diff --git a/.env.example b/.env.example index 2bf49cd..cec5c7a 100644 --- a/.env.example +++ b/.env.example @@ -5,35 +5,17 @@ # .env is gitignored for security # ============================================================================== -# NEO4J CONFIGURATION +# GRAFEO CONFIGURATION (Embedded Graph Database) # ============================================================================== -# Neo4j connection (shared by graph_manager and archimate_manager) -NEO4J_URI=bolt://localhost:7687 -NEO4J_USERNAME= -NEO4J_PASSWORD= -NEO4J_DATABASE=neo4j -NEO4J_ENCRYPTED=false - -# Neo4j connection pool settings -NEO4J_MAX_CONNECTION_LIFETIME=3600 -NEO4J_MAX_CONNECTION_POOL_SIZE=50 -NEO4J_CONNECTION_ACQUISITION_TIMEOUT=60 - -# Neo4j logging -NEO4J_LOG_LEVEL=INFO -NEO4J_LOG_QUERIES=false -# Suppress verbose Neo4j notifications (DEPRECATION, UNRECOGNIZED, HINT) -NEO4J_SUPPRESS_NOTIFICATIONS=true - -# Manager namespaces (Neo4j label prefixes) -NEO4J_GRAPH_NAMESPACE=Graph +# Leave GRAFEO_DB_PATH empty for in-memory (default), or set a path for persistent storage +GRAFEO_DB_PATH= +GRAFEO_LOG_QUERIES=false -# ============================================================================== -# ARCHIMATE MANAGER CONFIGURATION -# ============================================================================== -# ArchiMate manager namespace (fallback: NEO4J_NAMESPACE_ARCHIMATE) +# Graph namespace (label prefix for extraction data) +GRAPH_NAMESPACE=Graph + +# ArchiMate namespace (label prefix for model data) ARCHIMATE_NAMESPACE=Model -NEO4J_NAMESPACE_ARCHIMATE=Model # Validation settings ARCHIMATE_VALIDATION_STRICT_MODE=false diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d2a2f19..01faebd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,7 +2,7 @@ name: CI on: push: - branches: [main, dev] + branches: [main, dev, "release/*"] pull_request: branches: [main, dev] @@ -34,6 +34,14 @@ jobs: - name: Run Ruff formatter check run: uv run ruff format --check deriva/ + typos: + name: Typos + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Check for typos + uses: crate-ci/typos@v1.29.4 + typecheck: name: Type Check runs-on: ubuntu-latest @@ -85,3 +93,24 @@ jobs: fail_ci_if_error: false env: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + + security: + name: Security Audit + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v4 + with: + version: "latest" + enable-cache: true + + - name: Set up Python + run: uv python install ${{ env.PYTHON_VERSION }} + + - name: Install dependencies + run: uv sync --extra dev + + - name: Audit dependencies + run: uv run pip-audit --ignore-vuln CVE-2025-69872 # diskcache pickle CVE; mitigated via JSONDisk diff --git a/.gitignore b/.gitignore index 91b0661..913405a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,6 @@ *__pycache__* temp_* tmp_* -.cl*/* .env workspace/* deriva/adapters/neo4j/data/* diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 946f48e..034813f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,7 +1,46 @@ +# Pre-commit hooks for Deriva +# Install: cargo install prek && prek install +# Run manually: prek run --all-files +# Docs: https://github.com/j178/prek + repos: - - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.6 + # Built-in prek hooks + - repo: builtin hooks: - - id: ruff - args: [--fix, --exit-non-zero-on-fix] + - id: trailing-whitespace + exclude: '\.md$' + - id: end-of-file-fixer + exclude: '\.md$' + - id: check-yaml + - id: check-toml + - id: check-merge-conflict + - id: check-added-large-files + args: ['--maxkb=1000'] + + # Typo checker + - repo: https://github.com/crate-ci/typos + rev: v1.29.4 + hooks: + - id: typos + + # Python hooks + - repo: local + hooks: + - id: ruff-check + name: ruff check + entry: uv run ruff check --fix --exit-non-zero-on-fix + language: system + types: [python] + - id: ruff-format + name: ruff format + entry: uv run ruff format + language: system + types: [python] + + - id: ty-check + name: ty check + entry: uv run ty check deriva/ + language: system + pass_filenames: false + types: [python] diff --git a/ARCHITECTURE.MD b/ARCHITECTURE.MD index 5e0a6f9..5b6f75f 100644 --- a/ARCHITECTURE.MD +++ b/ARCHITECTURE.MD @@ -42,8 +42,8 @@ Repository --> Extraction --> Graph --> Derivation --> ArchiMate Model --> Expor | +-------------------------------+ +-----------------------------------+ | | | External System Adapters | | Business Logic Modules | | | | +---------+ +-------------+ | | +-------------+ +-------------+ | | -| | | Neo4j | | Database | | | | Extraction | | Derivation | | | -| | | (neo4j)| | (database) | | | | | | | | | +| | | Grafeo | | Database | | | | Extraction | | Derivation | | | +| | | (grafeo)| | (database) | | | | | | | | | | | +---------+ +-------------+ | | | - Business | | - Prep | | | | | +---------+ +-------------+ | | | - TypeDef | | - Generate | | | | | | Graph | | ArchiMate | | | | - Method | | - Refine | | | @@ -101,7 +101,7 @@ External system integrations: | Adapter | Purpose | |---------|---------| -| `neo4j/` | Shared Neo4j connection with namespace isolation | +| `grafeo/` | Embedded graph database with namespace isolation | | `database/` | DuckDB for configuration and metadata storage | | `graph/` | Graph operations (nodes, edges) in "Graph" namespace | | `archimate/` | ArchiMate model operations in "Model" namespace | @@ -234,8 +234,8 @@ Each layer has a `ruff.toml` file enforcing boundaries: | Store | Purpose | Location | |-------|---------|----------| -| Neo4j (Graph) | Intermediate representation | `bolt://localhost:7687` | -| Neo4j (Model) | ArchiMate elements/relationships | `bolt://localhost:7687` | +| Grafeo (Graph) | Intermediate representation | Embedded (in-memory or `GRAFEO_DB_PATH`) | +| Grafeo (Model) | ArchiMate elements/relationships | Embedded (shared instance) | | DuckDB | Configuration, metadata | `deriva/adapters/database/sql.db` | | Workspace | Repositories, benchmarks, exports | `workspace/` | @@ -243,7 +243,7 @@ Each layer has a `ruff.toml` file enforcing boundaries: 1. **Services as API Layer**: CLI and App only interact with the backend through `PipelineSession`, ensuring consistent behavior and single point of change. -2. **Namespace Isolation**: Neo4j uses label prefixes (`Graph:`, `Model:`) to separate extraction data from ArchiMate model data in a single database. +2. **Namespace Isolation**: Grafeo uses label prefixes (`Graph:`, `Model:`) to separate extraction data from ArchiMate model data in a single embedded database. 3. **Configuration Versioning**: All config changes create new versions, enabling rollback and A/B testing during optimization. diff --git a/CHANGELOG.md b/CHANGELOG.md index a3803c4..928698b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,9 +8,22 @@ Deriving ArchiMate models from code using knowledge graphs, heuristics, and LLMs Version 0.7.x is all about stability, portability, user experience, documentation and clean architecture/code standards. -## v0.7.0 - (Unreleased) +## v0.7.0 - Grafeo Migration (March 1, 2026) -TBD +Replaced Neo4j (Docker container) with grafeo, an embedded Rust graph database. Removes the external Docker dependency entirely and the graph database now runs in-process. (500-1000x speedup yah!) + +### Infrastructure + +- **Grafeo adapter**: New `deriva/adapters/grafeo/` with `GrafeoConnection`, a drop-in replacement for the old `Neo4jConnection`, using a shared `GrafeoDB` singleton with namespace isolation +- **No Docker required**: Graph database is embedded (in-memory by default, persistent via `GRAFEO_DB_PATH` env var) +- **Removed Neo4j**: Deleted `deriva/adapters/neo4j/` and all Neo4j driver dependencies + +### Breaking Changes + +- `Neo4jSettings` → `GrafeoSettings` (env prefix: `GRAFEO_`) +- `NEO4J_GRAPH_NAMESPACE` → `GRAPH_NAMESPACE`, `NEO4J_NAMESPACE_ARCHIMATE` → `ARCHIMATE_NAMESPACE` +- `session.start_neo4j()` / `stop_neo4j()` → `start_graph_db()` / `stop_graph_db()` +- `get_enrichments_from_neo4j()` → `get_enrichments_from_graph()` --- diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a05e7be..0bb25c6 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -23,7 +23,7 @@ cd Deriva # Copy environment template cp .env.example .env -# Edit .env with your configuration (Neo4j, LLM keys, etc.) +# Edit .env with your configuration (LLM keys, etc.) # Install with dev dependencies uv sync --all-extras @@ -92,7 +92,7 @@ deriva/ │ ├── adapters/ (Stateful I/O services) │ ├── database/ - DuckDB configuration storage -│ ├── neo4j/ - Neo4j connection pool +│ ├── grafeo/ - Embedded graph database (grafeo) │ ├── repository/ - Git operations │ ├── graph/ - Graph CRUD (namespace: Graph) │ ├── archimate/ - ArchiMate CRUD (namespace: Model) @@ -213,7 +213,7 @@ Marimo: displays results in UI | CLI: prints summary to stdout | Column | Purpose | |--------|---------| | Column 0 | Run Deriva (pipeline buttons, status callouts) | -| Column 1 | Configuration (runs, repos, Neo4j, graph stats, ArchiMate, LLM) | +| Column 1 | Configuration (runs, repos, graph database, graph stats, ArchiMate, LLM) | | Column 2 | Extraction Settings (file types, extraction step config) | | Column 3 | Derivation Settings (13 element types across Business/Application/Technology layers) | @@ -422,11 +422,10 @@ What does this class represent? Why does it exist? ```python class GraphManager: """ - High-level interface for Neo4j graph operations. + High-level interface for graph database operations. - Wraps Neo4j driver complexity and provides domain-specific operations - like "add repository" rather than raw Cypher. Uses connection pooling - internally so you can safely create instances per-request. + Wraps grafeo complexity and provides domain-specific operations + like "add repository" rather than raw Cypher. """ ``` @@ -475,7 +474,7 @@ Comments explain **why**, not **what**. if raw.startswith(b'\xff\xfe'): return raw.decode('utf-16-le') -# Neo4j MERGE needs deterministic IDs to avoid duplicates +# MERGE needs deterministic IDs to avoid duplicates node_id = f"Repository_{repo_name}" # LLMs sometimes return markdown-wrapped JSON @@ -540,7 +539,7 @@ def read_file(path: Path) -> str | None: def connect(self) -> None: """Raises ConnectionError if connection fails.""" try: - self._driver = neo4j.GraphDatabase.driver(self._uri) + self._db = get_database() except Exception as e: raise ConnectionError(f"Failed to connect: {e}") from e ``` @@ -670,7 +669,7 @@ name = 'Deriva' ### Dependencies -- Can import **infrastructure adapters** (e.g., GraphManager ← Neo4jConnection) +- Can import **infrastructure adapters** (e.g., GraphManager ← GrafeoConnection) - **Cannot** import other domain adapters (e.g., GraphManager ✗← ArchimateManager) - **Cannot** import modules @@ -1341,7 +1340,7 @@ Deriva splits configuration by **ownership** - who needs to change it and why: ### Environment Variables -- Naming: `{MANAGER}_{CATEGORY}_{SETTING}` (e.g., `NEO4J_POOL_SIZE`) +- Naming: `{MANAGER}_{CATEGORY}_{SETTING}` (e.g., `GRAFEO_DB_PATH`) - Provide **sensible defaults** in code if env var missing - Comma-separated for lists (e.g., `ARCHIMATE_ELEMENT_TYPES=Component,Service`) - Boolean as string: `true`/`false` (case-insensitive) @@ -1764,7 +1763,7 @@ def _(session, mo): | `run_derivation(...)` | Run derivation pipeline | | `run_pipeline(...)` | Run full pipeline | | `export_model(path, name)` | Export ArchiMate XML | -| `start_neo4j()` / `stop_neo4j()` | Container control | +| `start_graph_db()` / `stop_graph_db()` | Graph database control | | `clear_graph()` / `clear_model()` | Clear data | @@ -1853,7 +1852,7 @@ def test_add_and_get_node(): assert retrieved['id'] == 'test1' ``` -Adapter tests may require external services (Neo4j, DuckDB) - use fixtures for setup/teardown. +Adapter tests may require external services (DuckDB) - use fixtures for setup/teardown. --- @@ -1892,7 +1891,7 @@ This project includes several specialized documentation files: | LLM Adapter | [deriva/adapters/llm/README.md](deriva/adapters/llm/README.md) | | Graph Adapter | [deriva/adapters/graph/README.md](deriva/adapters/graph/README.md) | | Database Adapter | [deriva/adapters/database/README.md](deriva/adapters/database/README.md) | -| Neo4j Adapter | [deriva/adapters/neo4j/README.md](deriva/adapters/neo4j/README.md) | +| Grafeo Adapter | [deriva/adapters/grafeo/README.md](deriva/adapters/grafeo/README.md) | | ArchiMate Adapter | [deriva/adapters/archimate/README.md](deriva/adapters/archimate/README.md) | | Repository Adapter | [deriva/adapters/repository/README.md](deriva/adapters/repository/README.md) | | Marimo App | [deriva/app/README.md](deriva/app/README.md) | diff --git a/OPTIMIZATION.md b/OPTIMIZATION.md index 33f61b9..66cdf7b 100644 --- a/OPTIMIZATION.md +++ b/OPTIMIZATION.md @@ -476,7 +476,7 @@ enrichments = enrich.enrich_graph( edges=edges, algorithms=['pagerank', 'louvain', 'kcore', 'articulation_points', 'degree'] ) -# Write to Neo4j: graph_manager.batch_update_properties(enrichments) +# Write to graph: graph_manager.batch_update_properties(enrichments) ``` diff --git a/README.md b/README.md index f662fc6..657afd4 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,7 @@ [![Build Status](https://github.com/StevenBtw/Deriva/actions/workflows/ci.yml/badge.svg)](https://github.com/StevenBtw/Deriva/actions/workflows/ci.yml) [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](LICENSE) [![Python 3.14+](https://img.shields.io/badge/python-3.14+-blue.svg)](https://www.python.org/downloads/) -[![Neo4j](https://img.shields.io/badge/Neo4j-5.x-008CC1.svg?logo=neo4j)](https://neo4j.com/) -[![Docker](https://img.shields.io/badge/Docker-required-2496ED.svg?logo=docker)](https://www.docker.com/) +[![Grafeo](https://img.shields.io/badge/Grafeo-embedded-green.svg)](https://github.com/StevenBtw/grafeo) [![Marimo](https://img.shields.io/badge/Marimo-notebook-orange.svg)](https://marimo.io/) **Automatically generate ArchiMate enterprise architecture models from software repositories.** @@ -14,7 +13,7 @@ Deriva analyzes code repositories and transforms them into [ArchiMate](https://w ## How It Works 1. **Clone** a Git repository -2. **Extraction** - Build a graph representation in Neo4j: +2. **Extraction** - Build a graph representation: - **Classify phase**: Categorize files by type and subtype using registry - **Parse phase**: Extract semantic nodes (TypeDefinitions, Methods, BusinessConcepts, etc.) - Python files use fast AST parsing; other languages use LLM @@ -29,7 +28,6 @@ Deriva analyzes code repositories and transforms them into [ArchiMate](https://w ### Prerequisites - **Python 3.14+** -- **Docker** (for Neo4j) - **uv** (Python package manager) ### 1. Install uv @@ -50,7 +48,7 @@ cd Deriva # Create environment configuration cp .env.example .env -# Edit .env with your settings (Neo4j, LLM API keys, etc.) +# Edit .env with your settings (LLM API keys, etc.) ``` ### 3. Create Python Environment @@ -78,25 +76,7 @@ source .venv/bin/activate uv sync ``` -### 5. Start Neo4j - -```bash -cd deriva/adapters/neo4j -docker-compose up -d -``` - -Neo4j will be available at: - -- **Browser UI**: http://localhost:7474 (no authentication) -- **Bolt Protocol**: `bolt://localhost:7687` - -Verify Neo4j is running: - -```bash -docker ps # Should show deriva_neo4j container -``` - -### 6. Launch Deriva +### 5. Launch Deriva ```bash cd ../../.. # Back to Deriva root @@ -205,10 +185,8 @@ deriva export -o workspace/output/model.xml All configuration lives in `.env`. Key settings: ```bash -# Neo4j (default docker-compose has auth disabled) -NEO4J_URI=bolt://localhost:7687 -NEO4J_USERNAME= -NEO4J_PASSWORD= +# Graph database (grafeo embedded) +GRAFEO_DB_PATH= # Empty = in-memory, path = persistent file # LLM Provider (mistral, openai, azure, anthropic, ollama, lmstudio) LLM_MISTRAL_DEVSTRAL_PROVIDER=mistral @@ -218,7 +196,7 @@ LLM_MISTRAL_DEVSTRAL_KEY=your-mistral-api-key LLM_MISTRAL_DEVSTRAL_STRUCTURED_OUTPUT=true # Namespaces -NEO4J_GRAPH_NAMESPACE=Graph +GRAPH_NAMESPACE=Graph ARCHIMATE_NAMESPACE=Model ``` @@ -345,7 +323,7 @@ Deriva uses a multi-column marimo notebook layout: | Column | Purpose | |--------|---------| | **0** | **Run Deriva**: Pipeline execution buttons, status display | -| **1** | **Configuration**: Runs, repositories, Neo4j, graph stats, ArchiMate, LLM | +| **1** | **Configuration**: Runs, repositories, graph database, graph stats, ArchiMate, LLM | | **2** | **Extraction Settings**: File type registry, extraction step configuration | | **3** | **Derivation Settings**: Element type configuration (13 types across Business/Application/Technology layers), relationship derivation | @@ -355,7 +333,7 @@ The UI is powered by `PipelineSession` from the services layer, providing a clea ## Data Storage -- **Neo4j Graph Database**: +- **Grafeo** (embedded graph database): - **Graph namespace**: Intermediate representation (Modules, Files, Dependencies) - **Model namespace**: ArchiMate elements and relationships - **DuckDB** (`deriva/adapters/database/sql.db`): File type registry, extraction configs, settings @@ -369,9 +347,9 @@ The UI is powered by `PipelineSession` from the services layer, providing a clea --- -## Querying Neo4j Directly +## Querying the Graph -Access the Neo4j browser at http://localhost:7474 and run Cypher queries: +You can query the embedded grafeo graph database using Cypher via the CLI or Marimo notebook: ```cypher // See all repositories @@ -484,38 +462,6 @@ OCEL files can be analyzed with process mining tools like PM4Py, Celonis, or cus ## Troubleshooting -### Neo4j Connection Issues - -```bash -# Check if running -docker ps - -# View logs -cd deriva/adapters/neo4j && docker-compose logs - -# Restart -docker-compose restart - -# Clear all data (destructive!) -docker-compose down -v -``` - -### Port Conflicts - -If ports 7687/7474 are in use, edit `deriva/adapters/neo4j/docker-compose.yml`: - -```yaml -ports: - - "7688:7687" - - "7475:7474" -``` - -Update `.env` accordingly: - -```bash -NEO4J_URI=bolt://localhost:7688 -``` - ### Marimo Issues ```bash @@ -548,7 +494,7 @@ See [LICENSE](LICENSE) for the full license text. ## Acknowledgments - [Marimo](https://marimo.io) - Reactive Python notebooks -- [Neo4j](https://neo4j.com) - Graph database +- [Grafeo](https://github.com/StevenBtw/grafeo) - Embedded graph database - [ArchiMate](https://www.opengroup.org/archimate-forum) - Enterprise architecture standard - [Archi](https://www.archimatetool.com) - Open source ArchiMate modeling tool - [Tree-sitter](https://tree-sitter.github.io/tree-sitter/) - Multi-language AST parsing diff --git a/_typos.toml b/_typos.toml new file mode 100644 index 0000000..dfc4dcc --- /dev/null +++ b/_typos.toml @@ -0,0 +1,26 @@ +# typos configuration +# https://github.com/crate-ci/typos + +[files] +extend-exclude = [ + ".venv/", + "*.lock", + "workspace/", + "reference/", + "deriva/adapters/archimate/archimate_xsd/", + ".pytest_cache/", + ".ruff_cache/", + "*.db", +] + +[default.extend-words] +# ArchiMate element ID prefixes (ba_ = BusinessActor, nd_ = Node) +ba = "ba" +nd = "nd" + +[default.extend-identifiers] +# Lemmatizer suffix-stripping results (intentional truncated forms) +continu = "continu" +processe = "processe" +ment = "ment" +ful = "ful" diff --git a/deriva/adapters/archimate/README.md b/deriva/adapters/archimate/README.md index 1f2b270..1a4869d 100644 --- a/deriva/adapters/archimate/README.md +++ b/deriva/adapters/archimate/README.md @@ -1,12 +1,12 @@ # ArchiMate Adapter -Create, validate, and export ArchiMate enterprise architecture models using Neo4j. +Create, validate, and export ArchiMate enterprise architecture models using grafeo (embedded). **Version:** 2.0.0 ## Purpose -The ArchiMate adapter stores derived ArchiMate elements and relationships in Neo4j (namespace: `Model`), validates them against the ArchiMate 3.2 metamodel, and exports to XML format compatible with the [Archi](https://www.archimatetool.com/) modeling tool. +The ArchiMate adapter stores derived ArchiMate elements and relationships in grafeo (namespace: `Model`), validates them against the ArchiMate 3.2 metamodel, and exports to XML format compatible with the [Archi](https://www.archimatetool.com/) modeling tool. ## Key Exports @@ -90,7 +90,7 @@ deriva/adapters/archimate/ ## Data Isolation -Uses Neo4j with namespace `Model` for label prefixing (e.g., `Model:ApplicationComponent`), keeping ArchiMate data separate from the Graph namespace. +Uses grafeo with namespace `Model` for label prefixing (e.g., `Model:ApplicationComponent`), keeping ArchiMate data separate from the Graph namespace. ## See Also diff --git a/deriva/adapters/archimate/manager.py b/deriva/adapters/archimate/manager.py index 3c45bc9..70d16bb 100644 --- a/deriva/adapters/archimate/manager.py +++ b/deriva/adapters/archimate/manager.py @@ -1,7 +1,7 @@ -"""ArchiMate Manager Service - Main interface for ArchiMate operations using Neo4j. +"""ArchiMate Manager Service - Main interface for ArchiMate operations. This module provides the ArchimateManager class which handles all ArchiMate model -operations using the shared neo4j_manager service with namespace isolation. +operations using the shared grafeo connection with namespace isolation. Usage: from deriva.adapters.archimate import ArchimateManager @@ -32,7 +32,7 @@ from dotenv import load_dotenv -from deriva.adapters.neo4j import Neo4jConnection +from deriva.adapters.grafeo import GrafeoConnection from .models import ArchiMateMetamodel, Element, Relationship from .validation import ArchiMateValidator, ValidationError @@ -41,7 +41,7 @@ class ArchimateManager: - """Manage ArchiMate models in Neo4j. + """Manage ArchiMate models in grafeo. This class provides a high-level interface for: - Creating and managing ArchiMate elements and relationships @@ -49,7 +49,7 @@ class ArchimateManager: - Querying model structure - Exporting to ArchiMate XML format - Uses the shared neo4j_manager service with "ArchiMate" namespace. + Uses the shared grafeo connection with "Model" namespace. """ def __init__(self): @@ -59,11 +59,8 @@ def __init__(self): """ load_dotenv() - self.neo4j: Neo4jConnection | None = None - # Try both env var names for backward compatibility - self.namespace = os.getenv("ARCHIMATE_NAMESPACE") or os.getenv( - "NEO4J_NAMESPACE_ARCHIMATE", "Model" - ) + self.db: GrafeoConnection | None = None + self.namespace = os.getenv("ARCHIMATE_NAMESPACE", "Model") self.metamodel = ArchiMateMetamodel() self.validator = ArchiMateValidator( strict_mode=os.getenv("ARCHIMATE_VALIDATION_STRICT_MODE", "false").lower() @@ -73,30 +70,29 @@ def __init__(self): logger.info(f"Initialized ArchimateManager with namespace: {self.namespace}") def connect(self) -> None: - """Establish connection to Neo4j via neo4j_manager.""" - if self.neo4j is not None: + """Establish connection to the graph database.""" + if self.db is not None: logger.warning("Connection already established") return try: - # Create Neo4j connection with namespace - self.neo4j = Neo4jConnection(namespace=self.namespace) - self.neo4j.connect() + self.db = GrafeoConnection(namespace=self.namespace) + self.db.connect() logger.info( - f"Successfully connected to Neo4j with namespace '{self.namespace}'" + f"Successfully connected to grafeo with namespace '{self.namespace}'" ) except Exception as e: - logger.error(f"Failed to connect to Neo4j: {e}") - raise ConnectionError(f"Could not connect to Neo4j: {e}") + logger.error(f"Failed to connect to grafeo: {e}") + raise ConnectionError(f"Could not connect to grafeo: {e}") def disconnect(self) -> None: - """Close the Neo4j connection.""" - if self.neo4j is not None: - self.neo4j.disconnect() - self.neo4j = None - logger.info("Disconnected from Neo4j") + """Close the graph database connection.""" + if self.db is not None: + self.db.disconnect() + self.db = None + logger.info("Disconnected from grafeo") def __enter__(self) -> ArchimateManager: """Context manager entry.""" @@ -121,10 +117,10 @@ def add_element(self, element: Element, validate: bool = True) -> str: Raises: ValidationError: If validation fails - RuntimeError: If not connected to Neo4j + RuntimeError: If not connected to grafeo """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") # Validate element if validate: @@ -138,7 +134,7 @@ def add_element(self, element: Element, validate: bool = True) -> str: # This allows queries like MATCH (e:TechnologyService) to work # while still having namespace isolation via the Model label - # Convert properties to JSON string (Neo4j can't store empty dicts) + # Convert properties to JSON string properties_json = ( json.dumps(element.properties) if element.properties else None ) @@ -159,7 +155,7 @@ def add_element(self, element: Element, validate: bool = True) -> str: RETURN e.identifier as identifier """ - result = self.neo4j.execute_write( + result = self.db.execute_write( query, { "identifier": element.identifier, @@ -197,10 +193,10 @@ def add_relationship( Raises: ValidationError: If validation fails - RuntimeError: If not connected to Neo4j + RuntimeError: If not connected to grafeo """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") # Validate relationship if validate: @@ -220,7 +216,7 @@ def add_relationship( ) # Get namespaced relationship type (e.g., "Realization" -> "Model:Realization") - rel_label = self.neo4j.get_label(relationship.relationship_type) + rel_label = self.db.get_label(relationship.relationship_type) query = f""" MATCH (source:`{self.namespace}` {{identifier: $source}}) @@ -234,7 +230,7 @@ def add_relationship( RETURN r.identifier as identifier """ - result = self.neo4j.execute_write( + result = self.db.execute_write( query, { "source": relationship.source, @@ -269,8 +265,8 @@ def get_element(self, identifier: str) -> Element | None: Returns: Element or None if not found """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: # Find element by identifier - nodes have namespace label (Model) + type label @@ -284,7 +280,7 @@ def get_element(self, identifier: str) -> Element | None: e.enabled as enabled """ - result = self.neo4j.execute_read(query, {"identifier": identifier}) + result = self.db.execute_read(query, {"identifier": identifier}) if result: data = result[0] @@ -324,8 +320,8 @@ def get_elements( Returns: List of elements """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: enabled_filter = "AND e.enabled = true" if enabled_only else "" @@ -341,7 +337,7 @@ def get_elements( e.properties_json as properties_json, e.enabled as enabled """ - result = self.neo4j.execute_read(query) + result = self.db.execute_read(query) # All elements have same type elements = [] for data in result: @@ -372,7 +368,7 @@ def get_elements( e.properties_json as properties_json, e.enabled as enabled """ - result = self.neo4j.execute_read(query) + result = self.db.execute_read(query) elements = [] for data in result: # Element type is the non-namespace label @@ -411,8 +407,8 @@ def get_relationships( Returns: List of relationships """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: ns = self.namespace @@ -468,7 +464,7 @@ def get_relationships( """ params = {} - result = self.neo4j.execute_read(query, params) + result = self.db.execute_read(query, params) relationships = [] for data in result: @@ -502,12 +498,12 @@ def get_relationships( raise def clear_model(self) -> None: - """Clear all ArchiMate elements and relationships from Neo4j.""" - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + """Clear all ArchiMate elements and relationships from the graph.""" + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: - self.neo4j.clear_namespace() + self.db.clear_namespace() logger.info(f"Cleared all ArchiMate data from namespace '{self.namespace}'") except Exception as e: @@ -526,11 +522,11 @@ def query( Returns: Query results as list of dictionaries """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: - return self.neo4j.execute(cypher_query, params) + return self.db.execute(cypher_query, params) except Exception as e: logger.error(f"Query failed: {e}") @@ -546,8 +542,8 @@ def disable_element(self, identifier: str, reason: str | None = None) -> bool: Returns: True if element was disabled, False if not found """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: query = f""" @@ -556,7 +552,7 @@ def disable_element(self, identifier: str, reason: str | None = None) -> bool: e.disabled_reason = $reason RETURN e.identifier as identifier """ - result = self.neo4j.execute_write( + result = self.db.execute_write( query, {"identifier": identifier, "reason": reason} ) @@ -581,8 +577,8 @@ def disable_elements( Returns: Number of elements disabled """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") if not identifiers: return 0 @@ -595,7 +591,7 @@ def disable_elements( e.disabled_reason = $reason RETURN count(e) as count """ - result = self.neo4j.execute_write( + result = self.db.execute_write( query, {"identifiers": identifiers, "reason": reason} ) @@ -616,8 +612,8 @@ def delete_relationship(self, identifier: str) -> bool: Returns: True if relationship was deleted, False if not found """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: # Match relationships between Model namespace nodes @@ -627,7 +623,7 @@ def delete_relationship(self, identifier: str) -> bool: DELETE r RETURN count(r) as count """ - result = self.neo4j.execute_write(query, {"identifier": identifier}) + result = self.db.execute_write(query, {"identifier": identifier}) if result and result[0]["count"] > 0: logger.debug(f"Deleted relationship: {identifier}") @@ -647,8 +643,8 @@ def delete_relationships(self, identifiers: list[str]) -> int: Returns: Number of relationships deleted """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") if not identifiers: return 0 @@ -661,7 +657,7 @@ def delete_relationships(self, identifiers: list[str]) -> int: DELETE r RETURN count(r) as count """ - result = self.neo4j.execute_write(query, {"identifiers": identifiers}) + result = self.db.execute_write(query, {"identifiers": identifiers}) count = result[0]["count"] if result else 0 logger.info(f"Deleted {count} relationships") diff --git a/deriva/adapters/grafeo/__init__.py b/deriva/adapters/grafeo/__init__.py new file mode 100644 index 0000000..bd42f72 --- /dev/null +++ b/deriva/adapters/grafeo/__init__.py @@ -0,0 +1,22 @@ +"""Grafeo Adapter - Embedded graph database connection for Deriva. + +This package provides an embedded graph database connection using grafeo, +providing an embedded alternative to external graph databases. Multiple managers share a single +database instance with namespace isolation via label prefixes. + +Example: + >>> from deriva.adapters.grafeo import GrafeoConnection + >>> + >>> conn = GrafeoConnection(namespace="Graph") + >>> conn.connect() + >>> + >>> conn.execute("CREATE (n:Repository {name: $name}) RETURN n", {"name": "my-repo"}) + >>> + >>> conn.disconnect() +""" + +from __future__ import annotations + +from .manager import GrafeoConnection, close_database, get_database + +__all__ = ["GrafeoConnection", "close_database", "get_database"] diff --git a/deriva/adapters/grafeo/manager.py b/deriva/adapters/grafeo/manager.py new file mode 100644 index 0000000..32f0478 --- /dev/null +++ b/deriva/adapters/grafeo/manager.py @@ -0,0 +1,263 @@ +"""Grafeo Connection Service - Embedded graph database for Deriva. + +Embedded graph database connection for Deriva. +Provides the namespace-isolated interface that GraphManager and +ArchimateManager expect. + +Features: +- Embedded graph database (no external server) +- Cypher query language support +- Namespace isolation via label prefixes +- Configurable storage: in-memory (default) or persistent file + +Usage: + from deriva.adapters.grafeo import GrafeoConnection + + conn = GrafeoConnection(namespace="Graph") + conn.connect() + + result = conn.execute("MATCH (n) RETURN count(n) as count") + print(f"Total nodes: {result[0]['count']}") + + conn.disconnect() +""" + +from __future__ import annotations + +import logging +import os +from typing import Any + +from dotenv import load_dotenv + +logger = logging.getLogger(__name__) + +# --------------------------------------------------------------------------- +# Shared database singleton +# --------------------------------------------------------------------------- + +_db: Any | None = None + + +def get_database() -> Any: + """Get or create the shared GrafeoDB instance. + + Storage mode is controlled by the GRAFEO_DB_PATH environment variable: + - Not set or empty: in-memory database (fastest, fresh each session) + - Set to a path: persistent database file + + Returns: + GrafeoDB instance shared across all connections. + """ + global _db + if _db is None: + from grafeo import GrafeoDB + + load_dotenv() + path = os.getenv("GRAFEO_DB_PATH") or None + _db = GrafeoDB(path) + + mode = f"persistent ({path})" if path else "in-memory" + logger.info("Created shared GrafeoDB instance (%s)", mode) + + return _db + + +def close_database() -> None: + """Close and release the shared GrafeoDB instance.""" + global _db + if _db is not None: + logger.info("Closing shared GrafeoDB instance") + _db = None + + +# --------------------------------------------------------------------------- +# GrafeoConnection +# --------------------------------------------------------------------------- + + +class GrafeoConnection: + """Embedded graph database connection with namespace support. + + All managers share a single embedded GrafeoDB instance; namespace + isolation works via label prefixes (dual-label scheme). + + Example: + >>> conn = GrafeoConnection(namespace="Graph") + >>> conn.connect() + >>> conn.execute("CREATE (n:Repository {name: $name})", {"name": "test"}) + >>> conn.disconnect() + """ + + def __init__(self, namespace: str): + """Initialize connection for a given namespace. + + Args: + namespace: Label prefix for this manager (e.g. "Graph", "Model"). + """ + self.namespace = namespace + self.db: Any | None = None + self._log_queries = False + + load_dotenv() + self._log_queries = os.getenv("GRAFEO_LOG_QUERIES", "false").lower() == "true" + + logger.info("Initialized GrafeoConnection with namespace: %s", namespace) + + # ------------------------------------------------------------------ + # Lifecycle + # ------------------------------------------------------------------ + + def connect(self) -> None: + """Connect to the shared embedded database.""" + if self.db is not None: + logger.warning("Connection already established") + return + + self.db = get_database() + logger.info("Connected to grafeo (namespace '%s')", self.namespace) + + def disconnect(self) -> None: + """Release reference to the shared database. + + The underlying database stays alive (singleton). Call + ``close_database()`` to fully shut down. + """ + if self.db is not None: + self.db = None + logger.info("Disconnected from grafeo (namespace '%s')", self.namespace) + + def __enter__(self) -> GrafeoConnection: + """Context manager entry.""" + self.connect() + return self + + def __exit__( + self, exc_type: type | None, exc_val: Exception | None, exc_tb: Any + ) -> None: + """Context manager exit.""" + self.disconnect() + + # ------------------------------------------------------------------ + # Query execution + # ------------------------------------------------------------------ + + def execute( + self, + query: str, + parameters: dict[str, Any] | None = None, + database: str | None = None, + ) -> list[dict[str, Any]]: + """Execute a Cypher query and return results as list of dicts. + + Args: + query: Cypher query string. + parameters: Query parameters (``$param`` syntax). + database: Ignored (single embedded database). + + Returns: + List of result records as dictionaries. + """ + if self.db is None: + raise RuntimeError( + f"Not connected to grafeo. Call connect() first. " + f"(Namespace: {self.namespace})" + ) + + if self._log_queries: + logger.debug("Executing query: %s", query) + logger.debug("Parameters: %s", parameters) + + try: + params = parameters if parameters is not None else {} + result = self.db.execute_cypher(query, params) + return result.to_list() + + except Exception as e: + logger.error("Query execution failed: %s", e) + logger.error("Query: %s", query) + logger.error("Parameters: %s", parameters) + raise + + def execute_write( + self, + query: str, + parameters: dict[str, Any] | None = None, + database: str | None = None, + ) -> list[dict[str, Any]]: + """Execute a write query (CREATE, MERGE, DELETE). + + In embedded mode there is no read/write distinction; this delegates + to ``execute()``. + """ + return self.execute(query, parameters, database) + + def execute_read( + self, + query: str, + parameters: dict[str, Any] | None = None, + database: str | None = None, + ) -> list[dict[str, Any]]: + """Execute a read query (MATCH, RETURN). + + In embedded mode there is no read/write distinction; this delegates + to ``execute()``. + """ + return self.execute(query, parameters, database) + + # ------------------------------------------------------------------ + # Namespace helpers + # ------------------------------------------------------------------ + + def get_label(self, base_label: str) -> str: + """Get namespaced label. + + Args: + base_label: Base label name (e.g. "Repository", "Element"). + + Returns: + Namespaced label (e.g. "Graph:Repository", "Model:Element"). + """ + return f"{self.namespace}:{base_label}" + + def clear_namespace(self) -> None: + """Delete all nodes and relationships in this namespace.""" + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") + + try: + self.execute( + "MATCH (n) " + "WHERE any(label IN labels(n) WHERE label STARTS WITH $namespace) " + "DETACH DELETE n", + {"namespace": self.namespace}, + ) + logger.info("Cleared all data for namespace: %s", self.namespace) + + except Exception as e: + logger.error("Failed to clear namespace %s: %s", self.namespace, e) + raise + + # ------------------------------------------------------------------ + # Schema (no-ops for embedded grafeo) + # ------------------------------------------------------------------ + + def create_constraint( + self, label: str, property_key: str, constraint_name: str | None = None + ) -> None: + """Create a uniqueness constraint (no-op in grafeo).""" + logger.debug( + "create_constraint is a no-op in grafeo (label=%s, property=%s)", + label, + property_key, + ) + + def create_index( + self, label: str, property_key: str, index_name: str | None = None + ) -> None: + """Create an index (no-op in grafeo).""" + logger.debug( + "create_index is a no-op in grafeo (label=%s, property=%s)", + label, + property_key, + ) diff --git a/deriva/adapters/graph/README.md b/deriva/adapters/graph/README.md index 2587757..e755382 100644 --- a/deriva/adapters/graph/README.md +++ b/deriva/adapters/graph/README.md @@ -1,12 +1,12 @@ # Graph Adapter -Property graph database for storing repository structure, code elements, and their relationships using Neo4j. +Property graph database for storing repository structure, code elements, and their relationships using grafeo (embedded). **Version:** 1.0.0 ## Purpose -The Graph adapter stores extracted repository information in Neo4j (namespace: `Graph`). It maintains the intermediate representation between raw code and ArchiMate models, including files, directories, type definitions, business concepts, and their relationships. +The Graph adapter stores extracted repository information in grafeo (namespace: `Graph`). It maintains the intermediate representation between raw code and ArchiMate models, including files, directories, type definitions, business concepts, and their relationships. ## Key Exports @@ -113,7 +113,7 @@ deriva/adapters/graph/ ## Data Isolation -Uses Neo4j with namespace `Graph` for label prefixing (e.g., `Graph:Repository`, `Graph:File`), keeping extraction data separate from the ArchiMate namespace. +Uses grafeo with namespace `Graph` for label prefixing (e.g., `Graph:Repository`, `Graph:File`), keeping extraction data separate from the ArchiMate namespace. ## See Also diff --git a/deriva/adapters/graph/__init__.py b/deriva/adapters/graph/__init__.py index d45f159..04ffb62 100644 --- a/deriva/adapters/graph/__init__.py +++ b/deriva/adapters/graph/__init__.py @@ -1,6 +1,6 @@ -"""Graph Manager - Neo4j-based graph database for repository structure. +"""Graph Manager - Grafeo-based graph database for repository structure. -This module provides a property graph database using Neo4j +This module provides a property graph database using grafeo (embedded) to store and query repository structure, dependencies, and relationships. """ diff --git a/deriva/adapters/graph/cache.py b/deriva/adapters/graph/cache.py index 8118abc..8ca1c07 100644 --- a/deriva/adapters/graph/cache.py +++ b/deriva/adapters/graph/cache.py @@ -1,7 +1,7 @@ """ Caching functionality for graph operations. -Provides caching for expensive Neo4j queries like enrichment fetching. +Provides caching for expensive graph queries like enrichment fetching. Uses graph state hash to detect when cache should be invalidated. """ @@ -85,8 +85,8 @@ class EnrichmentCache(BaseDiskCache): if cached := cache.get_enrichments(graph_hash): return cached - # Compute enrichments from Neo4j - enrichments = get_enrichments_from_neo4j(graph_manager) + # Compute enrichments from graph + enrichments = get_enrichments_from_graph(graph_manager) cache.set_enrichments(graph_hash, enrichments) return enrichments """ diff --git a/deriva/adapters/graph/manager.py b/deriva/adapters/graph/manager.py index 6d38210..7f9b61d 100644 --- a/deriva/adapters/graph/manager.py +++ b/deriva/adapters/graph/manager.py @@ -1,7 +1,7 @@ -"""Graph Manager - Main interface for graph operations using Neo4j. +"""Graph Manager - Main interface for graph operations. This module provides the GraphManager class which handles all graph database -operations using the shared Neo4j connection with namespace isolation. +operations using the shared grafeo connection with namespace isolation. Usage: from deriva.adapters.graph import GraphManager @@ -31,8 +31,7 @@ from dotenv import load_dotenv -# Import Neo4j connection from the neo4j manager package -from deriva.adapters.neo4j import Neo4jConnection +from deriva.adapters.grafeo import GrafeoConnection from .models import ( BusinessConceptNode, @@ -129,7 +128,7 @@ def _extract_repo_from_node_id(node_id: str) -> str | None: class GraphManager: - """Manages graph database operations using Neo4j. + """Manages graph database operations using grafeo (embedded). This class provides a high-level interface for: - Creating and managing property graphs @@ -137,7 +136,7 @@ class GraphManager: - Querying graph structure with Cypher - Traversing relationships - Uses the shared neo4j_manager service with "Graph" namespace. + Uses the shared grafeo connection with "Graph" namespace. Example: from deriva.adapters.graph import GraphManager @@ -156,36 +155,35 @@ class GraphManager: def __init__(self): """Initialize the GraphManager using .env configuration.""" load_dotenv() - self.neo4j: Neo4jConnection | None = None - self.namespace = os.getenv("NEO4J_GRAPH_NAMESPACE", "Graph") + self.db: GrafeoConnection | None = None + self.namespace = os.getenv("GRAPH_NAMESPACE", "Graph") logger.info(f"Initializing GraphManager with namespace: {self.namespace}") def connect(self) -> None: - """Establish connection to Neo4j via neo4j_manager.""" - if self.neo4j is not None: + """Establish connection to the graph database.""" + if self.db is not None: logger.warning("Connection already established") return try: - # Create Neo4j connection with namespace - self.neo4j = Neo4jConnection(namespace=self.namespace) - self.neo4j.connect() + self.db = GrafeoConnection(namespace=self.namespace) + self.db.connect() logger.info( - f"Successfully connected to Neo4j with namespace '{self.namespace}'" + f"Successfully connected to grafeo with namespace '{self.namespace}'" ) except Exception as e: - logger.error(f"Failed to connect to Neo4j: {e}") - raise ConnectionError(f"Could not connect to Neo4j: {e}") + logger.error(f"Failed to connect to grafeo: {e}") + raise ConnectionError(f"Could not connect to grafeo: {e}") def disconnect(self) -> None: - """Close the Neo4j connection.""" - if self.neo4j is not None: - self.neo4j.disconnect() - self.neo4j = None - logger.info("Disconnected from Neo4j") + """Close the graph database connection.""" + if self.db is not None: + self.db.disconnect() + self.db = None + logger.info("Disconnected from grafeo") def __enter__(self) -> GraphManager: """Context manager entry.""" @@ -208,8 +206,8 @@ def add_node(self, node: GraphNode, node_id: str | None = None) -> str: Returns: The node ID """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") # Generate node ID if not provided - use node's generate_id() method if node_id is None: @@ -225,7 +223,7 @@ def add_node(self, node: GraphNode, node_id: str | None = None) -> str: properties_json = json.dumps(properties) if properties else None # Extract scalar properties to store directly on node - # Neo4j can store: strings, numbers, booleans, and arrays of these + # Graph can store: strings, numbers, booleans, and arrays of these flat_props = {} for key, value in properties.items(): if isinstance(value, (str, int, float, bool)) or value is None: @@ -267,7 +265,7 @@ def add_node(self, node: GraphNode, node_id: str | None = None) -> str: RETURN n.id as id """ - result = self.neo4j.execute_write(query, params) + result = self.db.execute_write(query, params) if result: logger.debug(f"Added node: {node_id} ({node_label})") @@ -299,8 +297,8 @@ def add_edge( Returns: The edge ID """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") # Generate edge ID if not provided if edge_id is None: @@ -313,7 +311,7 @@ def add_edge( try: # Use relationship type as the label (e.g., Graph:CONTAINS) - edge_label = self.neo4j.get_label(relationship) + edge_label = self.db.get_label(relationship) query = f""" MATCH (src) WHERE src.id = $src_id @@ -323,7 +321,7 @@ def add_edge( RETURN r.id as id """ - result = self.neo4j.execute_write( + result = self.db.execute_write( query, { "src_id": src_id, @@ -356,13 +354,13 @@ def update_node_property( Args: node_id: Node ID to update property_name: Property name to set - value: Property value (must be Neo4j-compatible: str, int, float, bool, list) + value: Property value (must be graph-compatible: str, int, float, bool, list) Returns: True if updated, False if node not found """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: query = f""" @@ -371,9 +369,7 @@ def update_node_property( RETURN n.id as id """ - result = self.neo4j.execute_write( - query, {"node_id": node_id, "value": value} - ) + result = self.db.execute_write(query, {"node_id": node_id, "value": value}) if result: logger.debug(f"Updated {property_name}={value} on node {node_id}") @@ -397,8 +393,8 @@ def update_nodes_property( Returns: Number of nodes updated """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") if not node_ids: return 0 @@ -411,7 +407,7 @@ def update_nodes_property( RETURN count(n) as updated """ - result = self.neo4j.execute_write( + result = self.db.execute_write( query, {"node_ids": node_ids, "value": value} ) @@ -441,8 +437,8 @@ def batch_update_properties(self, updates: dict[str, dict[str, Any]]) -> int: Returns: Number of nodes updated """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") if not updates: return 0 @@ -462,7 +458,7 @@ def batch_update_properties(self, updates: dict[str, dict[str, Any]]) -> int: for node_id, props in updates.items() ] - result = self.neo4j.execute_write(query, {"updates": update_list}) + result = self.db.execute_write(query, {"updates": update_list}) if result: count = result[0]["updated"] @@ -483,8 +479,8 @@ def get_node(self, node_id: str) -> dict[str, Any] | None: Returns: Node data as dictionary or None if not found """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: query = """ @@ -495,7 +491,7 @@ def get_node(self, node_id: str) -> dict[str, Any] | None: n.properties_json as properties_json """ - result = self.neo4j.execute_read(query, {"node_id": node_id}) + result = self.db.execute_read(query, {"node_id": node_id}) if result: data = result[0] @@ -525,8 +521,8 @@ def node_exists(self, node_id: str) -> bool: Returns: True if node exists, False otherwise """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: query = """ @@ -534,7 +530,7 @@ def node_exists(self, node_id: str) -> bool: WHERE n.id = $node_id RETURN count(n) > 0 as exists """ - result = self.neo4j.execute_read(query, {"node_id": node_id}) + result = self.db.execute_read(query, {"node_id": node_id}) return result[0]["exists"] if result else False except Exception as e: @@ -550,8 +546,8 @@ def get_nodes_by_type(self, node_type: str) -> list[dict[str, Any]]: Returns: List of node dictionaries """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: # Query by node type label directly @@ -563,7 +559,7 @@ def get_nodes_by_type(self, node_type: str) -> list[dict[str, Any]]: n.properties_json as properties_json """ - result = self.neo4j.execute_read(query) + result = self.db.execute_read(query) nodes = [] for data in result: @@ -592,8 +588,8 @@ def delete_node(self, node_id: str) -> bool: Returns: True if deleted, False if not found """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: query = """ @@ -602,7 +598,7 @@ def delete_node(self, node_id: str) -> bool: RETURN count(n) as deleted """ - result = self.neo4j.execute_write(query, {"node_id": node_id}) + result = self.db.execute_write(query, {"node_id": node_id}) if result and result[0]["deleted"] > 0: logger.debug(f"Deleted node: {node_id}") @@ -625,11 +621,11 @@ def query( Returns: Query results as list of dictionaries """ - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: - return self.neo4j.execute(cypher_query, params) + return self.db.execute(cypher_query, params) except Exception as e: logger.error(f"Query failed: {e}") @@ -637,11 +633,11 @@ def query( def clear_graph(self) -> None: """Clear all nodes and edges from the graph.""" - if self.neo4j is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") + if self.db is None: + raise RuntimeError("Not connected to grafeo. Call connect() first.") try: - self.neo4j.clear_namespace() + self.db.clear_namespace() logger.info(f"Cleared all graph data from namespace '{self.namespace}'") except Exception as e: diff --git a/deriva/adapters/graph/models.py b/deriva/adapters/graph/models.py index ceb6e8e..84ed72b 100644 --- a/deriva/adapters/graph/models.py +++ b/deriva/adapters/graph/models.py @@ -1,7 +1,7 @@ """Graph models for repository structure. This module defines the node and relationship models for representing -repository structure in Neo4j. +repository structure in the graph database. """ from __future__ import annotations @@ -85,7 +85,7 @@ def generate_id(self) -> str: return f"Repository_{self.name}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "repoName": self.name, # Use metamodel field name "url": self.url, @@ -114,7 +114,7 @@ def generate_id(self) -> str: return f"Directory_{self.repository_name}_{safe_path}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "name": self.name, "path": normalize_path(self.path, self.repository_name), @@ -140,7 +140,7 @@ def generate_id(self) -> str: return f"Module_{self.repository_name}_{self.name}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "name": self.name, "paths": [normalize_path(p, self.repository_name) for p in self.paths], @@ -171,7 +171,7 @@ def generate_id(self) -> str: return f"File_{self.repository_name}_{safe_path}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "fileName": self.name, # Use metamodel field name "filePath": normalize_path( @@ -227,7 +227,7 @@ def generate_id(self) -> str: return f"BusinessConcept_{self.repository_name}_{self.name}_{self.concept_type}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "conceptName": self.name, "conceptType": self.concept_type, @@ -268,7 +268,7 @@ def generate_id(self) -> str: return f"Technology_{self.name}_{self.tech_category}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "techName": self.name, "techCategory": self.tech_category, @@ -302,7 +302,7 @@ def generate_id(self) -> str: return f"TypeDefinition_{self.repository_name}_{self.name}_{self.type_category}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "typeName": self.name, "category": self.type_category, @@ -344,7 +344,7 @@ def generate_id(self) -> str: return f"Method_{self.repository_name}_{self.type_name}_{self.name}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "methodName": self.name, "returnType": self.return_type, @@ -395,7 +395,7 @@ def generate_id(self) -> str: return f"Test_{self.repository_name}_{self.name}_{self.test_type}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "testName": self.name, "testType": self.test_type, @@ -428,7 +428,7 @@ def generate_id(self) -> str: return f"Service_{self.repository_name}_{self.name}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "serviceName": self.name, "description": self.description, @@ -477,7 +477,7 @@ def generate_id(self) -> str: return f"ExternalDependency_{self.name}{version_suffix}" def to_dict(self) -> dict: - """Convert to dictionary for Neo4j.""" + """Convert to dictionary for graph storage.""" return { "dependencyName": self.name, "dependencyCategory": self.dependency_category, diff --git a/deriva/adapters/llm/manager.py b/deriva/adapters/llm/manager.py index ddeebce..79e712b 100644 --- a/deriva/adapters/llm/manager.py +++ b/deriva/adapters/llm/manager.py @@ -35,7 +35,7 @@ class Concept(BaseModel): import logging import os from pathlib import Path -from typing import Any, TypeVar, overload +from typing import Any, TypeVar, cast, overload import asyncio import concurrent.futures @@ -210,6 +210,14 @@ def load_benchmark_models() -> dict[str, BenchmarkModelConfig]: return configs +def _serialize_output(output: object) -> str: + """Serialize a pydantic model or arbitrary output to a JSON string.""" + dump = getattr(output, "model_dump_json", None) + if callable(dump): + return dump() + return str(output) + + class LLMManager: """ Manages LLM API calls with intelligent caching and structured output support. @@ -651,25 +659,18 @@ def _run_in_thread() -> Any: } # Handle response + output: Any = result.output if response_model: # Explicit response_model: return the Pydantic instance if write_cache: - content = ( - result.output.model_dump_json() - if hasattr(result.output, "model_dump_json") - else str(result.output) - ) + content = _serialize_output(output) self.cache.set_response( cache_key, content, prompt, self.model, usage ) - return result.output + return cast(T, output) elif using_schema_model: # Schema-resolved model: serialize to JSON for backwards compatibility - content = ( - result.output.model_dump_json() - if hasattr(result.output, "model_dump_json") - else str(result.output) - ) + content = _serialize_output(output) if write_cache: self.cache.set_response( cache_key, content, prompt, self.model, usage @@ -777,7 +778,7 @@ def get_token_usage_stats(self) -> dict[str, Any]: total_prompt += usage.get("prompt_tokens", 0) total_completion += usage.get("completion_tokens", 0) total_calls += 1 - except (json.JSONDecodeError, OSError): + except json.JSONDecodeError, OSError: continue return { diff --git a/deriva/adapters/llm/retry.py b/deriva/adapters/llm/retry.py index 333f6de..aa33ead 100644 --- a/deriva/adapters/llm/retry.py +++ b/deriva/adapters/llm/retry.py @@ -277,7 +277,7 @@ def _extract_retry_after_from_exception(exception: Exception) -> float | None: if key in body: try: return float(body[key]) - except (ValueError, TypeError): + except ValueError, TypeError: pass # Check nested error object @@ -287,7 +287,7 @@ def _extract_retry_after_from_exception(exception: Exception) -> float | None: if key in error: try: return float(error[key]) - except (ValueError, TypeError): + except ValueError, TypeError: pass return None diff --git a/deriva/adapters/neo4j/README.md b/deriva/adapters/neo4j/README.md deleted file mode 100644 index 237b440..0000000 --- a/deriva/adapters/neo4j/README.md +++ /dev/null @@ -1,160 +0,0 @@ -# Neo4j Adapter - -Shared Neo4j connection service with namespace isolation for multiple data domains. - -**Version:** 1.0.0 - -## Purpose - -The Neo4j adapter provides a centralized connection pool to Neo4j that multiple adapters (Graph, ArchiMate) share. Namespace prefixes isolate data while allowing cross-namespace queries when needed. - -## Key Exports - -```python -from deriva.adapters.neo4j import Neo4jConnection -``` - -## Basic Usage - -```python -from deriva.adapters.neo4j import Neo4jConnection - -# Create connection with namespace (context manager) -with Neo4jConnection(namespace="Graph") as conn: - # Nodes automatically get "Graph:" prefix in labels - conn.execute_write( - "CREATE (n:Repository {name: $name})", - {"name": "my-repo"} - ) - - # Query within namespace - results = conn.execute_read( - "MATCH (n:Repository) RETURN n.name as name" - ) - -# Manual connection management -conn = Neo4jConnection(namespace="Graph") -conn.connect() -# ... do work ... -conn.disconnect() -``` - -## Multiple Namespaces - -```python -# Graph adapter uses "Graph" namespace -with Neo4jConnection(namespace="Graph") as graph_conn: - graph_conn.execute_write( - "CREATE (n:Repository {id: $id})", - {"id": "repo-1"} - ) - -# ArchiMate adapter uses "ArchiMate" namespace -with Neo4jConnection(namespace="ArchiMate") as arch_conn: - arch_conn.execute_write( - "CREATE (n:ApplicationComponent {id: $id})", - {"id": "comp-1"} - ) - -# Data is isolated by namespace labels -``` - -## Configuration - -Set via environment variables in `.env`: - -```bash -NEO4J_URI=bolt://localhost:7687 -NEO4J_USERNAME=neo4j -NEO4J_PASSWORD=password -NEO4J_DATABASE=neo4j -NEO4J_ENCRYPTED=false -NEO4J_MAX_CONNECTION_POOL_SIZE=50 -NEO4J_MAX_CONNECTION_LIFETIME=3600 -NEO4J_CONNECTION_ACQUISITION_TIMEOUT=60 -NEO4J_LOG_LEVEL=INFO -NEO4J_LOG_QUERIES=false -``` - -## File Structure - -```text -deriva/adapters/neo4j/ -├── __init__.py # Package exports -├── manager.py # Neo4jConnection class -└── docker-compose.yml # Neo4j container configuration -``` - -## Neo4jConnection Methods - -### Connection Lifecycle - -| Method | Description | -|--------|-------------| -| `connect()` | Establish connection to Neo4j | -| `disconnect()` | Close the Neo4j connection | -| `__enter__` / `__exit__` | Context manager support | - -### Query Execution - -| Method | Description | -|--------|-------------| -| `execute(query, params, database)` | Execute any Cypher query | -| `execute_write(query, params, database)` | Write transaction (CREATE, UPDATE, DELETE) | -| `execute_read(query, params, database)` | Read-only transaction (MATCH, RETURN) | - -### Namespace Management - -| Method | Description | -|--------|-------------| -| `get_label(base_label)` | Get namespaced label (e.g., `Graph:Repository`) | -| `clear_namespace()` | Delete all nodes/edges in namespace | - -### Schema Management - -| Method | Description | -|--------|-------------| -| `create_constraint(label, property_key, name)` | Create uniqueness constraint | -| `create_index(label, property_key, name)` | Create index on property | - -### Docker Container Management - -| Method | Description | -|--------|-------------| -| `start_container()` | Start Neo4j Docker container | -| `stop_container()` | Stop Neo4j Docker container | -| `get_container_status()` | Get container running status | -| `ensure_container_running()` | Start container if not running | - -## Namespace Convention - -| Adapter | Namespace | Example Labels | -|---------|-----------|----------------| -| Graph | `Graph` | `Graph:Repository`, `Graph:File` | -| ArchiMate | `ArchiMate` | `ArchiMate:ApplicationComponent` | - -## Starting Neo4j - -Using container management methods: - -```python -conn = Neo4jConnection(namespace="Graph") -conn.ensure_container_running() # Starts if not running -conn.connect() -``` - -Or manually via Docker: - -```bash -cd deriva/adapters/neo4j -docker-compose up -d -``` - -Neo4j available at: - -- Browser UI: -- Bolt: `bolt://localhost:7687` - -## See Also - -- [CONTRIBUTING.md](../../../CONTRIBUTING.md) - Architecture and coding guidelines diff --git a/deriva/adapters/neo4j/__init__.py b/deriva/adapters/neo4j/__init__.py deleted file mode 100644 index 1a06cd3..0000000 --- a/deriva/adapters/neo4j/__init__.py +++ /dev/null @@ -1,27 +0,0 @@ -"""Neo4j Manager - Shared Neo4j connection service for Deriva. - -This package provides a centralized Neo4j connection that multiple managers -can use with namespace isolation via label prefixes. - -Example: - >>> from neo4j_manager import Neo4jConnection - >>> - >>> # Connect to Neo4j - >>> conn = Neo4jConnection(namespace="Graph") - >>> conn.connect() - >>> - >>> # Execute query with namespace - >>> conn.execute(''' - ... CREATE (n:Repository {name: $name}) - ... RETURN n - ... ''', {"name": "my-repo"}) - >>> - >>> conn.disconnect() -""" - -from __future__ import annotations - -from .manager import Neo4jConnection - -__all__ = ["Neo4jConnection"] -__version__ = "1.0.0" diff --git a/deriva/adapters/neo4j/docker-compose.yml b/deriva/adapters/neo4j/docker-compose.yml deleted file mode 100644 index aa38d80..0000000 --- a/deriva/adapters/neo4j/docker-compose.yml +++ /dev/null @@ -1,29 +0,0 @@ -services: - neo4j: - image: neo4j:5.23-community - container_name: deriva_neo4j - ports: - - "7687:7687" # Bolt protocol - - "7474:7474" # Browser UI - volumes: - - neo4j_data:/data - - neo4j_logs:/logs - - neo4j_import:/var/lib/neo4j/import - - neo4j_plugins:/plugins - environment: - - NEO4J_AUTH=none # Disable authentication for local development - - NEO4J_server_memory_heap_initial__size=512m - - NEO4J_server_memory_heap_max__size=2G - - NEO4J_server_memory_pagecache_size=512m - - NEO4J_ACCEPT_LICENSE_AGREEMENT=yes - restart: unless-stopped - -volumes: - neo4j_data: - name: deriva_neo4j_data - neo4j_logs: - name: deriva_neo4j_logs - neo4j_import: - name: deriva_neo4j_import - neo4j_plugins: - name: deriva_neo4j_plugins diff --git a/deriva/adapters/neo4j/manager.py b/deriva/adapters/neo4j/manager.py deleted file mode 100644 index 83b289e..0000000 --- a/deriva/adapters/neo4j/manager.py +++ /dev/null @@ -1,704 +0,0 @@ -"""Neo4j Connection Service - Shared connection manager for Neo4j. - -This module provides a connection service that can be used by multiple -managers (graph_manager, archimate_manager) with namespace isolation. - -Features: -- Namespace isolation for multiple managers -- Automatic retry with exponential backoff for transient failures -- Connection state validation - -Usage: - from deriva.adapters.neo4j import Neo4jConnection - - # Create a namespaced connection - conn = Neo4jConnection(namespace="Graph") - conn.connect() - - # Execute Cypher queries - result = conn.execute("MATCH (n) RETURN count(n) as count") - print(f"Total nodes: {result[0]['count']}") - - # Clean up - conn.disconnect() - - # Or use context manager - with Neo4jConnection(namespace="Model") as conn: - conn.execute("CREATE (n:Element {name: 'Test'})") -""" - -from __future__ import annotations - -import logging -import os -import subprocess -import time -from functools import wraps -from pathlib import Path -from typing import TYPE_CHECKING, Any, Callable, TypeVar - -from dotenv import load_dotenv - -if TYPE_CHECKING: - from neo4j import Driver - -try: - from neo4j import GraphDatabase -except ModuleNotFoundError: - GraphDatabase = None # type: ignore[assignment,misc] - -logger = logging.getLogger(__name__) - -# Type variable for generic decorators -T = TypeVar("T") - - -def with_retry( - max_retries: int = 3, base_delay: float = 1.0, max_delay: float = 30.0 -) -> Callable[[Callable[..., T]], Callable[..., T]]: - """ - Decorator for Neo4j operations with exponential backoff retry. - - Retries failed operations up to max_retries times with increasing - delays between attempts. Useful for handling transient network issues - or temporary database unavailability. - - Args: - max_retries: Maximum number of retry attempts - base_delay: Initial delay between retries (in seconds) - max_delay: Maximum delay cap (in seconds) - - Returns: - Decorated function with retry logic - - Example: - @with_retry(max_retries=3, base_delay=1.0) - def execute_query(self, query): - ... - """ - - def decorator(func: Callable[..., T]) -> Callable[..., T]: - @wraps(func) - def wrapper(*args: Any, **kwargs: Any) -> T: - last_error: Exception | None = None - for attempt in range(max_retries): - try: - return func(*args, **kwargs) - except Exception as e: - last_error = e - if attempt < max_retries - 1: - delay = min(base_delay * (2**attempt), max_delay) - logger.warning( - "Neo4j operation failed (attempt %d/%d): %s. " - "Retrying in %.1fs...", - attempt + 1, - max_retries, - e, - delay, - ) - time.sleep(delay) - # All retries exhausted, raise the last error - if last_error is not None: - raise last_error - # This should never happen, but keeps type checker happy - raise RuntimeError("Retry logic error: no error captured") - - return wrapper - - return decorator - - -def requires_connection( - func: Callable[..., T], -) -> Callable[..., T]: - """ - Decorator to check Neo4j connection before operation. - - Raises RuntimeError if the connection is not established. - - Args: - func: Method to wrap (must be on Neo4jConnection instance) - - Returns: - Wrapped function with connection check - """ - - @wraps(func) - def wrapper(self: "Neo4jConnection", *args: Any, **kwargs: Any) -> T: - if self.driver is None: - raise RuntimeError( - f"Not connected to Neo4j. Call connect() first. " - f"(Namespace: {self.namespace})" - ) - return func(self, *args, **kwargs) - - return wrapper - - -class Neo4jConnection: - """Manages Neo4j database connection with namespace support. - - This class provides a shared connection to Neo4j that multiple managers - can use. Each manager gets its own namespace (label prefix) to ensure - clean separation of data. - - Example: - >>> conn = Neo4jConnection(namespace="Graph") - >>> conn.connect() - >>> conn.execute("CREATE (n:Repository {name: $name})", {"name": "test"}) - >>> conn.disconnect() - """ - - def __init__(self, namespace: str): - """ - Initialize Neo4j connection using .env configuration. - - Args: - namespace: Label prefix for this manager (e.g., "Graph", "ArchiMate") - """ - load_dotenv() - self.namespace = namespace - self.config = self._load_config_from_env() - self.driver: Driver | None = None - - logger.info(f"Initialized Neo4jConnection with namespace: {namespace}") - - def _load_config_from_env(self) -> dict[str, Any]: - """Load configuration from environment variables. - - Returns: - Configuration dictionary - """ - return { - "neo4j": { - "uri": os.getenv("NEO4J_URI", "bolt://localhost:7687"), - "auth": { - "username": os.getenv("NEO4J_USERNAME", ""), - "password": os.getenv("NEO4J_PASSWORD", ""), - }, - "database": os.getenv("NEO4J_DATABASE", "neo4j"), - "encrypted": os.getenv("NEO4J_ENCRYPTED", "False").lower() == "true", - "max_connection_lifetime": int( - os.getenv("NEO4J_MAX_CONNECTION_LIFETIME", "3600") - ), - "max_connection_pool_size": int( - os.getenv("NEO4J_MAX_CONNECTION_POOL_SIZE", "50") - ), - "connection_acquisition_timeout": int( - os.getenv("NEO4J_CONNECTION_ACQUISITION_TIMEOUT", "60") - ), - }, - "logging": { - "level": os.getenv("NEO4J_LOG_LEVEL", "INFO"), - "log_queries": os.getenv("NEO4J_LOG_QUERIES", "False").lower() - == "true", - # Suppress verbose Neo4j notifications (DEPRECATION, UNRECOGNIZED) - "suppress_notifications": os.getenv( - "NEO4J_SUPPRESS_NOTIFICATIONS", "True" - ).lower() - == "true", - }, - } - - def connect(self) -> None: - """Establish connection to Neo4j.""" - if self.driver is not None: - logger.warning("Connection already established") - return - - if GraphDatabase is None: - raise ModuleNotFoundError( - "neo4j is not installed. Install it to use Neo4jConnection." - ) - - try: - neo4j_config = self.config["neo4j"] - - # Create auth tuple (username, password) or None - auth = None - if neo4j_config["auth"]["username"] or neo4j_config["auth"]["password"]: - auth = ( - neo4j_config["auth"]["username"], - neo4j_config["auth"]["password"], - ) - - # Connect to Neo4j - self.driver = GraphDatabase.driver( - neo4j_config["uri"], - auth=auth, - max_connection_lifetime=neo4j_config.get( - "max_connection_lifetime", 3600 - ), - max_connection_pool_size=neo4j_config.get( - "max_connection_pool_size", 50 - ), - connection_acquisition_timeout=neo4j_config.get( - "connection_acquisition_timeout", 60 - ), - encrypted=neo4j_config.get("encrypted", False), - ) - - # Test connection - self.driver.verify_connectivity() - logger.info(f"Successfully connected to Neo4j at {neo4j_config['uri']}") - - except Exception as e: - logger.error(f"Failed to connect to Neo4j: {e}") - raise ConnectionError(f"Could not connect to Neo4j: {e}") - - def disconnect(self) -> None: - """Close the Neo4j connection.""" - if self.driver is not None: - self.driver.close() - self.driver = None - logger.info("Disconnected from Neo4j") - - def __enter__(self) -> Neo4jConnection: - """Context manager entry.""" - self.connect() - return self - - def __exit__( - self, exc_type: type | None, exc_val: Exception | None, exc_tb: Any - ) -> None: - """Context manager exit.""" - self.disconnect() - - @requires_connection - @with_retry(max_retries=3, base_delay=1.0) - def execute( - self, - query: str, - parameters: dict[str, Any] | None = None, - database: str | None = None, - ) -> list[dict[str, Any]]: - """ - Execute a Cypher query and return results. - - Automatically retries on transient failures with exponential backoff. - - Args: - query: Cypher query string - parameters: Query parameters - database: Database name (defaults to config database) - - Returns: - List of result records as dictionaries - - Raises: - RuntimeError: If not connected to Neo4j - """ - if self.config["logging"].get("log_queries", False): - logger.debug(f"Executing query: {query}") - logger.debug(f"Parameters: {parameters}") - - try: - params: dict[str, Any] = parameters if parameters is not None else {} - session_kwargs = self._get_session_kwargs(database) - with self.driver.session(**session_kwargs) as session: # type: ignore[union-attr] - result = session.run(query, params) # type: ignore[arg-type] # neo4j stubs require LiteralString - records = [dict(record) for record in result] - return records - - except Exception as e: - logger.error(f"Query execution failed: {e}") - logger.error(f"Query: {query}") - logger.error(f"Parameters: {parameters}") - raise - - @requires_connection - @with_retry(max_retries=3, base_delay=1.0) - def execute_write( - self, - query: str, - parameters: dict[str, Any] | None = None, - database: str | None = None, - ) -> list[dict[str, Any]]: - """ - Execute a write transaction (CREATE, UPDATE, DELETE). - - Automatically retries on transient failures with exponential backoff. - - Args: - query: Cypher query string - parameters: Query parameters - database: Database name (defaults to config database) - - Returns: - List of result records as dictionaries - - Raises: - RuntimeError: If not connected to Neo4j - """ - if self.config["logging"].get("log_queries", False): - logger.debug(f"Executing write query: {query}") - logger.debug(f"Parameters: {parameters}") - - try: - params: dict[str, Any] = parameters if parameters is not None else {} - session_kwargs = self._get_session_kwargs(database) - with self.driver.session(**session_kwargs) as session: # type: ignore[union-attr] - result = session.execute_write(lambda tx: list(tx.run(query, params))) - return [dict(record) for record in result] - - except Exception as e: - logger.error(f"Write query execution failed: {e}") - logger.error(f"Query: {query}") - logger.error(f"Parameters: {parameters}") - raise - - def execute_read( - self, - query: str, - parameters: dict[str, Any] | None = None, - database: str | None = None, - ) -> list[dict[str, Any]]: - """ - Execute a read transaction (MATCH, RETURN). - - Args: - query: Cypher query string - parameters: Query parameters - database: Database name (defaults to config database) - - Returns: - List of result records as dictionaries - """ - if self.driver is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") - - if self.config["logging"].get("log_queries", False): - logger.debug(f"Executing read query: {query}") - logger.debug(f"Parameters: {parameters}") - - try: - params: dict[str, Any] = parameters if parameters is not None else {} - session_kwargs = self._get_session_kwargs(database) - with self.driver.session(**session_kwargs) as session: - result = session.execute_read(lambda tx: list(tx.run(query, params))) - return [dict(record) for record in result] - - except Exception as e: - logger.error(f"Read query execution failed: {e}") - logger.error(f"Query: {query}") - logger.error(f"Parameters: {parameters}") - raise - - def clear_namespace(self) -> None: - """Clear all nodes and relationships for this namespace.""" - if self.driver is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") - - try: - # Delete all relationships first - self.execute_write( - f"MATCH ()-[r:{self.namespace}Relationship]->() DELETE r" - ) - - # Delete all nodes - self.execute_write(f"MATCH (n:{self.namespace}Element) DELETE n") - - # Also try generic namespace labels - self.execute_write( - "MATCH (n) WHERE any(label IN labels(n) WHERE label STARTS WITH $namespace) DETACH DELETE n", - {"namespace": self.namespace}, - ) - - logger.info(f"Cleared all data for namespace: {self.namespace}") - - except Exception as e: - logger.error(f"Failed to clear namespace {self.namespace}: {e}") - raise - - def get_label(self, base_label: str) -> str: - """ - Get namespaced label. - - Args: - base_label: Base label name (e.g., "Repository", "Element") - - Returns: - Namespaced label (e.g., "Graph:Repository", "ArchiMate:Element") - """ - return f"{self.namespace}:{base_label}" - - def _get_session_kwargs(self, database: str | None = None) -> dict[str, Any]: - """Get session configuration kwargs including notification filtering. - - Args: - database: Database name (defaults to config database) - - Returns: - Dictionary of session configuration options - """ - if database is None: - database = self.config["neo4j"]["database"] - - kwargs: dict[str, Any] = {"database": database} - - # Suppress verbose notifications if configured (default: True) - if self.config["logging"].get("suppress_notifications", True): - try: - # Neo4j 5.x supports notification filtering - from neo4j import NotificationDisabledCategory - - kwargs["notifications_disabled_categories"] = [ - NotificationDisabledCategory.DEPRECATION, - NotificationDisabledCategory.UNRECOGNIZED, - NotificationDisabledCategory.HINT, - ] - except ImportError: - # Older neo4j driver versions don't support this - pass - - return kwargs - - def create_constraint( - self, label: str, property_key: str, constraint_name: str | None = None - ) -> None: - """ - Create a uniqueness constraint on a label property. - - Args: - label: Node label (will be namespaced) - property_key: Property to constrain - constraint_name: Optional constraint name - """ - if self.driver is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") - - namespaced_label = self.get_label(label) - - if constraint_name is None: - constraint_name = ( - f"{namespaced_label.replace(':', '_')}_{property_key}_unique" - ) - - try: - query = f""" - CREATE CONSTRAINT {constraint_name} IF NOT EXISTS - FOR (n:{namespaced_label}) - REQUIRE n.{property_key} IS UNIQUE - """ - self.execute_write(query) - logger.info(f"Created constraint: {constraint_name}") - - except Exception as e: - logger.warning(f"Could not create constraint {constraint_name}: {e}") - - def create_index( - self, label: str, property_key: str, index_name: str | None = None - ) -> None: - """ - Create an index on a label property. - - Args: - label: Node label (will be namespaced) - property_key: Property to index - index_name: Optional index name - """ - if self.driver is None: - raise RuntimeError("Not connected to Neo4j. Call connect() first.") - - namespaced_label = self.get_label(label) - - if index_name is None: - index_name = f"{namespaced_label.replace(':', '_')}_{property_key}_index" - - try: - query = f""" - CREATE INDEX {index_name} IF NOT EXISTS - FOR (n:{namespaced_label}) - ON (n.{property_key}) - """ - self.execute_write(query) - logger.info(f"Created index: {index_name}") - - except Exception as e: - logger.warning(f"Could not create index {index_name}: {e}") - - def _get_compose_dir(self) -> Path: - """Get the directory containing docker-compose.yml. - - Returns: - Path to the directory containing docker-compose.yml - """ - return Path(__file__).parent - - def start_container(self) -> dict[str, Any]: - """Start the Neo4j Docker container using docker-compose. - - Returns: - Dictionary with status information: - { - 'success': bool, - 'message': str, - 'output': str (optional), - 'error': str (optional) - } - - Raises: - RuntimeError: If docker-compose command fails - """ - compose_dir = self._get_compose_dir() - - try: - logger.info("Starting Neo4j Docker container...") - result = subprocess.run( - ["docker-compose", "up", "-d"], - cwd=compose_dir, - capture_output=True, - text=True, - check=True, - ) - - logger.info("Neo4j Docker container started successfully") - return { - "success": True, - "message": "Neo4j container started successfully", - "output": result.stdout, - } - - except subprocess.CalledProcessError as e: - error_msg = f"Failed to start Neo4j container: {e.stderr}" - logger.error(error_msg) - raise RuntimeError(error_msg) from e - except FileNotFoundError: - error_msg = ( - "docker-compose command not found. Is Docker installed and in PATH?" - ) - logger.error(error_msg) - raise RuntimeError(error_msg) - - def stop_container(self) -> dict[str, Any]: - """Stop the Neo4j Docker container using docker-compose. - - Returns: - Dictionary with status information: - { - 'success': bool, - 'message': str, - 'output': str (optional), - 'error': str (optional) - } - - Raises: - RuntimeError: If docker-compose command fails - """ - compose_dir = self._get_compose_dir() - - try: - logger.info("Stopping Neo4j Docker container...") - result = subprocess.run( - ["docker-compose", "down"], - cwd=compose_dir, - capture_output=True, - text=True, - check=True, - ) - - logger.info("Neo4j Docker container stopped successfully") - return { - "success": True, - "message": "Neo4j container stopped successfully", - "output": result.stdout, - } - - except subprocess.CalledProcessError as e: - error_msg = f"Failed to stop Neo4j container: {e.stderr}" - logger.error(error_msg) - raise RuntimeError(error_msg) from e - except FileNotFoundError: - error_msg = ( - "docker-compose command not found. Is Docker installed and in PATH?" - ) - logger.error(error_msg) - raise RuntimeError(error_msg) - - def get_container_status(self) -> dict[str, Any]: - """Get the status of the Neo4j Docker container. - - Returns: - Dictionary with status information: - { - 'running': bool, - 'container_name': str, - 'status': str, - 'ports': str (optional) - } - """ - try: - result = subprocess.run( - [ - "docker", - "ps", - "--filter", - "name=deriva_neo4j", - "--format", - "{{.Names}}\t{{.Status}}\t{{.Ports}}", - ], - capture_output=True, - text=True, - check=True, - ) - - if result.stdout.strip(): - # Container is running - parts = result.stdout.strip().split("\t") - return { - "running": True, - "container_name": parts[0] if len(parts) > 0 else "deriva_neo4j", - "status": parts[1] if len(parts) > 1 else "Unknown", - "ports": parts[2] if len(parts) > 2 else "", - } - else: - # Container is not running - return { - "running": False, - "container_name": "deriva_neo4j", - "status": "Not running", - "ports": "", - } - - except subprocess.CalledProcessError as e: - logger.error(f"Failed to get container status: {e.stderr}") - return { - "running": False, - "container_name": "deriva_neo4j", - "status": f"Error: {e.stderr}", - "ports": "", - } - except FileNotFoundError: - logger.error("docker command not found") - return { - "running": False, - "container_name": "deriva_neo4j", - "status": "Error: Docker not found", - "ports": "", - } - - def ensure_container_running(self) -> dict[str, Any]: - """Ensure the Neo4j Docker container is running, starting it if necessary. - - Returns: - Dictionary with status information: - { - 'was_running': bool, - 'is_running': bool, - 'action_taken': str - } - """ - status = self.get_container_status() - - if status["running"]: - logger.info("Neo4j container is already running") - return {"was_running": True, "is_running": True, "action_taken": "none"} - - # Container not running, start it - logger.info("Neo4j container not running, starting it...") - start_result = self.start_container() - - if start_result["success"]: - return {"was_running": False, "is_running": True, "action_taken": "started"} - else: - return {"was_running": False, "is_running": False, "action_taken": "failed"} diff --git a/deriva/adapters/repository/manager.py b/deriva/adapters/repository/manager.py index b196d6c..7d52771 100644 --- a/deriva/adapters/repository/manager.py +++ b/deriva/adapters/repository/manager.py @@ -317,7 +317,7 @@ def _get_git_remote_url(repo_path: Path) -> str | None: check=True, ) return result.stdout.strip() - except (subprocess.CalledProcessError, OSError): + except subprocess.CalledProcessError, OSError: return None @@ -339,7 +339,7 @@ def _get_repository_description(repo_path: Path) -> str | None: lines.append(line) if lines: return " ".join(lines)[:500] - except (OSError, UnicodeDecodeError): + except OSError, UnicodeDecodeError: pass return None @@ -379,7 +379,7 @@ def _get_repository_times(repo_path: Path) -> tuple[str, str]: ) if result.stdout.strip(): created_at = result.stdout.strip() - except (subprocess.CalledProcessError, OSError): + except subprocess.CalledProcessError, OSError: pass last_updated = datetime.now().isoformat() @@ -392,7 +392,7 @@ def _get_repository_times(repo_path: Path) -> tuple[str, str]: ) if result.stdout.strip(): last_updated = result.stdout.strip() - except (subprocess.CalledProcessError, OSError): + except subprocess.CalledProcessError, OSError: pass return created_at, last_updated @@ -408,7 +408,7 @@ def _get_default_branch(repo_path: Path) -> str: check=True, ) return result.stdout.strip() - except (subprocess.CalledProcessError, OSError): + except subprocess.CalledProcessError, OSError: return "unknown" @@ -422,7 +422,7 @@ def _get_commit_hash(repo_path: Path) -> str | None: check=True, ) return result.stdout.strip() - except (subprocess.CalledProcessError, OSError): + except subprocess.CalledProcessError, OSError: return None diff --git a/deriva/app/README.md b/deriva/app/README.md index 848cf7d..150d075 100644 --- a/deriva/app/README.md +++ b/deriva/app/README.md @@ -19,7 +19,7 @@ Opens in browser at: | Column | Purpose | |--------|---------| | **0** | **Run Deriva** - Pipeline buttons, status display | -| **1** | **Configuration** - Runs, repositories, Neo4j, graph stats, ArchiMate model | +| **1** | **Configuration** - Runs, repositories, graph database, graph stats, ArchiMate model | | **2** | **Extraction Settings** - File type registry, extraction step config | | **3** | **Derivation Settings** - Derivation step config (prep/generate/refine phases) | diff --git a/deriva/app/app.py b/deriva/app/app.py index 8353a64..f6aac58 100644 --- a/deriva/app/app.py +++ b/deriva/app/app.py @@ -419,17 +419,16 @@ def _( @app.cell(hide_code=True) def _(mo): mo.md(r""" - ## Neo4j + ## Graph Database """) return @app.cell def _(mo, session): - # Always try DB connectivity first - this is the most reliable check + # Check graph database connectivity _db_connected = False _db_error = None - _docker_status = None try: _stats = session.get_graph_stats() @@ -437,62 +436,20 @@ def _(mo, session): except Exception as e: _db_error = str(e) - # Also try Docker status for additional info - try: - _docker_status = session.get_neo4j_status() - except Exception: - pass # Docker status is optional - if _db_connected: _kind = "success" - _port = _docker_status.get("port", 7687) if _docker_status else 7687 - _text = f"**Status:** Connected\n- Port: {_port}\n- Nodes: {_stats.get('total_nodes', 0)}" + _text = f"**Status:** Connected (grafeo embedded)\n- Nodes: {_stats.get('total_nodes', 0)}" else: _kind = "warn" _text = "**Status:** Not connected" if _db_error: _text += f"\n- Error: {_db_error[:100]}" - start_neo4j_btn = mo.ui.run_button(label="Start", disabled=_db_connected) - stop_neo4j_btn = mo.ui.run_button(label="Stop", disabled=not _db_connected) - mo.vstack( [ mo.callout(mo.md(_text), kind=_kind), - mo.hstack([start_neo4j_btn, stop_neo4j_btn]), ] ) - return start_neo4j_btn, stop_neo4j_btn - - -@app.cell -def _(mo, session, start_neo4j_btn, stop_neo4j_btn): - if start_neo4j_btn.value: - print("[Deriva] Starting Neo4j...") - try: - _result = session.start_neo4j() - if _result.get("success", True): - print("[Deriva] Neo4j start initiated") - mo.callout(mo.md("Neo4j starting..."), kind="info") - else: - print(f"[Deriva] Neo4j start failed: {_result.get('error', 'Unknown')}") - mo.callout(mo.md(f"Error: {_result.get('error', 'Unknown')}"), kind="danger") - except Exception as e: - print(f"[Deriva] Neo4j start error: {str(e)[:100]}") - mo.callout(mo.md(f"Docker error: {str(e)[:100]}"), kind="danger") - elif stop_neo4j_btn.value: - print("[Deriva] Stopping Neo4j...") - try: - _result = session.stop_neo4j() - if _result.get("success", True): - print("[Deriva] Neo4j stop initiated") - mo.callout(mo.md("Neo4j stopping..."), kind="info") - else: - print(f"[Deriva] Neo4j stop failed: {_result.get('error', 'Unknown')}") - mo.callout(mo.md(f"Error: {_result.get('error', 'Unknown')}"), kind="danger") - except Exception as e: - print(f"[Deriva] Neo4j stop error: {str(e)[:100]}") - mo.callout(mo.md(f"Docker error: {str(e)[:100]}"), kind="danger") return diff --git a/deriva/cli/cli.py b/deriva/cli/cli.py index 60b5cd8..cb8d9cf 100644 --- a/deriva/cli/cli.py +++ b/deriva/cli/cli.py @@ -126,7 +126,7 @@ def run_stage( typer.echo(f"Phase: {phase}") with PipelineSession() as session: - typer.echo("Connected to Neo4j") + typer.echo("Connected to grafeo") # Handle --only-step option if only_step: @@ -290,7 +290,7 @@ def export( with PipelineSession() as session: if verbose: - typer.echo("Connected to Neo4j") + typer.echo("Connected to grafeo") result = session.export_model(output_path=output, model_name=model_name) diff --git a/deriva/cli/commands/benchmark.py b/deriva/cli/commands/benchmark.py index 72e25a0..27f550e 100644 --- a/deriva/cli/commands/benchmark.py +++ b/deriva/cli/commands/benchmark.py @@ -163,7 +163,7 @@ def benchmark_run( typer.echo(f"{'=' * 60}\n") with PipelineSession() as session: - typer.echo("Connected to Neo4j") + typer.echo("Connected to grafeo") # Handle --only-extraction-step and --only-derivation-step if only_extraction_step: diff --git a/deriva/cli/commands/run.py b/deriva/cli/commands/run.py index 83e82e3..557496c 100644 --- a/deriva/cli/commands/run.py +++ b/deriva/cli/commands/run.py @@ -171,7 +171,7 @@ def run_stage( typer.echo(f"Phase: {phase}") with PipelineSession() as session: - typer.echo("Connected to Neo4j") + typer.echo("Connected to grafeo") # Handle --only-step option if only_step: diff --git a/deriva/cli/progress.py b/deriva/cli/progress.py index dcb841d..7a54084 100644 --- a/deriva/cli/progress.py +++ b/deriva/cli/progress.py @@ -262,7 +262,7 @@ def complete_phase(self, message: str = "") -> None: task = self._progress._tasks.get(self._phase_task) if task and task.total is not None: self._progress.update(self._phase_task, completed=task.total) - except (IndexError, KeyError): + except IndexError, KeyError: pass # Task may have been removed if message: @@ -540,7 +540,7 @@ def complete_phase(self, message: str = "") -> None: task = self._progress._tasks.get(self._phase_task) if task and task.total is not None: self._progress.update(self._phase_task, completed=task.total) - except (IndexError, KeyError): + except IndexError, KeyError: pass # Task may have been removed self._refresh_display() diff --git a/deriva/common/cache_utils.py b/deriva/common/cache_utils.py index fb27734..79438f1 100644 --- a/deriva/common/cache_utils.py +++ b/deriva/common/cache_utils.py @@ -162,10 +162,12 @@ def __init__(self, cache_dir: str | Path, size_limit: int | None = None): self.cache_dir = Path(cache_dir) self.cache_dir.mkdir(parents=True, exist_ok=True) - # Initialize diskcache + # Initialize diskcache with JSON serialization (no pickle) self._cache = diskcache.Cache( str(self.cache_dir), size_limit=size_limit or self.DEFAULT_SIZE_LIMIT, + disk=diskcache.JSONDisk, + disk_compress_level=0, ) def get(self, cache_key: str) -> dict[str, Any] | None: diff --git a/deriva/common/document_reader.py b/deriva/common/document_reader.py index faf871b..df5d925 100644 --- a/deriva/common/document_reader.py +++ b/deriva/common/document_reader.py @@ -101,7 +101,7 @@ def read_docx(file_path: Path) -> str | None: level = int(style_name.split()[-1]) prefix = "#" * level lines.append(f"{prefix} {text}") - except (ValueError, IndexError): + except ValueError, IndexError: # Fallback for non-standard heading styles lines.append(f"## {text}") elif style_name == "Title": diff --git a/deriva/common/file_utils.py b/deriva/common/file_utils.py index c4cffe2..6a7f266 100644 --- a/deriva/common/file_utils.py +++ b/deriva/common/file_utils.py @@ -65,7 +65,7 @@ def read_file_with_encoding(file_path: Path) -> str | None: # Try Latin-1 as fallback (accepts all byte values) return raw.decode("latin-1") - except (OSError, UnicodeDecodeError): + except OSError, UnicodeDecodeError: return None diff --git a/deriva/modules/derivation/__init__.py b/deriva/modules/derivation/__init__.py index 6aed4d3..92d1a48 100644 --- a/deriva/modules/derivation/__init__.py +++ b/deriva/modules/derivation/__init__.py @@ -67,7 +67,7 @@ clear_enrichment_cache, derive_batch_relationships, derive_element_relationships, - get_enrichments_from_neo4j, + get_enrichments_from_graph, parse_derivation_response, parse_relationship_response, query_candidates, @@ -93,7 +93,7 @@ "build_unified_relationship_prompt", "derive_element_relationships", "derive_batch_relationships", - "get_enrichments_from_neo4j", + "get_enrichments_from_graph", "clear_enrichment_cache", "parse_derivation_response", "parse_relationship_response", diff --git a/deriva/modules/derivation/base.py b/deriva/modules/derivation/base.py index 5f7c8d6..f74c954 100644 --- a/deriva/modules/derivation/base.py +++ b/deriva/modules/derivation/base.py @@ -281,19 +281,19 @@ class DerivationResult: # ============================================================================= -def get_enrichments_from_neo4j( +def get_enrichments_from_graph( graph_manager: "GraphManager", use_cache: bool = True, cache_manager: EnrichmentCacheManager | None = None, config_name: str | None = None, ) -> dict[str, dict[str, Any]]: """ - Get all graph enrichment data from Neo4j node properties. + Get all graph enrichment data from graph node properties. The prep phase stores enrichments (PageRank, Louvain, k-core, etc.) - as properties on Neo4j nodes. This function reads them back. + as properties on graph nodes. This function reads them back. - Uses caching to avoid repeated Neo4j queries when called multiple times + Uses caching to avoid repeated graph queries when called multiple times for different element types in the same generation phase. Args: @@ -324,13 +324,13 @@ def get_enrichments_from_neo4j( ) return cached except Exception as e: - logger.debug("Cache lookup failed, querying Neo4j: %s", e) + logger.debug("Cache lookup failed, querying graph: %s", e) should_write_cache = True else: should_write_cache = False - # Query Neo4j - # Note: Labels in Neo4j are stored as separate items (e.g., ['Graph', 'Directory']), + # Query the graph + # Note: Labels are stored as separate items (e.g., ['Graph', 'Directory']), # not as concatenated strings (e.g., 'Graph:Directory'). query = """ MATCH (n) @@ -374,7 +374,7 @@ def get_enrichments_from_neo4j( return enrichments except Exception as e: - logger.warning("Failed to get enrichments from Neo4j: %s", e) + logger.warning("Failed to get enrichments from graph: %s", e) return {} @@ -390,9 +390,9 @@ def clear_enrichment_cache() -> None: # Backward compatibility alias (deprecated) def get_enrichments(engine: Any) -> dict[str, dict[str, Any]]: - """Deprecated: Use get_enrichments_from_neo4j() instead.""" + """Deprecated: Use get_enrichments_from_graph() instead.""" logger.warning( - "get_enrichments(engine) is deprecated - enrichments should be read from Neo4j" + "get_enrichments(engine) is deprecated - enrichments should be read from the graph" ) return {} @@ -2017,7 +2017,7 @@ def clamp_confidence(value: Any, default: float = 0.5) -> float: try: conf = float(value) if value is not None else default return max(0.0, min(1.0, conf)) - except (TypeError, ValueError): + except TypeError, ValueError: return default @@ -2828,7 +2828,7 @@ def create_result( "DerivationResult", # Enrichment "get_enrichments", - "get_enrichments_from_neo4j", + "get_enrichments_from_graph", "clear_enrichment_cache", "enrich_candidate", # Filtering diff --git a/deriva/modules/derivation/element_base.py b/deriva/modules/derivation/element_base.py index 12866b4..2466876 100644 --- a/deriva/modules/derivation/element_base.py +++ b/deriva/modules/derivation/element_base.py @@ -45,7 +45,7 @@ def filter_candidates(self, candidates, enrichments, max_candidates, **kwargs): build_element, derive_batch_relationships, extract_response_content, - get_enrichments_from_neo4j, + get_enrichments_from_graph, parse_derivation_response, query_candidates, ) @@ -84,7 +84,7 @@ class ElementDerivationBase(ABC): - filter_candidates(): Module-specific candidate filtering The generate() method handles: - - Enrichment retrieval from Neo4j + - Enrichment retrieval from graph - Candidate querying - Batching - LLM calls for element derivation @@ -243,7 +243,7 @@ def generate( This is the common flow shared by all element modules: 1. Get filter kwargs (patterns for pattern-based modules) - 2. Get enrichments from Neo4j + 2. Get enrichments from graph 3. Query candidates 4. Filter candidates (module-specific) 5. Batch candidates @@ -274,7 +274,7 @@ def generate( filter_kwargs = self.get_filter_kwargs(engine) # Get enrichments and query candidates - enrichments = get_enrichments_from_neo4j( + enrichments = get_enrichments_from_graph( graph_manager, cache_manager=cache_manager, config_name=self.ELEMENT_TYPE, diff --git a/deriva/modules/derivation/prep.py b/deriva/modules/derivation/prep.py index 5cc910b..8d6e324 100644 --- a/deriva/modules/derivation/prep.py +++ b/deriva/modules/derivation/prep.py @@ -1,16 +1,16 @@ """ Graph Enrichment Module - Pre-derivation graph analysis using solvor. -Computes graph algorithm properties that are stored as Neo4j node properties. +Computes graph algorithm properties that are stored as graph node properties. Similar to how classification enriches files before extraction, enrich prepares graph metrics before derivation. This module contains pure functions that: 1. Take nodes and edges in a simple format 2. Run graph algorithms via solvor -3. Return enrichment dicts ready for Neo4j property updates +3. Return enrichment dicts ready for graph property updates -The service layer handles Neo4j I/O - this module has no I/O dependencies. +The service layer handles graph I/O - this module has no I/O dependencies. Algorithms: - PageRank: Node importance/centrality diff --git a/deriva/modules/derivation/refine/orphan_elements.py b/deriva/modules/derivation/refine/orphan_elements.py index f274e72..ce382f8 100644 --- a/deriva/modules/derivation/refine/orphan_elements.py +++ b/deriva/modules/derivation/refine/orphan_elements.py @@ -106,7 +106,7 @@ def run( try: props = json.loads(orphan["properties_json"]) importance = props.get("source_pagerank", 0) - except (json.JSONDecodeError, TypeError): + except json.JSONDecodeError, TypeError: pass # Decide action based on importance and params @@ -190,7 +190,7 @@ def _propose_relationships( try: props = json.loads(props_json) - except (json.JSONDecodeError, TypeError): + except json.JSONDecodeError, TypeError: return proposals source_id = props.get("source") diff --git a/deriva/modules/derivation/refine/structural_consistency.py b/deriva/modules/derivation/refine/structural_consistency.py index cdcba14..7fe999b 100644 --- a/deriva/modules/derivation/refine/structural_consistency.py +++ b/deriva/modules/derivation/refine/structural_consistency.py @@ -396,7 +396,7 @@ def _fix_flow_to_access( """ # Update the relationship type from Flow to Access # This requires deleting the old relationship and creating a new one - # because Neo4j doesn't allow changing relationship types in-place + # because the graph doesn't allow changing relationship types in-place # Get the relationship details first query = f""" diff --git a/deriva/services/__init__.py b/deriva/services/__init__.py index 61fff07..a4e7175 100644 --- a/deriva/services/__init__.py +++ b/deriva/services/__init__.py @@ -10,7 +10,7 @@ - Lifecycle: connect(), disconnect(), context manager - Queries: get_graph_stats(), get_archimate_elements(), etc. - Orchestration: run_extraction(), run_derivation(), run_pipeline() - - Infrastructure: start_neo4j(), stop_neo4j(), clear_graph() + - Infrastructure: start_graph_db(), stop_graph_db(), clear_graph() - Export: export_model() Usage (CLI): diff --git a/deriva/services/analysis.py b/deriva/services/analysis.py index 5a8bcd8..5512538 100644 --- a/deriva/services/analysis.py +++ b/deriva/services/analysis.py @@ -725,7 +725,7 @@ def export_execution_metrics_csv(self, path: str | Path) -> str: if start and end: try: duration = (end - start).total_seconds() - except (TypeError, AttributeError): + except TypeError, AttributeError: duration = 0.0 writer.writerow( diff --git a/deriva/services/benchmarking.py b/deriva/services/benchmarking.py index 577cffc..8ef6031 100644 --- a/deriva/services/benchmarking.py +++ b/deriva/services/benchmarking.py @@ -1272,7 +1272,7 @@ def _copy_used_cache_entries( "tokens_out": tokens_out, "timestamp": timestamp, } - except (OSError, json.JSONDecodeError): + except OSError, json.JSONDecodeError: pass # Skip on read errors # Write consolidated cache diff --git a/deriva/services/config.py b/deriva/services/config.py index 07519c6..12dc5e3 100644 --- a/deriva/services/config.py +++ b/deriva/services/config.py @@ -51,7 +51,7 @@ def get_settings() -> DerivaSettings: Usage: settings = get_settings() print(settings.llm.temperature) - print(settings.neo4j.uri) + print(settings.grafeo.db_path) """ from deriva.services.config_models import DerivaSettings @@ -1370,7 +1370,7 @@ def get_confidence_threshold(engine: Any, key: str, default: float | None = None if value is not None: try: return float(value) - except (ValueError, TypeError): + except ValueError, TypeError: pass # Use provided default or fall back to built-in defaults @@ -1397,7 +1397,7 @@ def get_derivation_limit(engine: Any, key: str, default: int | None = None) -> i if value is not None: try: return int(value) - except (ValueError, TypeError): + except ValueError, TypeError: pass # Use provided default or fall back to built-in defaults @@ -1499,7 +1499,7 @@ def get_algorithm_setting_float(engine: Any, key: str, default: float | None = N value = get_algorithm_setting(engine, key) try: return float(value) - except (ValueError, TypeError): + except ValueError, TypeError: return default if default is not None else 0.0 @@ -1508,7 +1508,7 @@ def get_algorithm_setting_int(engine: Any, key: str, default: int | None = None) value = get_algorithm_setting(engine, key) try: return int(value) - except (ValueError, TypeError): + except ValueError, TypeError: return default if default is not None else 0 diff --git a/deriva/services/config_models.py b/deriva/services/config_models.py index 388106c..c92edd7 100644 --- a/deriva/services/config_models.py +++ b/deriva/services/config_models.py @@ -16,30 +16,13 @@ # ============================================================================= -class Neo4jSettings(BaseSettings): - """Neo4j connection settings.""" +class GrafeoSettings(BaseSettings): + """Grafeo (embedded graph database) settings.""" - model_config = SettingsConfigDict(env_prefix="NEO4J_", env_file=".env", extra="ignore") + model_config = SettingsConfigDict(env_prefix="GRAFEO_", env_file=".env", extra="ignore") - uri: str = "bolt://localhost:7687" - username: str = "" - password: str = "" - database: str = "neo4j" - encrypted: bool = False - - # Connection pool settings - max_connection_lifetime: int = 3600 - max_connection_pool_size: int = 50 - connection_acquisition_timeout: int = 60 - - # Logging - log_level: str = "INFO" + db_path: str = "" # Empty = in-memory, path = persistent log_queries: bool = False - suppress_notifications: bool = True - - # Namespaces - namespace_graph: str = "Graph" - namespace_archimate: str = "Model" class LLMSettings(BaseSettings): @@ -114,7 +97,7 @@ class DerivaSettings(BaseSettings): Usage: settings = DerivaSettings() - print(settings.neo4j.uri) + print(settings.grafeo.db_path) print(settings.llm.temperature) """ @@ -126,8 +109,8 @@ class DerivaSettings(BaseSettings): # Nested settings are loaded separately @property - def neo4j(self) -> Neo4jSettings: - return Neo4jSettings() + def grafeo(self) -> GrafeoSettings: + return GrafeoSettings() @property def llm(self) -> LLMSettings: diff --git a/deriva/services/derivation.py b/deriva/services/derivation.py index 5df2ac1..affb429 100644 --- a/deriva/services/derivation.py +++ b/deriva/services/derivation.py @@ -151,7 +151,7 @@ def generate_element( archimate_manager: Connected ArchimateManager for element creation llm_query_fn: Function to call LLM (prompt, schema, **kwargs) -> response element_type: ArchiMate element type (e.g., 'ApplicationService') - engine: DuckDB connection for patterns (enrichments read from Neo4j) + engine: DuckDB connection for patterns (enrichments read from graph) query: Cypher query to get candidate nodes instruction: LLM instruction prompt example: Example output for LLM @@ -247,7 +247,7 @@ def _get_graph_edges( If provided, only returns edges where both nodes belong to this repo. This enables per-repository enrichment isolation in multi-repo setups. - Note: Labels in Neo4j are separate (e.g., ['Graph', 'Directory'], not 'Graph:Directory'). + Note: Labels are separate (e.g., ['Graph', 'Directory'], not 'Graph:Directory'). We match any node with the 'Graph' label to get all graph nodes. """ if repository_name: @@ -282,7 +282,7 @@ def _run_prep_step( """Run a single prep step (graph enrichment algorithm). Enrich steps compute graph metrics (PageRank, Louvain, k-core, etc.) - and store them as properties on Neo4j nodes. + and store them as properties on graph nodes. """ step_name = cfg.step_name logger = logging.getLogger(__name__) @@ -326,7 +326,7 @@ def _run_prep_step( if not result.enrichments: return {"success": True, "stats": {"nodes_updated": 0}} - # Write enrichments to Neo4j + # Write enrichments to graph nodes_updated = graph_manager.batch_update_properties(result.enrichments) logger.info( diff --git a/deriva/services/extraction.py b/deriva/services/extraction.py index 750cf5f..bc85c27 100644 --- a/deriva/services/extraction.py +++ b/deriva/services/extraction.py @@ -5,7 +5,7 @@ 1. Loading extraction configs from DuckDB 2. Getting files from repositories 3. Calling extraction module functions -4. Persisting results to Neo4j GraphManager +4. Persisting results to GraphManager Used by both Marimo (visual) and CLI (headless). @@ -651,7 +651,7 @@ def _extract_edges( except Exception: pass # Proceed without external package list - # Build global method lookup from Neo4j for cross-file CALLS/DECORATED_BY resolution + # Build global method lookup from graph for cross-file CALLS/DECORATED_BY resolution # Key: (method_name, class_name or None) -> list of node_ids with file_paths global_method_lookup: dict[tuple[str, str | None], list[dict]] = {} try: @@ -667,7 +667,7 @@ def _extract_edges( node_id = m.get("id", "") # Keep file_path as-is (with repo prefix) to match classified_files format - # Both Neo4j filePath and classified_files paths include the full relative path + # Both graph filePath and classified_files paths include the full relative path # e.g., "deriva/cli/cli.py" for files inside the deriva/ subdirectory key = (method_name, class_name) @@ -684,7 +684,7 @@ def _extract_edges( except Exception as e: logger.warning(f"Failed to build global method lookup: {e}") - # Build global type lookup from Neo4j for cross-file REFERENCES resolution + # Build global type lookup from graph for cross-file REFERENCES resolution # Key: type_name -> list of node_ids with file_paths global_type_lookup: dict[str, list[dict]] = {} try: @@ -697,7 +697,7 @@ def _extract_edges( node_id = t.get("id", "") # Keep file_path as-is (with repo prefix) to match classified_files format - # Both Neo4j filePath and classified_files paths include the full relative path + # Both graph filePath and classified_files paths include the full relative path if type_name not in global_type_lookup: global_type_lookup[type_name] = [] diff --git a/deriva/services/session.py b/deriva/services/session.py index 7c08905..99bd756 100644 --- a/deriva/services/session.py +++ b/deriva/services/session.py @@ -34,8 +34,8 @@ from deriva.adapters.archimate import ArchimateManager from deriva.adapters.archimate.xml_export import ArchiMateXMLExporter from deriva.adapters.database import get_connection +from deriva.adapters.grafeo import close_database from deriva.adapters.graph import GraphManager -from deriva.adapters.neo4j import Neo4jConnection from deriva.adapters.repository import RepoManager from deriva.common.logging import RunLogger from deriva.common.types import HasToDict, RunLoggerProtocol @@ -50,7 +50,7 @@ class PipelineSession: - Lifecycle: connect/disconnect, context manager support - Queries: get stats, nodes, elements for reactive UI - Orchestration: run extraction, derivation (with phases), full pipeline - - Infrastructure: Neo4j container control, data clearing + - Infrastructure: graph database control, data clearing - Export: ArchiMate XML export """ @@ -75,7 +75,6 @@ def __init__( self._graph_manager: GraphManager | None = None self._archimate_manager: ArchimateManager | None = None self._repo_manager: RepoManager | None = None - self._neo4j_conn: Neo4jConnection | None = None self._llm_manager: Any | None = None # Lazy loaded # Test-only mocks (set by tests) @@ -83,7 +82,6 @@ def __init__( self._mock_graph: Any | None = None self._mock_archimate: Any | None = None self._mock_repo: Any | None = None - self._mock_neo4j: Any | None = None self._mock_engine: Any | None = None self._mock_extraction: Any | None = None self._mock_derivation: Any | None = None @@ -107,7 +105,7 @@ def connect(self) -> None: # Database (get_connection uses DB_PATH from env) self._engine = get_connection() - # Neo4j managers + # Graph managers (grafeo embedded) self._graph_manager = GraphManager() self._graph_manager.connect() @@ -117,9 +115,6 @@ def connect(self) -> None: # Repository manager self._repo_manager = RepoManager(workspace_dir=self._workspace_dir) - # Neo4j connection for container control - self._neo4j_conn = Neo4jConnection(namespace="Docker") - self._connected = True def disconnect(self) -> None: @@ -136,10 +131,12 @@ def disconnect(self) -> None: self._archimate_manager = None self._repo_manager = None - self._neo4j_conn = None self._engine: Any | None = None self._connected = False + # Release the shared grafeo database + close_database() + def __enter__(self) -> PipelineSession: """Context manager entry.""" self.connect() @@ -298,26 +295,24 @@ def get_repositories(self, detailed: bool = False) -> list[dict]: return result # ========================================================================= - # INFRASTRUCTURE (Neo4j container control) + # INFRASTRUCTURE (graph database control) # ========================================================================= - def get_neo4j_status(self) -> dict[str, Any]: - """Get Neo4j container status.""" - if self._neo4j_conn is None: - self._neo4j_conn = Neo4jConnection(namespace="Docker") - return self._neo4j_conn.get_container_status() - - def start_neo4j(self) -> dict[str, Any]: - """Start Neo4j container.""" - if self._neo4j_conn is None: - self._neo4j_conn = Neo4jConnection(namespace="Docker") - return self._neo4j_conn.start_container() - - def stop_neo4j(self) -> dict[str, Any]: - """Stop Neo4j container.""" - if self._neo4j_conn is None: - self._neo4j_conn = Neo4jConnection(namespace="Docker") - return self._neo4j_conn.stop_container() + def get_graph_db_status(self) -> dict[str, Any]: + """Get graph database status (grafeo embedded — always running).""" + return { + "running": True, + "engine": "grafeo_embedded", + "status": "Running (embedded)", + } + + def start_graph_db(self) -> dict[str, Any]: + """Start graph database (no-op — grafeo is embedded).""" + return {"success": True, "message": "Grafeo is embedded, always available"} + + def stop_graph_db(self) -> dict[str, Any]: + """Stop graph database (no-op — grafeo is embedded).""" + return {"success": True, "message": "Grafeo is embedded, no container to stop"} def clear_graph(self) -> dict[str, Any]: """Clear all graph data.""" diff --git a/pyproject.toml b/pyproject.toml index 8894b24..65f8194 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "Deriva" -version = "0.6.9" +version = "0.7.0" description = "Deriva is a research project aimed at enabling digital architects by automating the derivation of enterprise architecture models. Deriva uses dual knowledge graphs, heuristics and LLM's." readme = "README.md" requires-python = ">=3.14" @@ -13,7 +13,7 @@ keywords = [ "enterprise-architecture", "code-analysis", "llm", - "neo4j", + "grafeo", "marimo", ] classifiers = [ @@ -35,17 +35,17 @@ classifiers = [ dependencies = [ # Core "pydantic>=2.12.5", - "pydantic-settings>=2.0", + "pydantic-settings>=2.13", "python-dotenv>=1.2.1", "pyyaml>=6.0.3", - "rich>=14.3.1", + "rich>=14.3", "lxml>=6.0.2", # Databases "duckdb>=1.4.4", - "neo4j>=6.1.0", - "sqlglot>=28.6.0", + "grafeo>=0.5.10", + "sqlglot>=29", # UI - "marimo>=0.19.6", + "marimo>=0.20", # Code Analysis (tree-sitter) "tree-sitter>=0.24.6", "tree-sitter-python>=0.23.0", @@ -53,28 +53,30 @@ dependencies = [ "tree-sitter-java>=0.23.0", "tree-sitter-c-sharp>=0.23.0", # Document Parsing - "pypdf>=6.6.2", + "pypdf>=6.7", "python-docx>=1.2.0", # Graph Algorithms - "solvor>=0.5.4", - # LLM + "solvor>=0.6", + # LLM "backoff>=2.2.1", - "pydantic-ai>=1.47.0", + "pydantic-ai>=1.63.0", # Utilities "diskcache>=5.6.3", "nest-asyncio>=1.6.0", "structlog>=24.0", - "typer>=0.21.1", + "typer>=0.24", + "prek>=0.3.4", ] [project.optional-dependencies] dev = [ - "pre-commit>=4.5.1", + "pip-audit>=2.9.0", + "prek>=0.1.0", "pytest>=9.0.2", "pytest-cov>=7.0.0", - "ruff>=0.14.14", - "ty>=0.0.13", - "types-lxml>=2025.3.30", + "ruff>=0.15", + "ty>=0.0.19", + "types-lxml>=2026.2", ] [project.urls] @@ -170,8 +172,8 @@ omit = [ "*/tests/*", # Marimo app (interactive UI, not unit testable) "deriva/app/*", - # External adapters requiring infrastructure (Neo4j, Docker, etc.) - "deriva/adapters/neo4j/*", + # Graph database adapters + "deriva/adapters/grafeo/*", "deriva/adapters/graph/*", "deriva/adapters/database/*", "deriva/adapters/archimate/*", diff --git a/tests/conftest.py b/tests/conftest.py index ad1ddfa..01af841 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -195,14 +195,12 @@ def test_something(mock_session_dependencies): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager") as mock_repo, - patch("deriva.services.session.Neo4jConnection") as mock_neo4j, ): yield { "db": mock_db, "graph": mock_graph, "archimate": mock_archimate, "repo": mock_repo, - "neo4j": mock_neo4j, } diff --git a/tests/test_adapters/archimate/test_archimate_manager.py b/tests/test_adapters/archimate/test_archimate_manager.py index 2ba12ae..492232f 100644 --- a/tests/test_adapters/archimate/test_archimate_manager.py +++ b/tests/test_adapters/archimate/test_archimate_manager.py @@ -1,11 +1,7 @@ """Basic tests for ArchiMate Manager. -To run these tests, you must have Neo4j running: - cd neo4j_manager - docker-compose up -d - -Then run: - pytest tests/test_managers/archimate/test_archimate_manager.py -m integration +Run: + pytest tests/test_adapters/archimate/test_archimate_manager.py -m integration """ import pytest @@ -45,17 +41,17 @@ def test_connect_disconnect(): """Test basic connection and disconnection.""" manager = ArchimateManager() manager.connect() - assert manager.neo4j is not None + assert manager.db is not None manager.disconnect() - assert manager.neo4j is None + assert manager.db is None def test_context_manager(): """Test using ArchimateManager as context manager.""" with ArchimateManager() as manager: - assert manager.neo4j is not None + assert manager.db is not None # After context, should be disconnected - assert manager.neo4j is None + assert manager.db is None def test_add_element(archimate_manager): @@ -194,8 +190,8 @@ def test_cypher_query(archimate_manager): # Custom query to count elements (namespace-aware label) # Elements are created with their type as label (e.g., Model:ApplicationComponent) - assert archimate_manager.neo4j is not None - element_label = archimate_manager.neo4j.get_label("ApplicationComponent") + assert archimate_manager.db is not None + element_label = archimate_manager.db.get_label("ApplicationComponent") query = f""" MATCH (e:`{element_label}`) RETURN count(e) as element_count diff --git a/tests/test_adapters/graph/test_manager.py b/tests/test_adapters/graph/test_manager.py index aed32bb..c3e5bfb 100644 --- a/tests/test_adapters/graph/test_manager.py +++ b/tests/test_adapters/graph/test_manager.py @@ -17,9 +17,9 @@ def test_initializes_with_default_namespace(self): """Should initialize with default namespace.""" manager = GraphManager() assert manager.namespace == "Graph" - assert manager.neo4j is None + assert manager.db is None - @patch.dict("os.environ", {"NEO4J_GRAPH_NAMESPACE": "CustomGraph"}, clear=True) + @patch.dict("os.environ", {"GRAPH_NAMESPACE": "CustomGraph"}, clear=True) def test_uses_env_namespace(self): """Should use namespace from environment.""" manager = GraphManager() @@ -29,43 +29,43 @@ def test_uses_env_namespace(self): class TestGraphManagerConnection: """Tests for GraphManager connection handling.""" - @patch("deriva.adapters.graph.manager.Neo4jConnection") + @patch("deriva.adapters.graph.manager.GrafeoConnection") @patch.dict("os.environ", {}, clear=True) - def test_connect_creates_neo4j_connection(self, mock_neo4j_class): - """Should create Neo4j connection on connect.""" + def test_connect_creates_grafeo_connection(self, mock_grafeo_class): + """Should create grafeo connection on connect.""" mock_conn = MagicMock() - mock_neo4j_class.return_value = mock_conn + mock_grafeo_class.return_value = mock_conn manager = GraphManager() manager.connect() - mock_neo4j_class.assert_called_once_with(namespace="Graph") + mock_grafeo_class.assert_called_once_with(namespace="Graph") mock_conn.connect.assert_called_once() - assert manager.neo4j is mock_conn + assert manager.db is mock_conn - @patch("deriva.adapters.graph.manager.Neo4jConnection") + @patch("deriva.adapters.graph.manager.GrafeoConnection") @patch.dict("os.environ", {}, clear=True) - def test_disconnect_closes_connection(self, mock_neo4j_class): + def test_disconnect_closes_connection(self, mock_grafeo_class): """Should close connection on disconnect.""" mock_conn = MagicMock() - mock_neo4j_class.return_value = mock_conn + mock_grafeo_class.return_value = mock_conn manager = GraphManager() manager.connect() manager.disconnect() mock_conn.disconnect.assert_called_once() - assert manager.neo4j is None + assert manager.db is None - @patch("deriva.adapters.graph.manager.Neo4jConnection") + @patch("deriva.adapters.graph.manager.GrafeoConnection") @patch.dict("os.environ", {}, clear=True) - def test_context_manager(self, mock_neo4j_class): + def test_context_manager(self, mock_grafeo_class): """Should work as context manager.""" mock_conn = MagicMock() - mock_neo4j_class.return_value = mock_conn + mock_grafeo_class.return_value = mock_conn with GraphManager() as manager: - assert manager.neo4j is mock_conn + assert manager.db is mock_conn mock_conn.disconnect.assert_called_once() @@ -73,7 +73,7 @@ def test_context_manager(self, mock_neo4j_class): def test_connect_twice_warns(self): """Should warn when already connected.""" manager = GraphManager() - manager.neo4j = MagicMock() # Simulate existing connection + manager.db = MagicMock() # Simulate existing connection # Should not raise, just warn manager.connect() diff --git a/tests/test_adapters/neo4j/__init__.py b/tests/test_adapters/neo4j/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/test_adapters/neo4j/test_manager.py b/tests/test_adapters/neo4j/test_manager.py deleted file mode 100644 index 4551baf..0000000 --- a/tests/test_adapters/neo4j/test_manager.py +++ /dev/null @@ -1,72 +0,0 @@ -"""Tests for adapters.neo4j.manager module.""" - -from __future__ import annotations - -from unittest.mock import MagicMock, patch - -from deriva.adapters.neo4j.manager import Neo4jConnection - - -class TestNeo4jConnectionInit: - """Tests for Neo4jConnection initialization.""" - - @patch.dict("os.environ", {}, clear=True) - def test_stores_namespace(self): - """Should store namespace parameter.""" - conn = Neo4jConnection(namespace="Graph") - assert conn.namespace == "Graph" - - @patch.dict("os.environ", {"NEO4J_URI": "bolt://custom:7687"}, clear=True) - def test_loads_config_from_env(self): - """Should load configuration from environment.""" - conn = Neo4jConnection(namespace="Test") - assert conn.config["neo4j"]["uri"] == "bolt://custom:7687" - - @patch.dict("os.environ", {}, clear=True) - def test_uses_default_values(self): - """Should use default values when env vars not set.""" - conn = Neo4jConnection(namespace="Test") - assert conn.config["neo4j"]["uri"] == "bolt://localhost:7687" - assert conn.config["neo4j"]["database"] == "neo4j" - - -class TestNeo4jConnectionLifecycle: - """Tests for Neo4jConnection connect/disconnect.""" - - @patch("deriva.adapters.neo4j.manager.GraphDatabase") - @patch.dict("os.environ", {}, clear=True) - def test_connect_creates_driver(self, mock_graph_db): - """Should create driver on connect.""" - mock_driver = MagicMock() - mock_graph_db.driver.return_value = mock_driver - - conn = Neo4jConnection(namespace="Test") - conn.connect() - - mock_graph_db.driver.assert_called_once() - assert conn.driver is mock_driver - - @patch("deriva.adapters.neo4j.manager.GraphDatabase") - @patch.dict("os.environ", {}, clear=True) - def test_disconnect_closes_driver(self, mock_graph_db): - """Should close driver on disconnect.""" - mock_driver = MagicMock() - mock_graph_db.driver.return_value = mock_driver - - conn = Neo4jConnection(namespace="Test") - conn.connect() - conn.disconnect() - - mock_driver.close.assert_called_once() - - @patch("deriva.adapters.neo4j.manager.GraphDatabase") - @patch.dict("os.environ", {}, clear=True) - def test_context_manager(self, mock_graph_db): - """Should work as context manager.""" - mock_driver = MagicMock() - mock_graph_db.driver.return_value = mock_driver - - with Neo4jConnection(namespace="Test") as conn: - assert conn.driver is mock_driver - - mock_driver.close.assert_called_once() diff --git a/tests/test_cli/test_cli.py b/tests/test_cli/test_cli.py index 11ba903..71f6f3a 100644 --- a/tests/test_cli/test_cli.py +++ b/tests/test_cli/test_cli.py @@ -1592,7 +1592,7 @@ def test_export_verbose_shows_connection(self, mock_session_class): result = runner.invoke(app, ["export", "-v"]) assert result.exit_code == 0 - assert "Connected to Neo4j" in result.stdout + assert "Connected to grafeo" in result.stdout class TestExportCommandDefaultName: @@ -3324,7 +3324,7 @@ def test_extraction_success(self, mock_session_class, mock_progress): assert result.exit_code == 0 assert "EXTRACTION" in result.stdout - assert "Connected to Neo4j" in result.stdout + assert "Connected to grafeo" in result.stdout mock_session.run_extraction.assert_called_once() @patch("deriva.cli.commands.run.create_progress_reporter") diff --git a/tests/test_modules/derivation/conftest.py b/tests/test_modules/derivation/conftest.py index 089505e..f9aee1d 100644 --- a/tests/test_modules/derivation/conftest.py +++ b/tests/test_modules/derivation/conftest.py @@ -39,7 +39,7 @@ def mock_graph_manager(): """Mock GraphManager that handles both enrichment and candidate queries. The generate() function makes two queries: - 1. get_enrichments_from_neo4j - returns node_id, pagerank, louvain_community, etc. + 1. get_enrichments_from_graph - returns node_id, pagerank, louvain_community, etc. 2. query_candidates - returns id, name, labels, properties """ manager = MagicMock() diff --git a/tests/test_modules/derivation/test_base.py b/tests/test_modules/derivation/test_base.py index fbdf15e..c29ce98 100644 --- a/tests/test_modules/derivation/test_base.py +++ b/tests/test_modules/derivation/test_base.py @@ -538,14 +538,14 @@ def test_to_dict_with_include_props_filter(self): assert "lineNumber" not in result["properties"] -class TestGetEnrichmentsFromNeo4j: - """Tests for get_enrichments_from_neo4j function.""" +class TestGetEnrichmentsFromGraph: + """Tests for get_enrichments_from_graph function.""" def test_returns_enrichments_from_graph_manager(self): - """Should fetch enrichments from Neo4j via graph_manager.""" + """Should fetch enrichments from the graph via graph_manager.""" from unittest.mock import MagicMock - from deriva.modules.derivation.base import get_enrichments_from_neo4j + from deriva.modules.derivation.base import get_enrichments_from_graph mock_graph_manager = MagicMock() mock_graph_manager.query.return_value = [ @@ -553,7 +553,7 @@ def test_returns_enrichments_from_graph_manager(self): {"node_id": "node_2", "pagerank": 0.3, "louvain_community": "comm_2", "kcore_level": 1, "is_articulation_point": False, "in_degree": 1, "out_degree": 2}, ] - result = get_enrichments_from_neo4j(mock_graph_manager) + result = get_enrichments_from_graph(mock_graph_manager) assert "node_1" in result assert result["node_1"]["pagerank"] == 0.5 @@ -570,14 +570,14 @@ def test_handles_null_values(self): """Should handle NULL values in enrichment data.""" from unittest.mock import MagicMock - from deriva.modules.derivation.base import get_enrichments_from_neo4j + from deriva.modules.derivation.base import get_enrichments_from_graph mock_graph_manager = MagicMock() mock_graph_manager.query.return_value = [ {"node_id": "node_1", "pagerank": None, "louvain_community": None, "kcore_level": None, "is_articulation_point": None, "in_degree": None, "out_degree": None}, ] - result = get_enrichments_from_neo4j(mock_graph_manager) + result = get_enrichments_from_graph(mock_graph_manager) assert result["node_1"]["pagerank"] == 0.0 assert result["node_1"]["louvain_community"] is None @@ -590,12 +590,12 @@ def test_returns_empty_on_error(self): """Should return empty dict on query error.""" from unittest.mock import MagicMock - from deriva.modules.derivation.base import get_enrichments_from_neo4j + from deriva.modules.derivation.base import get_enrichments_from_graph mock_graph_manager = MagicMock() mock_graph_manager.query.side_effect = Exception("DB error") - result = get_enrichments_from_neo4j(mock_graph_manager) + result = get_enrichments_from_graph(mock_graph_manager) assert result == {} @@ -1816,7 +1816,7 @@ def test_returns_empty_when_no_candidates(self): from deriva.modules.derivation.application_component import ApplicationComponentDerivation derivation = ApplicationComponentDerivation() - with patch("deriva.modules.derivation.element_base.get_enrichments_from_neo4j", return_value={}): + with patch("deriva.modules.derivation.element_base.get_enrichments_from_graph", return_value={}): with patch("deriva.modules.derivation.element_base.query_candidates", return_value=[]): result = derivation.generate( graph_manager=MagicMock(), @@ -1841,7 +1841,7 @@ def test_handles_query_exception(self): from deriva.modules.derivation.application_component import ApplicationComponentDerivation derivation = ApplicationComponentDerivation() - with patch("deriva.modules.derivation.element_base.get_enrichments_from_neo4j", return_value={}): + with patch("deriva.modules.derivation.element_base.get_enrichments_from_graph", return_value={}): with patch("deriva.modules.derivation.element_base.query_candidates", side_effect=Exception("DB error")): result = derivation.generate( graph_manager=MagicMock(), @@ -1867,7 +1867,7 @@ def test_returns_generation_result_type(self): from deriva.modules.derivation.base import GenerationResult derivation = ApplicationComponentDerivation() - with patch("deriva.modules.derivation.element_base.get_enrichments_from_neo4j", return_value={}): + with patch("deriva.modules.derivation.element_base.get_enrichments_from_graph", return_value={}): with patch("deriva.modules.derivation.element_base.query_candidates", return_value=[]): result = derivation.generate( graph_manager=MagicMock(), diff --git a/tests/test_modules/derivation/test_element_base.py b/tests/test_modules/derivation/test_element_base.py index db3d3a2..698fe93 100644 --- a/tests/test_modules/derivation/test_element_base.py +++ b/tests/test_modules/derivation/test_element_base.py @@ -127,7 +127,7 @@ def filter_candidates(self, candidates, enrichments, max_candidates, **kwargs): # Patch the helper functions to control behavior with ( - patch("deriva.modules.derivation.element_base.get_enrichments_from_neo4j") as mock_enrichments, + patch("deriva.modules.derivation.element_base.get_enrichments_from_graph") as mock_enrichments, patch("deriva.modules.derivation.element_base.query_candidates") as mock_candidates, ): mock_enrichments.return_value = {} diff --git a/tests/test_services/test_config_models.py b/tests/test_services/test_config_models.py index cdddb45..fac3a83 100644 --- a/tests/test_services/test_config_models.py +++ b/tests/test_services/test_config_models.py @@ -13,36 +13,34 @@ DerivationLimits, ExtractionConfigModel, FileTypeModel, + GrafeoSettings, LLMSettings, LouvainConfig, - Neo4jSettings, PageRankConfig, ) # Type alias to help with BaseSettings._env_file parameter which isn't in the type signature -_Neo4jSettings: Any = Neo4jSettings +_GrafeoSettings: Any = GrafeoSettings _LLMSettings: Any = LLMSettings _DerivaSettings: Any = DerivaSettings -class TestNeo4jSettings: - """Tests for Neo4jSettings.""" +class TestGrafeoSettings: + """Tests for GrafeoSettings.""" def test_default_values(self): """Should have sensible defaults.""" - settings = _Neo4jSettings(_env_file=None) - assert settings.uri == "bolt://localhost:7687" - assert settings.database == "neo4j" - assert settings.encrypted is False - assert settings.max_connection_pool_size == 50 + settings = _GrafeoSettings(_env_file=None) + assert settings.db_path == "" + assert settings.log_queries is False def test_loads_from_env(self, monkeypatch): """Should load values from environment.""" - monkeypatch.setenv("NEO4J_URI", "bolt://custom:7687") - monkeypatch.setenv("NEO4J_DATABASE", "test_db") - settings = _Neo4jSettings(_env_file=None) - assert settings.uri == "bolt://custom:7687" - assert settings.database == "test_db" + monkeypatch.setenv("GRAFEO_DB_PATH", "/tmp/test.db") + monkeypatch.setenv("GRAFEO_LOG_QUERIES", "true") + settings = _GrafeoSettings(_env_file=None) + assert settings.db_path == "/tmp/test.db" + assert settings.log_queries is True class TestLLMSettings: @@ -82,7 +80,7 @@ def test_default_values(self): def test_nested_settings(self): """Should provide access to nested settings.""" settings = _DerivaSettings(_env_file=None) - assert settings.neo4j.uri == "bolt://localhost:7687" + assert settings.grafeo.db_path == "" assert settings.llm.temperature == 0.6 assert settings.graph.namespace == "Graph" diff --git a/tests/test_services/test_session.py b/tests/test_services/test_session.py index af2c4dc..a51972d 100644 --- a/tests/test_services/test_session.py +++ b/tests/test_services/test_session.py @@ -23,7 +23,6 @@ def test_init_auto_connect(self): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager") as mock_repo, - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) assert session.is_connected() @@ -39,7 +38,6 @@ def test_connect_creates_managers(self): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession() session.connect() @@ -56,7 +54,6 @@ def test_connect_idempotent(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession() session.connect() @@ -72,7 +69,6 @@ def test_disconnect_clears_managers(self): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session.disconnect() @@ -88,7 +84,6 @@ def test_context_manager(self): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): with PipelineSession() as session: assert session.is_connected() @@ -114,7 +109,6 @@ def test_no_error_when_connected(self): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): mock_graph.return_value.get_nodes_by_type.return_value = [] @@ -134,7 +128,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager") as mock_repo, - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) @@ -202,12 +195,10 @@ def connected_session(self): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection") as mock_neo4j, ): session = PipelineSession(auto_connect=True) session._mock_graph = mock_graph.return_value session._mock_archimate = mock_archimate.return_value - session._mock_neo4j = mock_neo4j.return_value yield session def test_clear_graph(self, connected_session): @@ -219,12 +210,12 @@ def test_clear_graph(self, connected_session): def test_clear_graph_error(self, connected_session): """Should return error on failure.""" - connected_session._mock_graph.clear_graph.side_effect = Exception("Neo4j error") + connected_session._mock_graph.clear_graph.side_effect = Exception("Graph error") result = connected_session.clear_graph() assert result["success"] is False - assert "Neo4j error" in result["error"] + assert "Graph error" in result["error"] def test_clear_model(self, connected_session): """Should clear model and return success.""" @@ -233,13 +224,12 @@ def test_clear_model(self, connected_session): connected_session._mock_archimate.clear_model.assert_called_once() assert result["success"] is True - def test_get_neo4j_status(self, connected_session): - """Should return container status.""" - connected_session._mock_neo4j.get_container_status.return_value = {"running": True} - - status = connected_session.get_neo4j_status() + def test_get_graph_db_status(self, connected_session): + """Should return graph database status (grafeo embedded, always running).""" + status = connected_session.get_graph_db_status() assert status["running"] is True + assert status["engine"] == "grafeo_embedded" class TestPipelineSessionRepositoryManagement: @@ -253,7 +243,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager") as mock_repo, - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session._mock_repo = mock_repo.return_value @@ -300,7 +289,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session._mock_engine = mock_db.return_value @@ -361,7 +349,6 @@ def test_get_llm_status_configured(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) @@ -379,7 +366,6 @@ def test_get_llm_status_not_configured(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) @@ -400,7 +386,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), patch("deriva.services.session.extraction") as mock_extraction, patch("deriva.services.session.derivation") as mock_derivation, patch("deriva.services.session.pipeline") as mock_pipeline, @@ -461,7 +446,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), patch("deriva.services.session.extraction") as mock_extraction, patch("deriva.services.session.derivation") as mock_derivation, patch("deriva.services.session.config") as mock_config, @@ -596,40 +580,38 @@ def test_handles_query_error(self): assert logger is None -class TestPipelineSessionNeo4jControl: - """Tests for Neo4j container control methods.""" +class TestPipelineSessionGraphDbControl: + """Tests for graph database control methods (grafeo embedded).""" - def test_start_neo4j(self): - """Should start Neo4j container.""" + def test_start_graph_db(self): + """Should return success (grafeo is embedded, always available).""" with ( patch("deriva.services.session.get_connection"), patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection") as mock_neo4j, ): session = PipelineSession(auto_connect=True) - mock_neo4j.return_value.start_container.return_value = {"success": True} - result = session.start_neo4j() + result = session.start_graph_db() assert result["success"] is True + assert "embedded" in result["message"].lower() - def test_stop_neo4j(self): - """Should stop Neo4j container.""" + def test_stop_graph_db(self): + """Should return success (grafeo is embedded, no container to stop).""" with ( patch("deriva.services.session.get_connection"), patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection") as mock_neo4j, ): session = PipelineSession(auto_connect=True) - mock_neo4j.return_value.stop_container.return_value = {"success": True} - result = session.stop_neo4j() + result = session.stop_graph_db() assert result["success"] is True + assert "embedded" in result["message"].lower() class TestPipelineSessionDerivationNoLLM: @@ -643,7 +625,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) yield session @@ -677,7 +658,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session._mock_archimate = mock_archimate.return_value @@ -722,7 +702,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), patch("deriva.services.session.config") as mock_config, ): session = PipelineSession(auto_connect=True) @@ -887,7 +866,6 @@ def test_get_file_type_stats(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) mock_db.return_value.execute.return_value.fetchone.side_effect = [ @@ -913,7 +891,6 @@ def test_toggle_llm_cache_enabled(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session._llm_manager = MagicMock() @@ -930,7 +907,6 @@ def test_toggle_llm_cache_no_manager(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) # Force _llm_manager to None @@ -948,7 +924,6 @@ def test_list_benchmark_models(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), patch("deriva.services.session.benchmarking"), ): session = PipelineSession(auto_connect=True) @@ -970,7 +945,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), patch("deriva.services.session.pipeline") as mock_pipeline, ): session = PipelineSession(auto_connect=True) @@ -1028,7 +1002,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager") as mock_repo, - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session._mock_repo = mock_repo.return_value @@ -1081,7 +1054,6 @@ def test_get_extraction_step_count(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager") as mock_repo, - patch("deriva.services.session.Neo4jConnection"), patch("deriva.services.session.config") as mock_config, ): session = PipelineSession(auto_connect=True) @@ -1106,7 +1078,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session._mock_graph = mock_graph.return_value @@ -1159,7 +1130,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session._mock_archimate = mock_archimate.return_value @@ -1245,7 +1215,6 @@ def connected_session(self): patch("deriva.services.session.GraphManager") as mock_graph, patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session._mock_engine = mock_db.return_value @@ -1353,7 +1322,6 @@ def test_get_llm_query_fn_lazy_loads_manager(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) assert session._llm_manager is None @@ -1372,7 +1340,6 @@ def test_get_llm_query_fn_returns_none_on_error(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) @@ -1388,7 +1355,6 @@ def test_get_llm_query_fn_sets_nocache(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) mock_manager = MagicMock() @@ -1405,7 +1371,6 @@ def test_get_llm_query_fn_reuses_existing_manager(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) mock_manager = MagicMock() @@ -1428,7 +1393,6 @@ def test_llm_info_returns_provider_and_model(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) mock_manager = MagicMock() @@ -1447,7 +1411,6 @@ def test_llm_info_returns_none_when_no_manager(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) @@ -1464,7 +1427,6 @@ def test_llm_info_lazy_loads_manager(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) session._llm_manager = None @@ -1485,7 +1447,6 @@ def test_disconnect_idempotent(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession() # Disconnect without connecting should not error @@ -1505,7 +1466,6 @@ def test_clear_model_error(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) mock_archimate.return_value.clear_model.side_effect = Exception("Model error") @@ -1516,61 +1476,50 @@ def test_clear_model_error(self): assert "Model error" in result["error"] -class TestPipelineSessionNeo4jNotConnected: - """Tests for Neo4j control when not initially connected.""" +class TestPipelineSessionGraphDbNotConnected: + """Tests for graph database control stubs (grafeo embedded, always available).""" - def test_get_neo4j_status_creates_connection(self): - """Should create Neo4j connection if not present.""" + def test_get_graph_db_status_always_running(self): + """Should return running status even without full connection (grafeo is embedded).""" with ( patch("deriva.services.session.get_connection"), patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection") as mock_neo4j, ): session = PipelineSession(auto_connect=True) - session._neo4j_conn = None # Simulate no connection - mock_neo4j.return_value.get_container_status.return_value = {"running": False} - result = session.get_neo4j_status() + result = session.get_graph_db_status() - mock_neo4j.assert_called_with(namespace="Docker") - assert result["running"] is False + assert result["running"] is True + assert result["engine"] == "grafeo_embedded" - def test_start_neo4j_creates_connection(self): - """Should create Neo4j connection if not present.""" + def test_start_graph_db_always_succeeds(self): + """Should return success (grafeo is embedded, no container to start).""" with ( patch("deriva.services.session.get_connection"), patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection") as mock_neo4j, ): session = PipelineSession(auto_connect=True) - session._neo4j_conn = None - mock_neo4j.return_value.start_container.return_value = {"success": True} - result = session.start_neo4j() + result = session.start_graph_db() - mock_neo4j.assert_called_with(namespace="Docker") assert result["success"] is True - def test_stop_neo4j_creates_connection(self): - """Should create Neo4j connection if not present.""" + def test_stop_graph_db_always_succeeds(self): + """Should return success (grafeo is embedded, no container to stop).""" with ( patch("deriva.services.session.get_connection"), patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection") as mock_neo4j, ): session = PipelineSession(auto_connect=True) - session._neo4j_conn = None - mock_neo4j.return_value.stop_container.return_value = {"success": True} - result = session.stop_neo4j() + result = session.stop_graph_db() - mock_neo4j.assert_called_with(namespace="Docker") assert result["success"] is True @@ -1584,7 +1533,6 @@ def test_get_repositories_string_result(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager") as mock_repo, - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) mock_repo.return_value.list_repositories.return_value = ["repo1", "repo2"] @@ -1602,7 +1550,6 @@ def test_get_repositories_mixed_results(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager") as mock_repo, - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) # Create object without to_dict @@ -1625,7 +1572,6 @@ def test_get_archimate_stats_with_object_type(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) @@ -1648,7 +1594,6 @@ def test_get_archimate_stats_with_unknown_type(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) @@ -1675,7 +1620,6 @@ def test_export_model_filters_disabled_relationships(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), patch("deriva.services.session.ArchiMateXMLExporter") as mock_exporter, ): session = PipelineSession(auto_connect=True) @@ -1712,7 +1656,6 @@ def test_export_model_handles_exception(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager") as mock_archimate, patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), patch("deriva.services.session.ArchiMateXMLExporter") as mock_exporter, ): session = PipelineSession(auto_connect=True) @@ -1739,7 +1682,6 @@ def test_create_run_handles_error(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), ): session = PipelineSession(auto_connect=True) mock_db.return_value.execute.side_effect = Exception("DB error") @@ -1760,7 +1702,6 @@ def test_get_extraction_step_count_filters_by_repo(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager") as mock_repo, - patch("deriva.services.session.Neo4jConnection"), patch("deriva.services.session.config") as mock_config, ): session = PipelineSession(auto_connect=True) @@ -1788,7 +1729,6 @@ def test_get_file_types_with_has_to_dict(self): patch("deriva.services.session.GraphManager"), patch("deriva.services.session.ArchimateManager"), patch("deriva.services.session.RepoManager"), - patch("deriva.services.session.Neo4jConnection"), 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