feat: add MCP tool wrappers for biomedical search tools

- Introduced a new module `mcp_tools.py` that provides asynchronous search functions for PubMed, ClinicalTrials.gov, and bioRxiv.
- Each function includes detailed Google-style docstrings and type hints, ensuring clarity and usability.
- Implemented a comprehensive search function that aggregates results from all sources, enhancing the search capabilities for biomedical literature.

Files added:
- src/mcp_tools.py

src/mcp_tools.py

@@ -0,0 +1,156 @@
+"""MCP tool wrappers for DeepCritical search tools.
+
+These functions expose our search tools via MCP protocol.
+Each function follows the MCP tool contract:
+- Full type hints
+- Google-style docstrings with Args section
+- Formatted string returns
+"""
+
+from src.tools.biorxiv import BioRxivTool
+from src.tools.clinicaltrials import ClinicalTrialsTool
+from src.tools.pubmed import PubMedTool
+
+# Singleton instances (avoid recreating on each call)
+_pubmed = PubMedTool()
+_trials = ClinicalTrialsTool()
+_biorxiv = BioRxivTool()
+
+
+async def search_pubmed(query: str, max_results: int = 10) -> str:
+    """Search PubMed for peer-reviewed biomedical literature.
+
+    Searches NCBI PubMed database for scientific papers matching your query.
+    Returns titles, authors, abstracts, and citation information.
+
+    Args:
+        query: Search query (e.g., "metformin alzheimer", "drug repurposing cancer")
+        max_results: Maximum results to return (1-50, default 10)
+
+    Returns:
+        Formatted search results with paper titles, authors, dates, and abstracts
+    """
+    max_results = max(1, min(50, max_results))  # Clamp to valid range
+
+    results = await _pubmed.search(query, max_results)
+
+    if not results:
+        return f"No PubMed results found for: {query}"
+
+    formatted = [f"## PubMed Results for: {query}\n"]
+    for i, evidence in enumerate(results, 1):
+        formatted.append(f"### {i}. {evidence.citation.title}")
+        formatted.append(f"**Authors**: {', '.join(evidence.citation.authors[:3])}")
+        formatted.append(f"**Date**: {evidence.citation.date}")
+        formatted.append(f"**URL**: {evidence.citation.url}")
+        formatted.append(f"\n{evidence.content}\n")
+
+    return "\n".join(formatted)
+
+
+async def search_clinical_trials(query: str, max_results: int = 10) -> str:
+    """Search ClinicalTrials.gov for clinical trial data.
+
+    Searches the ClinicalTrials.gov database for trials matching your query.
+    Returns trial titles, phases, status, conditions, and interventions.
+
+    Args:
+        query: Search query (e.g., "metformin alzheimer", "diabetes phase 3")
+        max_results: Maximum results to return (1-50, default 10)
+
+    Returns:
+        Formatted clinical trial information with NCT IDs, phases, and status
+    """
+    max_results = max(1, min(50, max_results))
+
+    results = await _trials.search(query, max_results)
+
+    if not results:
+        return f"No clinical trials found for: {query}"
+
+    formatted = [f"## Clinical Trials for: {query}\n"]
+    for i, evidence in enumerate(results, 1):
+        formatted.append(f"### {i}. {evidence.citation.title}")
+        formatted.append(f"**URL**: {evidence.citation.url}")
+        formatted.append(f"**Date**: {evidence.citation.date}")
+        formatted.append(f"\n{evidence.content}\n")
+
+    return "\n".join(formatted)
+
+
+async def search_biorxiv(query: str, max_results: int = 10) -> str:
+    """Search bioRxiv/medRxiv for preprint research.
+
+    Searches bioRxiv and medRxiv preprint servers for cutting-edge research.
+    Note: Preprints are NOT peer-reviewed but contain the latest findings.
+
+    Args:
+        query: Search query (e.g., "metformin neuroprotection", "long covid treatment")
+        max_results: Maximum results to return (1-50, default 10)
+
+    Returns:
+        Formatted preprint results with titles, authors, and abstracts
+    """
+    max_results = max(1, min(50, max_results))
+
+    results = await _biorxiv.search(query, max_results)
+
+    if not results:
+        return f"No bioRxiv/medRxiv preprints found for: {query}"
+
+    formatted = [f"## Preprint Results for: {query}\n"]
+    for i, evidence in enumerate(results, 1):
+        formatted.append(f"### {i}. {evidence.citation.title}")
+        formatted.append(f"**Authors**: {', '.join(evidence.citation.authors[:3])}")
+        formatted.append(f"**Date**: {evidence.citation.date}")
+        formatted.append(f"**URL**: {evidence.citation.url}")
+        formatted.append(f"\n{evidence.content}\n")
+
+    return "\n".join(formatted)
+
+
+async def search_all_sources(query: str, max_per_source: int = 5) -> str:
+    """Search all biomedical sources simultaneously.
+
+    Performs parallel search across PubMed, ClinicalTrials.gov, and bioRxiv.
+    This is the most comprehensive search option for drug repurposing research.
+
+    Args:
+        query: Search query (e.g., "metformin alzheimer", "aspirin cancer prevention")
+        max_per_source: Maximum results per source (1-20, default 5)
+
+    Returns:
+        Combined results from all sources with source labels
+    """
+    import asyncio
+
+    max_per_source = max(1, min(20, max_per_source))
+
+    # Run all searches in parallel
+    pubmed_task = search_pubmed(query, max_per_source)
+    trials_task = search_clinical_trials(query, max_per_source)
+    biorxiv_task = search_biorxiv(query, max_per_source)
+
+    pubmed_results, trials_results, biorxiv_results = await asyncio.gather(
+        pubmed_task, trials_task, biorxiv_task, return_exceptions=True
+    )
+
+    formatted = [f"# Comprehensive Search: {query}\n"]
+
+    # Add each result section (handle exceptions gracefully)
+    if isinstance(pubmed_results, str):
+        formatted.append(pubmed_results)
+    else:
+        formatted.append(f"## PubMed\n*Error: {pubmed_results}*\n")
+
+    if isinstance(trials_results, str):
+        formatted.append(trials_results)
+    else:
+        formatted.append(f"## Clinical Trials\n*Error: {trials_results}*\n")
+
+    if isinstance(biorxiv_results, str):
+        formatted.append(biorxiv_results)
+    else:
+        formatted.append(f"## Preprints\n*Error: {biorxiv_results}*\n")
+
+    return "\n---\n".join(formatted)