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

tooluniverse/tools/PubMed_search_articles.py

@@ -0,0 +1,55 @@
+"""
+PubMed_search_articles
+
+Search PubMed using NCBI E-utilities (esearch + esummary) and return articles. Returns articles w...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubMed_search_articles(
+    query: str,
+    limit: Optional[int] = 10,
+    api_key: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search PubMed using NCBI E-utilities (esearch + esummary) and return articles. Returns articles w...
+
+    Parameters
+    ----------
+    query : str
+        Search query for PubMed articles. Use keywords separated by spaces to refine ...
+    limit : int
+        Number of articles to return. This sets the maximum number of articles retrie...
+    api_key : str
+        Optional NCBI API key for higher rate limits. Get your free key at https://ww...
+    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": "PubMed_search_articles",
+            "arguments": {"query": query, "limit": limit, "api_key": api_key},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubMed_search_articles"]

tooluniverse/tools/PubTator3_EntityAutocomplete.py

@@ -0,0 +1,59 @@
+"""
+PubTator3_EntityAutocomplete
+
+Provides suggestions for the best‐matching standardized PubTator IDs for a partial biomedical ter...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubTator3_EntityAutocomplete(
+    text: str,
+    entity_type: str,
+    max_results: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Provides suggestions for the best‐matching standardized PubTator IDs for a partial biomedical ter...
+
+    Parameters
+    ----------
+    text : str
+        A few characters or the full name of the biomedical concept you are trying to...
+    entity_type : str
+        Optional filter to restrict suggestions to a single category such as GENE, DI...
+    max_results : int
+        Maximum number of suggestions to return (1 - 50, default = 10).
+    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": "PubTator3_EntityAutocomplete",
+            "arguments": {
+                "text": text,
+                "entity_type": entity_type,
+                "max_results": max_results,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubTator3_EntityAutocomplete"]

tooluniverse/tools/PubTator3_LiteratureSearch.py

@@ -0,0 +1,55 @@
+"""
+PubTator3_LiteratureSearch
+
+Find PubMed articles that match a keyword, a PubTator entity ID (e.g. “@GENE_BRAF”), or an entity...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubTator3_LiteratureSearch(
+    query: str,
+    page: int,
+    page_size: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Find PubMed articles that match a keyword, a PubTator entity ID (e.g. “@GENE_BRAF”), or an entity...
+
+    Parameters
+    ----------
+    query : str
+        What you want to search for. This can be plain keywords, a single PubTator ID...
+    page : int
+        Zero-based results page (optional; default = 0).
+    page_size : int
+        How many PMIDs to return per page (optional; default = 20, maximum = 200).
+    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": "PubTator3_LiteratureSearch",
+            "arguments": {"query": query, "page": page, "page_size": page_size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubTator3_LiteratureSearch"]

tooluniverse/tools/QuestionRephraser.py

@@ -0,0 +1,52 @@
+"""
+QuestionRephraser
+
+Generates three distinct paraphrases of a given question while ensuring answer options remain val...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def QuestionRephraser(
+    question: str,
+    options: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Generates three distinct paraphrases of a given question while ensuring answer options remain val...
+
+    Parameters
+    ----------
+    question : str
+        The original question text to be rephrased
+    options : str
+        Answer options (e.g., multiple choice options) that should remain valid for t...
+    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": "QuestionRephraser",
+            "arguments": {"question": question, "options": options},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["QuestionRephraser"]

tooluniverse/tools/Reactome_get_pathway_reactions.py

@@ -0,0 +1,46 @@
+"""
+Reactome_get_pathway_reactions
+
+Query all Reactions contained under a Pathway using Pathway Stable ID. This is currently the only...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Reactome_get_pathway_reactions(
+    stId: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Query all Reactions contained under a Pathway using Pathway Stable ID. This is currently the only...
+
+    Parameters
+    ----------
+    stId : str
+        Pathway Stable ID, e.g., 'R-HSA-73817' (verified valid).
+    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": "Reactome_get_pathway_reactions", "arguments": {"stId": stId}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Reactome_get_pathway_reactions"]

tooluniverse/tools/ReproducibilityTransparencyReviewer.py

@@ -0,0 +1,49 @@
+"""
+ReproducibilityTransparencyReviewer
+
+Evaluates data, code, and protocol availability for replication.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ReproducibilityTransparencyReviewer(
+    availability_statement: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Evaluates data, code, and protocol availability for replication.
+
+    Parameters
+    ----------
+    availability_statement : 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": "ReproducibilityTransparencyReviewer",
+            "arguments": {"availability_statement": availability_statement},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ReproducibilityTransparencyReviewer"]

tooluniverse/tools/ResultsInterpretationReviewer.py

@@ -0,0 +1,55 @@
+"""
+ResultsInterpretationReviewer
+
+Judges whether conclusions are data-justified and limitations addressed.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ResultsInterpretationReviewer(
+    results_section: str,
+    discussion_section: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Judges whether conclusions are data-justified and limitations addressed.
+
+    Parameters
+    ----------
+    results_section : str
+
+    discussion_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": "ResultsInterpretationReviewer",
+            "arguments": {
+                "results_section": results_section,
+                "discussion_section": discussion_section,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ResultsInterpretationReviewer"]

tooluniverse/tools/ScientificTextSummarizer.py

@@ -0,0 +1,59 @@
+"""
+ScientificTextSummarizer
+
+Summarizes biomedical research texts, abstracts, or papers with specified length and focus areas....
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ScientificTextSummarizer(
+    text: str,
+    summary_length: str,
+    focus_area: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Summarizes biomedical research texts, abstracts, or papers with specified length and focus areas....
+
+    Parameters
+    ----------
+    text : str
+        The biomedical text, abstract, or paper content to be summarized.
+    summary_length : str
+        Desired length of summary (e.g., '50', '100', '200 words').
+    focus_area : str
+        What to focus on in the summary (e.g., 'methodology', 'results', 'clinical im...
+    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": "ScientificTextSummarizer",
+            "arguments": {
+                "text": text,
+                "summary_length": summary_length,
+                "focus_area": focus_area,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ScientificTextSummarizer"]

tooluniverse/tools/SemanticScholar_search_papers.py

@@ -0,0 +1,55 @@
+"""
+SemanticScholar_search_papers
+
+Search for papers on Semantic Scholar including abstracts. This tool queries the Semantic Scholar...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def SemanticScholar_search_papers(
+    query: str,
+    limit: int,
+    api_key: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search for papers on Semantic Scholar including abstracts. This tool queries the Semantic Scholar...
+
+    Parameters
+    ----------
+    query : str
+        Search query for Semantic Scholar. Use keywords separated by spaces to refine...
+    limit : int
+        Maximum number of papers to return from Semantic Scholar.
+    api_key : str
+        Optional API key for Semantic Scholar to obtain a higher quota.
+    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": "SemanticScholar_search_papers",
+            "arguments": {"query": query, "limit": limit, "api_key": api_key},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["SemanticScholar_search_papers"]

tooluniverse/tools/TRIP_Database_Guidelines_Search.py

@@ -0,0 +1,55 @@
+"""
+TRIP_Database_Guidelines_Search
+
+Search TRIP Database (Turning Research into Practice) for evidence-based clinical guidelines. TRI...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def TRIP_Database_Guidelines_Search(
+    query: str,
+    limit: int,
+    search_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search TRIP Database (Turning Research into Practice) for evidence-based clinical guidelines. TRI...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition, treatment, or clinical question (e.g., 'diabetes managemen...
+    limit : int
+        Maximum number of guidelines to return (default: 10)
+    search_type : str
+        Type of content to search for (default: 'guideline'). Options include 'guidel...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "TRIP_Database_Guidelines_Search",
+            "arguments": {"query": query, "limit": limit, "search_type": search_type},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["TRIP_Database_Guidelines_Search"]

tooluniverse/tools/TestCaseGenerator.py

@@ -0,0 +1,46 @@
+"""
+TestCaseGenerator
+
+Generates diverse and representative ToolUniverse tool call dictionaries for a given tool based o...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def TestCaseGenerator(
+    tool_config: dict[str, Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Generates diverse and representative ToolUniverse tool call dictionaries for a given tool based o...
+
+    Parameters
+    ----------
+    tool_config : dict[str, Any]
+        The full configuration of the tool to generate test cases for. May include '_...
+    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": "TestCaseGenerator", "arguments": {"tool_config": tool_config}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["TestCaseGenerator"]

tooluniverse/tools/ToolCompatibilityAnalyzer.py

@@ -0,0 +1,59 @@
+"""
+ToolCompatibilityAnalyzer
+
+Analyzes two tool specifications to determine if one tool's output can be used as input for anoth...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ToolCompatibilityAnalyzer(
+    source_tool: str,
+    target_tool: str,
+    analysis_depth: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Analyzes two tool specifications to determine if one tool's output can be used as input for anoth...
+
+    Parameters
+    ----------
+    source_tool : str
+        The source tool specification (JSON string with name, description, parameter ...
+    target_tool : str
+        The target tool specification (JSON string with name, description, parameter ...
+    analysis_depth : str
+        Level of analysis depth - quick for basic compatibility, detailed for paramet...
+    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": "ToolCompatibilityAnalyzer",
+            "arguments": {
+                "source_tool": source_tool,
+                "target_tool": target_tool,
+                "analysis_depth": analysis_depth,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ToolCompatibilityAnalyzer"]