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

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/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/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"]

tooluniverse/tools/DBLP_search_publications.py

@@ -0,0 +1,52 @@
+"""
+DBLP_search_publications
+
+Search DBLP Computer Science Bibliography for publications. Returns publications with title, auth...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DBLP_search_publications(
+    query: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search DBLP Computer Science Bibliography for publications. Returns publications with title, auth...
+
+    Parameters
+    ----------
+    query : str
+        Search query for DBLP publications. Use keywords separated by spaces to refin...
+    limit : int
+        Number of publications to return. This sets the maximum number of publication...
+    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": "DBLP_search_publications",
+            "arguments": {"query": query, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DBLP_search_publications"]

tooluniverse/tools/DOAJ_search_articles.py

@@ -0,0 +1,55 @@
+"""
+DOAJ_search_articles
+
+Search DOAJ (Directory of Open Access Journals) for open-access articles. Returns articles with t...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DOAJ_search_articles(
+    query: str,
+    max_results: int,
+    type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search DOAJ (Directory of Open Access Journals) for open-access articles. Returns articles with t...
+
+    Parameters
+    ----------
+    query : str
+        Search query for DOAJ articles. Supports Lucene syntax for advanced queries.
+    max_results : int
+        Maximum number of articles to return. Default is 10, maximum is 100.
+    type : str
+        Type of search: 'articles' or 'journals'. Default is 'articles'.
+    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": "DOAJ_search_articles",
+            "arguments": {"query": query, "max_results": max_results, "type": type},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DOAJ_search_articles"]

tooluniverse/tools/DailyMed_get_spl_by_setid.py

@@ -0,0 +1,52 @@
+"""
+DailyMed_get_spl_by_setid
+
+Get complete label corresponding to SPL Set ID, returns content in XML or JSON format.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DailyMed_get_spl_by_setid(
+    setid: str,
+    format: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get complete label corresponding to SPL Set ID, returns content in XML or JSON format.
+
+    Parameters
+    ----------
+    setid : str
+        SPL Set ID to query.
+    format : str
+        Return format, only supports 'xml'.
+    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": "DailyMed_get_spl_by_setid",
+            "arguments": {"setid": setid, "format": format},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DailyMed_get_spl_by_setid"]

tooluniverse/tools/DailyMed_search_spls.py

@@ -0,0 +1,79 @@
+"""
+DailyMed_search_spls
+
+Search SPL list using multiple filter conditions (drug_name/ndc/rxcui/setid) and return metadata ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DailyMed_search_spls(
+    drug_name: str,
+    ndc: str,
+    rxcui: str,
+    setid: str,
+    published_date_gte: str,
+    published_date_eq: str,
+    pagesize: int,
+    page: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Search SPL list using multiple filter conditions (drug_name/ndc/rxcui/setid) and return metadata ...
+
+    Parameters
+    ----------
+    drug_name : str
+        Generic or brand name of the drug, e.g., 'TAMSULOSIN HYDROCHLORIDE'.
+    ndc : str
+        National Drug Code (NDC).
+    rxcui : str
+        RxNorm Code (RXCUI).
+    setid : str
+        Set ID corresponding to the SPL.
+    published_date_gte : str
+        Published date >= specified date, format 'YYYY-MM-DD'.
+    published_date_eq : str
+        Published date == specified date, format 'YYYY-MM-DD'.
+    pagesize : int
+        Number of items per page, maximum 100, default 100.
+    page : int
+        Page number, starts from 1, default 1.
+    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": "DailyMed_search_spls",
+            "arguments": {
+                "drug_name": drug_name,
+                "ndc": ndc,
+                "rxcui": rxcui,
+                "setid": setid,
+                "published_date_gte": published_date_gte,
+                "published_date_eq": published_date_eq,
+                "pagesize": pagesize,
+                "page": page,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DailyMed_search_spls"]

tooluniverse/tools/DataAnalysisValidityReviewer.py

@@ -0,0 +1,49 @@
+"""
+DataAnalysisValidityReviewer
+
+Checks statistical choices, assumption testing, and reporting transparency.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DataAnalysisValidityReviewer(
+    analysis_section: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Checks statistical choices, assumption testing, and reporting transparency.
+
+    Parameters
+    ----------
+    analysis_section : str
+
+    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": "DataAnalysisValidityReviewer",
+            "arguments": {"analysis_section": analysis_section},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DataAnalysisValidityReviewer"]

tooluniverse/tools/DescriptionAnalyzer.py

@@ -0,0 +1,55 @@
+"""
+DescriptionAnalyzer
+
+Analyzes a tool's original description and the results of multiple test cases, then suggests an i...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DescriptionAnalyzer(
+    original_description: str,
+    test_results: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Analyzes a tool's original description and the results of multiple test cases, then suggests an i...
+
+    Parameters
+    ----------
+    original_description : str
+        The original description of the tool.
+    test_results : str
+        A JSON string containing a list of test case input/output pairs.
+    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": "DescriptionAnalyzer",
+            "arguments": {
+                "original_description": original_description,
+                "test_results": test_results,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DescriptionAnalyzer"]

tooluniverse/tools/DescriptionQualityEvaluator.py

@@ -0,0 +1,59 @@
+"""
+DescriptionQualityEvaluator
+
+Evaluates the quality of tool descriptions and parameter descriptions, providing a score and spec...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DescriptionQualityEvaluator(
+    tool_description: str,
+    parameter_descriptions: str,
+    test_results: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Evaluates the quality of tool descriptions and parameter descriptions, providing a score and spec...
+
+    Parameters
+    ----------
+    tool_description : str
+        The tool description to evaluate.
+    parameter_descriptions : str
+        JSON string of parameter names and their descriptions.
+    test_results : str
+        JSON string containing test case results.
+    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": "DescriptionQualityEvaluator",
+            "arguments": {
+                "tool_description": tool_description,
+                "parameter_descriptions": parameter_descriptions,
+                "test_results": test_results,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DescriptionQualityEvaluator"]