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

tooluniverse/tools/ToolRelationshipDetector.py

@@ -0,0 +1,52 @@
+"""
+ToolRelationshipDetector
+
+Analyzes a primary tool against a list of other tools to identify meaningful, directional data fl...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ToolRelationshipDetector(
+    tool_a: str,
+    other_tools: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Analyzes a primary tool against a list of other tools to identify meaningful, directional data fl...
+
+    Parameters
+    ----------
+    tool_a : str
+        JSON string for the primary tool configuration (Tool A).
+    other_tools : str
+        JSON string of a list of other tool configurations to compare against Tool A.
+    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": "ToolRelationshipDetector",
+            "arguments": {"tool_a": tool_a, "other_tools": other_tools},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ToolRelationshipDetector"]

tooluniverse/tools/ToolSpecificationGenerator.py

@@ -0,0 +1,67 @@
+"""
+ToolSpecificationGenerator
+
+Generates complete ToolUniverse-compliant tool specifications based on a description and analysis...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ToolSpecificationGenerator(
+    tool_description: str,
+    tool_category: str,
+    tool_type: str,
+    similar_tools: str,
+    existing_tools_summary: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Generates complete ToolUniverse-compliant tool specifications based on a description and analysis...
+
+    Parameters
+    ----------
+    tool_description : str
+        Brief description of the desired tool functionality and purpose.
+    tool_category : str
+        Target category for the tool (e.g., 'biomedical', 'data_analysis', 'text_proc...
+    tool_type : str
+        Specific ToolUniverse tool type (e.g., 'AgenticTool', 'RESTTool', 'PythonTool').
+    similar_tools : str
+        JSON string containing configurations of similar existing tools for analysis ...
+    existing_tools_summary : str
+        Summary of existing tools in the ecosystem to avoid duplication and identify ...
+    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": "ToolSpecificationGenerator",
+            "arguments": {
+                "tool_description": tool_description,
+                "tool_category": tool_category,
+                "tool_type": tool_type,
+                "similar_tools": similar_tools,
+                "existing_tools_summary": existing_tools_summary,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ToolSpecificationGenerator"]

tooluniverse/tools/ToolSpecificationOptimizer.py

@@ -0,0 +1,63 @@
+"""
+ToolSpecificationOptimizer
+
+Optimizes tool specifications for clarity, completeness, and usability with comprehensive benchma...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ToolSpecificationOptimizer(
+    tool_config: str,
+    optimization_focus: Optional[str] = "all",
+    target_audience: Optional[str] = "mixed",
+    similar_tools: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Optimizes tool specifications for clarity, completeness, and usability with comprehensive benchma...
+
+    Parameters
+    ----------
+    tool_config : str
+        JSON string of current tool configuration to optimize
+    optimization_focus : str
+        Primary optimization focus
+    target_audience : str
+        Target user expertise level
+    similar_tools : str
+        JSON string array of similar tools for comparison and benchmarking
+    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": "ToolSpecificationOptimizer",
+            "arguments": {
+                "tool_config": tool_config,
+                "optimization_focus": optimization_focus,
+                "target_audience": target_audience,
+                "similar_tools": similar_tools,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ToolSpecificationOptimizer"]

tooluniverse/tools/Tool_Finder.py

@@ -0,0 +1,67 @@
+"""
+Tool_Finder
+
+Retrieve related tools from the toolbox based on the provided description, advanced version with ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Tool_Finder(
+    description: str,
+    limit: int,
+    picked_tool_names: Optional[list[Any]] = None,
+    return_call_result: Optional[bool] = None,
+    categories: Optional[list[Any]] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve related tools from the toolbox based on the provided description, advanced version with ...
+
+    Parameters
+    ----------
+    description : str
+        The description of the tool capability required.
+    limit : int
+        The number of tools to retrieve
+    picked_tool_names : list[Any]
+        Pre-selected tool names to process. If provided, tool selection will skip the...
+    return_call_result : bool
+        Whether to return both prompts and tool names. If false, returns only tool pr...
+    categories : list[Any]
+        Optional list of tool categories to filter by
+    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": "Tool_Finder",
+            "arguments": {
+                "description": description,
+                "limit": limit,
+                "picked_tool_names": picked_tool_names,
+                "return_call_result": return_call_result,
+                "categories": categories,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Tool_Finder"]

tooluniverse/tools/Tool_Finder_Keyword.py

@@ -0,0 +1,67 @@
+"""
+Tool_Finder_Keyword
+
+Simple keyword-based tool finder for discovering relevant tools using text matching
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Tool_Finder_Keyword(
+    description: str,
+    limit: int,
+    picked_tool_names: Optional[list[Any]] = None,
+    return_call_result: Optional[bool] = None,
+    categories: Optional[list[Any]] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Simple keyword-based tool finder for discovering relevant tools using text matching
+
+    Parameters
+    ----------
+    description : str
+        The description of the tool capability required.
+    limit : int
+        The number of tools to retrieve
+    picked_tool_names : list[Any]
+        Pre-selected tool names to process. If provided, tool selection will skip the...
+    return_call_result : bool
+        Whether to return both prompts and tool names. If false, returns only tool pr...
+    categories : list[Any]
+        Optional list of tool categories to filter by
+    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": "Tool_Finder_Keyword",
+            "arguments": {
+                "description": description,
+                "limit": limit,
+                "picked_tool_names": picked_tool_names,
+                "return_call_result": return_call_result,
+                "categories": categories,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Tool_Finder_Keyword"]

tooluniverse/tools/Tool_Finder_LLM.py

@@ -0,0 +1,67 @@
+"""
+Tool_Finder_LLM
+
+LLM-based tool finder that uses natural language processing to intelligently select relevant tool...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Tool_Finder_LLM(
+    description: str,
+    limit: int,
+    picked_tool_names: Optional[list[Any]] = None,
+    return_call_result: Optional[bool] = None,
+    categories: Optional[list[Any]] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    LLM-based tool finder that uses natural language processing to intelligently select relevant tool...
+
+    Parameters
+    ----------
+    description : str
+        The description of the tool capability required.
+    limit : int
+        The number of tools to retrieve
+    picked_tool_names : list[Any]
+        Pre-selected tool names to process. If provided, tool selection will skip the...
+    return_call_result : bool
+        Whether to return both prompts and tool names. If false, returns only tool pr...
+    categories : list[Any]
+        Optional list of tool categories to filter by
+    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": "Tool_Finder_LLM",
+            "arguments": {
+                "description": description,
+                "limit": limit,
+                "picked_tool_names": picked_tool_names,
+                "return_call_result": return_call_result,
+                "categories": categories,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Tool_Finder_LLM"]

tooluniverse/tools/Tool_RAG.py

@@ -0,0 +1,49 @@
+"""
+Tool_RAG
+
+Retrieve related tools from the toolbox based on the provided description
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Tool_RAG(
+    description: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve related tools from the toolbox based on the provided description
+
+    Parameters
+    ----------
+    description : str
+        The description of the tool capability required.
+    limit : int
+        The number of tools to retrieve
+    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": "Tool_RAG", "arguments": {"description": description, "limit": limit}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Tool_RAG"]

tooluniverse/tools/UCSC_get_genes_by_region.py

@@ -0,0 +1,67 @@
+"""
+UCSC_get_genes_by_region
+
+Query UCSC Genome Browser track API for knownGene features in a genomic window.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UCSC_get_genes_by_region(
+    chrom: str,
+    start: int,
+    end: int,
+    genome: Optional[str] = "hg38",
+    track: Optional[str] = "knownGene",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Query UCSC Genome Browser track API for knownGene features in a genomic window.
+
+    Parameters
+    ----------
+    genome : str
+        Genome assembly (e.g., hg38).
+    chrom : str
+        Chromosome (e.g., chr17).
+    start : int
+        Start position (0-based).
+    end : int
+        End position.
+    track : str
+        Track name.
+    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": "UCSC_get_genes_by_region",
+            "arguments": {
+                "genome": genome,
+                "chrom": chrom,
+                "start": start,
+                "end": end,
+                "track": track,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UCSC_get_genes_by_region"]

tooluniverse/tools/UniProt_get_alternative_names_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_alternative_names_by_accession
+
+Extract all alternative names (alternativeNames) from UniProtKB entry.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_alternative_names_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extract all alternative names (alternativeNames) 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_alternative_names_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_alternative_names_by_accession"]

tooluniverse/tools/UniProt_get_disease_variants_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_disease_variants_by_accession
+
+Extract all variants (feature type = VARIANT) and their related annotations from UniProtKB entry.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_disease_variants_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extract all variants (feature type = VARIANT) and their related annotations 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_disease_variants_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_disease_variants_by_accession"]

tooluniverse/tools/UniProt_get_entry_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_entry_by_accession
+
+Get the complete JSON entry for a specified UniProtKB accession.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_entry_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get the complete JSON entry for a specified UniProtKB accession.
+
+    Parameters
+    ----------
+    accession : str
+        UniProtKB entry 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_entry_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_entry_by_accession"]

tooluniverse/tools/UniProt_get_function_by_accession.py

@@ -0,0 +1,49 @@
+"""
+UniProt_get_function_by_accession
+
+Extract functional annotations from UniProtKB entry (Comment type = FUNCTION).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_get_function_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extract functional annotations from UniProtKB entry (Comment type = FUNCTION).
+
+    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_function_by_accession",
+            "arguments": {"accession": accession},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_get_function_by_accession"]