tooluniverse 1.0.10__py3-none-any.whl → 1.0.11__py3-none-any.whl

tooluniverse/tools/ToolDiscover.py

@@ -1,7 +1,7 @@
 """
 ToolDiscover
 
-Generates new ToolUniverse-compliant tools based on short descriptions through an intelligent dis...
+Generates new ToolUniverse-compliant tools based on short descriptions using XML format for simul...
 """
 
 from typing import Any, Optional, Callable
@@ -10,27 +10,27 @@ from ._shared_client import get_shared_client
 
 def ToolDiscover(
     tool_description: str,
-    max_iterations: int,
-    save_to_file: bool,
-    output_file: str,
+    max_iterations: Optional[int] = 2,
+    save_to_file: Optional[bool] = True,
+    output_file: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,
     validate: bool = True,
-) -> Any:
+) -> dict[str, Any]:
     """
-    Generates new ToolUniverse-compliant tools based on short descriptions through an intelligent dis...
+    Generates new ToolUniverse-compliant tools based on short descriptions using XML format for simul...
 
     Parameters
     ----------
     tool_description : str
-        Short description of the desired tool functionality and purpose. Tool Discove...
+        Short description of the desired tool functionality
     max_iterations : int
-        Maximum number of refinement iterations to perform.
+        Maximum number of optimization iterations
     save_to_file : bool
-        Whether to save the generated tool configuration and report to a file.
+        Whether to save the generated tool files
     output_file : str
-        Optional file path to save the generated tool. If not provided, uses auto-gen...
+        Optional file path to save the generated tool
     stream_callback : Callable, optional
         Callback for streaming output
     use_cache : bool, default False
@@ -40,7 +40,7 @@ def ToolDiscover(
 
     Returns
     -------
-    Any
+    dict[str, Any]
     """
     # Handle mutable defaults to avoid B006 linting error
 

tooluniverse/tools/UniProt_id_mapping.py

@@ -0,0 +1,63 @@
+"""
+UniProt_id_mapping
+
+Map IDs between different databases (e.g., Ensembl to UniProt, Gene Name to UniProt). Supports ba...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_id_mapping(
+    ids: str,
+    from_db: str,
+    to_db: Optional[str] = None,
+    max_wait_time: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Map IDs between different databases (e.g., Ensembl to UniProt, Gene Name to UniProt). Supports ba...
+
+    Parameters
+    ----------
+    ids : str
+        ID(s) to map. Can be single string or array of strings, e.g., 'ENSG0000014151...
+    from_db : str
+        Source database. Examples: 'Ensembl', 'Gene_Name', 'RefSeq_Protein', 'PDB', '...
+    to_db : str
+        Target database (default: 'UniProtKB')
+    max_wait_time : int
+        Maximum time to wait for async task completion in seconds (default: 30)
+    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_id_mapping",
+            "arguments": {
+                "ids": ids,
+                "from_db": from_db,
+                "to_db": to_db,
+                "max_wait_time": max_wait_time,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_id_mapping"]

tooluniverse/tools/UniProt_search.py

@@ -0,0 +1,63 @@
+"""
+UniProt_search
+
+Search UniProtKB database using flexible query syntax. Supports gene names (e.g., 'gene:TP53'), p...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UniProt_search(
+    query: str,
+    organism: Optional[str] = None,
+    limit: Optional[int] = None,
+    fields: Optional[list[Any]] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Search UniProtKB database using flexible query syntax. Supports gene names (e.g., 'gene:TP53'), p...
+
+    Parameters
+    ----------
+    query : str
+        Search query. Can be simple (e.g., 'MEIOB') or advanced ('gene:TP53 AND organ...
+    organism : str
+        Optional organism filter. Can use common name ('human') or taxonomy ID ('9606...
+    limit : int
+        Maximum number of results to return (default: 25, max: 500)
+    fields : list[Any]
+        Optional list of fields to return. Default returns: accession, id, protein_na...
+    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_search",
+            "arguments": {
+                "query": query,
+                "organism": organism,
+                "limit": limit,
+                "fields": fields,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UniProt_search"]

tooluniverse/tools/UnifiedToolGenerator.py

@@ -0,0 +1,59 @@
+"""
+UnifiedToolGenerator
+
+Generates complete ToolUniverse tools using simplified XML format that simultaneously creates bot...
+"""
+
+from typing import Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UnifiedToolGenerator(
+    tool_description: str,
+    reference_info: str,
+    xml_template: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> str:
+    """
+    Generates complete ToolUniverse tools using simplified XML format that simultaneously creates bot...
+
+    Parameters
+    ----------
+    tool_description : str
+        Description of the desired tool functionality
+    reference_info : str
+        JSON string containing curated reference information including API documentat...
+    xml_template : str
+        XML template example showing the expected format with code and spec sections
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    str
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "UnifiedToolGenerator",
+            "arguments": {
+                "tool_description": tool_description,
+                "reference_info": reference_info,
+                "xml_template": xml_template,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UnifiedToolGenerator"]

tooluniverse/tools/WoRMS_search_species.py

@@ -0,0 +1,49 @@
+"""
+WoRMS_search_species
+
+Search marine species in World Register of Marine Species
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def WoRMS_search_species(
+    query: str,
+    limit: Optional[int] = 20,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search marine species in World Register of Marine Species
+
+    Parameters
+    ----------
+    query : str
+        Species name or search term
+    limit : int
+        Number of results
+    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": "WoRMS_search_species", "arguments": {"query": query, "limit": limit}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["WoRMS_search_species"]

tooluniverse/tools/XMLToolOptimizer.py

@@ -0,0 +1,55 @@
+"""
+XMLToolOptimizer
+
+Optimizes tools defined in XML format based on test results and quality feedback
+"""
+
+from typing import Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def XMLToolOptimizer(
+    xml_tool: str,
+    optimization_context: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> str:
+    """
+    Optimizes tools defined in XML format based on test results and quality feedback
+
+    Parameters
+    ----------
+    xml_tool : str
+        Current XML-formatted tool definition with code and spec sections
+    optimization_context : str
+        JSON string containing test results, quality feedback, iteration info, improv...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    str
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "XMLToolOptimizer",
+            "arguments": {
+                "xml_tool": xml_tool,
+                "optimization_context": optimization_context,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["XMLToolOptimizer"]