diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..ac3c903 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,68 @@ +# Git +.git/ +.gitignore + +# Python +__pycache__/ +*.py[cod] +*$py.class +*.so +.Python +*.egg-info/ +dist/ +build/ +.pytest_cache/ +.coverage +htmlcov/ +.tox/ +.mypy_cache/ +.ruff_cache/ + +# Virtual environments +venv/ +env/ +ENV/ +.venv/ + +# IDEs +.vscode/ +.idea/ +*.swp +*.swo +*~ +.DS_Store + +# Project specific +tests/ +docs/ +examples/ +scripts/ +*.md +!README.md +pytest.ini +.github/ +.gitlab-ci.yml +coordination/ +memory/ +output/ +rdf_output/ +metadata-tmp/ +rdf-tmp/ +tmp/ +tmp-sample-data/ +sample_data/ +test-cli/ +task_log.jsonl +task_queue.jsonl + +# Docker +docker-compose*.yml +Dockerfile* +!Dockerfile +.dockerignore + +# Buildpack +project.toml +pack.toml + +# Keep only essential files for runtime \ No newline at end of file diff --git a/.github/workflows/build-artifacts.yml b/.github/workflows/build-artifacts.yml new file mode 100644 index 0000000..bfe4fbf --- /dev/null +++ b/.github/workflows/build-artifacts.yml @@ -0,0 +1,86 @@ +name: Build Artifacts + +on: + push: + branches: [ main ] + tags: [ 'v*' ] + pull_request: + branches: [ main ] + +jobs: + build-docker: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + + - name: Build Docker image + run: | + docker build -t knowledgebase-processor:latest . + docker save knowledgebase-processor:latest | gzip > knowledgebase-processor-docker.tar.gz + + - name: Upload Docker artifact + uses: actions/upload-artifact@v4 + with: + name: docker-image + path: knowledgebase-processor-docker.tar.gz + + build-wheel: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.12' + + - name: Install Poetry + uses: snok/install-poetry@v1 + + - name: Build wheel + run: | + poetry build + + - name: Upload wheel + uses: actions/upload-artifact@v4 + with: + name: python-wheel + path: dist/ + + # build-executable: + # runs-on: ${{ matrix.os }} + # strategy: + # matrix: + # os: [ubuntu-latest, windows-latest, macos-latest] + + # steps: + # - uses: actions/checkout@v4 + + # - name: Set up Python + # uses: actions/setup-python@v4 + # with: + # python-version: '3.12' + + # - name: Install Poetry + # uses: snok/install-poetry@v1 + + # - name: Install dependencies + # run: | + # poetry install --only=main + + # - name: Install PyInstaller + # run: | + # poetry add --group dev pyinstaller + + # - name: Build executable + # run: | + # poetry run pyinstaller --onefile --name kb src/knowledgebase_processor/cli_v2/main.py + + # - name: Upload executable + # uses: actions/upload-artifact@v4 + # with: + # name: executable-${{ matrix.os }} + # path: dist/kb* \ No newline at end of file diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..e4fba21 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..09fc616 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,45 @@ +# Multi-stage build to handle Python dependencies with C extensions +FROM python:3.12-slim as builder + +# Install build dependencies +RUN apt-get update && apt-get install -y \ + build-essential \ + gcc \ + g++ \ + && rm -rf /var/lib/apt/lists/* + +# Install poetry +RUN pip install poetry + +# Copy dependency files +COPY pyproject.toml poetry.lock ./ + +# Configure poetry to not create virtual environment +RUN poetry config virtualenvs.create false + +# Install dependencies +RUN poetry install --only=main --no-root + +# Production stage +FROM python:3.12-slim as runtime + +# Create non-root user +RUN useradd --create-home --shell /bin/bash kbp + +# Copy installed packages from builder +COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages +COPY --from=builder /usr/local/bin /usr/local/bin + +# Copy application code +COPY src/ /app/src/ +COPY pyproject.toml README.md /app/ + +WORKDIR /app + +# Install the package +RUN pip install -e . + +USER kbp + +# Default command +CMD ["kb", "--help"] \ No newline at end of file diff --git a/Dockerfile.alpine b/Dockerfile.alpine new file mode 100644 index 0000000..3d039b7 --- /dev/null +++ b/Dockerfile.alpine @@ -0,0 +1,75 @@ +# Alpine-based Dockerfile for knowledgebase-processor +# Smaller image size but requires more careful dependency management + +# Build stage +FROM python:3.12-alpine as builder + +# Install build dependencies for Alpine +# Note: Alpine uses musl libc which can cause compatibility issues +RUN apk add --no-cache \ + gcc \ + g++ \ + musl-dev \ + linux-headers \ + python3-dev \ + openblas-dev \ + gfortran \ + build-base \ + cmake \ + # Required for some Python packages + libffi-dev \ + openssl-dev + +# Install poetry +RUN pip install --no-cache-dir poetry==1.8.2 + +WORKDIR /app + +# Copy dependency files +COPY pyproject.toml poetry.lock ./ + +# Configure poetry +RUN poetry config virtualenvs.create false + +# Install dependencies - longer build time due to compilation +RUN poetry install --no-interaction --no-ansi --no-root --only main + +# Copy and install application +COPY src/ ./src/ +COPY README.md ./ +RUN poetry install --no-interaction --no-ansi --only-root + +# Runtime stage +FROM python:3.12-alpine + +# Install runtime dependencies only +RUN apk add --no-cache \ + openblas \ + libgfortran \ + libstdc++ \ + # For health checks + curl + +# Create non-root user +RUN adduser -D -u 1000 kbuser + +# Copy from builder +COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages +COPY --from=builder /usr/local/bin /usr/local/bin + +WORKDIR /app +COPY --from=builder /app/src ./src +COPY pyproject.toml README.md ./ + +# Create data directories +RUN mkdir -p /app/data /app/output /app/metadata && \ + chown -R kbuser:kbuser /app + +USER kbuser + +ENV PYTHONUNBUFFERED=1 + +HEALTHCHECK --interval=30s --timeout=3s --start-period=5s --retries=3 \ + CMD kb --version || exit 1 + +CMD ["kb", "--help"] \ No newline at end of file diff --git a/README-docker.md b/README-docker.md new file mode 100644 index 0000000..97fccc1 --- /dev/null +++ b/README-docker.md @@ -0,0 +1,284 @@ +# 🐳 Docker Usage Guide + +This guide shows you how to run the Knowledge Base Processor in different Docker scenarios. + +## 🚀 Quick Start + +### Option 1: Docker Run Script (Recommended) + +Use the provided wrapper script for easy Docker usage: + +```bash +# Make script executable (first time only) +chmod +x scripts/docker-run.sh + +# Show help +./scripts/docker-run.sh --help + +# Initialize in current directory +./scripts/docker-run.sh init + +# Process documents in specific directory +./scripts/docker-run.sh -w ~/Documents scan + +# Use custom config file +./scripts/docker-run.sh -c ./my-config.json publish --watch + +# Search your knowledge base +./scripts/docker-run.sh search "todo items" +``` + +### Option 2: Docker Compose + +For persistent services and easier management: + +```bash +# Build and run interactively +docker-compose -f docker-compose.app.yml up kbp + +# Run in watch mode (continuous processing) +docker-compose -f docker-compose.app.yml --profile watch up kbp-watch + +# Run with SPARQL server +docker-compose -f docker-compose.app.yml up fuseki kbp +``` + +### Option 3: Direct Docker Commands + +For full control over the container: + +```bash +# Build the image +docker build -t knowledgebase-processor:latest . + +# Run with volume mounts +docker run --rm -it \ + -v "$(pwd):/workspace" \ + -e KBP_WORK_DIR=/workspace \ + -e KBP_HOME=/workspace/.kbp \ + -w /workspace \ + knowledgebase-processor:latest kb --help +``` + +## 📁 Directory Structure + +The Docker setup creates this structure in your mounted directory: + +``` +your-documents/ +├── .kbp/ # KBP configuration directory +│ ├── config.yaml # Configuration file +│ ├── metadata/ # Document metadata and cache +│ └── cache/ # Processing cache +├── your-files.md # Your existing documents (unchanged) +└── kbp_config.json # Optional: custom config file +``` + +## 🔧 Environment Variables + +Configure the tool's behavior with environment variables: + +| Variable | Description | Default | +|----------|-------------|---------| +| `KBP_WORK_DIR` | Working directory path | `/workspace` | +| `KBP_HOME` | KBP configuration directory | `$KBP_WORK_DIR/.kbp` | +| `KBP_KNOWLEDGE_BASE_PATH` | Documents directory | `$KBP_WORK_DIR` | +| `KBP_METADATA_STORE_PATH` | Metadata storage path | `$KBP_HOME/metadata` | +| `KBP_CONFIG_PATH` | Custom config file path | *(auto-detected)* | + +## 📋 Common Use Cases + +### 1. Initialize New Project + +```bash +# Using wrapper script +./scripts/docker-run.sh -w ~/my-docs init + +# Using docker directly +docker run --rm -it \ + -v ~/my-docs:/workspace \ + -e KBP_WORK_DIR=/workspace \ + -e KBP_HOME=/workspace/.kbp \ + -w /workspace \ + knowledgebase-processor:latest kb init +``` + +### 2. Process Existing Documents + +```bash +# Scan and process all documents +./scripts/docker-run.sh -w ~/my-docs scan + +# With custom patterns +./scripts/docker-run.sh -w ~/my-docs scan --pattern "**/*.md" --pattern "**/*.txt" +``` + +### 3. Continuous Monitoring + +```bash +# Watch for changes and auto-process +./scripts/docker-run.sh -w ~/my-docs publish --watch + +# Or using docker-compose +docker-compose -f docker-compose.app.yml --profile watch up +``` + +### 4. Search Knowledge Base + +```bash +# Search for content +./scripts/docker-run.sh -w ~/my-docs search "project tasks" + +# Advanced search with filters +./scripts/docker-run.sh -w ~/my-docs search --type todo "deadlines" +``` + +### 5. Custom Configuration + +Create a `kbp_config.json` file: + +```json +{ + "file_patterns": ["**/*.md", "**/*.txt"], + "extract_frontmatter": true, + "sparql_endpoint_url": "http://localhost:3030/ds/query", + "sparql_update_endpoint_url": "http://localhost:3030/ds/update" +} +``` + +Then use it: + +```bash +./scripts/docker-run.sh -c ./kbp_config.json -w ~/my-docs scan +``` + +## 🔗 Integration with SPARQL + +### Using Fuseki Server + +1. Start Fuseki with docker-compose: +```bash +docker-compose -f docker-compose.app.yml up fuseki +``` + +2. Configure KBP to use Fuseki: +```bash +./scripts/docker-run.sh init --sparql-endpoint http://fuseki:3030/ds +``` + +3. Publish your knowledge base: +```bash +./scripts/docker-run.sh publish --sync +``` + +### Using External SPARQL Endpoint + +Set environment variables: + +```bash +docker run --rm -it \ + -v "$(pwd):/workspace" \ + -e KBP_WORK_DIR=/workspace \ + -e SPARQL_ENDPOINT=http://your-sparql-server/query \ + -e SPARQL_UPDATE_ENDPOINT=http://your-sparql-server/update \ + knowledgebase-processor:latest kb publish --sync +``` + +## 🛠️ Development & Debugging + +### Enable Verbose Output + +```bash +# With wrapper script +VERBOSE=1 ./scripts/docker-run.sh -w ~/my-docs scan --verbose + +# Direct docker command +docker run --rm -it \ + -v "$(pwd):/workspace" \ + -e KBP_WORK_DIR=/workspace \ + -w /workspace \ + knowledgebase-processor:latest kb scan --verbose +``` + +### Access Container Shell + +```bash +docker run --rm -it \ + -v "$(pwd):/workspace" \ + -e KBP_WORK_DIR=/workspace \ + -w /workspace \ + knowledgebase-processor:latest /bin/bash +``` + +### Build Custom Image + +```bash +# Build with custom tag +docker build -t my-kbp:latest . + +# Use custom image +./scripts/docker-run.sh -i my-kbp:latest scan +``` + +## 🔍 Troubleshooting + +### Permission Issues + +If you encounter permission errors: + +```bash +# Fix ownership (Linux/macOS) +sudo chown -R $(id -u):$(id -g) ./.kbp + +# Or run container with your user ID +docker run --rm -it \ + --user $(id -u):$(id -g) \ + -v "$(pwd):/workspace" \ + knowledgebase-processor:latest kb scan +``` + +### Config Not Found + +Ensure you're mounting the right directory: + +```bash +# Check what's mounted +./scripts/docker-run.sh ls -la + +# Verify config path +./scripts/docker-run.sh config show +``` + +### Volume Mount Issues + +On Windows, use full paths: + +```powershell +# PowerShell +./scripts/docker-run.sh -w "C:\Users\YourName\Documents" init + +# Or use WSL paths +./scripts/docker-run.sh -w "/mnt/c/Users/YourName/Documents" init +``` + +## 📊 Performance Tips + +1. **Use volume mounts** instead of copying files +2. **Persist the .kbp directory** to avoid reprocessing +3. **Use watch mode** for continuous updates +4. **Configure exclusion patterns** for large directories + +Example optimized setup: + +```yaml +# docker-compose.override.yml +version: '3.8' +services: + kbp: + volumes: + - ./docs:/workspace/docs + - ./.kbp:/workspace/.kbp + - /node_modules # Exclude from processing + environment: + - KBP_EXCLUDE_PATTERNS=["**/node_modules/**", "**/.git/**"] +``` \ No newline at end of file diff --git a/docker-compose.app.yml b/docker-compose.app.yml new file mode 100644 index 0000000..0e3a7ab --- /dev/null +++ b/docker-compose.app.yml @@ -0,0 +1,66 @@ +version: '3.8' + +services: + kbp: + build: . + image: knowledgebase-processor:latest + container_name: kbp-app + volumes: + # Mount your documents directory + - ./:/workspace + # Persist configuration and metadata + - kbp-data:/workspace/.kbp + environment: + # Configure paths for Docker environment + - KBP_WORK_DIR=/workspace + - KBP_HOME=/workspace/.kbp + - KBP_KNOWLEDGE_BASE_PATH=/workspace + - KBP_METADATA_STORE_PATH=/workspace/.kbp/metadata + # Optional: Set config file path + # - KBP_CONFIG_PATH=/workspace/kbp_config.json + working_dir: /workspace + # Run in interactive mode by default + stdin_open: true + tty: true + command: kb --help + + # Watch mode service for continuous processing + kbp-watch: + build: . + image: knowledgebase-processor:latest + container_name: kbp-watch + volumes: + - ./:/workspace + - kbp-data:/workspace/.kbp + environment: + - KBP_WORK_DIR=/workspace + - KBP_HOME=/workspace/.kbp + - KBP_KNOWLEDGE_BASE_PATH=/workspace + - KBP_METADATA_STORE_PATH=/workspace/.kbp/metadata + working_dir: /workspace + command: kb publish --watch + profiles: + - watch + + # Fuseki SPARQL server (from existing compose file) + fuseki: + image: stain/jena-fuseki:latest + container_name: fuseki-server + ports: + - "3030:3030" + environment: + ADMIN_PASSWORD: admin + JVM_ARGS: -Xmx2g + volumes: + - fuseki-data:/fuseki + command: --update --mem /ds + +volumes: + kbp-data: + driver: local + fuseki-data: + driver: local + +networks: + default: + name: kbp-network \ No newline at end of file diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml new file mode 100644 index 0000000..da6c010 --- /dev/null +++ b/docker-compose.prod.yml @@ -0,0 +1,83 @@ +version: '3.8' + +services: + # Knowledge Base Processor Application + kb-processor: + build: + context: . + dockerfile: Dockerfile + image: knowledgebase-processor:latest + container_name: kb-processor + networks: + - knowledgebase-processor + volumes: + # Mount data directory for input files + - ./data:/app/data:ro + # Mount output directory for results + - ./output:/app/output + # Mount metadata store + - ./metadata:/app/metadata + environment: + - LOG_LEVEL=INFO + - PYTHONUNBUFFERED=1 + depends_on: + fuseki: + condition: service_healthy + command: ["kb", "publish", "/app/data", "--watch"] + + # Knowledge Base API Service + kb-api: + build: + context: . + dockerfile: Dockerfile + image: knowledgebase-processor:latest + container_name: kb-api + networks: + - knowledgebase-processor + ports: + - "8000:8000" + volumes: + - ./metadata:/app/metadata:ro + environment: + - LOG_LEVEL=INFO + - PYTHONUNBUFFERED=1 + - FUSEKI_URL=http://fuseki:3030 + depends_on: + fuseki: + condition: service_healthy + command: ["kb", "serve", "--host", "0.0.0.0", "--port", "8000"] + healthcheck: + test: ["CMD", "curl", "-f", "http://localhost:8000/health"] + interval: 30s + timeout: 10s + retries: 3 + start_period: 10s + + # Fuseki Triple Store (existing service) + fuseki: + image: stain/jena-fuseki:latest + container_name: kb-fuseki + ports: + - "13030:3030" + networks: + - knowledgebase-processor + environment: + - ADMIN_PASSWORD=admin + - JVM_ARGS=-Xmx2g + volumes: + - fuseki-data:/fuseki + - ./data:/staging + command: ["/jena-fuseki/fuseki-server", "--update", "--mem", "/kb"] + healthcheck: + test: ["CMD", "curl", "-f", "http://localhost:3030/$/ping"] + interval: 30s + timeout: 10s + retries: 3 + start_period: 40s + +volumes: + fuseki-data: + +networks: + knowledgebase-processor: + external: true \ No newline at end of file diff --git a/docs/architecture/build-artifacts-options.md b/docs/architecture/build-artifacts-options.md new file mode 100644 index 0000000..2aa4821 --- /dev/null +++ b/docs/architecture/build-artifacts-options.md @@ -0,0 +1,337 @@ +# Knowledge Base Processor - Build Artifact Options + +## Executive Summary + +This document explores various build artifact options for the knowledgebase-processor project, with special consideration for the `srsly` compilation issue encountered with cloud native buildpacks. The `srsly` package is a dependency of spaCy and requires compilation of C extensions, which can be problematic in certain containerization approaches. + +## Current State + +### Dependencies +- Python 3.12 +- Poetry for dependency management +- spaCy (which depends on srsly, blis, and other C extensions) +- No existing Dockerfile +- docker-compose.yml only contains Fuseki service + +### The srsly Compilation Issue + +The `srsly` package (a serialization library used by spaCy) includes C extensions that need to be compiled during installation. This causes issues with: +1. Cloud Native Buildpacks that may not have required build tools +2. Alpine-based images lacking necessary headers/libraries +3. Multi-stage builds where build dependencies aren't properly handled + +## Build Artifact Options + +### Option 1: Traditional Dockerfile with Multi-Stage Build + +**Pros:** +- Full control over build environment +- Can optimize final image size +- Explicit dependency management +- Easy to debug + +**Cons:** +- Requires manual maintenance +- More complex than buildpacks + +**Implementation:** + +```dockerfile +# Build stage +FROM python:3.12-slim as builder + +# Install build dependencies +RUN apt-get update && apt-get install -y \ + build-essential \ + gcc \ + g++ \ + && rm -rf /var/lib/apt/lists/* + +# Install poetry +RUN pip install poetry + +# Copy project files +WORKDIR /app +COPY pyproject.toml poetry.lock ./ + +# Install dependencies +RUN poetry config virtualenvs.create false \ + && poetry install --no-interaction --no-ansi --no-root --only main + +# Runtime stage +FROM python:3.12-slim + +# Install runtime dependencies +RUN apt-get update && apt-get install -y \ + libgomp1 \ + && rm -rf /var/lib/apt/lists/* + +# Copy Python packages from builder +COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages +COPY --from=builder /usr/local/bin /usr/local/bin + +# Copy application +WORKDIR /app +COPY src/ ./src/ +COPY pyproject.toml ./ + +# Install the application +RUN pip install -e . + +CMD ["kb", "--help"] +``` + +### Option 2: Cloud Native Buildpacks with Custom Builder + +**Pros:** +- Automated dependency detection +- Security patches automatically applied +- Follows best practices +- Reproducible builds + +**Cons:** +- Less control over build process +- srsly compilation issues +- Larger images + +**Solutions for srsly issue:** + +1. **Use Paketo Full Builder:** +```bash +pack build knowledgebase-processor \ + --builder paketobuildpacks/builder:full \ + --env BP_CPYTHON_VERSION="3.12.*" +``` + +2. **Create project.toml with build dependencies:** +```toml +[[build.env]] +name = "BP_CPYTHON_VERSION" +value = "3.12.*" + +[[build.env]] +name = "BP_POETRY_VERSION" +value = "1.8.*" + +[[build.buildpacks]] +uri = "gcr.io/paketo-buildpacks/python" + +[build] +exclude = [ + "tests/", + "docs/", + "*.md", + ".git/" +] +``` + +3. **Pre-compile wheels approach:** +Create a custom buildpack extension that includes pre-compiled wheels for srsly and other C extensions. + +### Option 3: Distroless Images with Bazel + +**Pros:** +- Minimal attack surface +- Reproducible builds +- Efficient caching +- Handles C extensions well + +**Cons:** +- Steep learning curve +- Complex setup +- Less common in Python ecosystem + +**Implementation approach:** +```python +# BUILD.bazel +py_binary( + name = "kb", + srcs = ["src/knowledgebase_processor/cli_v2/main.py"], + deps = [ + requirement("spacy"), + requirement("srsly"), + # ... other deps + ], +) + +container_image( + name = "kb_image", + base = "@distroless_python3//image", + entrypoint = ["/kb"], + files = [":kb"], +) +``` + +### Option 4: Nix-based Builds + +**Pros:** +- Reproducible builds +- Handles C dependencies excellently +- Can generate Docker images +- Declarative configuration + +**Cons:** +- Nix learning curve +- Less mainstream + +**Implementation:** +```nix +# flake.nix +{ + inputs = { + nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable"; + poetry2nix.url = "github:nix-community/poetry2nix"; + }; + + outputs = { self, nixpkgs, poetry2nix }: + let + system = "x86_64-linux"; + pkgs = nixpkgs.legacyPackages.${system}; + poetry2nixLib = poetry2nix.lib.mkPoetry2Nix { inherit pkgs; }; + in { + packages.${system}.default = poetry2nixLib.mkPoetryApplication { + projectDir = self; + preferWheels = true; + }; + + dockerImage = pkgs.dockerTools.buildLayeredImage { + name = "knowledgebase-processor"; + contents = [ self.packages.${system}.default ]; + config.Cmd = [ "kb" ]; + }; + }; +} +``` + +### Option 5: Pre-built Wheels Strategy + +**Pros:** +- Avoids compilation entirely +- Fast builds +- Works with any containerization approach + +**Cons:** +- Requires wheel repository +- Platform-specific wheels needed + +**Implementation:** +1. Build wheels on CI for target platforms +2. Host in private PyPI or artifact repository +3. Modify pip/poetry to use pre-built wheels + +```dockerfile +FROM python:3.12-slim + +# Use pre-built wheels +RUN pip install --index-url https://your-pypi.com/simple \ + --trusted-host your-pypi.com \ + knowledgebase-processor + +CMD ["kb"] +``` + +### Option 6: Using Conda/Mamba + +**Pros:** +- Handles C dependencies well +- Pre-compiled packages available +- Cross-platform support + +**Cons:** +- Larger images +- Different ecosystem from pip/poetry + +**Implementation:** +```dockerfile +FROM continuumio/miniconda3:latest + +COPY environment.yml . +RUN conda env create -f environment.yml + +SHELL ["conda", "run", "-n", "kb-env", "/bin/bash", "-c"] + +COPY . /app +WORKDIR /app +RUN pip install -e . + +CMD ["conda", "run", "-n", "kb-env", "kb"] +``` + +## Recommended Approach + +Given the project's requirements and the srsly compilation issue, I recommend: + +### Primary: Traditional Dockerfile with Multi-Stage Build (Option 1) +- Provides full control over the build process +- Explicitly handles C compilation requirements +- Can be optimized for size and security +- Easy to debug and maintain + +### Secondary: Cloud Native Buildpacks with Full Builder (Option 2) +- Use for standardized CI/CD pipelines +- Requires the full builder (not tiny) for C compilation support +- Consider creating custom buildpack for spaCy dependencies + +### Future Consideration: Nix-based Builds (Option 4) +- Excellent for reproducibility +- Handles complex dependencies well +- Consider for long-term migration + +## Implementation Steps + +1. **Create Dockerfile** (Priority 1) + - Multi-stage build with explicit C compilation support + - Optimize for production use + - Include health checks and security scanning + +2. **Add project.toml for Buildpacks** (Priority 2) + - Configure for Paketo full builder + - Document buildpack usage + +3. **Set up CI/CD Pipeline** (Priority 3) + - Build and test multiple artifact types + - Publish to container registry + - Security scanning integration + +4. **Document Build Process** (Priority 4) + - Build commands + - Troubleshooting guide + - Performance optimization tips + +## Security Considerations + +1. **Base Image Selection** + - Use official Python images + - Consider distroless for production + - Regular security updates + +2. **Dependency Scanning** + - Integrate Trivy or similar + - Check for CVEs in dependencies + - Automated security patches + +3. **Runtime Security** + - Non-root user + - Read-only filesystem where possible + - Minimal attack surface + +## Performance Considerations + +1. **Image Size Optimization** + - Multi-stage builds + - Remove build dependencies + - Use slim base images + +2. **Build Cache Optimization** + - Layer caching strategy + - Dependency caching + - Parallel builds where possible + +3. **Startup Time** + - Pre-compile Python files + - Lazy loading of spaCy models + - Health check optimization + +## Conclusion + +The srsly compilation issue with cloud native buildpacks is solvable through multiple approaches. The traditional Dockerfile approach provides the most control and is recommended for immediate implementation, while buildpacks can be used with the full builder for standardized deployments. Long-term consideration should be given to more advanced solutions like Nix for better reproducibility and dependency management. \ No newline at end of file diff --git a/docs/troubleshooting/srsly-compilation-issues.md b/docs/troubleshooting/srsly-compilation-issues.md new file mode 100644 index 0000000..ce96b44 --- /dev/null +++ b/docs/troubleshooting/srsly-compilation-issues.md @@ -0,0 +1,237 @@ +# Troubleshooting srsly Compilation Issues + +## Overview + +The `srsly` package is a dependency of spaCy that provides high-performance serialization utilities. It includes C extensions that must be compiled during installation, which can cause issues in certain containerization scenarios. + +## Common Issues and Solutions + +### Issue 1: Missing Build Tools in Buildpacks + +**Symptoms:** +- Build fails with "error: Microsoft Visual C++ 14.0 is required" (Windows) +- Build fails with "gcc: command not found" (Linux) +- Error: "No module named '_srsly'" + +**Solution:** +Use the full builder instead of tiny/base builders: + +```bash +# Use full builder which includes build-essential +pack build myapp --builder paketobuildpacks/builder:full +``` + +### Issue 2: Alpine Linux Compatibility + +**Symptoms:** +- Segmentation faults at runtime +- "Error loading shared library" messages +- ImportError when importing srsly + +**Solution:** +Alpine uses musl libc instead of glibc. Install additional dependencies: + +```dockerfile +RUN apk add --no-cache \ + gcc \ + g++ \ + musl-dev \ + linux-headers \ + python3-dev \ + openblas-dev \ + gfortran +``` + +### Issue 3: Missing Runtime Dependencies + +**Symptoms:** +- Application starts but crashes when using spaCy +- "libgomp.so.1: cannot open shared object file" + +**Solution:** +Ensure runtime dependencies are installed in the final image: + +```dockerfile +# For Debian/Ubuntu based images +RUN apt-get update && apt-get install -y \ + libgomp1 \ + libopenblas0 + +# For Alpine +RUN apk add --no-cache \ + libgomp \ + openblas +``` + +### Issue 4: Platform-Specific Wheels + +**Symptoms:** +- Build works locally but fails in CI/CD +- "No matching distribution found for srsly" + +**Solution:** +Force compilation from source or use platform-specific wheels: + +```bash +# Force compilation from source +pip install --no-binary :all: srsly + +# Or use platform-specific index +pip install --index-url https://pypi.org/simple/ \ + --extra-index-url https://alpine-wheels.github.io/index \ + srsly +``` + +## Debugging Steps + +### 1. Check Compilation Environment + +```bash +# In your build container +python -c "import sysconfig; print(sysconfig.get_config_vars())" +gcc --version +python --version +``` + +### 2. Verify Installation + +```python +# Test srsly installation +try: + import srsly + print(f"srsly version: {srsly.__version__}") + # Test basic functionality + data = {"test": "data"} + json_bytes = srsly.json_dumps(data) + print("srsly is working correctly") +except Exception as e: + print(f"Error: {e}") +``` + +### 3. Check Shared Libraries + +```bash +# List dependencies +ldd $(python -c "import srsly; print(srsly.__file__)") + +# On Alpine +apk info -L py3-srsly +``` + +## Best Practices + +### 1. Use Multi-Stage Builds + +Separate build and runtime dependencies: + +```dockerfile +# Build stage with all compilation tools +FROM python:3.12 as builder +RUN apt-get update && apt-get install -y build-essential +# ... install packages ... + +# Runtime stage with minimal dependencies +FROM python:3.12-slim +COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages +``` + +### 2. Cache Dependencies + +Use Docker build cache effectively: + +```dockerfile +# Copy only dependency files first +COPY pyproject.toml poetry.lock ./ +RUN poetry install --no-root + +# Then copy source code +COPY . . +RUN poetry install +``` + +### 3. Pre-Built Wheels + +Consider maintaining pre-built wheels: + +```bash +# Build wheels for your platform +pip wheel --wheel-dir ./wheels srsly spacy + +# Use pre-built wheels in Dockerfile +COPY wheels/ /tmp/wheels/ +RUN pip install --find-links /tmp/wheels srsly spacy +``` + +### 4. Use Compatible Base Images + +Recommended base images: +- `python:3.12-slim-bookworm` (Debian-based, good compatibility) +- `python:3.12` (Full Python image with build tools) +- Avoid `python:3.12-alpine` unless you need the smaller size + +## Alternative Solutions + +### 1. Use Conda/Mamba + +Conda provides pre-compiled binaries: + +```dockerfile +FROM continuumio/miniconda3 +RUN conda install -c conda-forge spacy +``` + +### 2. Use Pre-Built Images + +Consider using images with spaCy pre-installed: + +```dockerfile +FROM explosion/spacy:latest +``` + +### 3. Build Custom Base Image + +Create a base image with all dependencies: + +```dockerfile +# base.Dockerfile +FROM python:3.12-slim +RUN apt-get update && apt-get install -y [all-deps] +RUN pip install spacy srsly +``` + +## CI/CD Considerations + +### GitHub Actions + +```yaml +- name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.12' + +- name: Install system dependencies + run: | + sudo apt-get update + sudo apt-get install -y build-essential + +- name: Install Python dependencies + run: | + pip install poetry + poetry install +``` + +### GitLab CI + +```yaml +before_script: + - apt-get update && apt-get install -y build-essential + - pip install poetry + - poetry install +``` + +## References + +- [srsly GitHub Repository](https://github.com/explosion/srsly) +- [spaCy Installation Guide](https://spacy.io/usage) +- [Cloud Native Buildpacks Python Guide](https://paketo.io/docs/howto/python/) +- [Alpine Linux Python Packages](https://pkgs.alpinelinux.org/packages?name=py3-*) \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index d51b333..08af7ff 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,65 +11,6 @@ files = [ {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, ] -[[package]] -name = "blis" -version = "1.0.2" -description = "The Blis BLAS-like linear algebra library, as a self-contained C-extension." -optional = false -python-versions = "*" -files = [ - 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Enable pip install for better C extension handling +[[build.env]] +name = "BP_PIP_INSTALL_FLAGS" +value = "--no-binary :all:" + +# Ensure we have compilation tools available +[[build.env]] +name = "BP_INCLUDE_FILES" +value = "pyproject.toml poetry.lock src/ README.md" + +# Buildpacks to use +[[build.buildpacks]] +uri = "gcr.io/paketo-buildpacks/python" + +# Or use specific buildpack versions +# [[build.buildpacks]] +# uri = "gcr.io/paketo-buildpacks/cpython" +# version = "latest" +# +# [[build.buildpacks]] +# uri = "gcr.io/paketo-buildpacks/poetry" +# version = "latest" +# +# [[build.buildpacks]] +# uri = "gcr.io/paketo-buildpacks/poetry-install" +# version = "latest" +# +# [[build.buildpacks]] +# uri = "gcr.io/paketo-buildpacks/python-start" +# version = "latest" + +# Process type +[[processes]] +type = "cli" +command = "kb" +default = true + +[[processes]] +type = "worker" +command = "kb publish --watch /workspace" + +# Slices for layer reuse +[slices] +paths = ["src/knowledgebase_processor"] + +# Metadata +[metadata] +include_files = ["README.md", "LICENSE"] + +# Build exclusions +[build] +exclude = [ + ".git", + ".github", + "tests", + "docs", + "examples", + "scripts", + "*.pyc", + "__pycache__", + ".pytest_cache", + "coordination", + "memory", + "output", + "sample_data", + "tmp*", + "*.log", + "*.db", + "*.ttl" +] \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 66e7ab2..beae663 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,11 +12,12 @@ pydantic = "^2.11.4" markdown-it-py = "^3.0.0" pyyaml = "^6.0.2" tomli = "^2.2.1" -spacy = "^3.7.0" +# spacy = "^3.7.0" # Removed to avoid C compilation issues in cloud builds rdflib = "^7.0.0" click = "^8.1.0" rich = "^13.7.0" watchdog = "^3.0.0" +SPARQLWrapper = "^2.0.0" [tool.poetry.group.test.dependencies] pytest = "^7.4.0" @@ -25,7 +26,6 @@ pytest-benchmark = "^4.0.0" psutil = "^5.9.0" docker = "^6.1.0" requests = "^2.31.0" -SPARQLWrapper = "^2.0.0" [tool.poetry.scripts] kbp = "knowledgebase_processor.cli:main" @@ -35,3 +35,4 @@ test = "scripts.run_tests:main" [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" + diff --git a/scripts/build.sh b/scripts/build.sh new file mode 100755 index 0000000..ec225dd --- /dev/null +++ b/scripts/build.sh @@ -0,0 +1,189 @@ +#!/bin/bash +# Build script for knowledgebase-processor +# Handles different build approaches including Docker and buildpacks + +set -e + +# Colors for output +RED='\033[0;31m' +GREEN='\033[0;32m' +YELLOW='\033[1;33m' +NC='\033[0m' # No Color + +# Default values +BUILD_TYPE="docker" +IMAGE_NAME="knowledgebase-processor" +IMAGE_TAG="latest" +DOCKERFILE="Dockerfile" +BUILDER="paketobuildpacks/builder:full" + +# Help function +show_help() { + echo "Knowledge Base Processor Build Script" + echo "" + echo "Usage: $0 [OPTIONS]" + echo "" + echo "Options:" + echo " -t, --type TYPE Build type: docker, docker-alpine, buildpack (default: docker)" + echo " -n, --name NAME Image name (default: knowledgebase-processor)" + echo " -v, --tag TAG Image tag (default: latest)" + echo " -f, --file FILE Dockerfile to use (default: Dockerfile)" + echo " -b, --builder BUILDER Buildpack builder (default: paketobuildpacks/builder:full)" + echo " -h, --help Show this help message" + echo "" + echo "Examples:" + echo " $0 # Build with Docker" + echo " $0 --type docker-alpine # Build Alpine variant" + echo " $0 --type buildpack # Build with Cloud Native Buildpacks" + echo " $0 --name myapp --tag v1.0.0 # Custom name and tag" +} + +# Parse arguments +while [[ $# -gt 0 ]]; do + case $1 in + -t|--type) + BUILD_TYPE="$2" + shift 2 + ;; + -n|--name) + IMAGE_NAME="$2" + shift 2 + ;; + -v|--tag) + IMAGE_TAG="$2" + shift 2 + ;; + -f|--file) + DOCKERFILE="$2" + shift 2 + ;; + -b|--builder) + BUILDER="$2" + shift 2 + ;; + -h|--help) + show_help + exit 0 + ;; + *) + echo -e "${RED}Unknown option: $1${NC}" + show_help + exit 1 + ;; + esac +done + +# Build functions +build_docker() { + echo -e "${GREEN}Building with Docker...${NC}" + echo "Image: ${IMAGE_NAME}:${IMAGE_TAG}" + echo "Dockerfile: ${DOCKERFILE}" + + docker build \ + -f "${DOCKERFILE}" \ + -t "${IMAGE_NAME}:${IMAGE_TAG}" \ + --build-arg BUILDKIT_INLINE_CACHE=1 \ + . + + echo -e "${GREEN}Build complete!${NC}" + echo "" + echo "To run the image:" + echo " docker run --rm ${IMAGE_NAME}:${IMAGE_TAG}" + echo "" + echo "To run with data volume:" + echo " docker run --rm -v \$(pwd)/data:/app/data ${IMAGE_NAME}:${IMAGE_TAG} kb scan /app/data" +} + +build_docker_alpine() { + echo -e "${GREEN}Building Alpine variant with Docker...${NC}" + DOCKERFILE="Dockerfile.alpine" + build_docker +} + +build_buildpack() { + echo -e "${GREEN}Building with Cloud Native Buildpacks...${NC}" + echo "Builder: ${BUILDER}" + echo "Image: ${IMAGE_NAME}:${IMAGE_TAG}" + + # Check if pack is installed + if ! command -v pack &> /dev/null; then + echo -e "${RED}Error: 'pack' CLI not found${NC}" + echo "Please install pack CLI: https://buildpacks.io/docs/tools/pack/" + exit 1 + fi + + # Build with pack + pack build "${IMAGE_NAME}:${IMAGE_TAG}" \ + --builder "${BUILDER}" \ + --env BP_CPYTHON_VERSION="3.12.*" \ + --env BP_POETRY_VERSION="1.8.*" \ + --path . + + echo -e "${GREEN}Build complete!${NC}" +} + +# Test the built image +test_image() { + echo -e "${YELLOW}Testing built image...${NC}" + + # Test if kb command works + if docker run --rm "${IMAGE_NAME}:${IMAGE_TAG}" kb --version; then + echo -e "${GREEN}✓ Version check passed${NC}" + else + echo -e "${RED}✗ Version check failed${NC}" + exit 1 + fi + + # Test help command + if docker run --rm "${IMAGE_NAME}:${IMAGE_TAG}" kb --help > /dev/null; then + echo -e "${GREEN}✓ Help command passed${NC}" + else + echo -e "${RED}✗ Help command failed${NC}" + exit 1 + fi + + echo -e "${GREEN}All tests passed!${NC}" +} + +# Main execution +echo "Knowledge Base Processor Build Script" +echo "=====================================" + +case ${BUILD_TYPE} in + docker) + build_docker + test_image + ;; + docker-alpine) + build_docker_alpine + test_image + ;; + buildpack) + build_buildpack + test_image + ;; + *) + echo -e "${RED}Unknown build type: ${BUILD_TYPE}${NC}" + echo "Valid types: docker, docker-alpine, buildpack" + exit 1 + ;; +esac + +# Show image info +echo "" +echo "Image Information:" +echo "==================" +docker images | grep "${IMAGE_NAME}" | grep "${IMAGE_TAG}" + +# Show usage examples +echo "" +echo "Usage Examples:" +echo "===============" +echo "# Run CLI" +echo "docker run --rm ${IMAGE_NAME}:${IMAGE_TAG} kb --help" +echo "" +echo "# Process files" +echo "docker run --rm -v \$(pwd)/data:/data ${IMAGE_NAME}:${IMAGE_TAG} kb scan /data" +echo "" +echo "# Run with docker-compose" +echo "docker-compose -f docker-compose.prod.yml up" \ No newline at end of file diff --git a/scripts/docker-run.sh b/scripts/docker-run.sh new file mode 100755 index 0000000..b9d644b --- /dev/null +++ b/scripts/docker-run.sh @@ -0,0 +1,111 @@ +#!/bin/bash +# Docker wrapper script for Knowledge Base Processor +# Makes it easy to run the tool with proper volume mounts and environment variables + +set -e + +# Default values +IMAGE_TAG="knowledgebase-processor:latest" +WORK_DIR="${PWD}" +CONFIG_FILE="" +COMMAND="" + +# Colors for output +RED='\033[0;31m' +GREEN='\033[0;32m' +YELLOW='\033[1;33m' +NC='\033[0m' # No Color + +usage() { + echo "Usage: $0 [OPTIONS] [COMMAND]" + echo "" + echo "Options:" + echo " -w, --work-dir PATH Working directory to mount (default: current directory)" + echo " -c, --config PATH Config file path (will be mounted)" + echo " -i, --image TAG Docker image tag (default: knowledgebase-processor:latest)" + echo " -h, --help Show this help" + echo "" + echo "Examples:" + echo " $0 --help # Show KB help" + echo " $0 init # Initialize in current directory" + echo " $0 -w ~/Documents init # Initialize in ~/Documents" + echo " $0 -c ./my-config.json scan # Use custom config" + echo " $0 publish --watch # Watch mode with current directory" + echo " $0 -w /data search \"todo\" # Search in /data directory" +} + +# Parse arguments +while [[ $# -gt 0 ]]; do + case $1 in + -w|--work-dir) + WORK_DIR="$2" + shift 2 + ;; + -c|--config) + CONFIG_FILE="$2" + shift 2 + ;; + -i|--image) + IMAGE_TAG="$2" + shift 2 + ;; + -h|--help) + if [[ -z "$COMMAND" ]]; then + usage + exit 0 + else + COMMAND="$COMMAND $1" + shift + fi + ;; + *) + COMMAND="$COMMAND $1" + shift + ;; + esac +done + +# Resolve paths +WORK_DIR=$(realpath "$WORK_DIR") + +# Build docker run command +DOCKER_CMD="docker run --rm -it --network host" + +# Volume mounts +DOCKER_CMD="$DOCKER_CMD -v \"$WORK_DIR:/workspace\"" + +# Environment variables +DOCKER_CMD="$DOCKER_CMD -e KBP_WORK_DIR=/workspace" +DOCKER_CMD="$DOCKER_CMD -e KBP_HOME=/workspace/.kbp" +DOCKER_CMD="$DOCKER_CMD -e KBP_KNOWLEDGE_BASE_PATH=/workspace" +DOCKER_CMD="$DOCKER_CMD -e KBP_METADATA_STORE_PATH=/workspace/.kbp/metadata" + +# Config file handling +if [[ -n "$CONFIG_FILE" ]]; then + if [[ ! -f "$CONFIG_FILE" ]]; then + echo -e "${RED}Error: Config file '$CONFIG_FILE' not found${NC}" >&2 + exit 1 + fi + CONFIG_FILE=$(realpath "$CONFIG_FILE") + DOCKER_CMD="$DOCKER_CMD -v \"$CONFIG_FILE:/workspace/kbp_config.json\"" + DOCKER_CMD="$DOCKER_CMD -e KBP_CONFIG_PATH=/workspace/kbp_config.json" +fi + +# Working directory +DOCKER_CMD="$DOCKER_CMD -w /workspace" + +# Image and command +DOCKER_CMD="$DOCKER_CMD $IMAGE_TAG" +if [[ -n "$COMMAND" ]]; then + DOCKER_CMD="$DOCKER_CMD kb$COMMAND" +else + DOCKER_CMD="$DOCKER_CMD kb --help" +fi + +# Print what we're running (if verbose) +if [[ "${VERBOSE:-}" == "1" ]]; then + echo -e "${YELLOW}Running: $DOCKER_CMD${NC}" >&2 +fi + +# Execute +eval $DOCKER_CMD \ No newline at end of file diff --git a/src/knowledgebase_processor/config/config.py b/src/knowledgebase_processor/config/config.py index eb95d21..3c23859 100644 --- a/src/knowledgebase_processor/config/config.py +++ b/src/knowledgebase_processor/config/config.py @@ -46,18 +46,29 @@ def load_config(config_path: Optional[str] = None) -> Config: Returns: Config object + Environment variables can override defaults: + - KBP_CONFIG_PATH: Path to config file + - KBP_KNOWLEDGE_BASE_PATH: Path to knowledge base directory + - KBP_METADATA_STORE_PATH: Path to metadata store directory + - KBP_HOME: Base directory for KBP files (defaults to ~/.kbp) + If config_path is not provided, the function will look for a config file in the following locations: - 1. ./kbp_config.json - 2. ~/.kbp_config.json - 3. /etc/kbp_config.json + 1. $KBP_CONFIG_PATH (if set) + 2. ./kbp_config.json + 3. $KBP_HOME/config.json or ~/.kbp/config.json + 4. ~/.kbp_config.json + 5. /etc/kbp_config.json If no config file is found, default values will be used. """ - # Default configuration + # Get environment variables + kbp_home = os.getenv("KBP_HOME", os.path.expanduser("~/.kbp")) + + # Default configuration with environment variable support default_config = { - "knowledge_base_path": os.path.expanduser("~/knowledge_base"), - "metadata_store_path": os.path.expanduser("~/.kbp/metadata"), + "knowledge_base_path": os.getenv("KBP_KNOWLEDGE_BASE_PATH", os.getenv("KBP_WORK_DIR", os.getcwd())), + "metadata_store_path": os.getenv("KBP_METADATA_STORE_PATH", os.path.join(kbp_home, "metadata")), "file_patterns": ["**/*.md"], "exclude_patterns": [], "extract_frontmatter": True, @@ -81,9 +92,19 @@ def load_config(config_path: Optional[str] = None) -> Config: config_data = json.load(f) return Config(**{**default_config, **config_data}) + # Check for environment variable config path first + env_config_path = os.getenv("KBP_CONFIG_PATH") + if env_config_path: + env_config_file = Path(env_config_path) + if env_config_file.exists(): + with open(env_config_file, 'r', encoding='utf-8') as f: + config_data = json.load(f) + return Config(**{**default_config, **config_data}) + # Otherwise, look for config files in standard locations config_paths = [ Path("./kbp_config.json"), + Path(kbp_home) / "config.json", Path(os.path.expanduser("~/.kbp_config.json")), Path("/etc/kbp_config.json") ]