id>`	Reconstruct document from chunks
`okf broken-links`	List orphaned links
`okf repair-links`	Repair broken links
`okf reindex [--if-dirty]`	Rebuild vector + FTS indexes
`okf shell`	Interactive REPL

Global Options

Option	Default	Description
`--db`	`okfgraph.db`	Database file path
`--bundle`	`.`	Bundle root directory
`--dim`	`512`	Embedding dimension (32–1024)
`--cache-dir`	`~/.cache/huggingface`	HuggingFace model cache
`--device`	`cuda`	`cpu` or `cuda`
`--omni-model-id`	`jinaai/jina-embeddings-v5-omni-small-retrieval`	Multimodal model ID
`--verbose, -v`	—	Verbose logging (Gap #10)
`--quiet, -q`	—	Suppress non-essential output
`--log-file`	—	Write logs to file
`--profile`	—	Enable cProfile profiling (Gap #10)

Import Options

Option	Default	Description
`--mode`	`text`	Image ingestion mode: `text`, `optional`, `omni`
`--allow-remote-images`	—	Fetch `http(s)://` image URLs
`--batch-size`	`32`	Batch size for encoding
`--purge`	—	Also purge concepts whose source files were deleted from disk

Performance

Metric	Time	Notes
Single import (100 concepts)	~140s	~1400ms per concept
Batch import (100 concepts)	~128s	1.1x faster than single
Hybrid search	107ms mean	5 repetitions
Export (100 concepts)	77ms	0.8ms per concept

Batch speedup comes from DB-level optimizations (single transaction, bulk directory/link building), not from ONNX batching — sequential single-pass encoding avoids padding overhead with variable-length documents.

Testing

# Run all tests
pytest tests/ -v
# Run just image tests (no heavy deps)
python tests/test_images.py
# Run integration tests (requires installed models)
pytest tests/test_integration.py -v

Test Suite	Tests	Status
`test_ingest.py`	39	✅ All passing (Gap #5b: ingest_pdf method, version checking, engine degradation, asset staging)
`test_router_misc.py`	33	✅ All passing (Gap #12a: reindex, repair_links, meta/epoch, error isolation, context window, schema migration)
`test_router.py`	29	✅ All passing
`test_chunking.py`	26	✅ All passing
`test_delta.py`	21	✅ All passing
`test_cli.py`	19	✅ All passing
`test_export_compliance.py`	13	✅ All passing
`test_integration.py`	11	✅ All passing
`test_images.py`	11	✅ All passing
`test_logging.py`	10	✅ All passing (Gap #10: logging setup, timing instrumentation, profiling)
`test_directory_hash.py`	10	✅ All passing (Gap #1b: directory-level hash aggregation, purge of deleted subtrees)
`test_search_browser.py`	9	✅ All passing (PySide6 stubbed)
`test_graph_enrichment.py`	9	✅ All passing
`test_chunk_search.py`	7	✅ All passing
`test_reconstruction.py`	5	✅ All passing
`test_okf_ingest_tool.py`	5	✅ All passing
`test_ingest_tool.py`	3	✅ All passing
`test_converter.py`	2	✅ All passing (PySide6 stubbed)
Total	262	All passing (0 warnings)

Gap Analysis & Production Readiness

OKFgraph has undergone a comprehensive gap analysis (docs/gap-analysis.md) assessing production-readiness across 15 areas:

Category	Status	Notes
Delta Detection	✅ Closed (v5.1, v5.5)	File-level SHA-256 + directory-level hash aggregation + purge
Schema Migration	✅ Closed (v5.3)	Versioned migrations (v1→v2→v3→v4)
PDF Ingestion	✅ Closed (v5.3)	CLI `okf ingest` command with `--auto-import`
Error Isolation	✅ Closed (v5.1)	Per-concept error isolation in import pipeline
Index Lifecycle	✅ Closed (v5.1)	Epoch-based dirty tracking + change-driven rebuild
Context Window	✅ Closed (v5.1)	90% threshold warning for oversized chunks
Missing Tests	✅ Closed (v5.7)	300 tests across 16 files (15 GPU tests)
RapidAI Pinning	✅ Closed (v5.4)	Version pins + runtime warning
Observability	✅ Closed (v5.4)	Structured logging + profiling hooks
PDF Ingest API	✅ Closed (v5.4)	`OKFRouter.ingest_pdf()` programmatic API
Open: Concurrency	⚠️ Open	WAL mode + single-writer constraint needed

See architecture.md §15 for details on open gaps.

Project Structure

okfgraph/
├── okfgraph/
│ ├── __init__.py # Exports: ConceptModel, OKFRouter, cli_main, ChunkModel
│ ├── models.py # ConceptModel + ImageAssetModel + ChunkModel
│ ├── router.py # OKFRouter — ~2700 lines (chunking, graph enrichment, export)
│ ├── cli.py # CLI + interactive shell — ~800 lines
│ ├── tools.py # LLM tool definitions (13 tools)
│ ├── images.py # Image ingestion logic
│ ├── ingest/ # ONNX/Rapid PDF ingestion engine
│ │ ├── __init__.py # Public API exports
│ │ ├── config.py # ConverterConfig + RoutingMode
│ │ ├── engine.py # OnnxRapidEngine (lazy ONNX loaders)
│ │ ├── converter.py # HybridConverter (core pipeline)
│ │ ├── tables.py # HTML → GFM pipe-table converter
│ │ ├── assets.py # okf-asset:// staging logic
│ │ └── versions.py # RapidAI version pinning + runtime checks (Gap #15)
│ └── docs/
│ ├── chunking-and-graph-retrieval.md # Chunking specification
│ └── chunking-status.md # Implementation status
├── tests/
│ ├── test_chunking.py # 13 chunking unit tests
│ ├── test_reconstruction.py # 9 document reconstruction tests
│ ├── test_chunk_search.py # 9 chunk search tests
│ ├── test_graph_enrichment.py # 11 graph enrichment tests
│ ├── test_integration.py # 16 end-to-end tests
│ ├── test_export_compliance.py # 13 OKF export compliance tests
│ ├── test_ingest.py # 39 ONNX/Rapid ingestion tests (version checking, ingest_pdf, asset staging)
│ ├── test_delta.py # 21 delta detection & purge tests
│ ├── test_router_misc.py # 23 router unit tests (reindex, repair_links, meta/epoch, error isolation, context window)
│ ├── test_router.py # 29 smoke & cache & device tests
│ ├── test_logging.py # 10 logging & profiling tests
│ ├── test_converter.py # 2 converter staging tests (PySide6 stubbed)
│ ├── test_search_browser.py # 9 search browser tests (PySide6 stubbed)
│ └── fixtures/bundle/ # Test markdown fixtures
├── benchmarks/
│ └── benchmark_500.py
├── examples/
│ ├── hybrid_pdf_converter.py # PySide6 UI (legacy Paddle stack)
│ └── oxide_to_markdown_converter.py
├── docs/
│ ├── okf-export-compliance.md # OKF export specification
│ ├── ONNX_RAPID_IMPLEMENTATION.md # ONNX/Rapid migration guide
│ └── gap-analysis.md # Production-readiness gap analysis (v3.0)
├── architecture.md # Full architecture specification (v5.4)
├── pyproject.toml # Project metadata
└── requirements.txt # Dependencies

Requirements

Core (required)

Python 3.10+
ladybug>=0.17
pydantic>=2.0
python-frontmatter>=1.0
pyyaml>=6.0
optimum[onnxruntime]>=1.20
transformers>=4.57
numpy>=1.24 (replaces torch for post-processing)
mordant>=0.12 (Rust-based Markdown chunker)
sentence-transformers>=3.0
Pillow>=10.0
pytest>=8.0 (dev)

PDF Ingestion (optional — ONNX/Rapid stack)

pdf_oxide — fast native PDF→Markdown (MIT)
rapidocr — text detection + recognition (Apache-2.0)
rapid_latex_ocr — formula image → LaTeX (MIT)
rapid_layout — layout region detection (Apache-2.0)
rapid_table — table structure → HTML (Apache-2.0)
onnxruntime-gpu or onnxruntime-directml or onnxruntime (pick one for your hardware)

All RapidAI imports are guarded — the ingestion sub-module loads cleanly without them installed.

License

See LICENSE for details.

Contributing

Contributions welcome! Please open an issue or pull request. Key areas for contribution (per gap analysis):

P1: RapidAI version pinning — pin exact versions + runtime warning ✅ (closed)
P2: Structured logging — replace print() with stdlib logging ✅ (closed)
P2: PDF Ingest API — OKFRouter.ingest_pdf() programmatic API ✅ (closed)
P2: WAL mode — enable SQLite WAL for concurrent read access ✅ (closed, v5.8)
P2: URL allowlist — restrict --allow-remote-images to safe domains ✅ (closed, v5.8)
P2: TOML config — add okfgraph.toml + env var support ✅ (closed, v5.8)
P2: Soft-delete recovery — undo purge within 24h recovery window ✅ (closed, v5.8)
P2: Query latency tracking — log search query latency
P2: Embedding cache hit rates — track ONNX model cache hit/miss
P3: LLM tool definition — add ingest_pdf tool to tools.py ✅ (closed)
P3: CLI okf ingest parity — fix stage_images 5-arg call + mordant linting ✅ (closed)
P3: ingest_thoughts linting — defensive in-memory lint via _lint_converted_md_str() ✅ (closed)
P3: Tool parameter parity — fix search_hybrid type filter, ingest_pdf bool default, traverse defaults ✅ (closed)
GPU performance benchmarking at scale (10k+ concepts)
Real-world OKF bundle testing
--skip-embedding flag for faster imports without ONNX encoding
ONNX/Rapid end-to-end PDF tests (see docs/ONNX_RAPID_IMPLEMENTATION.md testing checklist)
Office file conversion via office_oxide
Delta detection: directory-level hash aggregation (skip entire subtrees)
Delta detection: soft-delete with recovery window (undo purge within N hours)
okf index-status command — report epoch, dirty state, last rebuild time
okf schema --version command — inspect schema version

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OKFgraph

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Architecture

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Image Ingestion Modes

Database Schema

Chunking & Graph Retrieval

PDF Ingestion Engine (`okfgraph.ingest`)

Key Design Decisions

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`OKFRouter`

`IngestMode`

`ConceptModel`

CLI Reference

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OKFgraph

Features

Quick Start

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Chunking & Graph Retrieval

PDF Ingestion Engine (okfgraph.ingest)

Key Design Decisions

API Reference

OKFRouter

IngestMode

ConceptModel

CLI Reference

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