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

tooluniverse/tools/mesh_get_subjects_by_subject_scope_or_definition.py

@@ -0,0 +1,63 @@
+"""
+mesh_get_subjects_by_subject_scope_or_definition
+
+Find MeSH (Medical Subject Heading) subjects with matching scopes (definitions).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def mesh_get_subjects_by_subject_scope_or_definition(
+    query: str,
+    case_sensitive: bool,
+    exact_match: bool,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Find MeSH (Medical Subject Heading) subjects with matching scopes (definitions).
+
+    Parameters
+    ----------
+    query : str
+        Query string to search for in the scope notes of MeSH subjects
+    case_sensitive : bool
+        Select True to perform a case-sensitive search for the query
+    exact_match : bool
+        Select True to require an exact match for the query
+    limit : 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
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "mesh_get_subjects_by_subject_scope_or_definition",
+            "arguments": {
+                "query": query,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["mesh_get_subjects_by_subject_scope_or_definition"]

tooluniverse/tools/odphp_itemlist.py

@@ -0,0 +1,49 @@
+"""
+odphp_itemlist
+
+This tools browses and returns available topics and categories and it is helpful to help narrow a...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def odphp_itemlist(
+    lang: str,
+    type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    This tools browses and returns available topics and categories and it is helpful to help narrow a...
+
+    Parameters
+    ----------
+    lang : str
+        Language code (en or es)
+    type : str
+        topic or category
+    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": "odphp_itemlist", "arguments": {"lang": lang, "type": type}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["odphp_itemlist"]

tooluniverse/tools/odphp_myhealthfinder.py

@@ -0,0 +1,67 @@
+"""
+odphp_myhealthfinder
+
+This tool provides personalized preventive-care recommendations and it is helpful for different a...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def odphp_myhealthfinder(
+    lang: str,
+    age: int,
+    sex: str,
+    pregnant: str,
+    strip_html: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    This tool provides personalized preventive-care recommendations and it is helpful for different a...
+
+    Parameters
+    ----------
+    lang : str
+        Language code (en or es)
+    age : int
+        Age in years (0–120)
+    sex : str
+        Male or Female
+    pregnant : str
+        "Yes" or "No"
+    strip_html : bool
+        If true, also return PlainSections[] with HTML removed for each topic
+    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": "odphp_myhealthfinder",
+            "arguments": {
+                "lang": lang,
+                "age": age,
+                "sex": sex,
+                "pregnant": pregnant,
+                "strip_html": strip_html,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["odphp_myhealthfinder"]

tooluniverse/tools/odphp_outlink_fetch.py

@@ -0,0 +1,59 @@
+"""
+odphp_outlink_fetch
+
+This tool retrieves readable text from ODPHP article links and information sources. This is helpf...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def odphp_outlink_fetch(
+    urls: list[Any],
+    max_chars: int,
+    return_html: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    This tool retrieves readable text from ODPHP article links and information sources. This is helpf...
+
+    Parameters
+    ----------
+    urls : list[Any]
+        1–3 absolute URLs from AccessibleVersion or RelatedItems.Url
+    max_chars : int
+        Optional hard cap on extracted text length (e.g., 5000)
+    return_html : bool
+        If true, also return minimally cleaned HTML
+    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": "odphp_outlink_fetch",
+            "arguments": {
+                "urls": urls,
+                "max_chars": max_chars,
+                "return_html": return_html,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["odphp_outlink_fetch"]

tooluniverse/tools/odphp_topicsearch.py

@@ -0,0 +1,67 @@
+"""
+odphp_topicsearch
+
+Find specific health topics and get their full content. Use when the user mentions a keyword (e.g...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def odphp_topicsearch(
+    lang: str,
+    topicId: str,
+    categoryId: str,
+    keyword: str,
+    strip_html: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Find specific health topics and get their full content. Use when the user mentions a keyword (e.g...
+
+    Parameters
+    ----------
+    lang : str
+        Language code (en or es)
+    topicId : str
+        Comma-separated topic IDs
+    categoryId : str
+        Comma-separated category IDs
+    keyword : str
+        Keyword search for topics
+    strip_html : bool
+        If true, also return PlainSections[] with HTML removed for each topic
+    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": "odphp_topicsearch",
+            "arguments": {
+                "lang": lang,
+                "topicId": topicId,
+                "categoryId": categoryId,
+                "keyword": keyword,
+                "strip_html": strip_html,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["odphp_topicsearch"]

tooluniverse/tools/openalex_literature_search.py

@@ -0,0 +1,67 @@
+"""
+openalex_literature_search
+
+Search for academic literature using OpenAlex API. Retrieves papers with title, abstract, authors...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def openalex_literature_search(
+    search_keywords: str,
+    max_results: Optional[int] = 10,
+    year_from: Optional[int] = None,
+    year_to: Optional[int] = None,
+    open_access: Optional[bool] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search for academic literature using OpenAlex API. Retrieves papers with title, abstract, authors...
+
+    Parameters
+    ----------
+    search_keywords : str
+        Keywords to search for in paper titles, abstracts, and content. Use relevant ...
+    max_results : int
+        Maximum number of papers to retrieve (default: 10, maximum: 200).
+    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., 2023). Optional parameter to limi...
+    open_access : bool
+        Filter for open access papers only. Set to true for open access papers, false...
+    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": "openalex_literature_search",
+            "arguments": {
+                "search_keywords": search_keywords,
+                "max_results": max_results,
+                "year_from": year_from,
+                "year_to": year_to,
+                "open_access": open_access,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["openalex_literature_search"]

tooluniverse/tools/reactome_disease_target_score.py

@@ -0,0 +1,52 @@
+"""
+reactome_disease_target_score
+
+Extract disease-target association scores from Reactome pathway data. This includes pathway-based...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def reactome_disease_target_score(
+    efoId: str,
+    pageSize: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Extract disease-target association scores from Reactome pathway data. This includes pathway-based...
+
+    Parameters
+    ----------
+    efoId : str
+        The EFO (Experimental Factor Ontology) ID of the disease, e.g., 'EFO_0000339'...
+    pageSize : int
+        Number of results per page (default: 100, max: 100)
+    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": "reactome_disease_target_score",
+            "arguments": {"efoId": efoId, "pageSize": pageSize},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["reactome_disease_target_score"]

tooluniverse/tools/search_clinical_trials.py

@@ -0,0 +1,67 @@
+"""
+search_clinical_trials
+
+Search for clinical trials registered on clinicaltrials.gov based on title, conditions, intervent...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def search_clinical_trials(
+    query_term: str,
+    condition: Optional[str] = None,
+    intervention: Optional[str] = None,
+    pageSize: Optional[int] = None,
+    pageToken: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Search for clinical trials registered on clinicaltrials.gov based on title, conditions, intervent...
+
+    Parameters
+    ----------
+    condition : str
+        Query for condition or disease using Essie expression syntax (e.g., 'lung can...
+    intervention : str
+        Query for intervention/treatment using Essie expression syntax (e.g., 'chemot...
+    query_term : str
+        Query for 'other terms' with Essie expression syntax (e.g., 'combination', 'A...
+    pageSize : int
+        Maximum number of studies to return per page (default 10, max 1000).
+    pageToken : str
+        Token to retrieve the next page of results, obtained from the 'nextPageToken'...
+    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": "search_clinical_trials",
+            "arguments": {
+                "condition": condition,
+                "intervention": intervention,
+                "query_term": query_term,
+                "pageSize": pageSize,
+                "pageToken": pageToken,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["search_clinical_trials"]

tooluniverse/tools/visualize_molecule_2d.py

@@ -0,0 +1,83 @@
+"""
+visualize_molecule_2d
+
+Visualize 2D molecular structures using RDKit. Supports SMILES, InChI, molecule names, and variou...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def visualize_molecule_2d(
+    smiles: str,
+    inchi: str,
+    molecule_name: str,
+    width: Optional[int] = 400,
+    height: Optional[int] = 400,
+    output_format: Optional[str] = "png",
+    show_atom_numbers: Optional[bool] = False,
+    show_bond_numbers: Optional[bool] = False,
+    include_stereo: Optional[bool] = True,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Visualize 2D molecular structures using RDKit. Supports SMILES, InChI, molecule names, and variou...
+
+    Parameters
+    ----------
+    smiles : str
+        SMILES string representation of the molecule
+    inchi : str
+        InChI string representation of the molecule
+    molecule_name : str
+        Common name of the molecule (will be resolved to SMILES via PubChem)
+    width : int
+        Width of the visualization in pixels
+    height : int
+        Height of the visualization in pixels
+    output_format : str
+        Output format
+    show_atom_numbers : bool
+        Whether to show atom numbers
+    show_bond_numbers : bool
+        Whether to show bond numbers
+    include_stereo : bool
+        Whether to include stereochemistry information
+    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": "visualize_molecule_2d",
+            "arguments": {
+                "smiles": smiles,
+                "inchi": inchi,
+                "molecule_name": molecule_name,
+                "width": width,
+                "height": height,
+                "output_format": output_format,
+                "show_atom_numbers": show_atom_numbers,
+                "show_bond_numbers": show_bond_numbers,
+                "include_stereo": include_stereo,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["visualize_molecule_2d"]

tooluniverse/tools/visualize_molecule_3d.py

@@ -0,0 +1,91 @@
+"""
+visualize_molecule_3d
+
+Visualize 3D molecular structures using RDKit and py3Dmol. Supports SMILES, MOL files, SDF conten...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def visualize_molecule_3d(
+    smiles: str,
+    mol_content: str,
+    sdf_content: str,
+    style: Optional[str] = "stick",
+    color_scheme: Optional[str] = "default",
+    width: Optional[int] = 800,
+    height: Optional[int] = 600,
+    show_hydrogens: Optional[bool] = True,
+    show_surface: Optional[bool] = False,
+    generate_conformers: Optional[bool] = True,
+    conformer_count: Optional[int] = 1,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Visualize 3D molecular structures using RDKit and py3Dmol. Supports SMILES, MOL files, SDF conten...
+
+    Parameters
+    ----------
+    smiles : str
+        SMILES string representation of the molecule
+    mol_content : str
+        MOL file content as string
+    sdf_content : str
+        SDF file content as string
+    style : str
+        Visualization style
+    color_scheme : str
+        Color scheme for the molecule
+    width : int
+        Width of the visualization in pixels
+    height : int
+        Height of the visualization in pixels
+    show_hydrogens : bool
+        Whether to show hydrogen atoms
+    show_surface : bool
+        Whether to show molecular surface
+    generate_conformers : bool
+        Whether to generate multiple conformers
+    conformer_count : int
+        Number of conformers to generate
+    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": "visualize_molecule_3d",
+            "arguments": {
+                "smiles": smiles,
+                "mol_content": mol_content,
+                "sdf_content": sdf_content,
+                "style": style,
+                "color_scheme": color_scheme,
+                "width": width,
+                "height": height,
+                "show_hydrogens": show_hydrogens,
+                "show_surface": show_surface,
+                "generate_conformers": generate_conformers,
+                "conformer_count": conformer_count,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["visualize_molecule_3d"]