tooluniverse 1.0.11.2__py3-none-any.whl → 1.0.12__py3-none-any.whl

tooluniverse/tools/RNAcentral_search.py

@@ -0,0 +1,52 @@
+"""
+RNAcentral_search
+
+Search aggregated ncRNA records (miRNA, rRNA, lncRNA, etc.) across sources via RNAcentral. Use to...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def RNAcentral_search(
+    query: str,
+    page_size: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search aggregated ncRNA records (miRNA, rRNA, lncRNA, etc.) across sources via RNAcentral. Use to...
+
+    Parameters
+    ----------
+    query : str
+        Keyword, accession, or sequence-based query (per RNAcentral API).
+    page_size : int
+        Number of records per page (1–100).
+    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": "RNAcentral_search",
+            "arguments": {"query": query, "page_size": page_size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["RNAcentral_search"]

tooluniverse/tools/TestCaseGenerator.py

@@ -0,0 +1,46 @@
+"""
+TestCaseGenerator
+
+Generates diverse and representative ToolUniverse tool call dictionaries for a given tool based o...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def TestCaseGenerator(
+    tool_config: dict[str, Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Generates diverse and representative ToolUniverse tool call dictionaries for a given tool based o...
+
+    Parameters
+    ----------
+    tool_config : dict[str, Any]
+        The full configuration of the tool to generate test cases for. May include '_...
+    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": "TestCaseGenerator", "arguments": {"tool_config": tool_config}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["TestCaseGenerator"]

tooluniverse/tools/ToolDescriptionOptimizer.py

@@ -0,0 +1,67 @@
+"""
+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,
+) -> dict[str, 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
+    -------
+    dict[str, 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/ToolDiscover.py

@@ -13,6 +13,7 @@ def ToolDiscover(
     max_iterations: Optional[int] = 2,
     save_to_file: Optional[bool] = True,
     output_file: Optional[str] = None,
+    save_dir: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,
@@ -31,6 +32,8 @@ def ToolDiscover(
         Whether to save the generated tool files
     output_file : str
         Optional file path to save the generated tool
+    save_dir : str
+        Directory path to save the generated tool files (defaults to current working ...
     stream_callback : Callable, optional
         Callback for streaming output
     use_cache : bool, default False
@@ -52,6 +55,7 @@ def ToolDiscover(
                 "max_iterations": max_iterations,
                 "save_to_file": save_to_file,
                 "output_file": output_file,
+                "save_dir": save_dir,
             },
         },
         stream_callback=stream_callback,

tooluniverse/tools/UniProt_search.py

@@ -1,9 +1,7 @@
 """
 UniProt_search
 
-Search UniProtKB database using flexible query syntax.
-Supports gene names (e.g., 'gene:TP53'), protein names,
-organism filters, and complex queries.
+Search UniProtKB database with flexible query syntax. Returns protein entries with accession numb...
 """
 
 from typing import Any, Optional, Callable
@@ -14,49 +12,32 @@ def UniProt_search(
     query: str,
     organism: Optional[str] = None,
     limit: Optional[int] = None,
-    fields: Optional[list[Any]] = None,
     min_length: Optional[int] = None,
     max_length: 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 with flexible query syntax.
-
-    Search UniProtKB and return protein entries. Supports field searches,
-    ranges, wildcards, boolean operators, and parentheses for grouping.
+    Search UniProtKB database with flexible query syntax. Returns protein entries with accession numb...
 
     Parameters
     ----------
     query : str
-        Search query. Examples:
-        - Simple: 'MEIOB', 'insulin'
-        - Field: 'gene:TP53', 'organism_id:9606', 'reviewed:true'
-        - Range: 'length:[100 TO 500]', 'mass:[20000 TO 50000]'
-        - Wildcard: 'gene:MEIOB*'
-        - Boolean: 'gene:TP53 AND organism_id:9606'
-        - Grouped: '(organism_id:9606 OR organism_id:10090) AND
-          gene:TP53'
-    organism : str, optional
-        Organism filter. Use 'human', 'mouse', 'rat', 'yeast' or
-        taxonomy ID like '9606'. Combined with query using AND.
-    limit : int, optional
-        Maximum results to return (default: 25, max: 500).
-        Accepts string or integer.
-    fields : list[str], optional
-        Field names to return. When specified, returns raw API response.
-        Common: accession, id, gene_names, gene_primary, protein_name,
-        organism_name, organism_id, length, mass, sequence, reviewed,
-        cc_function.
-        Default: formatted response with accession, id, protein_name,
-        gene_names, organism, length.
-    min_length : int, optional
-        Minimum sequence length. Converts to 'length:[min TO *]'.
-    max_length : int, optional
-        Maximum sequence length. Converts to 'length:[* TO max]'.
-    stream_callback : callable, optional
+        Search query using UniProt syntax. Simple: 'MEIOB', 'insulin'. Field searches...
+    organism : str
+        Optional organism filter. Use common names ('human', 'mouse', 'rat', 'yeast')...
+    limit : int
+        Maximum number of results to return (default: 25, max: 500). Accepts string o...
+    min_length : int
+        Minimum sequence length. Auto-converts to 'length:[min TO *]' range query.
+    max_length : int
+        Maximum sequence length. Auto-converts to 'length:[* TO max]' range query.
+    fields : list[Any]
+        List of field names to return (e.g., ['accession','gene_primary','length','or...
+    stream_callback : Callable, optional
         Callback for streaming output
     use_cache : bool, default False
         Enable caching
@@ -65,15 +46,7 @@ def UniProt_search(
 
     Returns
     -------
-    dict
-        Search results with total_results, returned count, and results
-        list
-
-    Examples
-    --------
-    >>> UniProt_search("gene:TP53", organism="human", limit=5)
-    >>> UniProt_search("insulin", fields=['accession', 'length'])
-    >>> UniProt_search("gene:MEIOB", min_length=400, max_length=500)
+    Any
     """
     # Handle mutable defaults to avoid B006 linting error
 
@@ -84,9 +57,9 @@ def UniProt_search(
                 "query": query,
                 "organism": organism,
                 "limit": limit,
-                "fields": fields,
                 "min_length": min_length,
                 "max_length": max_length,
+                "fields": fields,
             },
         },
         stream_callback=stream_callback,

tooluniverse/tools/WikiPathways_get_pathway.py

@@ -0,0 +1,52 @@
+"""
+WikiPathways_get_pathway
+
+Fetch pathway content by WPID (JSON/GPML). Use to programmatically access pathway nodes/edges/met...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def WikiPathways_get_pathway(
+    wpid: str,
+    format: Optional[str] = "json",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Fetch pathway content by WPID (JSON/GPML). Use to programmatically access pathway nodes/edges/met...
+
+    Parameters
+    ----------
+    wpid : str
+        WikiPathways identifier (e.g., 'WP254').
+    format : str
+        Response format: 'json' for structured, 'gpml' for GPML XML.
+    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": "WikiPathways_get_pathway",
+            "arguments": {"wpid": wpid, "format": format},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["WikiPathways_get_pathway"]

tooluniverse/tools/WikiPathways_search.py

@@ -0,0 +1,52 @@
+"""
+WikiPathways_search
+
+Text search across community-curated pathways (disease, metabolic, signaling). Use to discover re...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def WikiPathways_search(
+    query: str,
+    organism: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Text search across community-curated pathways (disease, metabolic, signaling). Use to discover re...
+
+    Parameters
+    ----------
+    query : str
+        Free-text query (keywords, gene symbols, processes), e.g., 'p53', 'glycolysis'.
+    organism : str
+        Organism filter (scientific name), e.g., 'Homo sapiens'.
+    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": "WikiPathways_search",
+            "arguments": {"query": query, "organism": organism},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["WikiPathways_search"]

tooluniverse/tools/__init__.py

@@ -1,7 +1,7 @@
 """
 ToolUniverse Tools
 
-Type-safe Python interface to 713 scientific tools.
+Type-safe Python interface to 734 scientific tools.
 Each tool is in its own module for minimal import overhead.
 
 Usage:
@@ -42,6 +42,7 @@ from .AdverseEventPredictionQuestionGeneratorWithContext import (
     AdverseEventPredictionQuestionGeneratorWithContext,
 )
 from .ArXiv_search_papers import ArXiv_search_papers
+from .ArgumentDescriptionOptimizer import ArgumentDescriptionOptimizer
 from .BLAST_nucleotide_search import BLAST_nucleotide_search
 from .BLAST_protein_search import BLAST_protein_search
 from .BioRxiv_search_preprints import BioRxiv_search_preprints
@@ -68,6 +69,8 @@ from .DrugInteractionAnalyzerAgent import DrugInteractionAnalyzerAgent
 from .DrugOptimizationAgent import DrugOptimizationAgent
 from .DrugSafetyAnalyzer import DrugSafetyAnalyzer
 from .EMDB_get_structure import EMDB_get_structure
+from .ENCODE_list_files import ENCODE_list_files
+from .ENCODE_search_experiments import ENCODE_search_experiments
 from .EthicalComplianceReviewer import EthicalComplianceReviewer
 from .EuropePMC_Guidelines_Search import EuropePMC_Guidelines_Search
 from .EuropePMC_search_articles import EuropePMC_search_articles
@@ -449,12 +452,18 @@ from .FDA_retrieve_patient_medication_info_by_drug_name import (
 )
 from .Fatcat_search_scholar import Fatcat_search_scholar
 from .Finish import Finish
+from .GBIF_search_occurrences import GBIF_search_occurrences
+from .GBIF_search_species import GBIF_search_species
+from .GDC_list_files import GDC_list_files
+from .GDC_search_cases import GDC_search_cases
 from .GIN_Guidelines_Search import GIN_Guidelines_Search
 from .GO_get_annotations_for_gene import GO_get_annotations_for_gene
 from .GO_get_genes_for_term import GO_get_genes_for_term
 from .GO_get_term_by_id import GO_get_term_by_id
 from .GO_get_term_details import GO_get_term_details
 from .GO_search_terms import GO_search_terms
+from .GTEx_get_expression_summary import GTEx_get_expression_summary
+from .GTEx_query_eqtl import GTEx_query_eqtl
 from .GWAS_search_associations_by_gene import GWAS_search_associations_by_gene
 from .GtoPdb_get_targets import GtoPdb_get_targets
 from .HAL_search_archive import HAL_search_archive
@@ -490,6 +499,8 @@ from .LabelGenerator import LabelGenerator
 from .LiteratureContextReviewer import LiteratureContextReviewer
 from .LiteratureSearchTool import LiteratureSearchTool
 from .LiteratureSynthesisAgent import LiteratureSynthesisAgent
+from .MGnify_list_analyses import MGnify_list_analyses
+from .MGnify_search_studies import MGnify_search_studies
 from .MPD_get_phenotype_data import MPD_get_phenotype_data
 from .MedRxiv_search_preprints import MedRxiv_search_preprints
 from .MedicalLiteratureReviewer import MedicalLiteratureReviewer
@@ -505,6 +516,8 @@ from .MethodologyRigorReviewer import MethodologyRigorReviewer
 from .NICE_Clinical_Guidelines_Search import NICE_Clinical_Guidelines_Search
 from .NICE_Guideline_Full_Text import NICE_Guideline_Full_Text
 from .NoveltySignificanceReviewer import NoveltySignificanceReviewer
+from .OBIS_search_occurrences import OBIS_search_occurrences
+from .OBIS_search_taxa import OBIS_search_taxa
 from .OSF_search_preprints import OSF_search_preprints
 from .OSL_get_efo_id_by_disease_name import OSL_get_efo_id_by_disease_name
 from .OpenAIRE_search_publications import OpenAIRE_search_publications
@@ -698,6 +711,8 @@ from .PubTator3_EntityAutocomplete import PubTator3_EntityAutocomplete
 from .PubTator3_LiteratureSearch import PubTator3_LiteratureSearch
 from .PyPIPackageInspector import PyPIPackageInspector
 from .QuestionRephraser import QuestionRephraser
+from .RNAcentral_get_by_accession import RNAcentral_get_by_accession
+from .RNAcentral_search import RNAcentral_search
 from .ReMap_get_transcription_factor_binding import (
     ReMap_get_transcription_factor_binding,
 )
@@ -710,8 +725,10 @@ from .SCREEN_get_regulatory_elements import SCREEN_get_regulatory_elements
 from .ScientificTextSummarizer import ScientificTextSummarizer
 from .SemanticScholar_search_papers import SemanticScholar_search_papers
 from .TRIP_Database_Guidelines_Search import TRIP_Database_Guidelines_Search
+from .TestCaseGenerator import TestCaseGenerator
 from .TestResultsAnalyzer import TestResultsAnalyzer
 from .ToolCompatibilityAnalyzer import ToolCompatibilityAnalyzer
+from .ToolDescriptionOptimizer import ToolDescriptionOptimizer
 from .ToolDiscover import ToolDiscover
 from .ToolGraphComposer import ToolGraphComposer
 from .ToolGraphGenerationPipeline import ToolGraphGenerationPipeline
@@ -751,11 +768,14 @@ from .UnifiedToolGenerator import UnifiedToolGenerator
 from .Unpaywall_check_oa_status import Unpaywall_check_oa_status
 from .WHO_Guideline_Full_Text import WHO_Guideline_Full_Text
 from .WHO_Guidelines_Search import WHO_Guidelines_Search
+from .WikiPathways_get_pathway import WikiPathways_get_pathway
+from .WikiPathways_search import WikiPathways_search
 from .Wikidata_SPARQL_query import Wikidata_SPARQL_query
 from .WoRMS_search_species import WoRMS_search_species
 from .WritingPresentationReviewer import WritingPresentationReviewer
 from .XMLToolOptimizer import XMLToolOptimizer
 from .Zenodo_search_records import Zenodo_search_records
+from .advanced_literature_search_agent import advanced_literature_search_agent
 from .alphafold_get_annotations import alphafold_get_annotations
 from .alphafold_get_prediction import alphafold_get_prediction
 from .alphafold_get_summary import alphafold_get_summary
@@ -1128,6 +1148,7 @@ from .ols_get_term_children import ols_get_term_children
 from .ols_get_term_info import ols_get_term_info
 from .ols_search_ontologies import ols_search_ontologies
 from .ols_search_terms import ols_search_terms
+from .open_deep_research_agent import open_deep_research_agent
 from .openalex_literature_search import openalex_literature_search
 from .python_code_executor import python_code_executor
 from .python_script_runner import python_script_runner
@@ -1157,6 +1178,7 @@ __all__ = [
     "AdverseEventPredictionQuestionGenerator",
     "AdverseEventPredictionQuestionGeneratorWithContext",
     "ArXiv_search_papers",
+    "ArgumentDescriptionOptimizer",
     "BLAST_nucleotide_search",
     "BLAST_protein_search",
     "BioRxiv_search_preprints",
@@ -1183,6 +1205,8 @@ __all__ = [
     "DrugOptimizationAgent",
     "DrugSafetyAnalyzer",
     "EMDB_get_structure",
+    "ENCODE_list_files",
+    "ENCODE_search_experiments",
     "EthicalComplianceReviewer",
     "EuropePMC_Guidelines_Search",
     "EuropePMC_search_articles",
@@ -1360,12 +1384,18 @@ __all__ = [
     "FDA_retrieve_patient_medication_info_by_drug_name",
     "Fatcat_search_scholar",
     "Finish",
+    "GBIF_search_occurrences",
+    "GBIF_search_species",
+    "GDC_list_files",
+    "GDC_search_cases",
     "GIN_Guidelines_Search",
     "GO_get_annotations_for_gene",
     "GO_get_genes_for_term",
     "GO_get_term_by_id",
     "GO_get_term_details",
     "GO_search_terms",
+    "GTEx_get_expression_summary",
+    "GTEx_query_eqtl",
     "GWAS_search_associations_by_gene",
     "GtoPdb_get_targets",
     "HAL_search_archive",
@@ -1391,6 +1421,8 @@ __all__ = [
     "LiteratureContextReviewer",
     "LiteratureSearchTool",
     "LiteratureSynthesisAgent",
+    "MGnify_list_analyses",
+    "MGnify_search_studies",
     "MPD_get_phenotype_data",
     "MedRxiv_search_preprints",
     "MedicalLiteratureReviewer",
@@ -1404,6 +1436,8 @@ __all__ = [
     "NICE_Clinical_Guidelines_Search",
     "NICE_Guideline_Full_Text",
     "NoveltySignificanceReviewer",
+    "OBIS_search_occurrences",
+    "OBIS_search_taxa",
     "OSF_search_preprints",
     "OSL_get_efo_id_by_disease_name",
     "OpenAIRE_search_publications",
@@ -1485,6 +1519,8 @@ __all__ = [
     "PubTator3_LiteratureSearch",
     "PyPIPackageInspector",
     "QuestionRephraser",
+    "RNAcentral_get_by_accession",
+    "RNAcentral_search",
     "ReMap_get_transcription_factor_binding",
     "Reactome_get_pathway_reactions",
     "ReferenceInfoAnalyzer",
@@ -1495,8 +1531,10 @@ __all__ = [
     "ScientificTextSummarizer",
     "SemanticScholar_search_papers",
     "TRIP_Database_Guidelines_Search",
+    "TestCaseGenerator",
     "TestResultsAnalyzer",
     "ToolCompatibilityAnalyzer",
+    "ToolDescriptionOptimizer",
     "ToolDiscover",
     "ToolGraphComposer",
     "ToolGraphGenerationPipeline",
@@ -1526,11 +1564,14 @@ __all__ = [
     "Unpaywall_check_oa_status",
     "WHO_Guideline_Full_Text",
     "WHO_Guidelines_Search",
+    "WikiPathways_get_pathway",
+    "WikiPathways_search",
     "Wikidata_SPARQL_query",
     "WoRMS_search_species",
     "WritingPresentationReviewer",
     "XMLToolOptimizer",
     "Zenodo_search_records",
+    "advanced_literature_search_agent",
     "alphafold_get_annotations",
     "alphafold_get_prediction",
     "alphafold_get_summary",
@@ -1845,6 +1886,7 @@ __all__ = [
     "ols_get_term_info",
     "ols_search_ontologies",
     "ols_search_terms",
+    "open_deep_research_agent",
     "openalex_literature_search",
     "python_code_executor",
     "python_script_runner",

tooluniverse/tools/advanced_literature_search_agent.py

@@ -0,0 +1,46 @@
+"""
+advanced_literature_search_agent
+
+Advanced multi-agent literature search system. Required pipeline: (1) query_planner must produce ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def advanced_literature_search_agent(
+    query: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Advanced multi-agent literature search system. Required pipeline: (1) query_planner must produce ...
+
+    Parameters
+    ----------
+    query : str
+        Research query or topic to search in academic literature. The agent will auto...
+    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": "advanced_literature_search_agent", "arguments": {"query": query}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["advanced_literature_search_agent"]