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

tooluniverse/tools/get_viennarna_info.py

@@ -0,0 +1,49 @@
+"""
+get_viennarna_info
+
+Get comprehensive information about ViennaRNA – RNA structure prediction and analysis
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_viennarna_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about ViennaRNA – RNA structure prediction and analysis
+
+    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_viennarna_info",
+            "arguments": {"include_examples": include_examples},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_viennarna_info"]

tooluniverse/tools/get_webpage_text_from_url.py

@@ -0,0 +1,52 @@
+"""
+get_webpage_text_from_url
+
+Render a URL as PDF and extract its text (JavaScript supported).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_webpage_text_from_url(
+    url: str,
+    timeout: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Render a URL as PDF and extract its text (JavaScript supported).
+
+    Parameters
+    ----------
+    url : str
+        Webpage URL to fetch and render
+    timeout : int
+        Request timeout in seconds
+    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_webpage_text_from_url",
+            "arguments": {"url": url, "timeout": timeout},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_webpage_text_from_url"]

tooluniverse/tools/get_webpage_title.py

@@ -0,0 +1,49 @@
+"""
+get_webpage_title
+
+Fetch a webpage and return the content of its <title> tag.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_webpage_title(
+    url: str,
+    timeout: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Fetch a webpage and return the content of its <title> tag.
+
+    Parameters
+    ----------
+    url : str
+        HTTP or HTTPS URL to fetch (e.g. https://www.example.com)
+    timeout : int
+        Request timeout in seconds
+    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_webpage_title", "arguments": {"url": url, "timeout": timeout}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_webpage_title"]

tooluniverse/tools/get_xarray_info.py

@@ -0,0 +1,44 @@
+"""
+get_xarray_info
+
+Get information about the xarray package. N-D labeled arrays and datasets in Python
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_xarray_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the xarray package. N-D labeled arrays and datasets in 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_xarray_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_xarray_info"]

tooluniverse/tools/get_xesmf_info.py

@@ -0,0 +1,44 @@
+"""
+get_xesmf_info
+
+Get information about the xesmf package. Universal regridder for geospatial data
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_xesmf_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the xesmf package. Universal regridder for geospatial data
+
+    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_xesmf_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_xesmf_info"]

tooluniverse/tools/get_xgboost_info.py

@@ -0,0 +1,44 @@
+"""
+get_xgboost_info
+
+Get information about the xgboost package. Optimized gradient boosting framework
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_xgboost_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the xgboost package. Optimized gradient boosting framework
+
+    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_xgboost_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_xgboost_info"]

tooluniverse/tools/get_zarr_info.py

@@ -0,0 +1,44 @@
+"""
+get_zarr_info
+
+Get information about the zarr package. Chunked, compressed, N-dimensional arrays
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_zarr_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the zarr package. Chunked, compressed, N-dimensional arrays
+
+    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_zarr_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_zarr_info"]

tooluniverse/tools/gnomAD_query_variant.py

@@ -0,0 +1,52 @@
+"""
+gnomAD_query_variant
+
+Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gnomAD_query_variant(
+    variant_id: str,
+    dataset: Optional[str] = "gnomad_r4",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).
+
+    Parameters
+    ----------
+    variant_id : str
+        Variant ID like '1-230710048-A-G'.
+    dataset : str
+        Dataset ID (e.g., gnomad_r4).
+    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": "gnomAD_query_variant",
+            "arguments": {"variant_id": variant_id, "dataset": dataset},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gnomAD_query_variant"]

tooluniverse/tools/gwas_get_association_by_id.py

@@ -0,0 +1,49 @@
+"""
+gwas_get_association_by_id
+
+Get a specific GWAS association by its unique identifier.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_get_association_by_id(
+    association_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get a specific GWAS association by its unique identifier.
+
+    Parameters
+    ----------
+    association_id : str
+        GWAS association identifier
+    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_get_association_by_id",
+            "arguments": {"association_id": association_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_get_association_by_id"]

tooluniverse/tools/gwas_get_associations_for_snp.py

@@ -0,0 +1,67 @@
+"""
+gwas_get_associations_for_snp
+
+Get all associations for a specific SNP with optional sorting.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_get_associations_for_snp(
+    rs_id: str,
+    sort: Optional[str] = None,
+    direction: Optional[str] = None,
+    size: Optional[int] = None,
+    page: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get all associations for a specific SNP with optional sorting.
+
+    Parameters
+    ----------
+    rs_id : str
+        dbSNP rs identifier
+    sort : str
+        Sort field (e.g., 'p_value', 'or_value')
+    direction : str
+        Sort direction ('asc' or 'desc')
+    size : int
+        Number of results to return per page
+    page : int
+        Page number for pagination
+    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_get_associations_for_snp",
+            "arguments": {
+                "rs_id": rs_id,
+                "sort": sort,
+                "direction": direction,
+                "size": size,
+                "page": page,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_get_associations_for_snp"]

tooluniverse/tools/gwas_get_associations_for_study.py

@@ -0,0 +1,55 @@
+"""
+gwas_get_associations_for_study
+
+Get all associations for a specific study, sorted by p-value.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_get_associations_for_study(
+    accession_id: str,
+    size: Optional[int] = None,
+    page: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get all associations for a specific study, sorted by p-value.
+
+    Parameters
+    ----------
+    accession_id : str
+        Study accession identifier
+    size : int
+        Number of results to return per page
+    page : int
+        Page number for pagination
+    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_get_associations_for_study",
+            "arguments": {"accession_id": accession_id, "size": size, "page": page},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_get_associations_for_study"]

tooluniverse/tools/gwas_get_associations_for_trait.py

@@ -0,0 +1,55 @@
+"""
+gwas_get_associations_for_trait
+
+Get all associations for a specific trait, sorted by p-value (most significant first).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_get_associations_for_trait(
+    efo_trait: str,
+    size: Optional[int] = None,
+    page: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get all associations for a specific trait, sorted by p-value (most significant first).
+
+    Parameters
+    ----------
+    efo_trait : str
+        EFO trait identifier or name
+    size : int
+        Number of results to return per page
+    page : int
+        Page number for pagination
+    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_get_associations_for_trait",
+            "arguments": {"efo_trait": efo_trait, "size": size, "page": page},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_get_associations_for_trait"]

tooluniverse/tools/gwas_get_snp_by_id.py

@@ -0,0 +1,46 @@
+"""
+gwas_get_snp_by_id
+
+Get a specific GWAS SNP by its rs ID.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_get_snp_by_id(
+    rs_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get a specific GWAS SNP by its rs ID.
+
+    Parameters
+    ----------
+    rs_id : str
+        dbSNP rs identifier
+    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_get_snp_by_id", "arguments": {"rs_id": rs_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_get_snp_by_id"]