Convert binary to trigram name

Build Essie fragments for excluded mutations.

Build Essie fragments for progression on therapy search.

Build Essie fragments for required mutations.

Create a new HTTP client.

Remove duplicate articles based on DOI.

Execute a single tool and return the result.

Extract population frequencies from Ensembl response.

Fallback rule-based compression when LLM compression fails

Fetch drug shortage data from FDA. Returns: Dictionary with shortage data or None if fetch fails

Process all pending requests as a batch.

Format available tools with descriptions for display in evaluation prompt

Helper to format a single site/location.

Format a metric summary for display.

Generate cache key Args: server_name: Server name (e.g., Yahoo Finance) tool_name: Tool name (e.g.,

Generate tasks with retry logic Args: configs: Server configurations name: Name for logging progr

Get cBioPortal summary for the search request.

Helper method to extract post content based on type

Return default configuration (current hardcoded values). Returns: Dictionary containing all default configuration values

Helper method to determine post type

Check if the error is related to token limits.

Load configuration from file with environment overrides. Loads configuration in priority order: 1. Environment variables (hig

Parse single paper entry from Semantic Scholar HTML and optionally fetch detailed info

Acquire permission to make a request. Blocks if rate limit would be exceeded.

Optimized version of article_searcher with caching and context reuse.

Build a safe query dictionary with validated parameters. Args: params: Raw parameters dictionary Returns: Dictionary wi

혈압의 평균(mu)을 계산 Parameters: ----------- age : float 나이(년) zht : float 키의 z-score params : dict BP

혈압의 평균(mu)을 계산 Parameters: ----------- age : float 나이(년) zht : float 키의 z-score params : dict BP

Fetch the text of a list of PubMed IDs.

Calls a tool on the appropriate server by creating a new connection.

Check if token reduction is still possible.

Clean and parse JSON response with enhanced error handling.

Close all connection pools.

Convert a TrialQuery object to NCI CTS API parameters. Maps BioMCP's TrialQuery fields to NCI's parameter structure.

Convert single-server results to runner-compatible format

Create an LLM provider for the given model configuration. Creates appropriate client and provider instance based on the model

Create a new thinking session.

Create tool descriptions for Claude.

List all nix-darwin option categories. Enumerates all top-level categories with their option counts. Returns: Plain text list of cat

Discovers tools from HTTP MCP server.

Extract reaction terms from an adverse event result.

Format biomarker search results as markdown. Args: results: Search results dictionary Returns: Formatted markdown strin

Format disease search results as markdown. Args: results: Search results dictionary Returns: Formatted markdown string

Format intervention search results as markdown. Args: results: Search results dictionary Returns: Formatted markdown st

Format mutation search results as markdown.

Format organization search results as markdown. Args: results: Search results dictionary Returns: Formatted markdown st

Generate cache key using Python's built-in hash function for speed.

Maintain backward compatibility with existing interface

Generate multi-server tasks with incremental saving

Generate tasks for multi-server combinations with incremental saving

Generate single-server tasks with incremental saving

Generate tasks for individual servers with incremental saving

Get conference events matching the given keywords Args: keywords: Search terms for conferences limit: Maximum number of

Get summaries for all metrics. Returns: Dictionary of metric name to summary

Get OpenFDA API key from environment variable.

Get a full Wikipedia article.

Get article details handling both PMIDs and DOIs with proper output format.

Get cache instance (singleton pattern) Args: **kwargs: Arguments to pass to cache constructor Returns: Cache in

Retrieve a cached response if available and not expired. Args: endpoint: The API endpoint URL params: Query parameters

Get cancer type keywords for a given gene. Args: gene: Gene symbol (e.g., "BRAF") Returns: List of cancer type keywords to s

Get the display name for a cancer type ID. Args: cancer_type_id: The cancer type identifier Returns: Display

Get guidance for specific changing lines

Get context-specific interpretation

Get current weather for a city using WeatherAPI

Get current weather for a city using WeatherAPI

Get current weather for a city using WeatherAPI

Get drug/chemical information from MyChem.info. Args: drug_id_or_name: Drug ID (DrugBank, ChEMBL, etc.) or name field

Get gene information from MyGene.info. Args: gene_id_or_symbol: Gene ID (Entrez, Ensembl) or symbol (e.g., "TP53") fi

Get all available model configurations from environment variables. Scans environment variables to detect available API keys and endpo

Get list of problematic tools that should be filtered out. Returns: List of tool names that should be filtered due to issues (rate li

Get topics related to a Wikipedia article.

Get the complete field schema for discovery.

Get the current search context.

Get a summary of current execution state.

Get a summary of a Wikipedia article.

Get detailed trial information from NCI CTS API. Args: nct_id: NCT identifier (e.g., "NCT04280705") api_key: Optional API ke

Get weather forecast for a city using WeatherAPI

Determine if a request should be cached. Args: endpoint: The API endpoint URL params: Query parameters Returns:

Load local MCP server configurations.

Main entry point for multi-model benchmark runner

MCP Time Server - Time and timezone conversion functionality for MCP