tooluniverse 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl

tooluniverse/tools/MethodologyRigorReviewer.py

@@ -0,0 +1,49 @@
+"""
+MethodologyRigorReviewer
+
+Evaluates design appropriateness, sampling, and procedural transparency.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def MethodologyRigorReviewer(
+    methods_section: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Evaluates design appropriateness, sampling, and procedural transparency.
+
+    Parameters
+    ----------
+    methods_section : str
+        Full Methods text
+    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": "MethodologyRigorReviewer",
+            "arguments": {"methods_section": methods_section},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["MethodologyRigorReviewer"]

tooluniverse/tools/MultiAgentLiteratureSearch.py

@@ -0,0 +1,59 @@
+"""
+MultiAgentLiteratureSearch
+
+Multi-agent literature search system that uses AI agents to analyze intent, extract keywords, exe...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def MultiAgentLiteratureSearch(
+    query: str,
+    max_iterations: int,
+    quality_threshold: float,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Multi-agent literature search system that uses AI agents to analyze intent, extract keywords, exe...
+
+    Parameters
+    ----------
+    query : str
+        The research query to search for
+    max_iterations : int
+        Maximum number of iterations (default: 3)
+    quality_threshold : float
+        Quality threshold for completion (default: 0.7)
+    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": "MultiAgentLiteratureSearch",
+            "arguments": {
+                "query": query,
+                "max_iterations": max_iterations,
+                "quality_threshold": quality_threshold,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["MultiAgentLiteratureSearch"]

tooluniverse/tools/NICE_Clinical_Guidelines_Search.py

@@ -0,0 +1,52 @@
+"""
+NICE_Clinical_Guidelines_Search
+
+Search NICE (National Institute for Health and Care Excellence) clinical guidelines and evidence-...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def NICE_Clinical_Guidelines_Search(
+    query: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search NICE (National Institute for Health and Care Excellence) clinical guidelines and evidence-...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition, treatment, or clinical topic to search for in NICE guideli...
+    limit : int
+        Maximum number of clinical 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": "NICE_Clinical_Guidelines_Search",
+            "arguments": {"query": query, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["NICE_Clinical_Guidelines_Search"]

tooluniverse/tools/NICE_Guideline_Full_Text.py

@@ -0,0 +1,46 @@
+"""
+NICE_Guideline_Full_Text
+
+Fetch complete full text content from a NICE clinical guideline page. Takes a NICE guideline URL ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def NICE_Guideline_Full_Text(
+    url: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Fetch complete full text content from a NICE clinical guideline page. Takes a NICE guideline URL ...
+
+    Parameters
+    ----------
+    url : str
+        Full URL of the NICE guideline page (e.g., 'https://www.nice.org.uk/guidance/...
+    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": "NICE_Guideline_Full_Text", "arguments": {"url": url}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["NICE_Guideline_Full_Text"]

tooluniverse/tools/NoveltySignificanceReviewer.py

@@ -0,0 +1,59 @@
+"""
+NoveltySignificanceReviewer
+
+Provides a structured peer-review of the work's originality and potential impact.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def NoveltySignificanceReviewer(
+    paper_title: str,
+    abstract: str,
+    manuscript_text: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Provides a structured peer-review of the work's originality and potential impact.
+
+    Parameters
+    ----------
+    paper_title : str
+        Manuscript title
+    abstract : str
+        Manuscript abstract
+    manuscript_text : str
+        Full manuscript text
+    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": "NoveltySignificanceReviewer",
+            "arguments": {
+                "paper_title": paper_title,
+                "abstract": abstract,
+                "manuscript_text": manuscript_text,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["NoveltySignificanceReviewer"]

tooluniverse/tools/OSF_search_preprints.py

@@ -0,0 +1,59 @@
+"""
+OSF_search_preprints
+
+Search OSF (Open Science Framework) Preprints for research preprints and working papers. OSF Prep...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OSF_search_preprints(
+    query: str,
+    max_results: int,
+    provider: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search OSF (Open Science Framework) Preprints for research preprints and working papers. OSF Prep...
+
+    Parameters
+    ----------
+    query : str
+        Search query for OSF preprints. Use keywords to search across titles and abst...
+    max_results : int
+        Maximum number of results to return. Default is 10, maximum is 100.
+    provider : str
+        Optional preprint provider filter (e.g., 'osf', 'psyarxiv', 'socarxiv'). If n...
+    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": "OSF_search_preprints",
+            "arguments": {
+                "query": query,
+                "max_results": max_results,
+                "provider": provider,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OSF_search_preprints"]

tooluniverse/tools/OSL_get_efo_id_by_disease_name.py

@@ -0,0 +1,46 @@
+"""
+OSL_get_efo_id_by_disease_name
+
+Tool to lookup Experimental Factor Ontology (EFO) IDs for diseases via the EMBL-EBI OLS API.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OSL_get_efo_id_by_disease_name(
+    disease: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Tool to lookup Experimental Factor Ontology (EFO) IDs for diseases via the EMBL-EBI OLS API.
+
+    Parameters
+    ----------
+    disease : str
+        Search query for diseases. Provide the disease name to lookup the correspondi...
+    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": "OSL_get_efo_id_by_disease_name", "arguments": {"disease": disease}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OSL_get_efo_id_by_disease_name"]

tooluniverse/tools/OpenAIRE_search_publications.py

@@ -0,0 +1,55 @@
+"""
+OpenAIRE_search_publications
+
+Search OpenAIRE Explore for research products including publications, datasets, and software. Ope...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OpenAIRE_search_publications(
+    query: str,
+    max_results: int,
+    type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search OpenAIRE Explore for research products including publications, datasets, and software. Ope...
+
+    Parameters
+    ----------
+    query : str
+        Search query for OpenAIRE research products. Use keywords to search across ti...
+    max_results : int
+        Maximum number of results to return. Default is 10, maximum is 100.
+    type : str
+        Type of research product to search: 'publications', 'datasets', or 'software'...
+    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": "OpenAIRE_search_publications",
+            "arguments": {"query": query, "max_results": max_results, "type": type},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OpenAIRE_search_publications"]

tooluniverse/tools/OpenAlex_Guidelines_Search.py

@@ -0,0 +1,63 @@
+"""
+OpenAlex_Guidelines_Search
+
+Search for clinical practice guidelines using OpenAlex scholarly database. Provides access to a c...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OpenAlex_Guidelines_Search(
+    query: str,
+    limit: int,
+    year_from: int,
+    year_to: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search for clinical practice guidelines using OpenAlex scholarly database. Provides access to a c...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition or clinical topic to search for guidelines (e.g., 'diabetes...
+    limit : int
+        Maximum number of guidelines to return (default: 10)
+    year_from : int
+        Filter for guidelines published from this year onwards (optional)
+    year_to : int
+        Filter for guidelines published up to this year (optional)
+    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": "OpenAlex_Guidelines_Search",
+            "arguments": {
+                "query": query,
+                "limit": limit,
+                "year_from": year_from,
+                "year_to": year_to,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OpenAlex_Guidelines_Search"]

tooluniverse/tools/OpenTargets_drug_pharmacogenomics_data.py

@@ -0,0 +1,52 @@
+"""
+OpenTargets_drug_pharmacogenomics_data
+
+Retrieve pharmacogenomics data for a specific drug, including evidence levels and genotype annota...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OpenTargets_drug_pharmacogenomics_data(
+    chemblId: str,
+    page: Optional[dict[str, Any]] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve pharmacogenomics data for a specific drug, including evidence levels and genotype annota...
+
+    Parameters
+    ----------
+    chemblId : str
+        The ChEMBL ID of the drug.
+    page : dict[str, Any]
+        Pagination options.
+    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": "OpenTargets_drug_pharmacogenomics_data",
+            "arguments": {"chemblId": chemblId, "page": page},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OpenTargets_drug_pharmacogenomics_data"]

tooluniverse/tools/OpenTargets_get_approved_indications_by_drug_chemblId.py

@@ -0,0 +1,49 @@
+"""
+OpenTargets_get_approved_indications_by_drug_chemblId
+
+Retrieve detailed information about multiple drugs using a list of ChEMBL IDs.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OpenTargets_get_approved_indications_by_drug_chemblId(
+    chemblId: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve detailed information about multiple drugs using a list of ChEMBL IDs.
+
+    Parameters
+    ----------
+    chemblId : str
+        The ChEMBL ID 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": "OpenTargets_get_approved_indications_by_drug_chemblId",
+            "arguments": {"chemblId": chemblId},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OpenTargets_get_approved_indications_by_drug_chemblId"]

tooluniverse/tools/OpenTargets_get_associated_diseases_by_drug_chemblId.py

@@ -0,0 +1,49 @@
+"""
+OpenTargets_get_associated_diseases_by_drug_chemblId
+
+Retrieve the list of diseases associated with a specific drug chemblId based on clinical trial da...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OpenTargets_get_associated_diseases_by_drug_chemblId(
+    chemblId: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve the list of diseases associated with a specific drug chemblId based on clinical trial da...
+
+    Parameters
+    ----------
+    chemblId : str
+        The ChEMBL ID 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": "OpenTargets_get_associated_diseases_by_drug_chemblId",
+            "arguments": {"chemblId": chemblId},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OpenTargets_get_associated_diseases_by_drug_chemblId"]

tooluniverse/tools/OpenTargets_get_associated_drugs_by_disease_efoId.py

@@ -0,0 +1,52 @@
+"""
+OpenTargets_get_associated_drugs_by_disease_efoId
+
+Retrieve known drugs associated with a specific disease by disease efoId.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OpenTargets_get_associated_drugs_by_disease_efoId(
+    efoId: str,
+    size: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve known drugs associated with a specific disease by disease efoId.
+
+    Parameters
+    ----------
+    efoId : str
+        The EFO ID of the disease.
+    size : int
+        Number of entries to fetch, recomanding a large number to avoid missing drugs.
+    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": "OpenTargets_get_associated_drugs_by_disease_efoId",
+            "arguments": {"efoId": efoId, "size": size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OpenTargets_get_associated_drugs_by_disease_efoId"]