gnn-pipeline-orchestration

name	gnn-pipeline-orchestration
description	GNN pipeline orchestration and configuration management. Use when configuring pipeline execution, setting step inclusion/exclusion, managing pipeline state, or customizing the 25-step execution flow.

GNN Pipeline Orchestration

Purpose

Manages pipeline configuration, step ordering, execution state, and orchestration logic for the 25-step GNN pipeline. Controls which steps run, their order, and how data flows between them.

Key Commands

# Full pipeline
python src/main.py --target-dir input/gnn_files --verbose

# Run specific steps only
python src/main.py --only-steps "3,5,11,12" --verbose

# Skip specific steps
python src/main.py --skip-steps "15,16" --verbose

# Dry run (show what would execute)
python src/main.py --dry-run --verbose

API

from pipeline import (
    PipelineConfig, StepConfig, STEP_METADATA,
    get_pipeline_config, set_pipeline_config,
    run_pipeline, get_pipeline_status, validate_pipeline_config,
    create_pipeline_config, execute_pipeline_step, execute_pipeline_steps,
    get_output_dir_for_script, run_enhanced_health_check,
    EnhancedHealthChecker, StepExecutionResult
)

# Create and run pipeline
config = create_pipeline_config(target_dir="input/", output_dir="output/")
result = run_pipeline(config)

# Execute specific steps
result = execute_pipeline_step(step_number=3, config=config)
results = execute_pipeline_steps([3, 5, 11, 12], config=config)

# Get pipeline status
status = get_pipeline_status()

# Validate configuration
is_valid = validate_pipeline_config(config)

# Health checking
checker = EnhancedHealthChecker()
health = run_enhanced_health_check()

Key Exports

• PipelineConfig / StepConfig — configuration dataclasses
• STEP_METADATA — metadata for all 25 steps
• run_pipeline — execute the full pipeline
• execute_pipeline_step / execute_pipeline_steps — step-level execution
• create_pipeline_config / validate_pipeline_config — configuration
• EnhancedHealthChecker / run_enhanced_health_check — health monitoring
• StepExecutionResult — step result dataclass

Configuration Options

Option	Description
--target-dir	Input directory containing GNN files
--output-dir	Output directory for all results
--only-steps	Comma-separated list of steps to run
--skip-steps	Comma-separated list of steps to skip
--verbose	Enable detailed logging
--strict	Fail on warnings (default: continue)

Output

• output/pipeline_execution_summary.json — Comprehensive execution report
• Per-step output directories (output/N_step_output/)

MCP Tools

This module registers tools with the GNN MCP server (see mcp.py):

• get_pipeline_config_info
• get_pipeline_status
• get_pipeline_steps
• validate_pipeline_dependencies

References

• AGENTS.md — Module documentation
• README.md — Usage guide
• SPEC.md — Module specification
• ../main.py — Main orchestrator script

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Documentation

• README: Module Overview
• AGENTS: Agentic Workflows
• SPEC: Architectural Specification
• SKILL: Capability API