---
name: mcp-chaining
description: Research-to-implement pipeline chaining 5 MCP tools with graceful degradation
allowed-tools: [Bash, Read]
user-invocable: false
---

# MCP Chaining Pipeline

A research-to-implement pipeline that chains 5 MCP tools for end-to-end workflows.

## When to Use

- Building multi-tool MCP pipelines
- Understanding how to chain MCP calls with graceful degradation
- Debugging MCP environment variable issues
- Learning the tool naming conventions for different MCP servers

## What We Built

A pipeline that chains these tools:

| Step | Server | Tool ID | Purpose |
|------|--------|---------|---------|
| 1 | nia | `nia__search` | Search library documentation |
| 2 | ast-grep | `ast-grep__find_code` | Find AST code patterns |
| 3 | morph | `morph__warpgrep_codebase_search` | Fast codebase search |
| 4 | qlty | `qlty__qlty_check` | Code quality validation |
| 5 | git | `git__git_status` | Git operations |

## Key Files

- `scripts/research_implement_pipeline.py` - Main pipeline implementation
- `scripts/test_research_pipeline.py` - Test harness with isolated sandbox
- `workspace/pipeline-test/sample_code.py` - Test sample code

## Usage Examples

```bash
# Dry-run pipeline (preview plan without changes)
uv run python -m runtime.harness scripts/research_implement_pipeline.py \
    --topic "async error handling python" \
    --target-dir "./workspace/pipeline-test" \
    --dry-run --verbose

# Run tests
uv run python -m runtime.harness scripts/test_research_pipeline.py --test all

# View the pipeline script
cat scripts/research_implement_pipeline.py
```

## Critical Fix: Environment Variables

The MCP SDK's `get_default_environment()` only includes basic vars (PATH, HOME, etc.), NOT `os.environ`. We fixed `src/runtime/mcp_client.py` to pass full environment:

```python
# In _connect_stdio method:
full_env = {**os.environ, **(resolved_env or {})}
```

This ensures API keys from `~/.claude/.env` reach subprocesses.

## Graceful Degradation Pattern

Each tool is optional. If unavailable (disabled, no API key, etc.), the pipeline continues:

```python
async def check_tool_available(tool_id: str) -> bool:
    """Check if an MCP tool is available."""
    server_name = tool_id.split("__")[0]
    server_config = manager._config.get_server(server_name)
    if not server_config or server_config.disabled:
        return False
    return True

# In step function:
if not await check_tool_available("nia__search"):
    return StepResult(status=StepStatus.SKIPPED, message="Nia not available")
```

## Tool Name Reference

### nia (Documentation Search)
```
nia__search              - Universal documentation search
nia__nia_research        - Research with sources
nia__nia_grep            - Grep-style doc search
nia__nia_explore         - Explore package structure
```

### ast-grep (Structural Code Search)
```
ast-grep__find_code      - Find code by AST pattern
ast-grep__find_code_by_rule - Find by YAML rule
ast-grep__scan_code      - Scan with multiple patterns
```

### morph (Fast Text Search + Edit)
```
morph__warpgrep_codebase_search  - 20x faster grep
morph__edit_file                 - Smart file editing
```

### qlty (Code Quality)
```
qlty__qlty_check         - Run quality checks
qlty__qlty_fmt           - Auto-format code
qlty__qlty_metrics       - Get code metrics
qlty__smells             - Detect code smells
```

### git (Version Control)
```
git__git_status          - Get repo status
git__git_diff            - Show differences
git__git_log             - View commit history
git__git_add             - Stage files
```

## Pipeline Architecture

```
                    +----------------+
                    |   CLI Args     |
                    | (topic, dir)   |
                    +-------+--------+
                            |
                    +-------v--------+
                    | PipelineContext|
                    | (shared state) |
                    +-------+--------+
                            |
    +-------+-------+-------+-------+-------+
    |       |       |       |       |       |
+---v---+---v---+---v---+---v---+---v---+
| nia   |ast-grp| morph | qlty  | git   |
|search |pattern|search |check  |status |
+---+---+---+---+---+---+---+---+---+---+
    |       |       |       |       |
    +-------v-------v-------v-------+
                    |
            +-------v--------+
            | StepResult[]   |
            | (aggregated)   |
            +----------------+
```

## Error Handling

The pipeline captures errors without failing the entire run:

```python
try:
    result = await call_mcp_tool("nia__search", {"query": topic})
    return StepResult(status=StepStatus.SUCCESS, data=result)
except Exception as e:
    ctx.errors.append(f"nia: {e}")
    return StepResult(status=StepStatus.FAILED, error=str(e))
```

## Creating Your Own Pipeline

1. Copy the pattern from `scripts/research_implement_pipeline.py`
2. Define your steps as async functions
3. Use `check_tool_available()` for graceful degradation
4. Chain results through `PipelineContext`
5. Aggregate with `print_summary()`
