Parameters for querying clinical trial data from ClinicalTrials.gov.

Information about an external endpoint.

Client for OncoKB API interactions.

Result of a single environment check.

Definition of a searchable field.

Search parameters for querying variant data from MyVariant.info.

Raised when a search fails to execute.

Error raised when CTS API requests fail.

Configurable filter criteria for variants.

Filter mutations based on specific mutation or pattern.

Unified client for BioThings APIs (MyGene, MyVariant, MyDisease, MyChem).

Raised when invalid parameters are provided.

Raised when FDA response validation fails.

Configuration for retry behavior.

Custom assertion error for test framework.

Aggregates variant data from multiple external sources.

Result of samplesheet validation.

Rate-limited, caching HTTP client for genomic REST APIs.

Circuit breaker implementation.

Configuration for circuit breaker behavior.

Rate-limited, caching HTTP client for the ClinPGx REST API.

Complete polygenic risk score result. Attributes: trait: Disease or trait name snp_count: Number of SNPs in the PRS

A single SNP with its effect size for PRS calculation. Attributes: rs_id: dbSNP rs identifier (e.g., 'rs7903146') chromosome

Refactored cBioPortal client using centralized HTTP.

Research information lookup using Perplexity Sonar models via OpenRouter.

Client for cBioPortal search operations.

Test exception for circuit breaker tests.

Registry for tracking all external endpoints.

Single metric measurement.

Mock mutation object for testing.

A specific mutation occurrence in a study.

Token bucket rate limiter implementation.

Raised when results cannot be parsed.

Client for TCGA/GDC API.

Client for 1000 Genomes data via Ensembl REST API.

A comprehensive tool for medical image registration using SimpleITK. Supports rigid, affine, and deformable registration with preprocessing a

TCGA/GDC variant annotation data.

cBioPortal variant annotation data.

Gene information from MyGene.info.

Result of meta-analysis for a locus.

Client for interacting with Reactome REST APIs

Result of replication analysis between discovery and replication studies.

Context manager for timing operations.

Filter out non-critical ASGI/Starlette middleware errors.

Client for bioRxiv/medRxiv API. IMPORTANT LIMITATION: bioRxiv/medRxiv APIs do not provide a search endpoint. This implementation works around

Adapter for cBioPortal API calls using centralized HTTP client.

Client for mutation-specific searches in cBioPortal.

Enhanced variant annotation combining multiple sources.

Client for Europe PMC API.

Manages connection pools per event loop. This class ensures that each asyncio event loop has its own set of connection pools, preventing cros

Raised when an invalid domain is specified.

Mock LLM for testing and demonstration.

Client for OpenAlex API with rate limiting and error handling.

Client for interacting with the FDA's OpenFDA API. Provides comprehensive drug safety monitoring, adverse event analysis, and regulatory

Handles searching across multiple preprint sources.

A comprehensive tool for medical image segmentation using nnUNet. Handles BRATS dataset processing, modality splitting, and segmentation visu

Represents a single variant from a VCF file.

Circuit breaker to prevent cascading failures.

A clinical example for few-shot learning.

Custom Dataset implementation. Replace this with your actual dataset implementation.

Disease information from MyDisease.info.

Drug/chemical information from MyChem.info.

Result of a mutation-specific search.

Metadata for a GWAS study.

Summary of mutations in a specific study.

Integration tests for assembly parameter.

Integration tests for OncoKB demo server (no auth required).

Represents a single thought in the thinking process.

1000 Genomes variant annotation data.

Result of annotating a single variant.

A lightweight implementation of Bayesian Optimization using Gaussian Processes (GP). Crucial for 'Self-Driving Labs' to select the next exper

Summary data from cBioPortal for a gene search.

CheckAgent, core functions: - Verify expected output files exist and are non-empty (0 bytes) - Scan directory and use LLM to identify pos

Request parameters for Europe PMC API.

Main class for querying FDA databases.

Locus-to-gene (L2G) prediction linking a variant to its likely causal gene.

Exception raised for errors related to the LLM.

Simple LRU cache with TTL support.

Production MedPrompt engine with full feature set. This class provides all methods required by dependent modules: - generate_chain_of_th

Collects and manages performance metrics.

Container for molecular property calculations.

Data structure for paragraph properties extracted from a PowerPoint paragraph.

Validates presentations for common issues.