ontorag 0.1.0__tar.gz

ontorag-0.1.0/.example.env

@@ -0,0 +1,17 @@
+
+OPENROUTER_API_KEY="..."
+OPENROUTER_MODEL="xiaomi/mimo-v2-flash:free"
+OPENROUTER_BASE_URL="https://openrouter.ai/api/v1"
+OPENROUTER_APP_NAME="OntoRAG"
+OPENROUTER_SITE_URL="https://ontorag.github.io"
+
+# PageIndex (document ingestion) — hosted API at pageindex.ai
+PAGEINDEX_API_KEY="..."
+
+# OntoRAG Hub (ontorag hub command)
+GITHUB_CLIENT_ID=""
+GITHUB_CLIENT_SECRET=""
+HUB_JWT_SECRET="change-me-in-production"
+HUB_JWT_EXPIRY_HOURS=24
+HUB_ONTOLOGY_DIR="./data/hub_ontologies"
+HUB_BASE_URL="http://localhost:8000"

ontorag-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: python -m pip install --upgrade pip
+      - run: pip install -e ".[dev]"
+      - run: pytest -q

ontorag-0.1.0/.github/workflows/release.yml

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+name: Release to PyPI
+
+# Publishes to PyPI via Trusted Publishing (OIDC — no API token stored).
+# One-time setup on PyPI: add a "pending publisher" for project `ontorag`
+#   owner: ontorag  repo: ontorag  workflow: release.yml  environment: pypi
+# Then push a tag: `git tag v0.1.0 && git push origin v0.1.0`.
+
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: python -m pip install --upgrade pip build twine
+      - run: python -m build
+      - run: twine check dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ontorag
+    permissions:
+      id-token: write   # required for Trusted Publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1

ontorag-0.1.0/.gitignore

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+.env
+__pycache__/*
+*.pyc
+data/*
+!data/ontologies/
+!data/ontologies/catalog.json
+*.egg-info/*

ontorag-0.1.0/ARCHITECTURE_REVIEW.md

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+# OntoRAG System Architecture Review
+
+## Overall Assessment
+
+The architecture is **coherent and well-designed**. The pipeline follows a clear, principled flow:
+
+```
+Documents → DTOs → LLM Proposals → Schema Card → Instance Extraction → RDF/TTL → SPARQL/MCP
+```
+
+The core philosophy — "LLMs propose, Code decides, Humans govern" — is consistently applied throughout. Each stage has a clear responsibility, data flows forward through well-defined interfaces, and the separation between LLM-generated proposals and deterministic merging is sound.
+
+---
+
+## What Works Well
+
+1. **DTO-first ingestion** (`dto.py`, `extractor_ingest.py`, `storage_jsonl.py`) — Clean Pydantic models with stable IDs (SHA1-based), provenance tracking, and JSONL persistence. The DTOs serve as a replayable checkpoint.
+
+2. **Two-phase schema evolution** — LLM proposals (`ontology_extractor_openrouter.py`) are aggregated (`proposal_aggregator.py`) then deterministically merged into the schema card (`schema_card.py`). No hidden ML decisions in the merge step.
+
+3. **Evidence/provenance threading** — Every proposed class, property, and instance carries evidence quotes back to source chunks. The instance RDF embeds PROV-style mention nodes linking facts to their textual origin.
+
+4. **Schema card as governance artifact** — Versioned, human-reviewable JSON that guides all downstream extraction. This prevents schema drift and makes the ontology auditable.
+
+5. **Multi-backend design** — Local rdflib for inspection, Blazegraph for production. SPARQL as the universal query interface.
+
+6. **MCP integration** — Exposes the knowledge graph as structured tools for LLM agents, cleanly separating reasoning from data.
+
+---
+
+## Critical Issues
+
+### 1. Missing `mcp_backend` module
+
+**Files affected:** `cli.py:228`, `mcp_server.py:7`
+
+Both files import from `ontorag.mcp_backend`:
+- `cli.py`: `from ontorag.mcp_backend import LocalRdfBackend, RemoteSparqlBackend`
+- `mcp_server.py`: `from ontorag.mcp_backend import SparqlBackend`
+
+**No `mcp_backend.py` file exists in the codebase.** This means:
+- The `ontorag mcp-server` CLI command will crash with `ModuleNotFoundError`
+- The `mcp_server.py` module cannot be imported at all
+
+**Expected contents:** A `SparqlBackend` abstract base class with `select()` and `construct()` methods, and two implementations: `LocalRdfBackend` (wrapping rdflib in-memory graph) and `RemoteSparqlBackend` (wrapping a remote SPARQL endpoint via HTTP).
+
+### 2. SPARQL server filename is both misspelled and uses an invalid Python module name
+
+**File:** `ontorag/saprql-server.py`
+**Import in CLI:** `from ontorag.sparql_server import create_app` (`cli.py:199`)
+
+Two problems:
+- The filename is misspelled: `saprql-server.py` instead of `sparql_server.py`
+- Hyphens are invalid in Python module names — Python cannot import `saprql-server` as a module
+
+The `ontorag sparql-server` CLI command will fail with `ModuleNotFoundError`.
+
+**Fix:** Rename `saprql-server.py` → `sparql_server.py`
+
+### 3. `ontology_extractor.py` has a broken import and is dead code
+
+**File:** `ontorag/ontology_extractor.py:5`
+
+```python
+from ontology_proposal import ChunkOntologyProposal
+```
+
+This imports from a root-level file (`ontology_proposal.py`) using a bare import. As a package module, this will fail unless the root directory is manually added to `sys.path`. Additionally, nothing in the codebase imports `ontology_extractor.py` — the actual extractor used is `ontology_extractor_openrouter.py`.
+
+---
+
+## Moderate Issues
+
+### 4. `blazegraph_upload_ttl` injects raw TTL into SPARQL UPDATE
+
+**File:** `blazegraph.py:20-27`
+
+Raw Turtle content is string-interpolated directly into a SPARQL UPDATE query:
+```python
+update = f"""
+INSERT DATA {{
+  GRAPH <{graph_iri}> {{
+{ttl}
+  }}
+}}
+"""
+```
+
+Turtle syntax can contain curly braces, angle brackets, and other characters that conflict with SPARQL syntax. This will break for non-trivial TTL files. A more robust approach would use Blazegraph's REST API for bulk graph loading (e.g., POST to the endpoint with `Content-Type: application/x-turtle`).
+
+### 5. No rate limiting in instance extraction
+
+**File:** `instance_extractor_openrouter.py:118-139`
+
+The schema extractor (`ontology_extractor_openrouter.py:98`) includes `time.sleep(10)` between chunk calls, but the instance extractor has no inter-chunk delay. For documents with many chunks, this will likely hit OpenRouter rate limits.
+
+### 6. SPARQL query type detection is fragile
+
+**File:** `saprql-server.py:12-22`
+
+`_detect_query_kind()` checks if the query starts with a SPARQL keyword, then checks for keywords after newlines. Single-line queries with PREFIX blocks (e.g., `PREFIX foo: <...> SELECT ...`) will not be detected and will fall through to the "unknown" fallback. The fallback does work (it tries the query and checks the result type), so this is not fatal, but it's fragile.
+
+### 7. SPARQL injection in MCP server tools
+
+**File:** `mcp_server.py:26-51`
+
+Tools like `describe()`, `list_by_class()`, `outgoing()`, and `incoming()` inject IRIs directly into SPARQL query strings via f-strings:
+```python
+q = f"DESCRIBE <{iri}>"
+```
+
+If an IRI contains `>` or other special characters, the query will break or behave unexpectedly. Since these are MCP tools exposed to LLM agents, malformed input is plausible.
+
+### 8. `pyproject.toml` missing runtime dependencies
+
+**File:** `pyproject.toml`
+
+Only 6 dependencies are listed (typer, requests, pydantic, rdflib, llama-index, python-dotenv), but the codebase also requires at runtime:
+- `fastapi` + `uvicorn` (SPARQL server)
+- `fastmcp` (MCP server)
+- `openai` (used by `openrouter_client.py`)
+
+Users installing via `pip install .` will get incomplete dependencies.
+
+---
+
+## Minor Issues
+
+### 9. `datetime.utcnow()` is deprecated
+
+**Files:** `dto.py:34,43`, `schema_card.py:9`
+
+Since Python 3.12, `datetime.utcnow()` is deprecated in favor of `datetime.now(datetime.timezone.utc)`.
+
+### 10. Legacy root-level files with broken imports
+
+Three files at the project root are leftover from an earlier iteration:
+- `cli_extract.py` — imports `from extractor import ...` (should be `extractor_ingest`)
+- `openrouter_client.py` — standalone OpenAI client factory, unused by package
+- `ontology_proposal.py` — Pydantic models superseded by the dict-based approach in the package
+
+None of these are importable from the package or referenced by it.
+
+### 11. `openrouter_client.py` returns string, not dict
+
+**File:** `openrouter_client.py:28`
+
+The function `chat_json` returns `resp.choices[0].message.content` which is a raw string, not parsed JSON, despite the function name suggesting otherwise. The comment acknowledges this (`# JSON string (poi json.loads)`), but the API is misleading.
+
+### 12. Schema card class name validation is case-sensitive for warnings but case-insensitive for dedup
+
+**File:** `schema_card.py:215-223`
+
+Classes are deduplicated by lowercase key (`_key_class`), but the warning check `p["domain"] not in class_names` uses the original-case `name` field. If a property references a class with different casing (e.g., "person" vs "Person"), it will exist in the deduplicated map but trigger a spurious warning.
+
+---
+
+## Data Flow Verification
+
+| Step | Input | Output | Verified |
+|------|-------|--------|----------|
+| `ingest` | File path | DocumentDTO + ChunkDTOs (JSONL) | OK |
+| `extract-schema` | Chunks JSONL + schema card | Aggregated proposal JSON | OK |
+| `build-schema-card` | Previous card + proposal | New schema card JSON | OK |
+| `export-schema-ttl` | Proposal JSON | OWL/RDFS Turtle | OK |
+| `extract-instances` | Chunks JSONL + schema card | Instance RDF TTL with provenance | OK |
+| `load-ttl` | TTL file + graph IRI | Blazegraph upload | OK (with caveat #4) |
+| `sparql-server` | Ontology TTL + Instances TTL | FastAPI SPARQL endpoint | BROKEN (issue #2) |
+| `mcp-server` | TTL or SPARQL endpoint | MCP tools | BROKEN (issue #1) |
+
+---
+
+## Recommendations (Priority Order)
+
+1. **Create `ontorag/mcp_backend.py`** with `SparqlBackend`, `LocalRdfBackend`, and `RemoteSparqlBackend`
+2. **Rename `saprql-server.py` → `sparql_server.py`**
+3. **Fix `blazegraph_upload_ttl`** to use Blazegraph REST API instead of SPARQL INSERT DATA
+4. **Add missing dependencies** to `pyproject.toml` (fastapi, uvicorn, fastmcp)
+5. **Add inter-chunk delay** in `instance_extractor_openrouter.py`
+6. **Sanitize IRI inputs** in MCP server SPARQL templates
+7. **Remove or relocate legacy files** (`cli_extract.py`, `openrouter_client.py`, `ontology_proposal.py`, `ontology_extractor.py`)
+8. **Add a test suite** — the project has zero tests
+
+---
+
+## Conclusion
+
+The OntoRAG system architecture is **fundamentally sound**. The pipeline design, governance model, and separation of concerns are well thought out. The two blocking issues (missing `mcp_backend` module and misspelled SPARQL server filename) prevent two CLI commands from working, but the core extraction pipeline (`ingest` → `extract-schema` → `build-schema-card` → `export-schema-ttl` → `extract-instances`) is complete and internally consistent.

ontorag-0.1.0/CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Setup
+
+```bash
+uv sync          # installs core deps; rebuilds .venv if broken
+cp .example.env .env   # fill in OPENROUTER_API_KEY and optionally BLAZEGRAPH_ENDPOINT
+```
+
+Requires Python 3.12. Uses `uv` (see `uv.lock`). `pymupdf`, `pageindex`, and `llama-index` are optional extras:
+
+```bash
+uv sync --extra pdf        # for PDF ingest via PyMuPDF
+uv sync --extra pageindex  # for hierarchical PDF ingest via PageIndex
+uv sync --extra llamaindex # for LlamaIndex fixed-chunk ingest
+```
+
+## CLI
+
+The shell `PYTHONPATH` on this server is polluted with old system Python paths. Always invoke as:
+
+```bash
+PYTHONPATH=/srv/sembase/extractor_new uv run ontorag <command>
+```
+
+Verbosity flags go before the subcommand: `uv run ontorag -v <command>` or `-vv` for debug traces.
+
+## Key commands
+
+| Command | Purpose |
+|---|---|
+| `ontorag ingest <file> --out data/dto` | Parse document → DocumentDTO + ChunkDTOs (content-addressed, skips re-runs) |
+| `ontorag extract-schema --chunks ... --schema-card ... --out ...` | LLM per-chunk ontology proposals → aggregated proposal JSON |
+| `ontorag align-schema --proposal ... --baseline ... --out ...` | LLM alignment of induced items against baseline ontologies |
+| `ontorag build-schema-card --previous ... --proposal ... --out ...` | Deterministic merge of proposal into schema card |
+| `ontorag export-schema-ttl --proposal ... --out ... --namespace ...` | Proposal/alignment JSON → OWL/RDFS Turtle |
+| `ontorag extract-instances --chunks ... --schema-card ... --out-ttl ...` | LLM instance extraction → RDF TTL with PROV provenance |
+| `ontorag sparql-server --onto ... --inst ...` | FastAPI in-memory SPARQL endpoint (port 8890) |
+| `ontorag mcp-server --onto ... --inst ...` | Knowledge graph MCP server (port 9010) |
+| `ontorag ontology-mcp --catalog ...` | Ontology catalog MCP server (port 9020) |
+| `ontorag register-ontology <slug> <ttl>` | Register a baseline OWL/TTL into the catalog |
+| `ontorag init-schema-card --baselines foaf,prov --out ...` | Compose baselines → initial schema card |
+| `ontorag hub` | Start Hub API server (requires GitHub OAuth env vars) |
+
+## Architecture
+
+The core philosophy: **LLMs propose. Code decides. Humans govern.**
+
+Pipeline flow:
+```
+Baseline Ontologies (TTL)
+    → init-schema-card  → schema_card.json
+Documents
+    → ingest            → data/dto/documents/*.json + data/dto/chunks/*.jsonl
+    → extract-schema    → data/proposals/*.json         (LLM, per-chunk → aggregated)
+    → align-schema      → alignment JSON                (LLM, optional baseline alignment)
+    → build-schema-card → schema_card.json              (deterministic merge)
+    → export-schema-ttl → staging_schema.ttl
+    → extract-instances → instances.ttl                 (LLM, RDF + PROV provenance)
+    → sparql-server / mcp-server
+```
+
+### Module map (`ontorag/`)
+
+| File | Role |
+|---|---|
+| `cli.py` | Typer CLI — all 13 commands |
+| `dto.py` | `DocumentDTO`, `ChunkDTO`, `ProvenanceDTO`; content-hash (`stable_document_id`) |
+| `extractor_ingest.py` | Document parsing via PageIndex (hierarchical) or LlamaIndex (fixed chunks) |
+| `storage_jsonl.py` | JSONL persistence for DTOs |
+| `ontology_extractor_openrouter.py` | LLM schema proposal extraction (per chunk) |
+| `instance_extractor_openrouter.py` | LLM instance extraction (per chunk) |
+| `proposal_aggregator.py` | Merge per-chunk proposals into one document-level proposal |
+| `schema_card.py` | Deterministic schema card merge with origin tracking |
+| `schema_alignment.py` | LLM-based alignment of induced items against baselines |
+| `proposal_to_ttl.py` | Schema proposal/alignment JSON → rdflib `Graph` (OWL/RDFS) |
+| `instances_to_ttl.py` | Instance proposals → rdflib `Graph` with PROV mention nodes |
+| `blazegraph.py` | Blazegraph REST API (upload TTL, SPARQL UPDATE) |
+| `sparql_server.py` | FastAPI SPARQL endpoint (SELECT/ASK/CONSTRUCT/DESCRIBE, content negotiation) |
+| `mcp_backend.py` | `SparqlBackend` ABC + `LocalRdfBackend` + `RemoteSparqlBackend` |
+| `mcp_server.py` | Knowledge graph MCP tools (`sparql_select`, `describe`, `list_by_class`, etc.) |
+| `mcp_client.py` | Async SSE client for remote MCP |
+| `ontology_catalog.py` | Local catalog + OWL/TTL → schema card converter; remote baseline fetch |
+| `ontology_mcp.py` | Ontology catalog MCP server |
+| `verbosity.py` | Logging setup (`-v`/`-vv` flags) |
+| `hub/` | Hub FastAPI app, GitHub OAuth, GitHub storage backend |
+
+### Schema card format
+
+The schema card (`schema_card.json`) is the central governance artifact:
+
+```json
+{
+  "version": "<ISO timestamp>",
+  "namespace": "http://my.org/ns/",
+  "classes": [{"name": "...", "description": "...", "origin": "foaf|schema_org|induced|..."}],
+  "datatype_properties": [{"name": "...", "domain": "...", "range": "string|integer|...", "description": "...", "origin": "..."}],
+  "object_properties": [{"name": "...", "domain": "...", "range": "...", "description": "...", "origin": "..."}],
+  "events": [],
+  "aliases": [{"names": [...], "rationale": "..."}],
+  "warnings": []
+}
+```
+
+Dedup is by normalized (lowercased) name. Baseline origins are preserved across merges; LLM-induced items get `"origin": "induced"`.
+
+### LLM integration
+
+All LLM calls go through OpenRouter (`OPENROUTER_API_KEY`, `OPENROUTER_MODEL`). The modules `ontology_extractor_openrouter.py`, `instance_extractor_openrouter.py`, and `schema_alignment.py` each manage their own `requests` calls directly (no shared client abstraction). The `extract-schema` command adds a 10-second inter-chunk delay; `extract-instances` does not.
+
+`align-schema` supports **partial-save and auto-resume**: if the output file exists with `"_partial": true`, it resumes from the last completed category.
+
+### Ingest engines
+
+`ontorag ingest` supports two engines via `--engine`:
+- `llamaindex` (default): fixed-size chunks (1024 tokens, 120 overlap)
+- `pageindex`: hierarchical section detection, requires `PAGEINDEX_API_KEY`
+
+Documents are content-hashed (SHA-256); re-ingesting the same file is a no-op unless `--force` is passed.
+
+### Data directories
+
+```
+data/dto/documents/    DocumentDTO JSON files (doc_<hash>.json)
+data/dto/chunks/       ChunkDTO JSONL files (doc_<hash>.jsonl)
+data/proposals/        Aggregated schema proposals and alignment JSON
+data/schema/           Schema cards and exported TTL
+data/instances/        Instance RDF TTL
+data/ontologies/       Baseline catalog (catalog.json + *.ttl)
+data/ttl/              Misc TTL files
+```
+
+## Environment variables
+
+| Variable | Required for |
+|---|---|
+| `OPENROUTER_API_KEY` | All LLM commands |
+| `OPENROUTER_MODEL` | LLM model selection (default: `openai/gpt-4o-mini`) |
+| `OPENROUTER_BASE_URL` | OpenRouter endpoint |
+| `BLAZEGRAPH_ENDPOINT` | `load-ttl`, `sparql-update` commands |
+| `PAGEINDEX_API_KEY` | `ingest --engine pageindex` |
+| `GITHUB_CLIENT_ID` / `GITHUB_CLIENT_SECRET` / `HUB_JWT_SECRET` | `hub` command |
+| `ONTORAG_MCP_URL` | Remote baseline resolution in `init-schema-card` (default: `https://mcp.rpg-schema.org`) |
+
+## Known issues
+
+- `blazegraph.py`: raw TTL is string-interpolated into SPARQL UPDATE — breaks for non-trivial TTL; Blazegraph REST bulk load is the proper fix.
+- Hub async endpoints block the event loop (sync LLM calls inside `async def`).
+- No test suite exists in this repository.

ontorag-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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