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

tooluniverse/tools/get_cftime_info.py

@@ -0,0 +1,44 @@
+"""
+get_cftime_info
+
+Get information about the cftime package. Time-handling functionality from netcdf4-python
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_cftime_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the cftime package. Time-handling functionality from netcdf4-python
+
+    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": "get_cftime_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_cftime_info"]

tooluniverse/tools/get_chem_comp_audit_info.py

@@ -0,0 +1,46 @@
+"""
+get_chem_comp_audit_info
+
+Fetch audit history for a chemical component: action type, date, details, ordinal, and processing...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_chem_comp_audit_info(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Fetch audit history for a chemical component: action type, date, details, ordinal, and processing...
+
+    Parameters
+    ----------
+    pdb_id : str
+        Chemical component ID to retrieve audit info for
+    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": "get_chem_comp_audit_info", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_chem_comp_audit_info"]

tooluniverse/tools/get_chem_comp_charge_and_ambiguity.py

@@ -0,0 +1,46 @@
+"""
+get_chem_comp_charge_and_ambiguity
+
+Retrieve the formal charge and ambiguity flag of a chemical component.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_chem_comp_charge_and_ambiguity(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve the formal charge and ambiguity flag of a chemical component.
+
+    Parameters
+    ----------
+    pdb_id : str
+        Chemical component ID to query charge and ambiguity
+    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": "get_chem_comp_charge_and_ambiguity", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_chem_comp_charge_and_ambiguity"]

tooluniverse/tools/get_chembl_webresource_client_info.py

@@ -0,0 +1,44 @@
+"""
+get_chembl_webresource_client_info
+
+Get information about the chembl-webresource-client package. Python client for ChEMBL web services
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_chembl_webresource_client_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the chembl-webresource-client package. Python client for ChEMBL web services
+
+    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": "get_chembl_webresource_client_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_chembl_webresource_client_info"]

tooluniverse/tools/get_citation_info_by_pdb_id.py

@@ -0,0 +1,46 @@
+"""
+get_citation_info_by_pdb_id
+
+Retrieve citation information (authors, journal, year) for a given PDB structure.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_citation_info_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve citation information (authors, journal, year) for a given PDB structure.
+
+    Parameters
+    ----------
+    pdb_id : str
+        4-character RCSB PDB 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": "get_citation_info_by_pdb_id", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_citation_info_by_pdb_id"]

tooluniverse/tools/get_clair3_info.py

@@ -0,0 +1,46 @@
+"""
+get_clair3_info
+
+Get comprehensive information about Clair3 – variant calling for long-read sequencing
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_clair3_info(
+    info_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about Clair3 – variant calling for long-read sequencing
+
+    Parameters
+    ----------
+    info_type : str
+        Type of information to retrieve about Clair3
+    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": "get_clair3_info", "arguments": {"info_type": info_type}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_clair3_info"]

tooluniverse/tools/get_clinical_trial_conditions_and_interventions.py

@@ -0,0 +1,55 @@
+"""
+get_clinical_trial_conditions_and_interventions
+
+Retrieves the list of conditions or diseases and the interventions and arm groups that the clinic...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_clinical_trial_conditions_and_interventions(
+    nct_ids: list[Any],
+    condition_and_intervention: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieves the list of conditions or diseases and the interventions and arm groups that the clinic...
+
+    Parameters
+    ----------
+    nct_ids : list[Any]
+        List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).
+    condition_and_intervention : str
+        Placeholder.
+    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": "get_clinical_trial_conditions_and_interventions",
+            "arguments": {
+                "nct_ids": nct_ids,
+                "condition_and_intervention": condition_and_intervention,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_clinical_trial_conditions_and_interventions"]

tooluniverse/tools/get_clinical_trial_descriptions.py

@@ -0,0 +1,52 @@
+"""
+get_clinical_trial_descriptions
+
+Retrieves detailed identification information for trials, including titles, phases, and descripti...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_clinical_trial_descriptions(
+    nct_ids: list[Any],
+    description_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieves detailed identification information for trials, including titles, phases, and descripti...
+
+    Parameters
+    ----------
+    nct_ids : list[Any]
+        List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).
+    description_type : str
+        Type of information to retrieve. Options are 'brief' for brief descriptions o...
+    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": "get_clinical_trial_descriptions",
+            "arguments": {"nct_ids": nct_ids, "description_type": description_type},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_clinical_trial_descriptions"]

tooluniverse/tools/get_clinical_trial_eligibility_criteria.py

@@ -0,0 +1,55 @@
+"""
+get_clinical_trial_eligibility_criteria
+
+Retrieves the eligibility criteria for the clinical trials, using their NCT IDs.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_clinical_trial_eligibility_criteria(
+    nct_ids: list[Any],
+    eligibility_criteria: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieves the eligibility criteria for the clinical trials, using their NCT IDs.
+
+    Parameters
+    ----------
+    nct_ids : list[Any]
+        List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).
+    eligibility_criteria : str
+        Placeholder.
+    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": "get_clinical_trial_eligibility_criteria",
+            "arguments": {
+                "nct_ids": nct_ids,
+                "eligibility_criteria": eligibility_criteria,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_clinical_trial_eligibility_criteria"]

tooluniverse/tools/get_clinical_trial_locations.py

@@ -0,0 +1,52 @@
+"""
+get_clinical_trial_locations
+
+Retrieves the locations where the clinical trials are being conducted, using their NCT IDs.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_clinical_trial_locations(
+    nct_ids: list[Any],
+    location: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieves the locations where the clinical trials are being conducted, using their NCT IDs.
+
+    Parameters
+    ----------
+    nct_ids : list[Any]
+        List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).
+    location : str
+        Placeholder.
+    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": "get_clinical_trial_locations",
+            "arguments": {"nct_ids": nct_ids, "location": location},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_clinical_trial_locations"]

tooluniverse/tools/get_clinical_trial_outcome_measures.py

@@ -0,0 +1,52 @@
+"""
+get_clinical_trial_outcome_measures
+
+Retrieves the outcome measures for the clinical trials, using their NCT IDs.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_clinical_trial_outcome_measures(
+    nct_ids: list[Any],
+    outcome_measures: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieves the outcome measures for the clinical trials, using their NCT IDs.
+
+    Parameters
+    ----------
+    nct_ids : list[Any]
+        List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).
+    outcome_measures : str
+        Decides whether to retrieve primary, secondary, or all outcome measures. Opti...
+    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": "get_clinical_trial_outcome_measures",
+            "arguments": {"nct_ids": nct_ids, "outcome_measures": outcome_measures},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_clinical_trial_outcome_measures"]

tooluniverse/tools/get_clinical_trial_references.py

@@ -0,0 +1,52 @@
+"""
+get_clinical_trial_references
+
+Retrieves the references (if any) for the clinical trials, using their NCT IDs.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_clinical_trial_references(
+    nct_ids: list[Any],
+    references: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieves the references (if any) for the clinical trials, using their NCT IDs.
+
+    Parameters
+    ----------
+    nct_ids : list[Any]
+        List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).
+    references : str
+        Placeholder.
+    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": "get_clinical_trial_references",
+            "arguments": {"nct_ids": nct_ids, "references": references},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_clinical_trial_references"]

tooluniverse/tools/get_clinical_trial_status_and_dates.py

@@ -0,0 +1,52 @@
+"""
+get_clinical_trial_status_and_dates
+
+Retrieves trial status and start and completion dates, using their NCT IDs.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_clinical_trial_status_and_dates(
+    nct_ids: list[Any],
+    status_and_date: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieves trial status and start and completion dates, using their NCT IDs.
+
+    Parameters
+    ----------
+    nct_ids : list[Any]
+        List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).
+    status_and_date : str
+        Placeholder.
+    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": "get_clinical_trial_status_and_dates",
+            "arguments": {"nct_ids": nct_ids, "status_and_date": status_and_date},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_clinical_trial_status_and_dates"]

tooluniverse/tools/get_cobra_info.py

@@ -0,0 +1,46 @@
+"""
+get_cobra_info
+
+Get comprehensive information about COBRApy – constraint-based metabolic modeling
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_cobra_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about COBRApy – constraint-based metabolic modeling
+
+    Parameters
+    ----------
+    include_examples : bool
+        Whether to include usage examples and quick start guide
+    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": "get_cobra_info", "arguments": {"include_examples": include_examples}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_cobra_info"]