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

tooluniverse/tools/UniProt_get_isoform_ids_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_isoform_ids_by_accession
+
+Extract all splice isoform IDs from UniProtKB entry (isoformNames).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_isoform_ids_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extract all splice isoform IDs from UniProtKB entry (isoformNames).
+
+    Parameters
+    ----------
+    accession : str
+        UniProtKB accession, e.g., P05067.
+    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": "UniProt_get_isoform_ids_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_isoform_ids_by_accession"]

tooluniverse/tools/UniProt_get_organism_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_organism_by_accession
+
+Extract the organism scientific name from UniProtKB entry.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_organism_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extract the organism scientific name from UniProtKB entry.
+
+    Parameters
+    ----------
+    accession : str
+        UniProtKB accession, e.g., P05067.
+    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": "UniProt_get_organism_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_organism_by_accession"]

tooluniverse/tools/UniProt_get_ptm_processing_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_ptm_processing_by_accession
+
+Extract all PTM and processing sites from UniProtKB entry (feature type = MODIFIED RESIDUE or SIG...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_ptm_processing_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extract all PTM and processing sites from UniProtKB entry (feature type = MODIFIED RESIDUE or SIG...
+
+    Parameters
+    ----------
+    accession : str
+        UniProtKB accession, e.g., P05067.
+    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": "UniProt_get_ptm_processing_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_ptm_processing_by_accession"]

tooluniverse/tools/UniProt_get_recommended_name_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_recommended_name_by_accession
+
+Extract the recommended protein name (recommendedName) from UniProtKB entry.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_recommended_name_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extract the recommended protein name (recommendedName) from UniProtKB entry.
+
+    Parameters
+    ----------
+    accession : str
+        UniProtKB accession, e.g., P05067.
+    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": "UniProt_get_recommended_name_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_recommended_name_by_accession"]

tooluniverse/tools/UniProt_get_sequence_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_sequence_by_accession
+
+Extract the canonical sequence from UniProtKB entry.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_sequence_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extract the canonical sequence from UniProtKB entry.
+
+    Parameters
+    ----------
+    accession : str
+        UniProtKB accession, e.g., P05067.
+    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": "UniProt_get_sequence_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_sequence_by_accession"]

tooluniverse/tools/UniProt_get_subcellular_location_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_subcellular_location_by_accession
+
+Extract subcellular localization annotations from UniProtKB entry (Comment type = SUBCELLULAR LOC...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_subcellular_location_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extract subcellular localization annotations from UniProtKB entry (Comment type = SUBCELLULAR LOC...
+
+    Parameters
+    ----------
+    accession : str
+        UniProtKB accession, e.g., P05067.
+    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": "UniProt_get_subcellular_location_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_subcellular_location_by_accession"]

tooluniverse/tools/Unpaywall_check_oa_status.py

@@ -0,0 +1,52 @@
+"""
+Unpaywall_check_oa_status
+
+Query Unpaywall by DOI to check open-access status and OA locations. Requires a contact email for...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Unpaywall_check_oa_status(
+    doi: str,
+    email: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Query Unpaywall by DOI to check open-access status and OA locations. Requires a contact email for...
+
+    Parameters
+    ----------
+    doi : str
+        DOI (Digital Object Identifier) of the article to check for open access status.
+    email : str
+        Contact email address required by Unpaywall API for polite usage tracking.
+    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": "Unpaywall_check_oa_status",
+            "arguments": {"doi": doi, "email": email},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Unpaywall_check_oa_status"]

tooluniverse/tools/WHO_Guideline_Full_Text.py

@@ -0,0 +1,46 @@
+"""
+WHO_Guideline_Full_Text
+
+Fetch full text content from a WHO (World Health Organization) guideline publication page. Extrac...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def WHO_Guideline_Full_Text(
+    url: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Fetch full text content from a WHO (World Health Organization) guideline publication page. Extrac...
+
+    Parameters
+    ----------
+    url : str
+        Full URL of the WHO publication page (e.g., 'https://www.who.int/publications...
+    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": "WHO_Guideline_Full_Text", "arguments": {"url": url}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["WHO_Guideline_Full_Text"]

tooluniverse/tools/WHO_Guidelines_Search.py

@@ -0,0 +1,52 @@
+"""
+WHO_Guidelines_Search
+
+Search WHO (World Health Organization) official clinical guidelines and health recommendations. P...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def WHO_Guidelines_Search(
+    query: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search WHO (World Health Organization) official clinical guidelines and health recommendations. P...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition, disease, or health topic to search for in WHO guidelines (...
+    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
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "WHO_Guidelines_Search",
+            "arguments": {"query": query, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["WHO_Guidelines_Search"]

tooluniverse/tools/Wikidata_SPARQL_query.py

@@ -0,0 +1,52 @@
+"""
+Wikidata_SPARQL_query
+
+Execute SPARQL queries against Wikidata to retrieve structured data. This tool powers Scholia-sty...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Wikidata_SPARQL_query(
+    sparql: str,
+    max_results: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Execute SPARQL queries against Wikidata to retrieve structured data. This tool powers Scholia-sty...
+
+    Parameters
+    ----------
+    sparql : str
+        SPARQL query string to execute against Wikidata. Use SPARQL syntax to query a...
+    max_results : int
+        Optional result limit override. If not specified, uses the LIMIT clause in th...
+    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": "Wikidata_SPARQL_query",
+            "arguments": {"sparql": sparql, "max_results": max_results},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Wikidata_SPARQL_query"]

tooluniverse/tools/WritingPresentationReviewer.py

@@ -0,0 +1,49 @@
+"""
+WritingPresentationReviewer
+
+Assesses clarity, organization, grammar, and visual presentation quality.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def WritingPresentationReviewer(
+    manuscript_text: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Assesses clarity, organization, grammar, and visual presentation quality.
+
+    Parameters
+    ----------
+    manuscript_text : str
+
+    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": "WritingPresentationReviewer",
+            "arguments": {"manuscript_text": manuscript_text},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["WritingPresentationReviewer"]

tooluniverse/tools/Zenodo_search_records.py

@@ -0,0 +1,59 @@
+"""
+Zenodo_search_records
+
+Search Zenodo for research data, publications, and datasets. Zenodo is an open-access repository ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Zenodo_search_records(
+    query: str,
+    max_results: int,
+    community: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search Zenodo for research data, publications, and datasets. Zenodo is an open-access repository ...
+
+    Parameters
+    ----------
+    query : str
+        Free text search query for Zenodo records. Use keywords to search across titl...
+    max_results : int
+        Maximum number of results to return. Must be between 1 and 200.
+    community : str
+        Optional community slug to filter results by specific research community (e.g...
+    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": "Zenodo_search_records",
+            "arguments": {
+                "query": query,
+                "max_results": max_results,
+                "community": community,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Zenodo_search_records"]