diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..ce02378 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,13 @@ +.git +.github +.Rproj.user +.Rhistory +.RData +*.Rproj +a4d-python/.pytest_cache +a4d-python/.ruff_cache +a4d-python/htmlcov +a4d-python/.coverage +a4d-python/profiling/*.prof +data/ +secrets/ diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 3048080..fe1b1d7 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -28,7 +28,7 @@ jobs: enable-cache: true - name: Set up Python - run: uv python install 3.11 + run: uv python install 3.14 - name: Install dependencies run: uv sync --all-extras diff --git a/a4d-python/Dockerfile b/a4d-python/Dockerfile index 1837bdf..de143cc 100644 --- a/a4d-python/Dockerfile +++ b/a4d-python/Dockerfile @@ -1,7 +1,7 @@ -FROM python:3.11-slim +FROM python:3.14-slim # Install system dependencies -RUN apt-get update && apt-get install -y \ +RUN apt-get update && apt-get install -y --no-install-recommends \ gcc \ g++ \ curl \ @@ -13,23 +13,22 @@ ENV PATH="/root/.cargo/bin:${PATH}" WORKDIR /app -# Copy dependency files -COPY pyproject.toml ./ +# Copy dependency files first to leverage Docker layer caching +COPY a4d-python/pyproject.toml a4d-python/uv.lock ./ -# Install dependencies -RUN uv sync --frozen +# Install production dependencies only +RUN uv sync --frozen --no-dev # Copy application code -COPY src/ src/ -COPY scripts/ scripts/ +COPY a4d-python/src/ src/ -# Copy reference data from parent directory -# (This will be mounted or copied during build) -COPY ../reference_data/ reference_data/ +# Copy reference data from the repo root +COPY reference_data/ reference_data/ # Set environment ENV PYTHONPATH=/app/src ENV PYTHONUNBUFFERED=1 +ENV A4D_DATA_ROOT=/workspace/data -# Default command -CMD ["uv", "run", "python", "scripts/run_pipeline.py"] +# Run the full pipeline: download → process → upload to GCS → ingest into BigQuery +CMD ["uv", "run", "a4d", "run-pipeline"] diff --git a/a4d-python/pyproject.toml b/a4d-python/pyproject.toml index d959a09..5bad486 100644 --- a/a4d-python/pyproject.toml +++ b/a4d-python/pyproject.toml @@ -3,7 +3,7 @@ name = "a4d" version = "2.0.0" description = "A4D Medical Tracker Data Processing Pipeline (Python)" readme = "README.md" -requires-python = ">=3.11" +requires-python = ">=3.14" authors = [ {name = "Michael Aydinbas", email = "michael.aydinbas@gmail.com"} ] @@ -11,7 +11,6 @@ license = {text = "MIT"} dependencies = [ "polars>=0.20.0", - "duckdb>=0.10.0", "pydantic>=2.6.0", "pydantic-settings>=2.2.0", "pandera[polars]>=0.18.0", @@ -47,7 +46,7 @@ build-backend = "hatchling.build" [tool.ruff] line-length = 100 -target-version = "py311" +target-version = "py314" lint.select = [ "E", # pycodestyle errors "W", # pycodestyle warnings diff --git a/a4d-python/src/a4d/cli.py b/a4d-python/src/a4d/cli.py index 51adbf1..6ab7cd7 100644 --- a/a4d-python/src/a4d/cli.py +++ b/a4d-python/src/a4d/cli.py @@ -446,8 +446,124 @@ def upload_output_cmd( raise typer.Exit(1) from e -@app.command("version") -def version_cmd(): +@app.command("run-pipeline") +def run_pipeline_cmd( + workers: Annotated[ + int, typer.Option("--workers", "-w", help="Number of parallel workers (1 = sequential)") + ] = 4, + force: Annotated[ + bool, typer.Option("--force", help="Force reprocessing (ignore existing outputs)") + ] = False, + skip_upload: Annotated[ + bool, + typer.Option("--skip-upload", help="Skip GCS and BigQuery uploads (local testing)"), + ] = False, +): + """Run the full end-to-end A4D pipeline. + + Executes all pipeline stages in sequence: + 1. Download tracker files from Google Cloud Storage + 2. Extract and clean all tracker files + 3. Create final tables (static, monthly, annual) + 4. Upload output files to Google Cloud Storage + 5. Ingest tables into BigQuery + + All configuration is read from environment variables (A4D_*) or a .env file. + + \b + Examples: + # Full pipeline with 4 workers + uv run a4d run-pipeline + + # Force reprocess all files + uv run a4d run-pipeline --force + + # Local testing without GCS/BigQuery uploads + uv run a4d run-pipeline --skip-upload + """ + from a4d.config import settings + from a4d.gcp.bigquery import load_pipeline_tables + from a4d.gcp.storage import download_tracker_files, upload_output + + console.print("\n[bold blue]A4D Full Pipeline[/bold blue]\n") + console.print(f"Data root: {settings.data_root}") + console.print(f"Output root: {settings.output_root}") + console.print(f"Workers: {workers}") + console.print(f"Project: {settings.project_id}") + console.print(f"Dataset: {settings.dataset}\n") + + # Step 1 – Download tracker files from GCS + if not skip_upload: + console.print("[bold]Step 1/5:[/bold] Downloading tracker files from GCS...") + try: + downloaded = download_tracker_files(destination=settings.data_root) + console.print(f" ✓ Downloaded {len(downloaded)} files\n") + except Exception as e: + console.print(f"\n[bold red]Error during download: {e}[/bold red]\n") + raise typer.Exit(1) from e + else: + console.print("[bold]Step 1/5:[/bold] Skipping GCS download (--skip-upload)\n") + + # Step 2+3 – Extract, clean and build tables + console.print("[bold]Steps 2–3/5:[/bold] Processing tracker files...\n") + try: + result = run_patient_pipeline( + max_workers=workers, + force=force, + show_progress=True, + console_log_level="WARNING", + ) + + console.print( + f" ✓ Processed {result.total_trackers} trackers " + f"({result.successful_trackers} ok, {result.failed_trackers} failed)\n" + ) + + if result.failed_trackers > 0: + console.print("[bold yellow]Failed trackers:[/bold yellow]") + for tr in result.tracker_results: + if not tr.success: + console.print(f" • {tr.tracker_file.name}: {tr.error}") + console.print() + + if not result.success: + console.print("[bold red]✗ Pipeline failed – aborting upload steps[/bold red]\n") + raise typer.Exit(1) + + except Exception as e: + console.print(f"\n[bold red]Error during processing: {e}[/bold red]\n") + raise typer.Exit(1) from e + + tables_dir = settings.output_root / "tables" + + # Step 4 – Upload output to GCS + if not skip_upload: + console.print("[bold]Step 4/5:[/bold] Uploading output files to GCS...") + try: + uploaded = upload_output(source_dir=settings.output_root) + console.print(f" ✓ Uploaded {len(uploaded)} files\n") + except Exception as e: + console.print(f"\n[bold red]Error during GCS upload: {e}[/bold red]\n") + raise typer.Exit(1) from e + else: + console.print("[bold]Step 4/5:[/bold] Skipping GCS upload (--skip-upload)\n") + + # Step 5 – Ingest tables into BigQuery + if not skip_upload: + console.print("[bold]Step 5/5:[/bold] Ingesting tables into BigQuery...") + try: + bq_results = load_pipeline_tables(tables_dir=tables_dir) + console.print(f" ✓ Loaded {len(bq_results)} tables into BigQuery\n") + except Exception as e: + console.print(f"\n[bold red]Error during BigQuery upload: {e}[/bold red]\n") + raise typer.Exit(1) from e + else: + console.print("[bold]Step 5/5:[/bold] Skipping BigQuery upload (--skip-upload)\n") + + console.print("[bold green]✓ Full pipeline completed successfully![/bold green]\n") + + + """Show version information.""" console.print("[bold cyan]A4D Pipeline v0.1.0[/bold cyan]") console.print("Python implementation of the A4D medical tracker processing pipeline") diff --git a/a4d-python/uv.lock b/a4d-python/uv.lock index 10cf087..5f5f2ad 100644 --- a/a4d-python/uv.lock +++ b/a4d-python/uv.lock @@ -1,18 +1,12 @@ version = 1 revision = 3 -requires-python = ">=3.11" -resolution-markers = [ - 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