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

tooluniverse/tools/FDA_retrieve_drug_name_by_device_use.py

@@ -0,0 +1,59 @@
+"""
+FDA_retrieve_drug_name_by_device_use
+
+Retrieve the drug name based on the intended use of the device.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def FDA_retrieve_drug_name_by_device_use(
+    intended_use_of_the_device: str,
+    limit: Optional[int] = None,
+    skip: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve the drug name based on the intended use of the device.
+
+    Parameters
+    ----------
+    intended_use_of_the_device : str
+        The intended use of the device.
+    limit : int
+        The number of records to return.
+    skip : int
+        The number of records to skip.
+    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": "FDA_retrieve_drug_name_by_device_use",
+            "arguments": {
+                "intended_use_of_the_device": intended_use_of_the_device,
+                "limit": limit,
+                "skip": skip,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["FDA_retrieve_drug_name_by_device_use"]

tooluniverse/tools/FDA_retrieve_drug_names_by_patient_medication_info.py

@@ -0,0 +1,55 @@
+"""
+FDA_retrieve_drug_names_by_patient_medication_info
+
+Retrieve drug names based on patient medication information, which is about safe use of the drug.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def FDA_retrieve_drug_names_by_patient_medication_info(
+    patient_info: str,
+    limit: Optional[int] = None,
+    skip: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve drug names based on patient medication information, which is about safe use of the drug.
+
+    Parameters
+    ----------
+    patient_info : str
+        Information or instructions to patients about safe use of the drug product.
+    limit : int
+        The number of records to return.
+    skip : int
+        The number of records to skip.
+    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": "FDA_retrieve_drug_names_by_patient_medication_info",
+            "arguments": {"patient_info": patient_info, "limit": limit, "skip": skip},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["FDA_retrieve_drug_names_by_patient_medication_info"]

tooluniverse/tools/FDA_retrieve_patient_medication_info_by_drug_name.py

@@ -0,0 +1,55 @@
+"""
+FDA_retrieve_patient_medication_info_by_drug_name
+
+Retrieve patient medication information (which is about safe use of the drug) based on drug names.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def FDA_retrieve_patient_medication_info_by_drug_name(
+    drug_name: str,
+    limit: Optional[int] = None,
+    skip: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve patient medication information (which is about safe use of the drug) based on drug names.
+
+    Parameters
+    ----------
+    drug_name : str
+        The name of the drug.
+    limit : int
+        The number of records to return.
+    skip : int
+        The number of records to skip.
+    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": "FDA_retrieve_patient_medication_info_by_drug_name",
+            "arguments": {"drug_name": drug_name, "limit": limit, "skip": skip},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["FDA_retrieve_patient_medication_info_by_drug_name"]

tooluniverse/tools/Fatcat_search_scholar.py

@@ -0,0 +1,52 @@
+"""
+Fatcat_search_scholar
+
+Search Internet Archive Scholar via Fatcat releases search. Fatcat is the underlying database pow...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Fatcat_search_scholar(
+    query: str,
+    max_results: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search Internet Archive Scholar via Fatcat releases search. Fatcat is the underlying database pow...
+
+    Parameters
+    ----------
+    query : str
+        Search query for Fatcat releases. Use keywords to search across titles, abstr...
+    max_results : int
+        Maximum number of results to return. Default is 10, maximum is 100.
+    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": "Fatcat_search_scholar",
+            "arguments": {"query": query, "max_results": max_results},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Fatcat_search_scholar"]

tooluniverse/tools/Finish.py

@@ -0,0 +1,44 @@
+"""
+Finish
+
+Indicate the end of multi-step reasoning.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Finish(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Indicate the end of multi-step reasoning.
+
+    Parameters
+    ----------
+    No parameters
+    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": "Finish", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Finish"]

tooluniverse/tools/GIN_Guidelines_Search.py

@@ -0,0 +1,52 @@
+"""
+GIN_Guidelines_Search
+
+Search Guidelines International Network (GIN) guidelines database. GIN maintains the world's larg...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GIN_Guidelines_Search(
+    query: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search Guidelines International Network (GIN) guidelines database. GIN maintains the world's larg...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition, treatment, or clinical topic to search for in GIN guidelin...
+    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
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "GIN_Guidelines_Search",
+            "arguments": {"query": query, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GIN_Guidelines_Search"]

tooluniverse/tools/GO_get_annotations_for_gene.py

@@ -0,0 +1,46 @@
+"""
+GO_get_annotations_for_gene
+
+Finds all GO annotations for a specific gene/protein using GOlr search.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GO_get_annotations_for_gene(
+    gene_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Finds all GO annotations for a specific gene/protein using GOlr search.
+
+    Parameters
+    ----------
+    gene_id : str
+        A gene identifier such as gene symbol (e.g., 'TP53') or database ID.
+    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": "GO_get_annotations_for_gene", "arguments": {"gene_id": gene_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GO_get_annotations_for_gene"]

tooluniverse/tools/GO_get_genes_for_term.py

@@ -0,0 +1,55 @@
+"""
+GO_get_genes_for_term
+
+Finds all genes/proteins associated with a specific Gene Ontology term using the Biolink API.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GO_get_genes_for_term(
+    id: str,
+    taxon: str,
+    rows: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Finds all genes/proteins associated with a specific Gene Ontology term using the Biolink API.
+
+    Parameters
+    ----------
+    id : str
+        The standard GO term ID, e.g., 'GO:0006915'.
+    taxon : str
+        Optional species filter using a NCBI taxon ID. For example, Human is 'NCBITax...
+    rows : int
+        The number of genes to return. Default is 100.
+    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": "GO_get_genes_for_term",
+            "arguments": {"id": id, "taxon": taxon, "rows": rows},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GO_get_genes_for_term"]

tooluniverse/tools/GO_get_term_by_id.py

@@ -0,0 +1,46 @@
+"""
+GO_get_term_by_id
+
+Retrieves basic GO term information by ID using GOlr search.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GO_get_term_by_id(
+    id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieves basic GO term information by ID using GOlr search.
+
+    Parameters
+    ----------
+    id : str
+        The standard GO term ID, e.g., 'GO:0006915' for apoptotic process.
+    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": "GO_get_term_by_id", "arguments": {"id": id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GO_get_term_by_id"]

tooluniverse/tools/GO_get_term_details.py

@@ -0,0 +1,46 @@
+"""
+GO_get_term_details
+
+Retrieves detailed information for a specific GO ID using the Biolink API, including definition, ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GO_get_term_details(
+    id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieves detailed information for a specific GO ID using the Biolink API, including definition, ...
+
+    Parameters
+    ----------
+    id : str
+        The standard GO term ID, e.g., 'GO:0006915' for apoptotic process.
+    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": "GO_get_term_details", "arguments": {"id": id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GO_get_term_details"]

tooluniverse/tools/GO_search_terms.py

@@ -0,0 +1,46 @@
+"""
+GO_search_terms
+
+Searches for Gene Ontology (GO) terms by a keyword using the GOlr search engine. Returns GO terms...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GO_search_terms(
+    query: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Searches for Gene Ontology (GO) terms by a keyword using the GOlr search engine. Returns GO terms...
+
+    Parameters
+    ----------
+    query : str
+        The keyword to search for, e.g., 'apoptosis' or 'kinase activity'.
+    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": "GO_search_terms", "arguments": {"query": query}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GO_search_terms"]

tooluniverse/tools/GWAS_search_associations_by_gene.py

@@ -0,0 +1,52 @@
+"""
+GWAS_search_associations_by_gene
+
+Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GWAS_search_associations_by_gene(
+    gene_name: str,
+    size: Optional[int] = 5,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene symbol (e.g., BRCA1).
+    size : int
+        Max associations 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": "GWAS_search_associations_by_gene",
+            "arguments": {"gene_name": gene_name, "size": size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GWAS_search_associations_by_gene"]

tooluniverse/tools/HAL_search_archive.py

@@ -0,0 +1,52 @@
+"""
+HAL_search_archive
+
+Search the French HAL open archive via its public API. Returns documents with title, authors, yea...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HAL_search_archive(
+    query: str,
+    max_results: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search the French HAL open archive via its public API. Returns documents with title, authors, yea...
+
+    Parameters
+    ----------
+    query : str
+        Search query for HAL archive. Supports Lucene syntax for advanced queries.
+    max_results : int
+        Maximum number of documents to return. Default is 10, maximum is 100.
+    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": "HAL_search_archive",
+            "arguments": {"query": query, "max_results": max_results},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HAL_search_archive"]