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

tooluniverse/tools/convert_to_markdown.py

@@ -0,0 +1,59 @@
+"""
+convert_to_markdown
+
+Convert a resource described by an http:, https:, file: or data: URI to markdown.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def convert_to_markdown(
+    uri: str,
+    output_path: Optional[str] = None,
+    enable_plugins: Optional[bool] = False,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Convert a resource described by an http:, https:, file: or data: URI to markdown.
+
+    Parameters
+    ----------
+    uri : str
+        URI of the resource to convert (supports http:, https:, file:, data: URIs)
+    output_path : str
+        Optional output file path
+    enable_plugins : bool
+        Enable 3rd-party plugins
+    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": "convert_to_markdown",
+            "arguments": {
+                "uri": uri,
+                "output_path": output_path,
+                "enable_plugins": enable_plugins,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["convert_to_markdown"]

tooluniverse/tools/dbSNP_get_variant_by_rsid.py

@@ -0,0 +1,46 @@
+"""
+dbSNP_get_variant_by_rsid
+
+Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def dbSNP_get_variant_by_rsid(
+    rsid: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).
+
+    Parameters
+    ----------
+    rsid : str
+        rsID without 'rs' prefix or with (e.g., rs699 or 699).
+    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": "dbSNP_get_variant_by_rsid", "arguments": {"rsid": rsid}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["dbSNP_get_variant_by_rsid"]

tooluniverse/tools/dict_search.py

@@ -0,0 +1,67 @@
+"""
+dict_search
+
+Search the DICTrank dataset for drug-induced cardiotoxicity (DICT) risk information by trade name...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def dict_search(
+    query: str,
+    search_fields: list[Any],
+    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]:
+    """
+    Search the DICTrank dataset for drug-induced cardiotoxicity (DICT) risk information by trade name...
+
+    Parameters
+    ----------
+    query : str
+        Free-text query (e.g. 'ZYPREXA', 'Olanzapine').
+    search_fields : list[Any]
+        Columns to search. Choose from: 'Trade Name', 'Generic/Proper Name(s)', 'Acti...
+    case_sensitive : bool
+        Match text with exact case if true.
+    exact_match : bool
+        Field value must equal query exactly if true; otherwise substring match.
+    limit : int
+        Maximum number of rows 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": "dict_search",
+            "arguments": {
+                "query": query,
+                "search_fields": search_fields,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["dict_search"]

tooluniverse/tools/dili_search.py

@@ -0,0 +1,67 @@
+"""
+dili_search
+
+Search the DILIrank dataset for drug-induced liver-injury (DILI) risk information by compound nam...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def dili_search(
+    query: str,
+    search_fields: list[Any],
+    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]:
+    """
+    Search the DILIrank dataset for drug-induced liver-injury (DILI) risk information by compound nam...
+
+    Parameters
+    ----------
+    query : str
+        Free-text query (e.g. 'acetaminophen').
+    search_fields : list[Any]
+        Columns to search. Choose from: 'Compound Name'.
+    case_sensitive : bool
+        Match text with exact case if true.
+    exact_match : bool
+        Field value must equal query exactly if true; otherwise substring match.
+    limit : int
+        Maximum number of rows 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": "dili_search",
+            "arguments": {
+                "query": query,
+                "search_fields": search_fields,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["dili_search"]

tooluniverse/tools/diqt_search.py

@@ -0,0 +1,67 @@
+"""
+diqt_search
+
+Search the DIQTA dataset for drug-induced QT-interval prolongation risk information by generic na...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def diqt_search(
+    query: str,
+    search_fields: list[Any],
+    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]:
+    """
+    Search the DIQTA dataset for drug-induced QT-interval prolongation risk information by generic na...
+
+    Parameters
+    ----------
+    query : str
+        Free-text query (e.g. 'Astemizole', 'DB00637').
+    search_fields : list[Any]
+        Columns to search. Choose from: 'Generic/Proper Name(s)', 'DrugBank ID'.
+    case_sensitive : bool
+        Match text with exact case if true.
+    exact_match : bool
+        Field value must equal query exactly if true; otherwise substring match.
+    limit : int
+        Maximum number of rows 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": "diqt_search",
+            "arguments": {
+                "query": query,
+                "search_fields": search_fields,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["diqt_search"]

tooluniverse/tools/disease_target_score.py

@@ -0,0 +1,59 @@
+"""
+disease_target_score
+
+Extract disease-target association scores from a specific data source using GraphQL API. This too...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def disease_target_score(
+    efoId: str,
+    datasourceId: 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 a specific data source using GraphQL API. This too...
+
+    Parameters
+    ----------
+    efoId : str
+        The EFO (Experimental Factor Ontology) ID of the disease, e.g., 'EFO_0000339'...
+    datasourceId : str
+        The datasource ID to extract scores from. Available options: 'chembl', 'eva',...
+    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": "disease_target_score",
+            "arguments": {
+                "efoId": efoId,
+                "datasourceId": datasourceId,
+                "pageSize": pageSize,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["disease_target_score"]

tooluniverse/tools/drugbank_filter_drugs_by_name.py

@@ -0,0 +1,55 @@
+"""
+drugbank_filter_drugs_by_name
+
+Filter DrugBank records based on conditions applied to drug names. For example, find drugs whose ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def drugbank_filter_drugs_by_name(
+    condition: str,
+    value: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Filter DrugBank records based on conditions applied to drug names. For example, find drugs whose ...
+
+    Parameters
+    ----------
+    condition : str
+        The condition to apply for filtering.
+    value : str
+        The value to use with the condition (e.g., 'Aspirin' for 'starts_with'). Requ...
+    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": "drugbank_filter_drugs_by_name",
+            "arguments": {"condition": condition, "value": value, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["drugbank_filter_drugs_by_name"]

tooluniverse/tools/drugbank_full_search.py

@@ -0,0 +1,67 @@
+"""
+drugbank_full_search
+
+Search the cleaned DrugBank dataframe (one row per drug) by ID, common name, or synonym. Returns ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def drugbank_full_search(
+    query: str,
+    search_fields: list[Any],
+    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]:
+    """
+    Search the cleaned DrugBank dataframe (one row per drug) by ID, common name, or synonym. Returns ...
+
+    Parameters
+    ----------
+    query : str
+        Free-text query (e.g. 'DB00945', 'acetylsalicylic', 'Acarbosa').
+    search_fields : list[Any]
+        Columns to search in. Choose from: 'drugbank_id', 'name', 'synonyms'.
+    case_sensitive : bool
+        Match text with exact case if true.
+    exact_match : bool
+        Field value must equal query exactly if true; otherwise substring match.
+    limit : int
+        Max number of rows 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": "drugbank_full_search",
+            "arguments": {
+                "query": query,
+                "search_fields": search_fields,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["drugbank_full_search"]

tooluniverse/tools/drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id.py

@@ -0,0 +1,63 @@
+"""
+drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id
+
+Get basic drug information including name, description, CAS number, and approval status by drug n...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id(
+    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]:
+    """
+    Get basic drug information including name, description, CAS number, and approval status by drug n...
+
+    Parameters
+    ----------
+    query : str
+        Drug name or DrugBank ID to search for
+    case_sensitive : bool
+        Select True to perform a case-sensitive search
+    exact_match : bool
+        Select True to require an exact match with the queried name or ID
+    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": "drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id",
+            "arguments": {
+                "query": query,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id"]

tooluniverse/tools/drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id.py

@@ -0,0 +1,63 @@
+"""
+drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id
+
+Get drug chemical properties including molecular formula, weight, and structure by drug name or D...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id(
+    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]:
+    """
+    Get drug chemical properties including molecular formula, weight, and structure by drug name or D...
+
+    Parameters
+    ----------
+    query : str
+        Drug name or Drugbank ID to search for
+    case_sensitive : bool
+        Select True to perform a case-sensitive search
+    exact_match : bool
+        Select True to require an exact match
+    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": "drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id",
+            "arguments": {
+                "query": query,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id"]

tooluniverse/tools/drugbank_get_drug_interactions_by_drug_name_or_drugbank_id.py

@@ -0,0 +1,63 @@
+"""
+drugbank_get_drug_interactions_by_drug_name_or_drugbank_id
+
+Get drug interactions and contraindications by drug name or DrugBank ID.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def drugbank_get_drug_interactions_by_drug_name_or_drugbank_id(
+    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]:
+    """
+    Get drug interactions and contraindications by drug name or DrugBank ID.
+
+    Parameters
+    ----------
+    query : str
+        Drug name to search for interactions
+    case_sensitive : bool
+        Select True to perform a case-sensitive search
+    exact_match : bool
+        Select True to require an exact match
+    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": "drugbank_get_drug_interactions_by_drug_name_or_drugbank_id",
+            "arguments": {
+                "query": query,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["drugbank_get_drug_interactions_by_drug_name_or_drugbank_id"]