tooluniverse 1.0.9.1__py3-none-any.whl → 1.0.11__py3-none-any.whl

tooluniverse/data/genomics_tools.json

@@ -1,174 +0,0 @@
-[
-  {
-    "type": "EnsemblTool",
-    "name": "Ensembl_lookup_gene_by_symbol",
-    "description": "Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xrefs/symbol then /lookup/id?expand=1).",
-    "parameter": {
-      "type": "object",
-      "properties": {
-        "species": {"type": "string", "description": "Species name (e.g., 'homo_sapiens').", "default": "homo_sapiens"},
-        "symbol": {"type": "string", "description": "Gene symbol (e.g., BRCA1)."}
-      },
-      "required": ["symbol"]
-    },
-    "return_schema": {
-      "type": "object",
-      "description": "Gene metadata including Ensembl ID, name, location, and transcripts count.",
-      "properties": {
-        "id": {"type": "string"},
-        "symbol": {"type": "string"},
-        "display_name": {"type": "string"},
-        "species": {"type": "string"},
-        "seq_region_name": {"type": "string"},
-        "start": {"type": "integer"},
-        "end": {"type": "integer"},
-        "strand": {"type": "integer"},
-        "biotype": {"type": "string"},
-        "transcript_count": {"type": "integer"}
-      }
-    }
-  },
-  {
-    "type": "ClinVarTool",
-    "name": "ClinVar_search_variants",
-    "description": "Search ClinVar via NCBI E-utilities (esearch→esummary) and return concise variant records for a query term.",
-    "parameter": {
-      "type": "object",
-      "properties": {
-        "query": {"type": "string", "description": "ClinVar search term (e.g., BRCA1)."},
-        "retmax": {"type": "integer", "description": "Max records.", "default": 5}
-      },
-      "required": ["query"]
-    },
-    "return_schema": {
-      "type": "array",
-      "items": {
-        "type": "object",
-        "properties": {
-          "uid": {"type": "string"},
-          "accession": {"type": "string"},
-          "title": {"type": "string"},
-          "gene": {"type": "string"},
-          "chr": {"type": "string"},
-          "start": {"type": "integer"},
-          "stop": {"type": "integer"},
-          "spdi": {"type": "string"},
-          "clinical_significance": {"type": "string"}
-        }
-      }
-    }
-  },
-  {
-    "type": "DbSnpTool",
-    "name": "dbSNP_get_variant_by_rsid",
-    "description": "Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).",
-    "parameter": {
-      "type": "object",
-      "properties": {
-        "rsid": {"type": "string", "description": "rsID without 'rs' prefix or with (e.g., rs699 or 699)."}
-      },
-      "required": ["rsid"]
-    },
-    "return_schema": {
-      "type": "object",
-      "properties": {
-        "refsnp_id": {"type": "string"},
-        "chrom": {"type": "string"},
-        "pos": {"type": "integer"},
-        "alleles": {"type": "array", "items": {"type": "string"}},
-        "hgvs": {"type": "array", "items": {"type": "string"}}
-      }
-    }
-  },
-  {
-    "type": "UCSCTool",
-    "name": "UCSC_get_genes_by_region",
-    "description": "Query UCSC Genome Browser track API for knownGene features in a genomic window.",
-    "parameter": {
-      "type": "object",
-      "properties": {
-        "genome": {"type": "string", "description": "Genome assembly (e.g., hg38).", "default": "hg38"},
-        "chrom": {"type": "string", "description": "Chromosome (e.g., chr17)."},
-        "start": {"type": "integer", "description": "Start position (0-based)."},
-        "end": {"type": "integer", "description": "End position."},
-        "track": {"type": "string", "description": "Track name.", "default": "knownGene"}
-      },
-      "required": ["chrom", "start", "end"]
-    },
-    "return_schema": {
-      "type": "object",
-      "properties": {
-        "itemsReturned": {"type": "integer"},
-        "features": {
-          "type": "array",
-          "items": {
-            "type": "object",
-            "properties": {
-              "name": {"type": "string"},
-              "geneName": {"type": "string"},
-              "chrom": {"type": "string"},
-              "chromStart": {"type": "integer"},
-              "chromEnd": {"type": "integer"},
-              "strand": {"type": "string"}
-            }
-          }
-        }
-      }
-    }
-  },
-  {
-    "type": "GnomadTool",
-    "name": "gnomAD_query_variant",
-    "description": "Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).",
-    "parameter": {
-      "type": "object",
-      "properties": {
-        "variant_id": {"type": "string", "description": "Variant ID like '1-230710048-A-G'."},
-        "dataset": {"type": "string", "description": "Dataset ID (e.g., gnomad_r4).", "default": "gnomad_r4"}
-      },
-      "required": ["variant_id"]
-    },
-    "return_schema": {
-      "type": "object",
-      "properties": {
-        "variantId": {"type": "string"},
-        "genome": {
-          "type": "object",
-          "properties": {"ac": {"type": "integer"}, "an": {"type": "integer"}, "af": {"type": "number"}}
-        }
-      }
-    }
-  },
-  {
-    "type": "GWASGeneSearch",
-    "name": "GWAS_search_associations_by_gene",
-    "description": "Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).",
-    "parameter": {
-      "type": "object",
-      "properties": {
-        "gene_name": {"type": "string", "description": "Gene symbol (e.g., BRCA1)."},
-        "size": {"type": "integer", "description": "Max associations to return.", "default": 5}
-      },
-      "required": ["gene_name"]
-    },
-    "return_schema": {
-      "type": "object",
-      "properties": {
-        "gene_name": {"type": "string"},
-        "association_count": {"type": "integer"},
-        "associations": {
-          "type": "array",
-          "items": {
-            "type": "object",
-            "properties": {
-              "study": {"type": "string"},
-              "strongestRiskAllele": {"type": "string"},
-              "pvalue": {"type": "number"}
-            }
-          }
-        },
-        "total_found": {"type": "integer"}
-      }
-    }
-  }
-]

tooluniverse/tools/ToolDescriptionOptimizer.py

@@ -1,67 +0,0 @@
-"""
-ToolDescriptionOptimizer
-
-Optimizes a tool's description and parameter descriptions by generating test cases, executing the...
-"""
-
-from typing import Any, Optional, Callable
-from ._shared_client import get_shared_client
-
-
-def ToolDescriptionOptimizer(
-    tool_config: dict[str, Any],
-    save_to_file: bool,
-    output_file: str,
-    max_iterations: int,
-    satisfaction_threshold: float,
-    *,
-    stream_callback: Optional[Callable[[str], None]] = None,
-    use_cache: bool = False,
-    validate: bool = True,
-) -> Any:
-    """
-    Optimizes a tool's description and parameter descriptions by generating test cases, executing the...
-
-    Parameters
-    ----------
-    tool_config : dict[str, Any]
-        The full configuration of the tool to optimize.
-    save_to_file : bool
-        If true, save the optimized description to a file (do not overwrite the origi...
-    output_file : str
-        Optional file path to save the optimized description. If not provided, use '<...
-    max_iterations : int
-        Maximum number of optimization rounds to perform.
-    satisfaction_threshold : float
-        Quality score threshold (1-10) to consider optimization satisfactory.
-    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": "ToolDescriptionOptimizer",
-            "arguments": {
-                "tool_config": tool_config,
-                "save_to_file": save_to_file,
-                "output_file": output_file,
-                "max_iterations": max_iterations,
-                "satisfaction_threshold": satisfaction_threshold,
-            },
-        },
-        stream_callback=stream_callback,
-        use_cache=use_cache,
-        validate=validate,
-    )
-
-
-__all__ = ["ToolDescriptionOptimizer"]

tooluniverse/tools/ToolImplementationGenerator.py

@@ -1,67 +0,0 @@
-"""
-ToolImplementationGenerator
-
-Generates domain-specific, functional code implementations based on tool descriptions and require...
-"""
-
-from typing import Any, Optional, Callable
-from ._shared_client import get_shared_client
-
-
-def ToolImplementationGenerator(
-    tool_description: str,
-    tool_parameters: str,
-    domain: Optional[str] = "general",
-    complexity_level: Optional[str] = "intermediate",
-    performance_requirements: Optional[str] = None,
-    *,
-    stream_callback: Optional[Callable[[str], None]] = None,
-    use_cache: bool = False,
-    validate: bool = True,
-) -> Any:
-    """
-    Generates domain-specific, functional code implementations based on tool descriptions and require...
-
-    Parameters
-    ----------
-    tool_description : str
-        Detailed description of what the tool should accomplish
-    tool_parameters : str
-        JSON string of parameter schema for the tool
-    domain : str
-        Domain area for specialized implementation
-    complexity_level : str
-        Desired complexity level of implementation
-    performance_requirements : str
-        Performance requirements or constraints
-    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": "ToolImplementationGenerator",
-            "arguments": {
-                "tool_description": tool_description,
-                "tool_parameters": tool_parameters,
-                "domain": domain,
-                "complexity_level": complexity_level,
-                "performance_requirements": performance_requirements,
-            },
-        },
-        stream_callback=stream_callback,
-        use_cache=use_cache,
-        validate=validate,
-    )
-
-
-__all__ = ["ToolImplementationGenerator"]

tooluniverse/tools/ToolOptimizer.py

@@ -1,59 +0,0 @@
-"""
-ToolOptimizer
-
-Optimizes tool configurations based on quality feedback. Improves tool specifications and impleme...
-"""
-
-from typing import Any, Optional, Callable
-from ._shared_client import get_shared_client
-
-
-def ToolOptimizer(
-    tool_config: str,
-    quality_feedback: str,
-    optimization_target: str,
-    *,
-    stream_callback: Optional[Callable[[str], None]] = None,
-    use_cache: bool = False,
-    validate: bool = True,
-) -> Any:
-    """
-    Optimizes tool configurations based on quality feedback. Improves tool specifications and impleme...
-
-    Parameters
-    ----------
-    tool_config : str
-        JSON string of the original tool configuration
-    quality_feedback : str
-        JSON string of quality evaluation feedback
-    optimization_target : str
-        What to optimize for (improve_quality, enhance_performance, etc.)
-    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": "ToolOptimizer",
-            "arguments": {
-                "tool_config": tool_config,
-                "quality_feedback": quality_feedback,
-                "optimization_target": optimization_target,
-            },
-        },
-        stream_callback=stream_callback,
-        use_cache=use_cache,
-        validate=validate,
-    )
-
-
-__all__ = ["ToolOptimizer"]

tooluniverse/tools/ToolSpecificationGenerator.py

@@ -1,67 +0,0 @@
-"""
-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

@@ -1,63 +0,0 @@
-"""
-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/ucsc_tool.py

@@ -1,60 +0,0 @@
-import requests
-from .base_tool import BaseTool
-from .tool_registry import register_tool
-
-
-@register_tool("UCSCTool")
-class UCSCTool(BaseTool):
-    """
-    Local tool wrapper for UCSC Genome Browser track API.
-    Queries knownGene track for genomic regions.
-    """
-
-    def __init__(self, tool_config):
-        super().__init__(tool_config)
-        self.base = "https://api.genome.ucsc.edu/getData/track"
-        self.session = requests.Session()
-
-    def run(self, arguments):
-        genome = arguments.get("genome", "hg38")
-        chrom = arguments.get("chrom")
-        start = arguments.get("start")
-        end = arguments.get("end")
-        track = arguments.get("track", "knownGene")
-
-        if not all([chrom, start is not None, end is not None]):
-            return {"error": "Missing required parameters: chrom, start, end"}
-
-        params = {
-            "genome": genome,
-            "track": track,
-            "chrom": chrom,
-            "start": start,
-            "end": end,
-        }
-
-        resp = self.session.get(self.base, params=params, timeout=30)
-        resp.raise_for_status()
-        data = resp.json()
-
-        features = data.get(track, [])
-        items_returned = len(features)
-
-        # Extract key fields from each feature
-        processed_features = []
-        for feature in features:
-            processed_features.append(
-                {
-                    "name": feature.get("name", ""),
-                    "geneName": feature.get("geneName", ""),
-                    "chrom": feature.get("chrom", ""),
-                    "chromStart": feature.get("chromStart"),
-                    "chromEnd": feature.get("chromEnd"),
-                    "strand": feature.get("strand", ""),
-                }
-            )
-
-        return {
-            "itemsReturned": items_returned,
-            "features": processed_features,
-        }