agr-mcp-server 4.0.0 → 4.0.2

package/README.md

@@ -1,531 +1,137 @@
-# Enhanced AGR MCP Server - JavaScript Implementation
+# AGR MCP Server
 
-**A high-performance, modern JavaScript implementation of the Alliance of Genome Resources MCP server with advanced natural language query capabilities and cross-entity search.**
+MCP server for querying [Alliance of Genome Resources](https://www.alliancegenome.org) - genomics data across model organisms.
 
-## NEW: Complex Query Engine
+## Installation
 
-This server now features a sophisticated natural language processing engine that understands:
-- **Boolean Logic**: `"breast cancer genes AND DNA repair NOT p53"`  
-- **Multi-Entity Search**: Simultaneously search genes, diseases, phenotypes, and alleles
-- **Smart Filtering**: Automatic detection of species, processes, functions, and locations
-- **Relationship Discovery**: Find connections between genes, diseases, and orthologs
-- **Faceted Search**: Multi-dimensional filtering with real-time aggregations
+### Claude Desktop
 
-## Why This JavaScript Version is Better
+Add to `~/Library/Application Support/Claude/claude_desktop_config.json` (macOS) or `%APPDATA%\Claude\claude_desktop_config.json` (Windows):
 
-This JavaScript implementation offers significant improvements over the Python version:
-
-### Performance Enhancements
-- **25-40% faster API responses** due to Node.js async I/O optimization
-- **Intelligent caching system** with configurable TTL and automatic cleanup
-- **Connection pooling** with optimized HTTP client settings
-- **Exponential backoff retry logic** for robust error recovery
-- **Rate limiting** to prevent API overwhelm
-
-### Advanced Features
-- **🧠 Complex Natural Language Queries** with Boolean operators (AND, OR, NOT)
-- **🎯 Multi-Entity Cross-Search** (genes + diseases + phenotypes + alleles)
-- **🔍 Advanced Query Parsing** with automatic species/process/function detection
-- **📊 Intelligent Aggregations** across multiple data types
-- **🔗 Relationship Discovery** between genes, diseases, and orthologs
-- **🎛️ Faceted Search** with multiple simultaneous filters
-- **📈 Real-time Query Analytics** and performance insights
-- **🏷️ Automatic Entity Classification** and metadata extraction
-
-### Reliability & Security
-- **Robust error boundaries** with detailed error reporting
-- **Input sanitization** to prevent injection attacks
-- **Request timeout handling** with configurable limits
-- **Process monitoring** with health check capabilities
-- **Memory leak prevention** with automated cache management
-
-### Monitoring & Observability
-- **Real-time performance metrics** 
-- **Cache hit/miss ratio tracking**
-- **API response time monitoring**
-- **Structured JSON logging**
-- **Health check endpoints**
-
-## Architecture
-
-```
-Enhanced AGR MCP Server (JavaScript)
-├── High-Performance HTTP Client (Axios)
-│   ├── Connection Pooling
-│   ├── Request/Response Interceptors
-│   └── Automatic Retry Logic
-│
-├── Intelligent Caching Layer (NodeCache)
-│   ├── Configurable TTL per endpoint
-│   ├── Memory-efficient storage
-│   └── Automatic cleanup
-│
-├── Rate Limiting System
-│   ├── Per-endpoint rate tracking
-│   ├── Sliding window algorithm
-│   └── Automatic throttling
-│
-├── Enhanced Logging (Pino)
-│   ├── Structured JSON output
-│   ├── Pretty console formatting
-│   └── Performance tracking
-│
-└── Advanced Validation
-    ├── Gene ID format validation
-    ├── Sequence validation
-    └── Input sanitization
-```
-
-## Quick Start
-
-### Prerequisites
-- Node.js 18+ 
-- npm 8+
-
-### Installation
-
-#### Option 1: npm Package (Recommended)
-```bash
-# Install globally from npm
-npm install -g agr-mcp-server-enhanced
-
-# Start the server
-agr-mcp-server
-
-# Or use the natural language server
-agr-mcp-natural
-
-# Or start interactive chat
-agr-chat
-```
-
-#### Option 2: From Source
-```bash
-# Clone the repository
-git clone https://github.com/nuin/agr-mcp-server-js.git
-cd agr-mcp-server-js
-
-# Install dependencies and validate setup
-npm run setup
-
-# Start the server
-npm start
-
-# Or start with development logging
-npm run dev
-```
-
-### Development Setup
-```bash
-# Complete development setup
-npm run setup
-
-# Run with hot reload and debugging
-npm run dev
-
-# Run tests
-npm test
-
-# Run with coverage
-npm run test:coverage
-
-# Lint and format code
-npm run lint:fix
-npm run format
-```
-
-## Available Tools (12 Advanced Tools)
-
-### Core Genomics Tools
-1. **`search_genes`** - Advanced gene search with natural language support
-2. **`get_gene_info`** - Comprehensive gene information
-3. **`get_gene_diseases`** - Disease associations and models
-4. **`search_diseases`** - Disease search with filtered results
-5. **`get_gene_expression`** - Expression data across tissues
-6. **`find_orthologs`** - Cross-species orthology analysis
-7. **`blast_sequence`** - BLAST search with auto-detection
-8. **`get_species_list`** - Supported model organisms
-
-### Advanced Query Tools
-9. **`complex_search`** - Natural language cross-entity search with relationships
-10. **`faceted_search`** - Multi-filter advanced search with aggregations
-
-### Performance & Monitoring Tools
-11. **`get_cache_stats`** - Real-time performance metrics
-12. **`clear_cache`** - Cache management (dev/testing)
-
-## Usage Examples
-
-### Complex Natural Language Queries (NEW!)
-
-The Enhanced AGR MCP Server now supports advanced Boolean queries with natural language processing:
-
-#### Working Complex Query Examples
-
-##### 1. Boolean NOT - Exclude specific genes
-```bash
-# Find DNA repair genes in breast cancer, excluding p53
-npm run query complex "breast cancer genes in human AND DNA repair NOT p53"
-# Returns: 6,021 genes (XRCC3, XRCC1, RAD50, ERCC1, etc.)
-```
-
-##### 2. Boolean OR - Multiple terms
-```bash
-# Find genes related to insulin OR glucose in mouse
-npm run query complex "insulin OR glucose in mouse"
-# Returns: 28 genes (Insl5, Igfbp7, Irs3, Ide, etc.)
-```
-
-##### 3. Species-specific search
-```bash
-# Find BRCA1 genes specifically in humans
-npm run query complex "BRCA1 in human"
-# Returns: 29 human-specific BRCA1-related genes
-```
-
-#### Advanced Query Features
-- **Boolean Operators**: AND, OR, NOT for precise filtering
-- **Species Filters**: "in human", "in mouse", "in zebrafish", etc.
-- **Disease Context**: Automatically recognizes disease terms
-- **Process Filters**: Detects biological processes (apoptosis, DNA repair, etc.)
-- **Cross-Entity Search**: Searches genes, diseases, phenotypes simultaneously
-
-#### JavaScript/Node.js Examples
-```javascript
-// Using complex_search tool with MCP
-{
-  "tool": "complex_search",
-  "arguments": {
-    "query": "breast cancer genes in human AND DNA repair NOT p53",
-    "limit": 5
-  }
-}
-
-// Species and process filtering
+```json
 {
-  "tool": "search_genes", 
-  "arguments": {
-    "query": "tumor suppressor genes in mouse involved in apoptosis",
-    "limit": 10
+  "mcpServers": {
+    "agr-genomics": {
+      "command": "npx",
+      "args": ["-y", "agr-mcp-server"]
+    }
   }
 }
 ```
 
-#### Cross-Entity Search with Relationships
-```javascript
-// Search across genes, diseases, and phenotypes simultaneously
-{
-  "tool": "complex_search",
-  "arguments": {
-    "query": "insulin resistance genes and diabetes diseases in human",
-    "limit": 10
-  }
-}
-```
+### Claude Code (CLI)
+
+Add to `~/.claude/settings.json`:
 
-### Advanced Faceted Search
-```javascript
-// Multi-dimensional filtering
+```json
 {
-  "tool": "faceted_search",
-  "arguments": {
-    "genes": ["BRCA1", "BRCA2", "TP53"],
-    "diseases": ["breast cancer", "ovarian cancer"],
-    "processes": ["DNA repair", "apoptosis"],
-    "species": "Homo sapiens",
-    "chromosome": "17",
-    "limit": 20
+  "mcpServers": {
+    "agr-genomics": {
+      "command": "npx",
+      "args": ["-y", "agr-mcp-server"]
+    }
   }
 }
 ```
 
-### Tested & Verified Query Examples
-
-#### Natural Language Queries That Work
-- `"breast cancer genes in human AND DNA repair NOT p53"` - 6,021 results
-- `"insulin OR glucose in mouse"` - 28 results  
-- `"BRCA1 in human"` - 29 results
-- `"kinase genes in mouse involved in signaling"` - Species + process filtering
-- `"tumor suppressor NOT p53 in zebrafish"` - Exclusion queries  
-- `"transcription factors NOT zinc finger in fly"` ✅
-- `"diabetes genes on chromosome 11 in human"` ✅
-- `"tumor suppressor genes involved in apoptosis NOT p53"` ✅
-
-#### Multi-Entity Discovery
-- `"insulin genes and diabetes diseases"` → Returns genes + related diseases
-- `"BRCA1 orthologs and cancer associations"` → Cross-species + disease links
-- `"DNA repair genes and associated phenotypes"` → Genes + phenotype relationships
+### Cursor
 
-### Basic Tool Usage
+Add to Cursor settings (Settings > MCP Servers):
 
-#### Gene Information
-```javascript
-{
-  "tool": "get_gene_info",
-  "arguments": {
-    "gene_id": "HGNC:1100"
-  }
-}
-```
-
-#### BLAST Search
-```javascript
+```json
 {
-  "tool": "blast_sequence", 
-  "arguments": {
-    "sequence": "ATCGATCGATCGATCG",
-    "max_target_seqs": 20
+  "agr-genomics": {
+    "command": "npx",
+    "args": ["-y", "agr-mcp-server"]
   }
 }
 ```
 
-#### Performance Monitoring
-```javascript
-{
-  "tool": "get_cache_stats",
-  "arguments": {}
-}
-```
-
-## Configuration
-
-### Environment Variables
-```bash
-# Logging level
-export LOG_LEVEL=debug
-
-# Custom timeouts
-export API_TIMEOUT=30000
-
-# Cache settings  
-export CACHE_TTL=300
-export CACHE_MAX_KEYS=1000
-```
-
-### Advanced Configuration
-The server automatically configures itself with optimal settings:
-
-- **Cache TTL**: 5 minutes (gene info cached 10 minutes)
-- **Rate Limiting**: 100 requests/minute per endpoint
-- **Retry Logic**: 3 attempts with exponential backoff
-- **Connection Pooling**: Optimized for genomics API patterns
-
-## Docker Support
-
-```bash
-# Build Docker image
-npm run docker:build
-
-# Run in container
-npm run docker:run
-
-# Or use docker-compose
-docker-compose up -d
-```
-
-## Performance Comparison
-
-| Metric | Python Version | **JavaScript Version** | Improvement |
-|--------|---------------|----------------------|-------------|
-| Cold Start | ~800ms | **~450ms** | **44% faster** |
-| API Response | ~200ms | **~120ms** | **40% faster** |
-| Memory Usage | ~45MB | **~28MB** | **38% less** |
-| Cache Hit Rate | ~65% | **~89%** | **37% better** |
-| Error Recovery | Basic | **Advanced** | Exponential backoff |
-| Input Validation | Limited | **Comprehensive** | Type safety |
-
-## Testing & Quality
-
-```bash
-# Run comprehensive tests
-npm test
-
-# Run with coverage reporting
-npm run test:coverage
-
-# Performance benchmarking
-npm run benchmark
-
-# Code quality checks
-npm run lint
-npm run validate
-
-# Health check
-npm run health-check
-```
-
-## Advanced Features
-
-### Intelligent Caching
-- **Per-endpoint TTL optimization**
-- **Memory-efficient storage**
-- **Automatic cache warming**
-- **Cache hit/miss analytics**
+### Windsurf
 
-### Enhanced Error Handling
-- **Detailed error classification**
-- **Automatic retry with backoff**
-- **Graceful degradation**
-- **Structured error reporting**
-
-### Performance Monitoring
-- **Real-time metrics collection**
-- **Cache performance tracking**
-- **API response time analysis**
-- **Memory usage monitoring**
-
-### Input Validation
-- **Gene ID format validation** (HGNC, MGI, RGD, etc.)
-- **Sequence validation** (DNA/RNA/Protein)
-- **Query sanitization**
-- **Parameter bounds checking**
-
-## Claude Integration
-
-### Claude Desktop Configuration
-
-#### Option 1: Global Installation (Recommended)
-```bash
-# Install globally for easy setup
-npm install -g .
-```
-
-Then configure Claude Desktop:
-
-**macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
-**Windows**: `%APPDATA%/Claude/claude_desktop_config.json`
+Add to `~/.codeium/windsurf/mcp_config.json`:
 
 ```json
 {
   "mcpServers": {
     "agr-genomics": {
-      "command": "agr-mcp-server",
-      "env": {
-        "LOG_LEVEL": "info"
-      }
+      "command": "npx",
+      "args": ["-y", "agr-mcp-server"]
     }
   }
 }
 ```
 
-#### Option 2: Local Development Setup
+### From source
+
+```bash
+git clone https://github.com/nuin/agr-mcp-server-js.git
+cd agr-mcp-server-js
+npm install && npm run build
+```
+
+Then use the local path in your config:
+
 ```json
 {
   "mcpServers": {
     "agr-genomics": {
       "command": "node",
-      "args": ["<PROJECT_PATH>/src/agr-server-enhanced.js"],
-      "cwd": "<PROJECT_PATH>",
-      "env": {
-        "LOG_LEVEL": "info"
-      }
+      "args": ["/path/to/agr-mcp-server-js/dist/index.js"]
     }
   }
 }
 ```
 
-Replace `<PROJECT_PATH>` with the absolute path to your cloned repository.
-
-### Advanced Natural Language Queries
-
-With the enhanced complex query system, Claude can now handle sophisticated genomic questions:
-
-#### Boolean Logic & Multi-Species Queries
-- "Find breast cancer genes in human AND DNA repair NOT p53"
-- "Search for kinase genes in mouse OR rat involved in signaling"
-- "Get tumor suppressor genes involved in apoptosis NOT p53"
-
-#### Cross-Entity Discovery
-- "Find insulin genes and related diabetes diseases"
-- "Show BRCA1 orthologs and their cancer associations"
-- "Get DNA repair genes and associated phenotypes"
-
-#### Location & Function Specific
-- "Find transcription factors on chromosome 17 in human"
-- "Search for kinase genes in mouse involved in development"
-- "Get membrane proteins in fly NOT channels"
-
-#### Traditional Queries (Still Supported)
-- "Find orthologs of BRCA1 in mouse and zebrafish"
-- "BLAST this DNA sequence and show top 10 matches"
-- "Get expression data for TP53 across all tissues"
-- "Show me cache performance statistics"
-
-## Monitoring Dashboard
-
-The server provides comprehensive monitoring:
-
-```javascript
-// Real-time performance metrics
-{
-  "cache": {
-    "keys": 156,
-    "hits": 1240,
-    "misses": 180,
-    "hitRate": "87.3%"
-  },
-  "rateLimits": {
-    "/search": [timestamps...],
-    "/gene": [timestamps...]
-  },
-  "uptime": 3600.5,
-  "memoryUsage": "28.4MB"
-}
-```
-
-## Production Deployment
-
-### PM2 Process Manager
-```bash
-# Install PM2
-npm install -g pm2
+## Usage
 
-# Start with PM2
-pm2 start src/agr-server-enhanced.js --name agr-mcp-server
+Ask questions naturally:
 
-# Monitor processes
-pm2 monit
+- "Search for BRCA1 genes in human"
+- "What genes are involved in DNA repair?"
+- "Get information about HGNC:1100"
+- "Find orthologs of insulin gene"
+- "What diseases are associated with TP53?"
+- "Show me expression data for daf-2 in worm"
 
-# View logs
-pm2 logs agr-mcp-server
-```
+### Supported Species
 
-### Health Monitoring
-```bash
-# Built-in health check
-npm run health-check
+Human, mouse, rat, zebrafish, fly, worm, yeast, xenopus
 
-# Custom monitoring script
-node scripts/monitor.js
-```
+## Tools
 
-## Key Advantages Over Python
+| Tool | Description |
+|------|-------------|
+| `search_genes` | Search genes with optional species filter |
+| `get_gene_info` | Detailed gene information (symbol, location, synonyms) |
+| `get_gene_diseases` | Disease associations for a gene |
+| `search_diseases` | Search diseases by name |
+| `get_gene_expression` | Expression data across tissues/stages |
+| `find_orthologs` | Cross-species homologs |
+| `get_gene_phenotypes` | Phenotype annotations |
+| `get_gene_interactions` | Molecular and genetic interactions |
+| `get_gene_alleles` | Alleles/variants for a gene |
+| `search_alleles` | Search alleles by name |
+| `get_species_list` | List supported model organisms |
 
-1. **Performance**: 25-40% faster response times
-2. **Smart Caching**: Intelligent TTL and automatic cleanup
-3. **Robust Validation**: Comprehensive input checking
-4. **Monitoring**: Real-time performance metrics
-5. **Error Handling**: Advanced retry and recovery logic
-6. **Configuration**: Flexible, environment-aware settings
-7. **Documentation**: TypeScript-style JSDoc throughout
-8. **DevOps**: Docker, PM2, and monitoring ready
+## Gene ID Formats
 
-## Support
+| Species | Format | Example |
+|---------|--------|---------|
+| Human | `HGNC:*` | `HGNC:1100` |
+| Mouse | `MGI:*` | `MGI:95892` |
+| Rat | `RGD:*` | `RGD:3889` |
+| Zebrafish | `ZFIN:ZDB-GENE-*` | `ZFIN:ZDB-GENE-990415-72` |
+| Fly | `FB:FBgn*` | `FB:FBgn0000017` |
+| Worm | `WB:WBGene*` | `WB:WBGene00000898` |
+| Yeast | `SGD:S*` | `SGD:S000002536` |
+| Xenopus | `Xenbase:XB-GENE-*` | `Xenbase:XB-GENE-485905` |
 
-- **Issues**: GitHub Issues
-- **Documentation**: JSDoc generated docs in `/docs`
-- **Health Check**: `npm run health-check`
-- **Performance**: `npm run benchmark`
+## Data Sources
 
-## Status: Production Ready
+- **Search & gene data**: [Alliance of Genome Resources API](https://www.alliancegenome.org/api)
+- **Advanced search**: [AllianceMine](https://www.alliancegenome.org/alliancemine)
 
-**Enhanced JavaScript Implementation Complete**
-- High-performance architecture with caching
-- Robust error handling and validation  
-- Comprehensive monitoring and logging
-- Advanced configuration management
-- Full testing and quality assurance
-- Production deployment ready
-- Complete documentation
+## License
 
-**Ready for immediate deployment as a faster, more reliable alternative to the Python version!**
+MIT

package/dist/client.d.ts

@@ -50,12 +50,9 @@ export declare class AllianceClient {
      */
     searchAlleles(query: string, limit?: number): Promise<SearchResponse>;
     /**
-     * Get list of supported species
+     * Get list of supported species from API
      */
-    getSpeciesList(): Array<{
-        name: Species;
-        shortName: string;
-    }>;
+    getSpeciesList(): Promise<unknown>;
     /**
      * Helper to resolve species short name
      */

package/dist/client.js

@@ -51,9 +51,8 @@ export class AllianceClient {
                     id: r.id,
                     symbol: r.symbol,
                     name: r.name || r.name_key || r.id,
-                    species: r.species?.name,
+                    species: r.species,
                     category: r.category,
-                    description: r.highlights?.description?.[0],
                     highlights: r.highlights,
                 })),
                 total: response.total,
@@ -202,22 +201,29 @@ export class AllianceClient {
         return this.search(query, "allele", undefined, limit);
     }
     /**
-     * Get list of supported species
+     * Get list of supported species from API
      */
-    getSpeciesList() {
-        // Return hardcoded list of Alliance model organisms
-        const speciesList = [
-            { name: "Homo sapiens", shortName: "human" },
-            { name: "Mus musculus", shortName: "mouse" },
-            { name: "Rattus norvegicus", shortName: "rat" },
-            { name: "Danio rerio", shortName: "zebrafish" },
-            { name: "Drosophila melanogaster", shortName: "fly" },
-            { name: "Caenorhabditis elegans", shortName: "worm" },
-            { name: "Saccharomyces cerevisiae", shortName: "yeast" },
-            { name: "Xenopus laevis", shortName: "frog" },
-            { name: "Xenopus tropicalis", shortName: "xenopus" },
-        ];
-        return speciesList;
+    async getSpeciesList() {
+        const url = `${this.agrApiUrl}/api/species`;
+        try {
+            return await this.fetch(url);
+        }
+        catch {
+            // Fallback to hardcoded list
+            return {
+                results: [
+                    { name: "Homo sapiens", shortName: "Hsa", commonNames: ["human"] },
+                    { name: "Mus musculus", shortName: "Mmu", commonNames: ["mouse"] },
+                    { name: "Rattus norvegicus", shortName: "Rno", commonNames: ["rat"] },
+                    { name: "Danio rerio", shortName: "Dre", commonNames: ["zebrafish"] },
+                    { name: "Drosophila melanogaster", shortName: "Dme", commonNames: ["fly"] },
+                    { name: "Caenorhabditis elegans", shortName: "Cel", commonNames: ["worm"] },
+                    { name: "Saccharomyces cerevisiae", shortName: "Sce", commonNames: ["yeast"] },
+                    { name: "Xenopus tropicalis", shortName: "Xtr", commonNames: ["xenopus"] },
+                ],
+                total: 8,
+            };
+        }
     }
     /**
      * Helper to resolve species short name

package/dist/index.js

@@ -220,17 +220,9 @@ server.tool("search_alleles", "Search for alleles/variants in the Alliance datab
 // Tool: Get Species List
 server.tool("get_species_list", "Get list of model organisms supported by Alliance of Genome Resources.", {}, async () => {
     try {
-        const species = client.getSpeciesList();
+        const data = await client.getSpeciesList();
         return {
-            content: [
-                {
-                    type: "text",
-                    text: JSON.stringify({
-                        description: "Model organisms in the Alliance of Genome Resources",
-                        species,
-                    }, null, 2),
-                },
-            ],
+            content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
         };
     }
     catch (error) {
@@ -259,18 +251,18 @@ server.resource("entity-types", "agr://entity-types", async () => ({
     ],
 }));
 // Resource: Species
-server.resource("species", "agr://species", async () => ({
-    contents: [
-        {
-            uri: "agr://species",
-            mimeType: "application/json",
-            text: JSON.stringify({
-                description: "Model organisms in Alliance of Genome Resources",
-                species: client.getSpeciesList(),
-            }, null, 2),
-        },
-    ],
-}));
+server.resource("species", "agr://species", async () => {
+    const data = await client.getSpeciesList();
+    return {
+        contents: [
+            {
+                uri: "agr://species",
+                mimeType: "application/json",
+                text: JSON.stringify(data, null, 2),
+            },
+        ],
+    };
+});
 function getEntityDescription(type) {
     const descriptions = {
         gene: "Genes across all model organisms",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agr-mcp-server",
-  "version": "4.0.0",
+  "version": "4.0.2",
   "description": "MCP server for Alliance of Genome Resources - access genomics data across model organisms",
   "main": "dist/index.js",
   "bin": {