tooluniverse 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.whl

tooluniverse/tools/expression_atlas_disease_target_score.py

@@ -0,0 +1,52 @@
+"""
+expression_atlas_disease_target_score
+
+Extract disease-target association scores from Expression Atlas. This provides gene expression data.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def expression_atlas_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 Expression Atlas. This provides gene expression data.
+
+    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": "expression_atlas_disease_target_score",
+            "arguments": {"efoId": efoId, "pageSize": pageSize},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["expression_atlas_disease_target_score"]

tooluniverse/tools/extract_clinical_trial_adverse_events.py

@@ -0,0 +1,59 @@
+"""
+extract_clinical_trial_adverse_events
+
+Extracts detailed adverse event results from clinicaltrials.gov, using their NCT IDs.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def extract_clinical_trial_adverse_events(
+    nct_ids: list[Any],
+    organ_systems: Optional[list[Any]] = None,
+    adverse_event_type: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extracts detailed adverse event results from clinicaltrials.gov, using their NCT IDs.
+
+    Parameters
+    ----------
+    nct_ids : list[Any]
+        List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).
+    organ_systems : list[Any]
+        List of organs or organ systems to filter adverse events (see enum for exact ...
+    adverse_event_type : str
+        Type of adverse events to extract. Options are 'serious' (serious adverse eve...
+    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": "extract_clinical_trial_adverse_events",
+            "arguments": {
+                "nct_ids": nct_ids,
+                "organ_systems": organ_systems,
+                "adverse_event_type": adverse_event_type,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["extract_clinical_trial_adverse_events"]

tooluniverse/tools/extract_clinical_trial_outcomes.py

@@ -0,0 +1,52 @@
+"""
+extract_clinical_trial_outcomes
+
+Extracts detailed trial outcome results (e.g., overall survival months, p-values, etc.) from clin...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def extract_clinical_trial_outcomes(
+    nct_ids: list[Any],
+    outcome_measure: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extracts detailed trial outcome results (e.g., overall survival months, p-values, etc.) from clin...
+
+    Parameters
+    ----------
+    nct_ids : list[Any]
+        List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).
+    outcome_measure : str
+        Outcome measure to extract. Example values include 'primary' (primary outcome...
+    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": "extract_clinical_trial_outcomes",
+            "arguments": {"nct_ids": nct_ids, "outcome_measure": outcome_measure},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["extract_clinical_trial_outcomes"]

tooluniverse/tools/genomics_england_disease_target_score.py

@@ -0,0 +1,52 @@
+"""
+genomics_england_disease_target_score
+
+Extract disease-target association scores from Genomics England data. This includes clinical geno...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def genomics_england_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 Genomics England data. This includes clinical geno...
+
+    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": "genomics_england_disease_target_score",
+            "arguments": {"efoId": efoId, "pageSize": pageSize},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["genomics_england_disease_target_score"]

tooluniverse/tools/get_HPO_ID_by_phenotype.py

@@ -0,0 +1,55 @@
+"""
+get_HPO_ID_by_phenotype
+
+Retrieve the HPO ID of a phenotype or symptom.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_HPO_ID_by_phenotype(
+    query: str,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve the HPO ID of a phenotype or symptom.
+
+    Parameters
+    ----------
+    query : str
+        One query phenotype or symptom.
+    limit : int
+        Number of entries to fetch.
+    offset : int
+        Number of initial entries 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": "get_HPO_ID_by_phenotype",
+            "arguments": {"query": query, "limit": limit, "offset": offset},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_HPO_ID_by_phenotype"]

tooluniverse/tools/get_albumentations_info.py

@@ -0,0 +1,44 @@
+"""
+get_albumentations_info
+
+Get information about the albumentations package. Fast image augmentation library
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_albumentations_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the albumentations package. Fast image augmentation library
+
+    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_albumentations_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_albumentations_info"]

tooluniverse/tools/get_altair_info.py

@@ -0,0 +1,44 @@
+"""
+get_altair_info
+
+Get information about the altair package. Declarative statistical visualization library
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_altair_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the altair package. Declarative statistical visualization library
+
+    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_altair_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_altair_info"]

tooluniverse/tools/get_anndata_info.py

@@ -0,0 +1,49 @@
+"""
+get_anndata_info
+
+Get comprehensive information about AnnData – annotated data for computational biology
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_anndata_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about AnnData – annotated data for computational biology
+
+    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_anndata_info",
+            "arguments": {"include_examples": include_examples},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_anndata_info"]

tooluniverse/tools/get_arboreto_info.py

@@ -0,0 +1,46 @@
+"""
+get_arboreto_info
+
+Get comprehensive information about Arboreto – gene regulatory network inference
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_arboreto_info(
+    info_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about Arboreto – gene regulatory network inference
+
+    Parameters
+    ----------
+    info_type : str
+        Type of information to retrieve about Arboreto
+    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_arboreto_info", "arguments": {"info_type": info_type}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_arboreto_info"]

tooluniverse/tools/get_arxiv_info.py

@@ -0,0 +1,46 @@
+"""
+get_arxiv_info
+
+Get comprehensive information about arxiv – access to arXiv preprint repository
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_arxiv_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about arxiv – access to arXiv preprint repository
+
+    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_arxiv_info", "arguments": {"include_examples": include_examples}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_arxiv_info"]

tooluniverse/tools/get_ase_info.py

@@ -0,0 +1,46 @@
+"""
+get_ase_info
+
+Get comprehensive information about ASE (Atomic Simulation Environment) – a toolkit for building,...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_ase_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about ASE (Atomic Simulation Environment) – a toolkit for building,...
+
+    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_ase_info", "arguments": {"include_examples": include_examples}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_ase_info"]

tooluniverse/tools/get_assembly_info_by_pdb_id.py

@@ -0,0 +1,46 @@
+"""
+get_assembly_info_by_pdb_id
+
+Retrieve all associated biological assembly details for a given PDB structure.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_assembly_info_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve all associated biological assembly details 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_assembly_info_by_pdb_id", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_assembly_info_by_pdb_id"]

tooluniverse/tools/get_assembly_summary.py

@@ -0,0 +1,46 @@
+"""
+get_assembly_summary
+
+Get key assembly composition and symmetry summary for an assembly associated with a PDB entry.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_assembly_summary(
+    assembly_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get key assembly composition and symmetry summary for an assembly associated with a PDB entry.
+
+    Parameters
+    ----------
+    assembly_id : str
+        Assembly ID in format 'PDBID-assemblyNumber' (e.g., '1A8M-1')
+    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_assembly_summary", "arguments": {"assembly_id": assembly_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_assembly_summary"]

tooluniverse/tools/get_astropy_info.py

@@ -0,0 +1,44 @@
+"""
+get_astropy_info
+
+Get information about the astropy package. Astronomy and astrophysics library
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_astropy_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the astropy package. Astronomy and astrophysics library
+
+    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_astropy_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_astropy_info"]