tooluniverse 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.whl

tooluniverse/tools/ADMETAI_predict_stress_response.py

@@ -0,0 +1,46 @@
+"""
+ADMETAI_predict_stress_response
+
+Predicts stress response endpoints (SR-ARE, SR-ATAD5, SR-HSE, SR-MMP, SR-p53) for a given list of...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ADMETAI_predict_stress_response(
+    smiles: list[Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Predicts stress response endpoints (SR-ARE, SR-ATAD5, SR-HSE, SR-MMP, SR-p53) for a given list of...
+
+    Parameters
+    ----------
+    smiles : list[Any]
+        The list of SMILES strings.
+    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": "ADMETAI_predict_stress_response", "arguments": {"smiles": smiles}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ADMETAI_predict_stress_response"]

tooluniverse/tools/ADMETAI_predict_toxicity.py

@@ -0,0 +1,46 @@
+"""
+ADMETAI_predict_toxicity
+
+Predicts toxicity endpoints (AMES, Carcinogens_Lagunin, ClinTox, DILI, LD50_Zhu, Skin_Reaction, h...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ADMETAI_predict_toxicity(
+    smiles: list[Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Predicts toxicity endpoints (AMES, Carcinogens_Lagunin, ClinTox, DILI, LD50_Zhu, Skin_Reaction, h...
+
+    Parameters
+    ----------
+    smiles : list[Any]
+        The list of SMILES strings.
+    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": "ADMETAI_predict_toxicity", "arguments": {"smiles": smiles}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ADMETAI_predict_toxicity"]

tooluniverse/tools/AdvancedCodeQualityAnalyzer.py

@@ -0,0 +1,63 @@
+"""
+AdvancedCodeQualityAnalyzer
+
+Performs deep analysis of code quality including complexity, security, performance, and maintaina...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def AdvancedCodeQualityAnalyzer(
+    source_code: str,
+    language: Optional[str] = "python",
+    analysis_depth: Optional[str] = "comprehensive",
+    domain_context: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Performs deep analysis of code quality including complexity, security, performance, and maintaina...
+
+    Parameters
+    ----------
+    source_code : str
+        The source code to analyze for quality assessment
+    language : str
+        Programming language (python, javascript, etc.)
+    analysis_depth : str
+        Level of analysis depth to perform
+    domain_context : str
+        Domain context for specialized analysis (e.g., bioinformatics, web development)
+    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": "AdvancedCodeQualityAnalyzer",
+            "arguments": {
+                "source_code": source_code,
+                "language": language,
+                "analysis_depth": analysis_depth,
+                "domain_context": domain_context,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["AdvancedCodeQualityAnalyzer"]

tooluniverse/tools/AdverseEventICDMapper.py

@@ -0,0 +1,46 @@
+"""
+AdverseEventICDMapper
+
+Extracts adverse events from narrative clinical or pharmacovigilance text and maps each event to ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def AdverseEventICDMapper(
+    source_text: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extracts adverse events from narrative clinical or pharmacovigilance text and maps each event to ...
+
+    Parameters
+    ----------
+    source_text : str
+        Unstructured narrative text that may mention adverse events.
+    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": "AdverseEventICDMapper", "arguments": {"source_text": source_text}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["AdverseEventICDMapper"]

tooluniverse/tools/AdverseEventPredictionQuestionGenerator.py

@@ -0,0 +1,52 @@
+"""
+AdverseEventPredictionQuestionGenerator
+
+Generates a set of personalized adverse‐event prediction questions for a given disease and drug, ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def AdverseEventPredictionQuestionGenerator(
+    disease_name: str,
+    drug_name: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Generates a set of personalized adverse‐event prediction questions for a given disease and drug, ...
+
+    Parameters
+    ----------
+    disease_name : str
+        The name of the disease or condition
+    drug_name : str
+        The name of the drug
+    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": "AdverseEventPredictionQuestionGenerator",
+            "arguments": {"disease_name": disease_name, "drug_name": drug_name},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["AdverseEventPredictionQuestionGenerator"]

tooluniverse/tools/AdverseEventPredictionQuestionGeneratorWithContext.py

@@ -0,0 +1,59 @@
+"""
+AdverseEventPredictionQuestionGeneratorWithContext
+
+Generates a set of personalized adverse‐event prediction questions for a given disease and drug, ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def AdverseEventPredictionQuestionGeneratorWithContext(
+    disease_name: str,
+    drug_name: str,
+    context_information: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Generates a set of personalized adverse‐event prediction questions for a given disease and drug, ...
+
+    Parameters
+    ----------
+    disease_name : str
+        The name of the disease or condition
+    drug_name : str
+        The name of the drug
+    context_information : str
+        Additional context information such as patient medical history, clinical find...
+    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": "AdverseEventPredictionQuestionGeneratorWithContext",
+            "arguments": {
+                "disease_name": disease_name,
+                "drug_name": drug_name,
+                "context_information": context_information,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["AdverseEventPredictionQuestionGeneratorWithContext"]

tooluniverse/tools/ArXiv_search_papers.py

@@ -0,0 +1,63 @@
+"""
+ArXiv_search_papers
+
+Search arXiv for papers by keyword using the public arXiv API. Returns papers with title, abstrac...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ArXiv_search_papers(
+    query: str,
+    limit: int,
+    sort_by: str,
+    sort_order: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search arXiv for papers by keyword using the public arXiv API. Returns papers with title, abstrac...
+
+    Parameters
+    ----------
+    query : str
+        Search query for arXiv papers. Use keywords separated by spaces to refine you...
+    limit : int
+        Number of papers to return. This sets the maximum number of papers retrieved ...
+    sort_by : str
+        Sort order for results. Options: 'relevance', 'lastUpdatedDate', 'submittedDate'
+    sort_order : str
+        Sort direction. Options: 'ascending', 'descending'
+    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": "ArXiv_search_papers",
+            "arguments": {
+                "query": query,
+                "limit": limit,
+                "sort_by": sort_by,
+                "sort_order": sort_order,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ArXiv_search_papers"]

tooluniverse/tools/ArgumentDescriptionOptimizer.py

@@ -0,0 +1,55 @@
+"""
+ArgumentDescriptionOptimizer
+
+Optimizes the descriptions of tool arguments/parameters based on test case results and actual usa...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ArgumentDescriptionOptimizer(
+    parameter_schema: str,
+    test_results: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Optimizes the descriptions of tool arguments/parameters based on test case results and actual usa...
+
+    Parameters
+    ----------
+    parameter_schema : str
+        JSON string of the original parameter schema with properties and descriptions.
+    test_results : str
+        A JSON string containing test case input/output pairs showing parameter usage.
+    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": "ArgumentDescriptionOptimizer",
+            "arguments": {
+                "parameter_schema": parameter_schema,
+                "test_results": test_results,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ArgumentDescriptionOptimizer"]

tooluniverse/tools/BioRxiv_search_preprints.py

@@ -0,0 +1,52 @@
+"""
+BioRxiv_search_preprints
+
+Search bioRxiv preprints using the public bioRxiv API. Returns preprints with title, authors, yea...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def BioRxiv_search_preprints(
+    query: str,
+    max_results: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search bioRxiv preprints using the public bioRxiv API. Returns preprints with title, authors, yea...
+
+    Parameters
+    ----------
+    query : str
+        Search query for bioRxiv preprints. Use keywords separated by spaces to refin...
+    max_results : int
+        Maximum number of preprints to return. Default is 10, maximum is 200.
+    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": "BioRxiv_search_preprints",
+            "arguments": {"query": query, "max_results": max_results},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["BioRxiv_search_preprints"]

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/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: int,
+    year_to: int,
+    language: str,
+    *,
+    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"]