tooluniverse 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

tooluniverse/tools/BiomarkerDiscoveryWorkflow.py

@@ -0,0 +1,55 @@
+"""
+BiomarkerDiscoveryWorkflow
+
+Discover and validate biomarkers for a specific disease condition using literature analysis, expr...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def BiomarkerDiscoveryWorkflow(
+    disease_condition: str,
+    sample_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Discover and validate biomarkers for a specific disease condition using literature analysis, expr...
+
+    Parameters
+    ----------
+    disease_condition : str
+        The disease condition to discover biomarkers for (e.g., 'breast cancer', 'Alz...
+    sample_type : str
+        The type of sample to analyze (e.g., 'blood', 'tissue', 'plasma')
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "BiomarkerDiscoveryWorkflow",
+            "arguments": {
+                "disease_condition": disease_condition,
+                "sample_type": sample_type,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["BiomarkerDiscoveryWorkflow"]

tooluniverse/tools/CMA_Guidelines_Search.py

@@ -0,0 +1,52 @@
+"""
+CMA_Guidelines_Search
+
+Search Canadian Medical Association (CMA) Infobase guidelines. Contains over 1200 evidence-based ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def CMA_Guidelines_Search(
+    query: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search Canadian Medical Association (CMA) Infobase guidelines. Contains over 1200 evidence-based ...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition, treatment, or clinical topic to search for in CMA guidelin...
+    limit : int
+        Maximum number of guidelines to return (default: 10)
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "CMA_Guidelines_Search",
+            "arguments": {"query": query, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["CMA_Guidelines_Search"]

tooluniverse/tools/CORE_search_papers.py

@@ -0,0 +1,67 @@
+"""
+CORE_search_papers
+
+Search for open access academic papers using CORE API. CORE is the world's largest collection of ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def CORE_search_papers(
+    query: str,
+    limit: int,
+    year_from: Optional[int] = None,
+    year_to: Optional[int] = None,
+    language: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search for open access academic papers using CORE API. CORE is the world's largest collection of ...
+
+    Parameters
+    ----------
+    query : str
+        Search query for CORE papers. Use keywords separated by spaces to refine your...
+    limit : int
+        Maximum number of papers to return. This sets the maximum number of papers re...
+    year_from : int
+        Start year for publication date filter (e.g., 2020). Optional parameter to li...
+    year_to : int
+        End year for publication date filter (e.g., 2024). Optional parameter to limi...
+    language : str
+        Language filter for papers (e.g., 'en', 'es', 'fr'). Optional parameter to li...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "CORE_search_papers",
+            "arguments": {
+                "query": query,
+                "limit": limit,
+                "year_from": year_from,
+                "year_to": year_to,
+                "language": language,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["CORE_search_papers"]

tooluniverse/tools/CallAgent.py

@@ -0,0 +1,46 @@
+"""
+CallAgent
+
+Give a solution plan to the agent and let it solve the problem. Solution plan should reflect a di...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def CallAgent(
+    solution: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Give a solution plan to the agent and let it solve the problem. Solution plan should reflect a di...
+
+    Parameters
+    ----------
+    solution : str
+        A feasible and concise solution plan that address the question.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "CallAgent", "arguments": {"solution": solution}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["CallAgent"]

tooluniverse/tools/ChEMBL_search_similar_molecules.py

@@ -0,0 +1,59 @@
+"""
+ChEMBL_search_similar_molecules
+
+Search for molecules similar to a given SMILES, chembl_id, or compound or drug name, using the Ch...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ChEMBL_search_similar_molecules(
+    query: str,
+    similarity_threshold: int,
+    max_results: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Search for molecules similar to a given SMILES, chembl_id, or compound or drug name, using the Ch...
+
+    Parameters
+    ----------
+    query : str
+        SMILES string, chembl_id, or compound or drug name.
+    similarity_threshold : int
+        Similarity threshold (0–100).
+    max_results : int
+        Maximum number of results to return.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "ChEMBL_search_similar_molecules",
+            "arguments": {
+                "query": query,
+                "similarity_threshold": similarity_threshold,
+                "max_results": max_results,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ChEMBL_search_similar_molecules"]

tooluniverse/tools/ClinVar_search_variants.py

@@ -0,0 +1,52 @@
+"""
+ClinVar_search_variants
+
+Search ClinVar via NCBI E-utilities (esearch→esummary) and return concise variant records for a q...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ClinVar_search_variants(
+    query: str,
+    retmax: Optional[int] = 5,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search ClinVar via NCBI E-utilities (esearch→esummary) and return concise variant records for a q...
+
+    Parameters
+    ----------
+    query : str
+        ClinVar search term (e.g., BRCA1).
+    retmax : int
+        Max records.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "ClinVar_search_variants",
+            "arguments": {"query": query, "retmax": retmax},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ClinVar_search_variants"]

tooluniverse/tools/ClinicalTrialDesignAgent.py

@@ -0,0 +1,63 @@
+"""
+ClinicalTrialDesignAgent
+
+AI agent that designs clinical trial protocols based on preclinical data and regulatory requirements
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ClinicalTrialDesignAgent(
+    drug_name: str,
+    indication: str,
+    preclinical_data: Optional[str] = "",
+    target_population: Optional[str] = "General adult population",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that designs clinical trial protocols based on preclinical data and regulatory requirements
+
+    Parameters
+    ----------
+    drug_name : str
+        Name of the drug candidate
+    indication : str
+        Disease indication
+    preclinical_data : str
+        Preclinical efficacy and safety data
+    target_population : str
+        Target patient population
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "ClinicalTrialDesignAgent",
+            "arguments": {
+                "drug_name": drug_name,
+                "indication": indication,
+                "preclinical_data": preclinical_data,
+                "target_population": target_population,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ClinicalTrialDesignAgent"]

tooluniverse/tools/CodeOptimizer.py

@@ -0,0 +1,55 @@
+"""
+CodeOptimizer
+
+Optimizes code implementation for tools based on quality evaluation. Takes tool configuration and...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def CodeOptimizer(
+    tool_config: str,
+    quality_evaluation: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Optimizes code implementation for tools based on quality evaluation. Takes tool configuration and...
+
+    Parameters
+    ----------
+    tool_config : str
+        JSON string containing the complete tool configuration including current impl...
+    quality_evaluation : str
+        JSON string containing quality evaluation results and feedback
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "CodeOptimizer",
+            "arguments": {
+                "tool_config": tool_config,
+                "quality_evaluation": quality_evaluation,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["CodeOptimizer"]

tooluniverse/tools/CodeQualityAnalyzer.py

@@ -0,0 +1,71 @@
+"""
+CodeQualityAnalyzer
+
+Analyzes code quality from multiple dimensions including algorithmic correctness, functional impl...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def CodeQualityAnalyzer(
+    tool_name: str,
+    tool_description: str,
+    tool_parameters: str,
+    implementation_code: str,
+    test_cases: str,
+    test_execution_results: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Analyzes code quality from multiple dimensions including algorithmic correctness, functional impl...
+
+    Parameters
+    ----------
+    tool_name : str
+        Name of the tool being analyzed
+    tool_description : str
+        Description of what the tool is supposed to do
+    tool_parameters : str
+        JSON string of tool parameters and their types
+    implementation_code : str
+        The actual implementation code to analyze
+    test_cases : str
+        JSON string of test cases for the tool
+    test_execution_results : str
+        JSON string of test execution results including pass/fail status and actual o...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "CodeQualityAnalyzer",
+            "arguments": {
+                "tool_name": tool_name,
+                "tool_description": tool_description,
+                "tool_parameters": tool_parameters,
+                "implementation_code": implementation_code,
+                "test_cases": test_cases,
+                "test_execution_results": test_execution_results,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["CodeQualityAnalyzer"]

tooluniverse/tools/CompoundDiscoveryAgent.py

@@ -0,0 +1,59 @@
+"""
+CompoundDiscoveryAgent
+
+AI agent that analyzes potential drug compounds using multiple strategies and LLM reasoning
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def CompoundDiscoveryAgent(
+    disease_name: str,
+    targets: str,
+    context: Optional[str] = "",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that analyzes potential drug compounds using multiple strategies and LLM reasoning
+
+    Parameters
+    ----------
+    disease_name : str
+        Name of the disease
+    targets : str
+        List of therapeutic targets (comma-separated)
+    context : str
+        Additional context or specific requirements
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "CompoundDiscoveryAgent",
+            "arguments": {
+                "disease_name": disease_name,
+                "targets": targets,
+                "context": context,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["CompoundDiscoveryAgent"]

tooluniverse/tools/ComprehensiveDrugDiscoveryPipeline.py

@@ -0,0 +1,49 @@
+"""
+ComprehensiveDrugDiscoveryPipeline
+
+Complete end-to-end drug discovery workflow from disease to optimized candidates. Identifies targ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ComprehensiveDrugDiscoveryPipeline(
+    disease_efo_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Complete end-to-end drug discovery workflow from disease to optimized candidates. Identifies targ...
+
+    Parameters
+    ----------
+    disease_efo_id : str
+        The EFO ID of the disease for drug discovery (e.g., 'EFO_0001074' for Alzheim...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "ComprehensiveDrugDiscoveryPipeline",
+            "arguments": {"disease_efo_id": disease_efo_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ComprehensiveDrugDiscoveryPipeline"]

tooluniverse/tools/Crossref_search_works.py

@@ -0,0 +1,55 @@
+"""
+Crossref_search_works
+
+Search Crossref Works API for articles by keyword. Returns articles with title, abstract, journal...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Crossref_search_works(
+    query: str,
+    limit: int,
+    filter: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search Crossref Works API for articles by keyword. Returns articles with title, abstract, journal...
+
+    Parameters
+    ----------
+    query : str
+        Search query for Crossref works. Use keywords separated by spaces to refine y...
+    limit : int
+        Number of articles to return. This sets the maximum number of articles retrie...
+    filter : str
+        Optional filter string for Crossref API. Examples: 'type:journal-article,from...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "Crossref_search_works",
+            "arguments": {"query": query, "limit": limit, "filter": filter},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Crossref_search_works"]