nsip-skills 1.4.7
Breeding decision support tools for sheep genetics using NSIP EBV data
License: MIT
Requires Python: >=3.12
Keywords: breeding, ebv, genetics, inbreeding, livestock, nsip, selection-index, sheep

# NSIP Search API Client

A Python client for the NSIP (National Sheep Improvement Program) Search API, reverse-engineered from http://nsipsearch.nsip.org

---

> **🐑 New to NSIP Tools?** Check out the **[Getting Started Guide](docs/getting-started-guide.md)** for step-by-step instructions on using these tools with Claude Desktop or other AI assistants. No programming experience required!
>
> **📚 Example Prompts**: Browse the **[Examples Library](docs/examples/)** for copy-paste prompts covering tools, workflows, resources, and skills.

---

## Overview

This client provides programmatic access to sheep breeding data including:
- Animal details and genetic traits (EBVs)
- Pedigree/lineage information
- Progeny records
- Breed groups and trait ranges
- Search and filtering capabilities

## Installation

> **Important:** This package is **NOT** published to PyPI. It is only available through GitHub Releases.
> See [DISTRIBUTION.md](DISTRIBUTION.md) for our distribution policy.

### From GitHub Release (Recommended)

Download the latest release from the [releases page](https://github.com/epicpast/nsip-api-client/releases):

```bash
# Install from wheel (recommended)
pip install https://github.com/epicpast/nsip-api-client/releases/latest/download/nsip_client-1.3.5-py3-none-any.whl

# Or install from source distribution
pip install https://github.com/epicpast/nsip-api-client/releases/download/v1.3.5/nsip-client-1.3.5.tar.gz
```

### From Git

```bash
# Install latest from main branch
pip install git+https://github.com/epicpast/nsip-api-client.git

# Install specific version tag
pip install git+https://github.com/epicpast/nsip-api-client.git@v1.3.5
```

### From Source

```bash
git clone https://github.com/epicpast/nsip-api-client.git
cd nsip-api-client
pip install -e .
```

---

## NSIP Skills: Breeding Decision Support Tools

The NSIP Skills module provides a suite of breeding decision support tools designed to help sheep breeders make data-driven genetic improvement decisions. These tools are available as both Python modules and Claude Code slash commands.

### Why Use NSIP Skills?

Genetic improvement in sheep breeding requires balancing multiple factors: growth traits, maternal ability, carcass quality, and inbreeding risk. The NSIP Skills module automates complex calculations that would otherwise require extensive spreadsheet work or specialized software.

**Key Benefits:**
- **Data-driven decisions**: Replace guesswork with EBV-based analysis
- **Inbreeding management**: Automatically calculate and flag high-risk matings
- **Multi-trait optimization**: Balance competing breeding goals
- **Time savings**: Automate repetitive analysis tasks
- **Accessible genetics**: Make NSIP data actionable for all breeders

### Quick Start

All tools can be run as Python modules or through Claude Code slash commands:

```bash
# Python module usage
uv run python -m nsip_skills.ebv_analysis LPN_ID1 LPN_ID2 LPN_ID3

# Claude Code slash command (when using Claude Code)
/nsip:ebv-analyzer LPN_ID1 LPN_ID2 LPN_ID3
```

### The 10 NSIP Skills

| Command | Purpose | Key Use Case |
|---------|---------|--------------|
| `/nsip:flock-import` | Import spreadsheet data and enrich with NSIP EBVs | Getting started with your flock data |
| `/nsip:ebv-analyzer` | Compare EBVs across animals | Evaluating purchase candidates |
| `/nsip:inbreeding` | Calculate inbreeding coefficients | Pre-mating risk assessment |
| `/nsip:mating-plan` | Optimize ram-ewe pairings | Breeding season planning |
| `/nsip:progeny-report` | Evaluate sires by offspring | Sire selection and evaluation |
| `/nsip:trait-improvement` | Multi-generation selection planning | Long-term genetic goals |
| `/nsip:ancestry` | Generate pedigree trees | Understanding genetic background |
| `/nsip:flock-dashboard` | Aggregate flock statistics | Flock performance overview |
| `/nsip:selection-index` | Calculate breeding indexes | Ranking animals by composite merit |
| `/nsip:breeding-recs` | AI-powered recommendations | Comprehensive breeding advice |

### Example Workflows

#### Workflow 1: Evaluating Ram Purchase Candidates

```bash
# Compare EBVs of rams you're considering
uv run python -m nsip_skills.ebv_analysis RAM_LPN_1 RAM_LPN_2 RAM_LPN_3

# Check progeny performance for proven sires
uv run python -m nsip_skills.progeny_analysis RAM_LPN_1 --compare RAM_LPN_2,RAM_LPN_3

# Calculate inbreeding risk with your ewes
uv run python -m nsip_skills.inbreeding --mating RAM_LPN_1,EWE_LPN_1
```

#### Workflow 2: Breeding Season Planning

```bash
# Import your flock data
uv run python -m nsip_skills.flock_import my_flock.csv

# Generate optimized mating plan
uv run python -m nsip_skills.mating_optimizer --rams rams.csv --ewes ewes.csv --goal terminal

# Get AI-powered recommendations
uv run python -m nsip_skills.recommendation_engine my_flock.csv --goal terminal
```

#### Workflow 3: Long-term Genetic Planning

```bash
# Analyze current flock performance
uv run python -m nsip_skills.flock_stats my_flock.csv --name "Valley Farm"

# Plan multi-generation improvement
uv run python -m nsip_skills.trait_planner my_flock.csv --targets '{"WWT": 5.0, "NLW": 0.20}'
```

### Understanding EBVs

Estimated Breeding Values (EBVs) predict an animal's genetic merit for specific traits. Key traits include:

| Trait | Description | Breeding Impact |
|-------|-------------|-----------------|
| BWT | Birth Weight | Lower values = easier lambing |
| WWT | Weaning Weight | Growth to weaning age |
| PWWT | Post-Weaning Weight | Growth potential |
| MWWT | Maternal Weaning Weight | Dam's milk/mothering effect |
| NLW | Number of Lambs Weaned | Fertility and lamb survival |
| YEMD | Yearling Eye Muscle Depth | Carcass muscling |
| YFAT | Yearling Fat Depth | Carcass fat cover |

### Selection Indexes

Selection indexes combine multiple traits into a single score based on economic weights:

| Index | Focus | Best For |
|-------|-------|----------|
| Terminal | Growth + carcass | Market lamb production |
| Maternal | Reproduction + milk | Replacement ewe selection |
| Range | Balanced traits | Extensive operations |
| Hair | Growth without wool | Hair sheep breeds |

### Detailed Documentation

For comprehensive documentation including:
- Detailed tool descriptions
- Input/output formats
- Real-world use cases
- Genetic concepts explained

See **[docs/nsip-skills.md](docs/nsip-skills.md)**

---

## API Endpoints Discovered

### Base URL
```
http://nsipsearch.nsip.org/api
```

### Authentication
No authentication required - this is a public API.

### Endpoints

#### Search & Metadata
- `GET /search/getDateLastUpdated` - Get database last update date
- `GET /search/getAvailableBreedGroups` - List all breed groups
- `GET /search/getStatusesByBreedGroup` - List animal statuses
- `GET /search/getTraitRangesByBreed?breedId={id}` - Get trait ranges for a breed
- `POST /search/getPageOfSearchResults?page={p}&pageSize={size}&breedId={id}` - Search animals

#### Animal Details
- `GET /details/getAnimalDetails?searchString={lpnId}` - Get animal details
- `GET /details/getLineage?lpnId={lpnId}` - Get pedigree/lineage
- `GET /details/getPageOfProgeny?lpnId={lpnId}&page={p}&pageSize={size}` - Get offspring

## Usage

### Basic Example

```python
from nsip_client import NSIPClient

# Initialize client
client = NSIPClient()

# Get animal details
animal = client.get_animal_details("6####92020###249")
print(f"Breed: {animal['Breed']}")
print(f"DOB: {animal['DateOfBirth']}")

# Get progeny
progeny = client.get_progeny("6####92020###249")
print(f"Total offspring: {progeny['TotalCount']}")

# Get lineage
lineage = client.get_lineage("6####92020###249")
```

### Search Animals

```python
# Search by breed
results = client.search_animals(
    breed_id=486,  # South African Meat Merino
    page=0,
    page_size=15
)

for animal in results['Results']:
    print(animal['LpnId'])
```

### Get Breed Information

```python
# Get all breed groups
breed_groups = client.get_available_breed_groups()
for group in breed_groups:
    print(f"{group['Id']}: {group['Name']}")

# Get trait ranges for a breed
trait_ranges = client.get_trait_ranges_by_breed(486)
```

### Complete Animal Profile

```python
# Get all information at once
profile = client.search_by_lpn("6####92020###249")
print(profile['details'])
print(profile['lineage'])
print(profile['progeny'])
```

## MCP Server

The NSIP API Client includes an MCP (Model Context Protocol) server that exposes NSIP sheep breeding data to LLM applications. The server provides intelligent context management with automatic response summarization to prevent LLM context window overflow.

### Features

- **15 MCP Tools**: 10 NSIP API tools + 5 Shepherd consultation tools
- **Context Management**: Automatic summarization of large responses (>2000 tokens)
- **Smart Caching**: 1-hour TTL cache with 40%+ hit rate target
- **Multiple Transports**: stdio (CLI), HTTP SSE (web), WebSocket (real-time)
- **Performance Optimized**: <3s startup, <5s tool discovery, 70% token reduction

### Installation

The MCP server is included with the package and accessible via the `nsip-mcp-server` command:

```bash
# Install from GitHub release
pip install git+https://github.com/epicpast/nsip-api-client@v1.0.0

# Or using uvx (no installation required)
uvx --from git+https://github.com/epicpast/nsip-api-client@v1.0.0 nsip-mcp-server
```

### Quick Start

**Start the server (stdio mode - default)**:
```bash
nsip-mcp-server
```

**Configure with Claude Desktop** (`claude_desktop_config.json`):
```json
{
  "mcpServers": {
    "nsip": {
      "command": "nsip-mcp-server",
      "env": {
        "MCP_TRANSPORT": "stdio"
      }
    }
  }
}
```

### Available MCP Tools (15 Total)

#### NSIP API Tools (10)

| Tool Name | Description | May Be Summarized |
|-----------|-------------|-------------------|
| `nsip_get_last_update` | Get database last updated timestamp | No |
| `nsip_list_breeds` | List breed groups with individual breeds | No |
| `nsip_get_statuses` | Get status options for breed group | No |
| `nsip_get_trait_ranges` | Get trait value ranges for breed | No |
| `nsip_search_animals` | Search animals by breed and traits | Yes |
| `nsip_get_animal` | Get detailed animal information | Yes |
| `nsip_get_lineage` | Get animal lineage/pedigree | Yes |
| `nsip_get_progeny` | Get animal progeny list | Yes |
| `nsip_search_by_lpn` | Comprehensive animal lookup | Optional |
| `get_server_health` | Get server metrics and health status | No |

#### Shepherd Consultation Tools (5)

| Tool Name | Description | Parameters |
|-----------|-------------|------------|
| `shepherd_consult` | General sheep husbandry advice | `question`, `region` |
| `shepherd_breeding` | EBV interpretation, mating advice | `question`, `region`, `production_goal` |
| `shepherd_health` | Disease prevention, nutrition, parasites | `question`, `region`, `life_stage` |
| `shepherd_calendar` | Seasonal planning, breeding schedules | `question`, `region`, `task_type` |
| `shepherd_economics` | Cost analysis, ROI, marketing | `question`, `flock_size`, `market_focus` |

### Transport Options

**stdio (Default - for MCP clients)**:
```bash
nsip-mcp-server
# Or explicitly:
MCP_TRANSPORT=stdio nsip-mcp-server
```

**Streamable HTTP (for web applications)**:
```bash
MCP_TRANSPORT=streamable-http MCP_PORT=8000 nsip-mcp-server
```

**WebSocket (for real-time bidirectional communication)**:
```bash
MCP_TRANSPORT=websocket MCP_PORT=9000 nsip-mcp-server
```

### Environment Variables

| Variable | Description | Default | Example |
|----------|-------------|---------|---------|
| `MCP_TRANSPORT` | Transport mechanism | `stdio` | `streamable-http`, `websocket` |
| `MCP_PORT` | Port for HTTP/WebSocket | None (required for non-stdio) | `8000`, `9000` |
| `MCP_HOST` | Host address to bind to | `0.0.0.0` | `127.0.0.1`, `localhost` |
| `MCP_PATH` | Path for HTTP endpoints | `/mcp` | `/api/mcp` |
| `TIKTOKEN_CACHE_DIR` | Token cache directory | OS default | `/tmp/tiktoken` |
| `LOG_LEVEL` | Logging verbosity | `INFO` | `DEBUG`, `WARNING` |

### Context Management

The server automatically manages response sizes to prevent LLM context overflow:

**Responses <=2000 tokens**: Pass through unmodified
**Responses >2000 tokens**: Automatically summarized to ~70% reduction

**What's preserved in summaries**:
- Identity: LPN ID, breed, sire, dam
- Progeny: Total count (not full list)
- Contact: All breeder information
- Top 3 traits by accuracy (>=50% accuracy only)

**What's omitted**:
- Low-accuracy traits (<50%)
- Verbose metadata
- Full progeny lists (count only)

**Example summarized response**:
```json
{
  "lpn_id": "6####92020###249",
  "breed": "Katahdin",
  "sire": "6####92019###124",
  "dam": "6####92018###035",
  "total_progeny": 6,
  "contact": {
    "farm_name": "[FARM_NAME]",
    "phone": "[PHONE_NUMBER]"
  },
  "top_traits": [
    {"trait": "WWT", "value": 3.051, "accuracy": 0.71},
    {"trait": "BWT", "value": 0.246, "accuracy": 0.74},
    {"trait": "YWT", "value": 5.123, "accuracy": 0.68}
  ],
  "_summarized": true,
  "_original_token_count": 3500,
  "_summary_token_count": 1050,
  "_reduction_percent": 70.0
}
```

### Caching

The server caches NSIP API responses with a **1-hour TTL** to reduce API load:

- **Cache Key**: `method_name:sorted_json_params`
- **Target Hit Rate**: 40%+ in typical usage
- **Max Size**: 1000 entries
- **Eviction**: FIFO (oldest removed first)

Example:
```python
# First call - API fetch
nsip_get_animal(search_string="6####92020###249")  # Cache miss

# Within 1 hour - cached response
nsip_get_animal(search_string="6####92020###249")  # Cache hit (fast)

# After 1 hour - fresh data
nsip_get_animal(search_string="6####92020###249")  # Cache expired
```

### Error Handling

All MCP tools return structured errors following JSON-RPC 2.0 with LLM-friendly suggestions:

```json
{
  "error": {
    "code": -32602,
    "message": "Invalid parameter: lpn_id",
    "data": {
      "parameter": "lpn_id",
      "value": "123",
      "expected": "Non-empty string with at least 5 characters",
      "suggestion": "Provide a valid LPN ID like '6####92020###249'"
    }
  }
}
```

**Common error codes**:
- `-32602`: Invalid parameters (check suggestion for fix)
- `-32000`: NSIP API error (verify API availability)
- `-32001`: Cache error (retry without cache)
- `-32002`: Summarization error (request smaller dataset)

### Health Monitoring

Get server health and performance metrics (HTTP SSE/WebSocket only):

```bash
curl http://localhost:8000/health
```

Response includes:
- Discovery times (target: <5s)
- Summarization reduction (target: >=70%)
- Validation success rate (target: >=95%)
- Cache hit rate (target: >=40%)
- Concurrent connections (support: 50+)
- Startup time (target: <3s)

### Performance

The MCP server is designed to meet these targets:

| Metric | Target |
|--------|--------|
| Tool Discovery | <5 seconds |
| Summarization Reduction | >=70% token reduction |
| Validation Success | >=95% caught before API |
| Cache Hit Rate | >=40% |
| Concurrent Connections | 50+ without degradation |
| Startup Time | <3 seconds |

### Advanced Usage

**Example MCP tool call**:
```json
{
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "name": "nsip_get_animal",
    "arguments": {
      "search_string": "6####92020###249"
    }
  },
  "id": 1
}
```

**Example search with traits**:
```json
{
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "name": "nsip_search_animals",
    "arguments": {
      "breed_id": 486,
      "page": 0,
      "page_size": 15
    }
  },
  "id": 2
}
```

For complete MCP server documentation, examples, and troubleshooting, see `specs/001-create-an-mcp/quickstart.md`.

## API Response Structure

### Animal Details Response
```json
{
  "LpnId": "6####92020###249",
  "Breed": "Katahdin",
  "BreedGroup": "Hair",
  "DateOfBirth": "2/5/2020",
  "Gender": "Female",
  "Status": "CURRENT",
  "Sire": "6####92019###124",
  "Dam": "6####92018###035",
  "TotalProgeny": 6,
  "Genotyped": "No",
  "Traits": {
    "BWT": {"Value": 0.246, "Accuracy": 74},
    "WWT": {"Value": 3.051, "Accuracy": 71},
    ...
  },
  "ContactInfo": {
    "FarmName": "[FARM_NAME]",
    "ContactName": "[OWNER_NAME]",
    "Phone": "[PHONE_NUMBER]",
    "Email": "[EMAIL_ADDRESS]"
  }
}
```

## Breed Groups

- **61** - Range
- **62** - Maternal Wool
- **64** - Hair
- **69** - Terminal

## Common Traits (EBVs)

### Growth Traits
- **BWT** - Birth Weight
- **WWT** - Weaning Weight
- **MWWT** - Maternal Weaning Weight
- **PWWT** - Post Weaning Weight
- **YWT** - Yearling Weight

### Carcass Traits
- **YEMD** - Yearling Eye Muscle Depth
- **YFAT** - Yearling Fat
- **PEMD** - Post Weaning Eye Muscle Depth
- **PFAT** - Post Weaning Fat

### Wool Traits (for wool breeds)
- **YGFW** - Yearling Greasy Fleece Weight
- **YFD** - Yearling Fibre Diameter
- **YSL** - Yearling Staple Length

### Reproduction
- **NLB** - Number of Lambs Born
- **NLW** - Number of Lambs Weaned

### Parasite Resistance
- **WFEC** - Weaning Fecal Egg Count
- **PFEC** - Post Weaning Fecal Egg Count

### Indexes
- **US Range Index**
- **US Hair Index**
- **SRC$ Index**

## Network Traffic Analysis

The API was reverse-engineered using Chrome DevTools by:
1. Loading http://nsipsearch.nsip.org/#!/search
2. Performing searches and viewing animal details
3. Capturing network requests to identify API endpoints
4. Analyzing request/response headers and payloads

### Headers Used
```
Accept: application/json, text/plain, */*
User-Agent: Mozilla/5.0...
```

No authentication headers, cookies, or API keys required.

## Limitations

- This is a reverse-engineered client based on public web traffic
- The API is not officially documented
- Endpoints may change without notice
- Rate limiting behavior is unknown
- Some endpoints (like breed list by group) may need additional discovery

## Example: Your Sheep

```python
client = NSIPClient()

# Get details for your sheep
my_sheep = client.search_by_lpn("6####92020###249")

print(f"Name/ID: {my_sheep['details']['LpnId']}")
print(f"Breed: {my_sheep['details']['Breed']}")
print(f"Farm: {my_sheep['details']['ContactInfo']['FarmName']}")
print(f"Total Progeny: {my_sheep['details']['TotalProgeny']}")
print(f"US Hair Index: {my_sheep['details']['Traits']['USHairIndex']['Value']}")
```

## License

MIT License - see [LICENSE](LICENSE) for details.

Note: The NSIP data accessed through this client remains property of the National Sheep Improvement Program.