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

tooluniverse/tools/Ensembl_lookup_gene_by_symbol.py

@@ -0,0 +1,52 @@
+"""
+Ensembl_lookup_gene_by_symbol
+
+Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xr...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Ensembl_lookup_gene_by_symbol(
+    symbol: str,
+    species: Optional[str] = "homo_sapiens",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xr...
+
+    Parameters
+    ----------
+    species : str
+        Species name (e.g., 'homo_sapiens').
+    symbol : str
+        Gene symbol (e.g., BRCA1).
+    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": "Ensembl_lookup_gene_by_symbol",
+            "arguments": {"species": species, "symbol": symbol},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Ensembl_lookup_gene_by_symbol"]

tooluniverse/tools/EthicalComplianceReviewer.py

@@ -0,0 +1,49 @@
+"""
+EthicalComplianceReviewer
+
+Checks adherence to ethical standards and disclosure practices.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def EthicalComplianceReviewer(
+    ethics_section: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Checks adherence to ethical standards and disclosure practices.
+
+    Parameters
+    ----------
+    ethics_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": "EthicalComplianceReviewer",
+            "arguments": {"ethics_section": ethics_section},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["EthicalComplianceReviewer"]

tooluniverse/tools/EuropePMC_Guidelines_Search.py

@@ -0,0 +1,52 @@
+"""
+EuropePMC_Guidelines_Search
+
+Search Europe PMC for clinical guidelines and evidence-based recommendations. Europe PMC provides...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def EuropePMC_Guidelines_Search(
+    query: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search Europe PMC for clinical guidelines and evidence-based recommendations. Europe PMC provides...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition, treatment, or clinical topic to search for (e.g., 'diabete...
+    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
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "EuropePMC_Guidelines_Search",
+            "arguments": {"query": query, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["EuropePMC_Guidelines_Search"]

tooluniverse/tools/EuropePMC_search_articles.py

@@ -0,0 +1,52 @@
+"""
+EuropePMC_search_articles
+
+Search for articles on Europe PMC including abstracts. The tool queries the Europe PMC web servic...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def EuropePMC_search_articles(
+    query: str,
+    limit: Optional[int] = 5,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search for articles on Europe PMC including abstracts. The tool queries the Europe PMC web servic...
+
+    Parameters
+    ----------
+    query : str
+        Search query for Europe PMC. Use keywords separated by spaces to refine your ...
+    limit : int
+        Number of articles to return. This sets the maximum number of articles retrie...
+    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": "EuropePMC_search_articles",
+            "arguments": {"query": query, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["EuropePMC_search_articles"]

tooluniverse/tools/ExperimentalDesignScorer.py

@@ -0,0 +1,55 @@
+"""
+ExperimentalDesignScorer
+
+Assesses a proposed experimental design by assigning scores and structured feedback on hypothesis...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ExperimentalDesignScorer(
+    hypothesis: str,
+    design_description: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Assesses a proposed experimental design by assigning scores and structured feedback on hypothesis...
+
+    Parameters
+    ----------
+    hypothesis : str
+        A clear statement of the research hypothesis to be tested.
+    design_description : str
+        A detailed description of the proposed experimental design, including variabl...
+    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": "ExperimentalDesignScorer",
+            "arguments": {
+                "hypothesis": hypothesis,
+                "design_description": design_description,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ExperimentalDesignScorer"]

tooluniverse/tools/FAERS_count_additive_administration_routes.py

@@ -0,0 +1,52 @@
+"""
+FAERS_count_additive_administration_routes
+
+Additive multi-drug data: Enumerate and count administration routes for adverse events across spe...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def FAERS_count_additive_administration_routes(
+    medicinalproducts: list[Any],
+    serious: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Additive multi-drug data: Enumerate and count administration routes for adverse events across spe...
+
+    Parameters
+    ----------
+    medicinalproducts : list[Any]
+        Array of medicinal product names.
+    serious : str
+        Filter by seriousness.
+    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": "FAERS_count_additive_administration_routes",
+            "arguments": {"medicinalproducts": medicinalproducts, "serious": serious},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["FAERS_count_additive_administration_routes"]

tooluniverse/tools/FAERS_count_additive_adverse_reactions.py

@@ -0,0 +1,71 @@
+"""
+FAERS_count_additive_adverse_reactions
+
+Additive multi-drug data: Aggregate adverse reaction counts across specified medicinal products, ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def FAERS_count_additive_adverse_reactions(
+    medicinalproducts: list[Any],
+    patientsex: str,
+    patientagegroup: str,
+    occurcountry: str,
+    serious: str,
+    seriousnessdeath: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Additive multi-drug data: Aggregate adverse reaction counts across specified medicinal products, ...
+
+    Parameters
+    ----------
+    medicinalproducts : list[Any]
+        Array of medicinal product names.
+    patientsex : str
+        Filter by patient sex.
+    patientagegroup : str
+        Filter by patient age group.
+    occurcountry : str
+        Filter by ISO2 country code of occurrence.
+    serious : str
+        Filter by seriousness classification.
+    seriousnessdeath : str
+        Filter for fatal outcomes.
+    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": "FAERS_count_additive_adverse_reactions",
+            "arguments": {
+                "medicinalproducts": medicinalproducts,
+                "patientsex": patientsex,
+                "patientagegroup": patientagegroup,
+                "occurcountry": occurcountry,
+                "serious": serious,
+                "seriousnessdeath": seriousnessdeath,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["FAERS_count_additive_adverse_reactions"]

tooluniverse/tools/FAERS_count_additive_event_reports_by_country.py

@@ -0,0 +1,63 @@
+"""
+FAERS_count_additive_event_reports_by_country
+
+Additive multi-drug data: Aggregate report counts by country of occurrence across specified medic...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def FAERS_count_additive_event_reports_by_country(
+    medicinalproducts: list[Any],
+    patientsex: str,
+    patientagegroup: str,
+    serious: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Additive multi-drug data: Aggregate report counts by country of occurrence across specified medic...
+
+    Parameters
+    ----------
+    medicinalproducts : list[Any]
+        Array of medicinal product names.
+    patientsex : str
+        Filter by sex.
+    patientagegroup : str
+        Filter by age group.
+    serious : str
+        Filter by seriousness.
+    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": "FAERS_count_additive_event_reports_by_country",
+            "arguments": {
+                "medicinalproducts": medicinalproducts,
+                "patientsex": patientsex,
+                "patientagegroup": patientagegroup,
+                "serious": serious,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["FAERS_count_additive_event_reports_by_country"]

tooluniverse/tools/FAERS_count_additive_reaction_outcomes.py

@@ -0,0 +1,63 @@
+"""
+FAERS_count_additive_reaction_outcomes
+
+Additive multi-drug data: Determine reaction outcome counts (e.g., recovered, resolving, fatal) a...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def FAERS_count_additive_reaction_outcomes(
+    medicinalproducts: list[Any],
+    patientsex: str,
+    patientagegroup: str,
+    occurcountry: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Additive multi-drug data: Determine reaction outcome counts (e.g., recovered, resolving, fatal) a...
+
+    Parameters
+    ----------
+    medicinalproducts : list[Any]
+        Array of medicinal product names.
+    patientsex : str
+
+    patientagegroup : str
+
+    occurcountry : 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": "FAERS_count_additive_reaction_outcomes",
+            "arguments": {
+                "medicinalproducts": medicinalproducts,
+                "patientsex": patientsex,
+                "patientagegroup": patientagegroup,
+                "occurcountry": occurcountry,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["FAERS_count_additive_reaction_outcomes"]

tooluniverse/tools/FAERS_count_additive_reports_by_reporter_country.py

@@ -0,0 +1,63 @@
+"""
+FAERS_count_additive_reports_by_reporter_country
+
+Additive multi-drug data: Aggregate adverse event reports by primary reporter country across medi...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def FAERS_count_additive_reports_by_reporter_country(
+    medicinalproducts: list[Any],
+    patientsex: str,
+    patientagegroup: str,
+    serious: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Additive multi-drug data: Aggregate adverse event reports by primary reporter country across medi...
+
+    Parameters
+    ----------
+    medicinalproducts : list[Any]
+        Array of medicinal product names.
+    patientsex : str
+        Filter by sex.
+    patientagegroup : str
+        Filter by age group.
+    serious : str
+        Filter by seriousness.
+    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": "FAERS_count_additive_reports_by_reporter_country",
+            "arguments": {
+                "medicinalproducts": medicinalproducts,
+                "patientsex": patientsex,
+                "patientagegroup": patientagegroup,
+                "serious": serious,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["FAERS_count_additive_reports_by_reporter_country"]

tooluniverse/tools/FAERS_count_additive_seriousness_classification.py

@@ -0,0 +1,63 @@
+"""
+FAERS_count_additive_seriousness_classification
+
+Additive multi-drug data: Quantify serious vs non-serious classifications across medicinal produc...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def FAERS_count_additive_seriousness_classification(
+    medicinalproducts: list[Any],
+    patientsex: str,
+    patientagegroup: str,
+    occurcountry: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Additive multi-drug data: Quantify serious vs non-serious classifications across medicinal produc...
+
+    Parameters
+    ----------
+    medicinalproducts : list[Any]
+        Array of medicinal product names.
+    patientsex : str
+        Filter by sex.
+    patientagegroup : str
+        Filter by age group.
+    occurcountry : str
+        ISO2 country code filter.
+    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": "FAERS_count_additive_seriousness_classification",
+            "arguments": {
+                "medicinalproducts": medicinalproducts,
+                "patientsex": patientsex,
+                "patientagegroup": patientagegroup,
+                "occurcountry": occurcountry,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["FAERS_count_additive_seriousness_classification"]