tooluniverse 1.0.11.1__py3-none-any.whl → 1.0.12__py3-none-any.whl
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- tooluniverse/alphafold_tool.py +47 -7
- tooluniverse/base_tool.py +9 -1
- tooluniverse/build_optimizer.py +115 -22
- tooluniverse/data/alphafold_tools.json +7 -12
- tooluniverse/data/encode_tools.json +139 -0
- tooluniverse/data/gbif_tools.json +152 -0
- tooluniverse/data/gdc_tools.json +116 -0
- tooluniverse/data/gtex_tools.json +116 -0
- tooluniverse/data/icgc_tools.json +0 -0
- tooluniverse/data/mgnify_tools.json +121 -0
- tooluniverse/data/obis_tools.json +122 -0
- tooluniverse/data/optimizer_tools.json +275 -0
- tooluniverse/data/rnacentral_tools.json +99 -0
- tooluniverse/data/smolagent_tools.json +206 -0
- tooluniverse/data/uniprot_tools.json +13 -5
- tooluniverse/data/wikipathways_tools.json +106 -0
- tooluniverse/default_config.py +12 -0
- tooluniverse/encode_tool.py +245 -0
- tooluniverse/execute_function.py +185 -17
- tooluniverse/gbif_tool.py +166 -0
- tooluniverse/gdc_tool.py +175 -0
- tooluniverse/generate_tools.py +121 -9
- tooluniverse/gtex_tool.py +168 -0
- tooluniverse/mgnify_tool.py +181 -0
- tooluniverse/obis_tool.py +185 -0
- tooluniverse/pypi_package_inspector_tool.py +3 -2
- tooluniverse/python_executor_tool.py +43 -13
- tooluniverse/rnacentral_tool.py +124 -0
- tooluniverse/smcp.py +17 -25
- tooluniverse/smcp_server.py +1 -1
- tooluniverse/smolagent_tool.py +555 -0
- tooluniverse/tools/ArgumentDescriptionOptimizer.py +55 -0
- tooluniverse/tools/ENCODE_list_files.py +59 -0
- tooluniverse/tools/ENCODE_search_experiments.py +67 -0
- tooluniverse/tools/GBIF_search_occurrences.py +67 -0
- tooluniverse/tools/GBIF_search_species.py +55 -0
- tooluniverse/tools/GDC_list_files.py +55 -0
- tooluniverse/tools/GDC_search_cases.py +55 -0
- tooluniverse/tools/GTEx_get_expression_summary.py +49 -0
- tooluniverse/tools/GTEx_query_eqtl.py +59 -0
- tooluniverse/tools/MGnify_list_analyses.py +52 -0
- tooluniverse/tools/MGnify_search_studies.py +55 -0
- tooluniverse/tools/OBIS_search_occurrences.py +59 -0
- tooluniverse/tools/OBIS_search_taxa.py +52 -0
- tooluniverse/tools/RNAcentral_get_by_accession.py +46 -0
- tooluniverse/tools/RNAcentral_search.py +52 -0
- tooluniverse/tools/TestCaseGenerator.py +46 -0
- tooluniverse/tools/ToolDescriptionOptimizer.py +67 -0
- tooluniverse/tools/ToolDiscover.py +4 -0
- tooluniverse/tools/UniProt_search.py +14 -6
- tooluniverse/tools/WikiPathways_get_pathway.py +52 -0
- tooluniverse/tools/WikiPathways_search.py +52 -0
- tooluniverse/tools/__init__.py +43 -1
- tooluniverse/tools/advanced_literature_search_agent.py +46 -0
- tooluniverse/tools/alphafold_get_annotations.py +4 -10
- tooluniverse/tools/download_binary_file.py +3 -6
- tooluniverse/tools/open_deep_research_agent.py +46 -0
- tooluniverse/uniprot_tool.py +51 -4
- tooluniverse/wikipathways_tool.py +122 -0
- {tooluniverse-1.0.11.1.dist-info → tooluniverse-1.0.12.dist-info}/METADATA +3 -1
- {tooluniverse-1.0.11.1.dist-info → tooluniverse-1.0.12.dist-info}/RECORD +65 -24
- {tooluniverse-1.0.11.1.dist-info → tooluniverse-1.0.12.dist-info}/WHEEL +0 -0
- {tooluniverse-1.0.11.1.dist-info → tooluniverse-1.0.12.dist-info}/entry_points.txt +0 -0
- {tooluniverse-1.0.11.1.dist-info → tooluniverse-1.0.12.dist-info}/licenses/LICENSE +0 -0
- {tooluniverse-1.0.11.1.dist-info → tooluniverse-1.0.12.dist-info}/top_level.txt +0 -0
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"""
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RNAcentral_search
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Search aggregated ncRNA records (miRNA, rRNA, lncRNA, etc.) across sources via RNAcentral. Use to...
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"""
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from typing import Any, Optional, Callable
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from ._shared_client import get_shared_client
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def RNAcentral_search(
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query: str,
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page_size: Optional[int] = 10,
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*,
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stream_callback: Optional[Callable[[str], None]] = None,
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use_cache: bool = False,
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validate: bool = True,
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) -> dict[str, Any]:
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"""
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Search aggregated ncRNA records (miRNA, rRNA, lncRNA, etc.) across sources via RNAcentral. Use to...
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Parameters
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----------
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query : str
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Keyword, accession, or sequence-based query (per RNAcentral API).
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page_size : int
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Number of records per page (1–100).
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stream_callback : Callable, optional
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Callback for streaming output
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use_cache : bool, default False
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Enable caching
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validate : bool, default True
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Validate parameters
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Returns
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-------
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dict[str, Any]
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"""
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# Handle mutable defaults to avoid B006 linting error
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return get_shared_client().run_one_function(
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{
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"name": "RNAcentral_search",
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"arguments": {"query": query, "page_size": page_size},
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},
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stream_callback=stream_callback,
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use_cache=use_cache,
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validate=validate,
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)
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__all__ = ["RNAcentral_search"]
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"""
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TestCaseGenerator
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Generates diverse and representative ToolUniverse tool call dictionaries for a given tool based o...
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"""
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from typing import Any, Optional, Callable
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from ._shared_client import get_shared_client
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def TestCaseGenerator(
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tool_config: dict[str, Any],
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*,
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stream_callback: Optional[Callable[[str], None]] = None,
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use_cache: bool = False,
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validate: bool = True,
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) -> dict[str, Any]:
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"""
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Generates diverse and representative ToolUniverse tool call dictionaries for a given tool based o...
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Parameters
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----------
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tool_config : dict[str, Any]
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The full configuration of the tool to generate test cases for. May include '_...
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stream_callback : Callable, optional
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Callback for streaming output
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use_cache : bool, default False
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Enable caching
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validate : bool, default True
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Validate parameters
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Returns
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-------
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dict[str, Any]
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"""
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# Handle mutable defaults to avoid B006 linting error
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return get_shared_client().run_one_function(
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{"name": "TestCaseGenerator", "arguments": {"tool_config": tool_config}},
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stream_callback=stream_callback,
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use_cache=use_cache,
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validate=validate,
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)
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__all__ = ["TestCaseGenerator"]
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"""
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ToolDescriptionOptimizer
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Optimizes a tool's description and parameter descriptions by generating test cases, executing the...
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"""
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from typing import Any, Optional, Callable
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from ._shared_client import get_shared_client
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def ToolDescriptionOptimizer(
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tool_config: dict[str, Any],
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save_to_file: bool,
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output_file: str,
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max_iterations: int,
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satisfaction_threshold: float,
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*,
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stream_callback: Optional[Callable[[str], None]] = None,
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use_cache: bool = False,
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validate: bool = True,
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) -> dict[str, Any]:
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"""
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Optimizes a tool's description and parameter descriptions by generating test cases, executing the...
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Parameters
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----------
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tool_config : dict[str, Any]
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The full configuration of the tool to optimize.
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save_to_file : bool
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If true, save the optimized description to a file (do not overwrite the origi...
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output_file : str
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Optional file path to save the optimized description. If not provided, use '<...
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max_iterations : int
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Maximum number of optimization rounds to perform.
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satisfaction_threshold : float
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Quality score threshold (1-10) to consider optimization satisfactory.
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stream_callback : Callable, optional
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Callback for streaming output
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use_cache : bool, default False
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Enable caching
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validate : bool, default True
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Validate parameters
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Returns
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-------
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dict[str, Any]
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"""
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# Handle mutable defaults to avoid B006 linting error
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return get_shared_client().run_one_function(
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{
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"name": "ToolDescriptionOptimizer",
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"arguments": {
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"tool_config": tool_config,
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"save_to_file": save_to_file,
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"output_file": output_file,
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"max_iterations": max_iterations,
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"satisfaction_threshold": satisfaction_threshold,
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},
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},
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stream_callback=stream_callback,
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use_cache=use_cache,
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validate=validate,
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)
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__all__ = ["ToolDescriptionOptimizer"]
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save_to_file: Optional[bool] = True,
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save_dir: Optional[str] = None,
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Optional file path to save the generated tool
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save_dir : str
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Directory path to save the generated tool files (defaults to current working ...
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"save_dir": save_dir,
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UniProt_search
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Search UniProtKB database
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Search UniProtKB database with flexible query syntax. Returns protein entries with accession numb...
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Search UniProtKB database
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Search UniProtKB database with flexible query syntax. Returns protein entries with accession numb...
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Search query
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Search query using UniProt syntax. Simple: 'MEIOB', 'insulin'. Field searches...
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Maximum number of results to return (default: 25, max: 500). Accepts string o...
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WikiPathways_get_pathway
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Fetch pathway content by WPID (JSON/GPML). Use to programmatically access pathway nodes/edges/met...
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def WikiPathways_get_pathway(
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format: Optional[str] = "json",
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Fetch pathway content by WPID (JSON/GPML). Use to programmatically access pathway nodes/edges/met...
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WikiPathways identifier (e.g., 'WP254').
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format : str
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Response format: 'json' for structured, 'gpml' for GPML XML.
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Callback for streaming output
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Enable caching
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Validate parameters
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dict[str, Any]
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"""
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# Handle mutable defaults to avoid B006 linting error
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return get_shared_client().run_one_function(
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{
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"name": "WikiPathways_get_pathway",
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"arguments": {"wpid": wpid, "format": format},
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},
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stream_callback=stream_callback,
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use_cache=use_cache,
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validate=validate,
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)
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__all__ = ["WikiPathways_get_pathway"]
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@@ -0,0 +1,52 @@
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"""
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2
|
+
WikiPathways_search
|
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+
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Text search across community-curated pathways (disease, metabolic, signaling). Use to discover re...
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+
"""
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+
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+
from typing import Any, Optional, Callable
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from ._shared_client import get_shared_client
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+
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+
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def WikiPathways_search(
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query: str,
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organism: Optional[str] = None,
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*,
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stream_callback: Optional[Callable[[str], None]] = None,
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use_cache: bool = False,
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validate: bool = True,
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) -> dict[str, Any]:
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"""
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Text search across community-curated pathways (disease, metabolic, signaling). Use to discover re...
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+
|
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+
Parameters
|
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+
----------
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query : str
|
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Free-text query (keywords, gene symbols, processes), e.g., 'p53', 'glycolysis'.
|
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organism : str
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Organism filter (scientific name), e.g., 'Homo sapiens'.
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stream_callback : Callable, optional
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Callback for streaming output
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use_cache : bool, default False
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Enable caching
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validate : bool, default True
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Validate parameters
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Returns
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-------
|
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dict[str, Any]
|
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+
"""
|
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+
# Handle mutable defaults to avoid B006 linting error
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+
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return get_shared_client().run_one_function(
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{
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"name": "WikiPathways_search",
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"arguments": {"query": query, "organism": organism},
|
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+
},
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stream_callback=stream_callback,
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use_cache=use_cache,
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validate=validate,
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)
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+
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+
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+
__all__ = ["WikiPathways_search"]
|
tooluniverse/tools/__init__.py
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
"""
|
|
2
2
|
ToolUniverse Tools
|
|
3
3
|
|
|
4
|
-
Type-safe Python interface to
|
|
4
|
+
Type-safe Python interface to 734 scientific tools.
|
|
5
5
|
Each tool is in its own module for minimal import overhead.
|
|
6
6
|
|
|
7
7
|
Usage:
|
|
@@ -42,6 +42,7 @@ from .AdverseEventPredictionQuestionGeneratorWithContext import (
|
|
|
42
42
|
AdverseEventPredictionQuestionGeneratorWithContext,
|
|
43
43
|
)
|
|
44
44
|
from .ArXiv_search_papers import ArXiv_search_papers
|
|
45
|
+
from .ArgumentDescriptionOptimizer import ArgumentDescriptionOptimizer
|
|
45
46
|
from .BLAST_nucleotide_search import BLAST_nucleotide_search
|
|
46
47
|
from .BLAST_protein_search import BLAST_protein_search
|
|
47
48
|
from .BioRxiv_search_preprints import BioRxiv_search_preprints
|
|
@@ -68,6 +69,8 @@ from .DrugInteractionAnalyzerAgent import DrugInteractionAnalyzerAgent
|
|
|
68
69
|
from .DrugOptimizationAgent import DrugOptimizationAgent
|
|
69
70
|
from .DrugSafetyAnalyzer import DrugSafetyAnalyzer
|
|
70
71
|
from .EMDB_get_structure import EMDB_get_structure
|
|
72
|
+
from .ENCODE_list_files import ENCODE_list_files
|
|
73
|
+
from .ENCODE_search_experiments import ENCODE_search_experiments
|
|
71
74
|
from .EthicalComplianceReviewer import EthicalComplianceReviewer
|
|
72
75
|
from .EuropePMC_Guidelines_Search import EuropePMC_Guidelines_Search
|
|
73
76
|
from .EuropePMC_search_articles import EuropePMC_search_articles
|
|
@@ -449,12 +452,18 @@ from .FDA_retrieve_patient_medication_info_by_drug_name import (
|
|
|
449
452
|
)
|
|
450
453
|
from .Fatcat_search_scholar import Fatcat_search_scholar
|
|
451
454
|
from .Finish import Finish
|
|
455
|
+
from .GBIF_search_occurrences import GBIF_search_occurrences
|
|
456
|
+
from .GBIF_search_species import GBIF_search_species
|
|
457
|
+
from .GDC_list_files import GDC_list_files
|
|
458
|
+
from .GDC_search_cases import GDC_search_cases
|
|
452
459
|
from .GIN_Guidelines_Search import GIN_Guidelines_Search
|
|
453
460
|
from .GO_get_annotations_for_gene import GO_get_annotations_for_gene
|
|
454
461
|
from .GO_get_genes_for_term import GO_get_genes_for_term
|
|
455
462
|
from .GO_get_term_by_id import GO_get_term_by_id
|
|
456
463
|
from .GO_get_term_details import GO_get_term_details
|
|
457
464
|
from .GO_search_terms import GO_search_terms
|
|
465
|
+
from .GTEx_get_expression_summary import GTEx_get_expression_summary
|
|
466
|
+
from .GTEx_query_eqtl import GTEx_query_eqtl
|
|
458
467
|
from .GWAS_search_associations_by_gene import GWAS_search_associations_by_gene
|
|
459
468
|
from .GtoPdb_get_targets import GtoPdb_get_targets
|
|
460
469
|
from .HAL_search_archive import HAL_search_archive
|
|
@@ -490,6 +499,8 @@ from .LabelGenerator import LabelGenerator
|
|
|
490
499
|
from .LiteratureContextReviewer import LiteratureContextReviewer
|
|
491
500
|
from .LiteratureSearchTool import LiteratureSearchTool
|
|
492
501
|
from .LiteratureSynthesisAgent import LiteratureSynthesisAgent
|
|
502
|
+
from .MGnify_list_analyses import MGnify_list_analyses
|
|
503
|
+
from .MGnify_search_studies import MGnify_search_studies
|
|
493
504
|
from .MPD_get_phenotype_data import MPD_get_phenotype_data
|
|
494
505
|
from .MedRxiv_search_preprints import MedRxiv_search_preprints
|
|
495
506
|
from .MedicalLiteratureReviewer import MedicalLiteratureReviewer
|
|
@@ -505,6 +516,8 @@ from .MethodologyRigorReviewer import MethodologyRigorReviewer
|
|
|
505
516
|
from .NICE_Clinical_Guidelines_Search import NICE_Clinical_Guidelines_Search
|
|
506
517
|
from .NICE_Guideline_Full_Text import NICE_Guideline_Full_Text
|
|
507
518
|
from .NoveltySignificanceReviewer import NoveltySignificanceReviewer
|
|
519
|
+
from .OBIS_search_occurrences import OBIS_search_occurrences
|
|
520
|
+
from .OBIS_search_taxa import OBIS_search_taxa
|
|
508
521
|
from .OSF_search_preprints import OSF_search_preprints
|
|
509
522
|
from .OSL_get_efo_id_by_disease_name import OSL_get_efo_id_by_disease_name
|
|
510
523
|
from .OpenAIRE_search_publications import OpenAIRE_search_publications
|
|
@@ -698,6 +711,8 @@ from .PubTator3_EntityAutocomplete import PubTator3_EntityAutocomplete
|
|
|
698
711
|
from .PubTator3_LiteratureSearch import PubTator3_LiteratureSearch
|
|
699
712
|
from .PyPIPackageInspector import PyPIPackageInspector
|
|
700
713
|
from .QuestionRephraser import QuestionRephraser
|
|
714
|
+
from .RNAcentral_get_by_accession import RNAcentral_get_by_accession
|
|
715
|
+
from .RNAcentral_search import RNAcentral_search
|
|
701
716
|
from .ReMap_get_transcription_factor_binding import (
|
|
702
717
|
ReMap_get_transcription_factor_binding,
|
|
703
718
|
)
|
|
@@ -710,8 +725,10 @@ from .SCREEN_get_regulatory_elements import SCREEN_get_regulatory_elements
|
|
|
710
725
|
from .ScientificTextSummarizer import ScientificTextSummarizer
|
|
711
726
|
from .SemanticScholar_search_papers import SemanticScholar_search_papers
|
|
712
727
|
from .TRIP_Database_Guidelines_Search import TRIP_Database_Guidelines_Search
|
|
728
|
+
from .TestCaseGenerator import TestCaseGenerator
|
|
713
729
|
from .TestResultsAnalyzer import TestResultsAnalyzer
|
|
714
730
|
from .ToolCompatibilityAnalyzer import ToolCompatibilityAnalyzer
|
|
731
|
+
from .ToolDescriptionOptimizer import ToolDescriptionOptimizer
|
|
715
732
|
from .ToolDiscover import ToolDiscover
|
|
716
733
|
from .ToolGraphComposer import ToolGraphComposer
|
|
717
734
|
from .ToolGraphGenerationPipeline import ToolGraphGenerationPipeline
|
|
@@ -751,11 +768,14 @@ from .UnifiedToolGenerator import UnifiedToolGenerator
|
|
|
751
768
|
from .Unpaywall_check_oa_status import Unpaywall_check_oa_status
|
|
752
769
|
from .WHO_Guideline_Full_Text import WHO_Guideline_Full_Text
|
|
753
770
|
from .WHO_Guidelines_Search import WHO_Guidelines_Search
|
|
771
|
+
from .WikiPathways_get_pathway import WikiPathways_get_pathway
|
|
772
|
+
from .WikiPathways_search import WikiPathways_search
|
|
754
773
|
from .Wikidata_SPARQL_query import Wikidata_SPARQL_query
|
|
755
774
|
from .WoRMS_search_species import WoRMS_search_species
|
|
756
775
|
from .WritingPresentationReviewer import WritingPresentationReviewer
|
|
757
776
|
from .XMLToolOptimizer import XMLToolOptimizer
|
|
758
777
|
from .Zenodo_search_records import Zenodo_search_records
|
|
778
|
+
from .advanced_literature_search_agent import advanced_literature_search_agent
|
|
759
779
|
from .alphafold_get_annotations import alphafold_get_annotations
|
|
760
780
|
from .alphafold_get_prediction import alphafold_get_prediction
|
|
761
781
|
from .alphafold_get_summary import alphafold_get_summary
|
|
@@ -1128,6 +1148,7 @@ from .ols_get_term_children import ols_get_term_children
|
|
|
1128
1148
|
from .ols_get_term_info import ols_get_term_info
|
|
1129
1149
|
from .ols_search_ontologies import ols_search_ontologies
|
|
1130
1150
|
from .ols_search_terms import ols_search_terms
|
|
1151
|
+
from .open_deep_research_agent import open_deep_research_agent
|
|
1131
1152
|
from .openalex_literature_search import openalex_literature_search
|
|
1132
1153
|
from .python_code_executor import python_code_executor
|
|
1133
1154
|
from .python_script_runner import python_script_runner
|
|
@@ -1157,6 +1178,7 @@ __all__ = [
|
|
|
1157
1178
|
"AdverseEventPredictionQuestionGenerator",
|
|
1158
1179
|
"AdverseEventPredictionQuestionGeneratorWithContext",
|
|
1159
1180
|
"ArXiv_search_papers",
|
|
1181
|
+
"ArgumentDescriptionOptimizer",
|
|
1160
1182
|
"BLAST_nucleotide_search",
|
|
1161
1183
|
"BLAST_protein_search",
|
|
1162
1184
|
"BioRxiv_search_preprints",
|
|
@@ -1183,6 +1205,8 @@ __all__ = [
|
|
|
1183
1205
|
"DrugOptimizationAgent",
|
|
1184
1206
|
"DrugSafetyAnalyzer",
|
|
1185
1207
|
"EMDB_get_structure",
|
|
1208
|
+
"ENCODE_list_files",
|
|
1209
|
+
"ENCODE_search_experiments",
|
|
1186
1210
|
"EthicalComplianceReviewer",
|
|
1187
1211
|
"EuropePMC_Guidelines_Search",
|
|
1188
1212
|
"EuropePMC_search_articles",
|
|
@@ -1360,12 +1384,18 @@ __all__ = [
|
|
|
1360
1384
|
"FDA_retrieve_patient_medication_info_by_drug_name",
|
|
1361
1385
|
"Fatcat_search_scholar",
|
|
1362
1386
|
"Finish",
|
|
1387
|
+
"GBIF_search_occurrences",
|
|
1388
|
+
"GBIF_search_species",
|
|
1389
|
+
"GDC_list_files",
|
|
1390
|
+
"GDC_search_cases",
|
|
1363
1391
|
"GIN_Guidelines_Search",
|
|
1364
1392
|
"GO_get_annotations_for_gene",
|
|
1365
1393
|
"GO_get_genes_for_term",
|
|
1366
1394
|
"GO_get_term_by_id",
|
|
1367
1395
|
"GO_get_term_details",
|
|
1368
1396
|
"GO_search_terms",
|
|
1397
|
+
"GTEx_get_expression_summary",
|
|
1398
|
+
"GTEx_query_eqtl",
|
|
1369
1399
|
"GWAS_search_associations_by_gene",
|
|
1370
1400
|
"GtoPdb_get_targets",
|
|
1371
1401
|
"HAL_search_archive",
|
|
@@ -1391,6 +1421,8 @@ __all__ = [
|
|
|
1391
1421
|
"LiteratureContextReviewer",
|
|
1392
1422
|
"LiteratureSearchTool",
|
|
1393
1423
|
"LiteratureSynthesisAgent",
|
|
1424
|
+
"MGnify_list_analyses",
|
|
1425
|
+
"MGnify_search_studies",
|
|
1394
1426
|
"MPD_get_phenotype_data",
|
|
1395
1427
|
"MedRxiv_search_preprints",
|
|
1396
1428
|
"MedicalLiteratureReviewer",
|
|
@@ -1404,6 +1436,8 @@ __all__ = [
|
|
|
1404
1436
|
"NICE_Clinical_Guidelines_Search",
|
|
1405
1437
|
"NICE_Guideline_Full_Text",
|
|
1406
1438
|
"NoveltySignificanceReviewer",
|
|
1439
|
+
"OBIS_search_occurrences",
|
|
1440
|
+
"OBIS_search_taxa",
|
|
1407
1441
|
"OSF_search_preprints",
|
|
1408
1442
|
"OSL_get_efo_id_by_disease_name",
|
|
1409
1443
|
"OpenAIRE_search_publications",
|
|
@@ -1485,6 +1519,8 @@ __all__ = [
|
|
|
1485
1519
|
"PubTator3_LiteratureSearch",
|
|
1486
1520
|
"PyPIPackageInspector",
|
|
1487
1521
|
"QuestionRephraser",
|
|
1522
|
+
"RNAcentral_get_by_accession",
|
|
1523
|
+
"RNAcentral_search",
|
|
1488
1524
|
"ReMap_get_transcription_factor_binding",
|
|
1489
1525
|
"Reactome_get_pathway_reactions",
|
|
1490
1526
|
"ReferenceInfoAnalyzer",
|
|
@@ -1495,8 +1531,10 @@ __all__ = [
|
|
|
1495
1531
|
"ScientificTextSummarizer",
|
|
1496
1532
|
"SemanticScholar_search_papers",
|
|
1497
1533
|
"TRIP_Database_Guidelines_Search",
|
|
1534
|
+
"TestCaseGenerator",
|
|
1498
1535
|
"TestResultsAnalyzer",
|
|
1499
1536
|
"ToolCompatibilityAnalyzer",
|
|
1537
|
+
"ToolDescriptionOptimizer",
|
|
1500
1538
|
"ToolDiscover",
|
|
1501
1539
|
"ToolGraphComposer",
|
|
1502
1540
|
"ToolGraphGenerationPipeline",
|
|
@@ -1526,11 +1564,14 @@ __all__ = [
|
|
|
1526
1564
|
"Unpaywall_check_oa_status",
|
|
1527
1565
|
"WHO_Guideline_Full_Text",
|
|
1528
1566
|
"WHO_Guidelines_Search",
|
|
1567
|
+
"WikiPathways_get_pathway",
|
|
1568
|
+
"WikiPathways_search",
|
|
1529
1569
|
"Wikidata_SPARQL_query",
|
|
1530
1570
|
"WoRMS_search_species",
|
|
1531
1571
|
"WritingPresentationReviewer",
|
|
1532
1572
|
"XMLToolOptimizer",
|
|
1533
1573
|
"Zenodo_search_records",
|
|
1574
|
+
"advanced_literature_search_agent",
|
|
1534
1575
|
"alphafold_get_annotations",
|
|
1535
1576
|
"alphafold_get_prediction",
|
|
1536
1577
|
"alphafold_get_summary",
|
|
@@ -1845,6 +1886,7 @@ __all__ = [
|
|
|
1845
1886
|
"ols_get_term_info",
|
|
1846
1887
|
"ols_search_ontologies",
|
|
1847
1888
|
"ols_search_terms",
|
|
1889
|
+
"open_deep_research_agent",
|
|
1848
1890
|
"openalex_literature_search",
|
|
1849
1891
|
"python_code_executor",
|
|
1850
1892
|
"python_script_runner",
|
|
@@ -0,0 +1,46 @@
|
|
|
1
|
+
"""
|
|
2
|
+
advanced_literature_search_agent
|
|
3
|
+
|
|
4
|
+
Advanced multi-agent literature search system. Required pipeline: (1) query_planner must produce ...
|
|
5
|
+
"""
|
|
6
|
+
|
|
7
|
+
from typing import Any, Optional, Callable
|
|
8
|
+
from ._shared_client import get_shared_client
|
|
9
|
+
|
|
10
|
+
|
|
11
|
+
def advanced_literature_search_agent(
|
|
12
|
+
query: str,
|
|
13
|
+
*,
|
|
14
|
+
stream_callback: Optional[Callable[[str], None]] = None,
|
|
15
|
+
use_cache: bool = False,
|
|
16
|
+
validate: bool = True,
|
|
17
|
+
) -> Any:
|
|
18
|
+
"""
|
|
19
|
+
Advanced multi-agent literature search system. Required pipeline: (1) query_planner must produce ...
|
|
20
|
+
|
|
21
|
+
Parameters
|
|
22
|
+
----------
|
|
23
|
+
query : str
|
|
24
|
+
Research query or topic to search in academic literature. The agent will auto...
|
|
25
|
+
stream_callback : Callable, optional
|
|
26
|
+
Callback for streaming output
|
|
27
|
+
use_cache : bool, default False
|
|
28
|
+
Enable caching
|
|
29
|
+
validate : bool, default True
|
|
30
|
+
Validate parameters
|
|
31
|
+
|
|
32
|
+
Returns
|
|
33
|
+
-------
|
|
34
|
+
Any
|
|
35
|
+
"""
|
|
36
|
+
# Handle mutable defaults to avoid B006 linting error
|
|
37
|
+
|
|
38
|
+
return get_shared_client().run_one_function(
|
|
39
|
+
{"name": "advanced_literature_search_agent", "arguments": {"query": query}},
|
|
40
|
+
stream_callback=stream_callback,
|
|
41
|
+
use_cache=use_cache,
|
|
42
|
+
validate=validate,
|
|
43
|
+
)
|
|
44
|
+
|
|
45
|
+
|
|
46
|
+
__all__ = ["advanced_literature_search_agent"]
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
"""
|
|
2
2
|
alphafold_get_annotations
|
|
3
3
|
|
|
4
|
-
Retrieve AlphaFold
|
|
4
|
+
Retrieve AlphaFold MUTAGEN annotations for a given UniProt accession. Returns experimental mutage...
|
|
5
5
|
"""
|
|
6
6
|
|
|
7
7
|
from typing import Any, Optional, Callable
|
|
@@ -10,21 +10,18 @@ from ._shared_client import get_shared_client
|
|
|
10
10
|
|
|
11
11
|
def alphafold_get_annotations(
|
|
12
12
|
qualifier: str,
|
|
13
|
-
type: str,
|
|
14
13
|
*,
|
|
15
14
|
stream_callback: Optional[Callable[[str], None]] = None,
|
|
16
15
|
use_cache: bool = False,
|
|
17
16
|
validate: bool = True,
|
|
18
17
|
) -> dict[str, Any]:
|
|
19
18
|
"""
|
|
20
|
-
Retrieve AlphaFold
|
|
19
|
+
Retrieve AlphaFold MUTAGEN annotations for a given UniProt accession. Returns experimental mutage...
|
|
21
20
|
|
|
22
21
|
Parameters
|
|
23
22
|
----------
|
|
24
23
|
qualifier : str
|
|
25
|
-
|
|
26
|
-
type : str
|
|
27
|
-
Annotation type (currently only 'MUTAGEN' is supported).
|
|
24
|
+
UniProt ACCESSION (e.g., 'P69905'). Must be an accession number, not an entry...
|
|
28
25
|
stream_callback : Callable, optional
|
|
29
26
|
Callback for streaming output
|
|
30
27
|
use_cache : bool, default False
|
|
@@ -39,10 +36,7 @@ def alphafold_get_annotations(
|
|
|
39
36
|
# Handle mutable defaults to avoid B006 linting error
|
|
40
37
|
|
|
41
38
|
return get_shared_client().run_one_function(
|
|
42
|
-
{
|
|
43
|
-
"name": "alphafold_get_annotations",
|
|
44
|
-
"arguments": {"qualifier": qualifier, "type": type},
|
|
45
|
-
},
|
|
39
|
+
{"name": "alphafold_get_annotations", "arguments": {"qualifier": qualifier}},
|
|
46
40
|
stream_callback=stream_callback,
|
|
47
41
|
use_cache=use_cache,
|
|
48
42
|
validate=validate,
|
|
@@ -1,8 +1,7 @@
|
|
|
1
1
|
"""
|
|
2
2
|
download_binary_file
|
|
3
3
|
|
|
4
|
-
Download binary files (images, videos, executables) with chunked
|
|
5
|
-
streaming for better memory management.
|
|
4
|
+
Download binary files (images, videos, executables) with chunked streaming for better memory mana...
|
|
6
5
|
"""
|
|
7
6
|
|
|
8
7
|
from typing import Any, Optional, Callable
|
|
@@ -20,16 +19,14 @@ def download_binary_file(
|
|
|
20
19
|
validate: bool = True,
|
|
21
20
|
) -> Any:
|
|
22
21
|
"""
|
|
23
|
-
Download binary files (images, videos, executables) with chunked
|
|
24
|
-
streaming for better memory management.
|
|
22
|
+
Download binary files (images, videos, executables) with chunked streaming for better memory mana...
|
|
25
23
|
|
|
26
24
|
Parameters
|
|
27
25
|
----------
|
|
28
26
|
url : str
|
|
29
27
|
HTTP or HTTPS URL to download from
|
|
30
28
|
output_path : str
|
|
31
|
-
Full path where to save the binary file
|
|
32
|
-
(e.g., /tmp/image.jpg or C:/Users/Downloads/file.pdf)
|
|
29
|
+
Full path where to save the binary file (e.g., /tmp/image.jpg or C:/Users/Dow...
|
|
33
30
|
chunk_size : int
|
|
34
31
|
Download chunk size in bytes (default: 1MB for binary files)
|
|
35
32
|
timeout : int
|