tooluniverse 1.0.7__py3-none-any.whl → 1.0.9__py3-none-any.whl

tooluniverse/tools/__init__.py

@@ -1,7 +1,7 @@
 """
 ToolUniverse Tools
 
-Type-safe Python interface to 654 scientific tools.
+Type-safe Python interface to 669 scientific tools.
 Each tool is in its own module for minimal import overhead.
 
 Usage:
@@ -32,6 +32,7 @@ from .ADMETAI_predict_solubility_lipophilicity_hydration import (
 )
 from .ADMETAI_predict_stress_response import ADMETAI_predict_stress_response
 from .ADMETAI_predict_toxicity import ADMETAI_predict_toxicity
+from .ADMETAnalyzerAgent import ADMETAnalyzerAgent
 from .AdvancedCodeQualityAnalyzer import AdvancedCodeQualityAnalyzer
 from .AdverseEventICDMapper import AdverseEventICDMapper
 from .AdverseEventPredictionQuestionGenerator import (
@@ -44,11 +45,15 @@ from .ArXiv_search_papers import ArXiv_search_papers
 from .ArgumentDescriptionOptimizer import ArgumentDescriptionOptimizer
 from .BioRxiv_search_preprints import BioRxiv_search_preprints
 from .BiomarkerDiscoveryWorkflow import BiomarkerDiscoveryWorkflow
+from .CMA_Guidelines_Search import CMA_Guidelines_Search
 from .CORE_search_papers import CORE_search_papers
 from .CallAgent import CallAgent
 from .ChEMBL_search_similar_molecules import ChEMBL_search_similar_molecules
+from .ClinVar_search_variants import ClinVar_search_variants
+from .ClinicalTrialDesignAgent import ClinicalTrialDesignAgent
 from .CodeOptimizer import CodeOptimizer
 from .CodeQualityAnalyzer import CodeQualityAnalyzer
+from .CompoundDiscoveryAgent import CompoundDiscoveryAgent
 from .ComprehensiveDrugDiscoveryPipeline import ComprehensiveDrugDiscoveryPipeline
 from .Crossref_search_works import Crossref_search_works
 from .DBLP_search_publications import DBLP_search_publications
@@ -58,8 +63,12 @@ from .DailyMed_search_spls import DailyMed_search_spls
 from .DataAnalysisValidityReviewer import DataAnalysisValidityReviewer
 from .DescriptionAnalyzer import DescriptionAnalyzer
 from .DescriptionQualityEvaluator import DescriptionQualityEvaluator
+from .DiseaseAnalyzerAgent import DiseaseAnalyzerAgent
 from .DomainExpertValidator import DomainExpertValidator
+from .DrugInteractionAnalyzerAgent import DrugInteractionAnalyzerAgent
+from .DrugOptimizationAgent import DrugOptimizationAgent
 from .DrugSafetyAnalyzer import DrugSafetyAnalyzer
+from .Ensembl_lookup_gene_by_symbol import Ensembl_lookup_gene_by_symbol
 from .EthicalComplianceReviewer import EthicalComplianceReviewer
 from .EuropePMC_Guidelines_Search import EuropePMC_Guidelines_Search
 from .EuropePMC_search_articles import EuropePMC_search_articles
@@ -441,11 +450,13 @@ from .FDA_retrieve_patient_medication_info_by_drug_name import (
 )
 from .Fatcat_search_scholar import Fatcat_search_scholar
 from .Finish import Finish
+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 .GWAS_search_associations_by_gene import GWAS_search_associations_by_gene
 from .HAL_search_archive import HAL_search_archive
 from .HPA_get_biological_processes_by_gene import HPA_get_biological_processes_by_gene
 from .HPA_get_cancer_prognostics_by_gene import HPA_get_cancer_prognostics_by_gene
@@ -474,6 +485,7 @@ from .HypothesisGenerator import HypothesisGenerator
 from .LabelGenerator import LabelGenerator
 from .LiteratureContextReviewer import LiteratureContextReviewer
 from .LiteratureSearchTool import LiteratureSearchTool
+from .LiteratureSynthesisAgent import LiteratureSynthesisAgent
 from .MedRxiv_search_preprints import MedRxiv_search_preprints
 from .MedicalLiteratureReviewer import MedicalLiteratureReviewer
 from .MedicalTermNormalizer import MedicalTermNormalizer
@@ -485,7 +497,6 @@ from .MedlinePlus_get_genetics_gene_by_name import MedlinePlus_get_genetics_gene
 from .MedlinePlus_get_genetics_index import MedlinePlus_get_genetics_index
 from .MedlinePlus_search_topics_by_keyword import MedlinePlus_search_topics_by_keyword
 from .MethodologyRigorReviewer import MethodologyRigorReviewer
-from .MultiAgentLiteratureSearch import MultiAgentLiteratureSearch
 from .NICE_Clinical_Guidelines_Search import NICE_Clinical_Guidelines_Search
 from .NICE_Guideline_Full_Text import NICE_Guideline_Full_Text
 from .NoveltySignificanceReviewer import NoveltySignificanceReviewer
@@ -704,6 +715,7 @@ from .Tool_Finder import Tool_Finder
 from .Tool_Finder_Keyword import Tool_Finder_Keyword
 from .Tool_Finder_LLM import Tool_Finder_LLM
 from .Tool_RAG import Tool_RAG
+from .UCSC_get_genes_by_region import UCSC_get_genes_by_region
 from .UniProt_get_alternative_names_by_accession import (
     UniProt_get_alternative_names_by_accession,
 )
@@ -744,6 +756,8 @@ from .cellosaurus_get_cell_line_info import cellosaurus_get_cell_line_info
 from .cellosaurus_query_converter import cellosaurus_query_converter
 from .cellosaurus_search_cell_lines import cellosaurus_search_cell_lines
 from .chembl_disease_target_score import chembl_disease_target_score
+from .convert_to_markdown import convert_to_markdown
+from .dbSNP_get_variant_by_rsid import dbSNP_get_variant_by_rsid
 from .dict_search import dict_search
 from .dili_search import dili_search
 from .diqt_search import diqt_search
@@ -1046,6 +1060,7 @@ from .get_xarray_info import get_xarray_info
 from .get_xesmf_info import get_xesmf_info
 from .get_xgboost_info import get_xgboost_info
 from .get_zarr_info import get_zarr_info
+from .gnomAD_query_variant import gnomAD_query_variant
 from .gwas_get_association_by_id import gwas_get_association_by_id
 from .gwas_get_associations_for_snp import gwas_get_associations_for_snp
 from .gwas_get_associations_for_study import gwas_get_associations_for_study
@@ -1090,6 +1105,7 @@ __all__ = [
     "ADMETAI_predict_solubility_lipophilicity_hydration",
     "ADMETAI_predict_stress_response",
     "ADMETAI_predict_toxicity",
+    "ADMETAnalyzerAgent",
     "AdvancedCodeQualityAnalyzer",
     "AdverseEventICDMapper",
     "AdverseEventPredictionQuestionGenerator",
@@ -1098,11 +1114,15 @@ __all__ = [
     "ArgumentDescriptionOptimizer",
     "BioRxiv_search_preprints",
     "BiomarkerDiscoveryWorkflow",
+    "CMA_Guidelines_Search",
     "CORE_search_papers",
     "CallAgent",
     "ChEMBL_search_similar_molecules",
+    "ClinVar_search_variants",
+    "ClinicalTrialDesignAgent",
     "CodeOptimizer",
     "CodeQualityAnalyzer",
+    "CompoundDiscoveryAgent",
     "ComprehensiveDrugDiscoveryPipeline",
     "Crossref_search_works",
     "DBLP_search_publications",
@@ -1112,8 +1132,12 @@ __all__ = [
     "DataAnalysisValidityReviewer",
     "DescriptionAnalyzer",
     "DescriptionQualityEvaluator",
+    "DiseaseAnalyzerAgent",
     "DomainExpertValidator",
+    "DrugInteractionAnalyzerAgent",
+    "DrugOptimizationAgent",
     "DrugSafetyAnalyzer",
+    "Ensembl_lookup_gene_by_symbol",
     "EthicalComplianceReviewer",
     "EuropePMC_Guidelines_Search",
     "EuropePMC_search_articles",
@@ -1291,11 +1315,13 @@ __all__ = [
     "FDA_retrieve_patient_medication_info_by_drug_name",
     "Fatcat_search_scholar",
     "Finish",
+    "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",
+    "GWAS_search_associations_by_gene",
     "HAL_search_archive",
     "HPA_get_biological_processes_by_gene",
     "HPA_get_cancer_prognostics_by_gene",
@@ -1314,6 +1340,7 @@ __all__ = [
     "LabelGenerator",
     "LiteratureContextReviewer",
     "LiteratureSearchTool",
+    "LiteratureSynthesisAgent",
     "MedRxiv_search_preprints",
     "MedicalLiteratureReviewer",
     "MedicalTermNormalizer",
@@ -1323,7 +1350,6 @@ __all__ = [
     "MedlinePlus_get_genetics_index",
     "MedlinePlus_search_topics_by_keyword",
     "MethodologyRigorReviewer",
-    "MultiAgentLiteratureSearch",
     "NICE_Clinical_Guidelines_Search",
     "NICE_Guideline_Full_Text",
     "NoveltySignificanceReviewer",
@@ -1430,6 +1456,7 @@ __all__ = [
     "Tool_Finder_Keyword",
     "Tool_Finder_LLM",
     "Tool_RAG",
+    "UCSC_get_genes_by_region",
     "UniProt_get_alternative_names_by_accession",
     "UniProt_get_disease_variants_by_accession",
     "UniProt_get_entry_by_accession",
@@ -1456,6 +1483,8 @@ __all__ = [
     "cellosaurus_query_converter",
     "cellosaurus_search_cell_lines",
     "chembl_disease_target_score",
+    "convert_to_markdown",
+    "dbSNP_get_variant_by_rsid",
     "dict_search",
     "dili_search",
     "diqt_search",
@@ -1708,6 +1737,7 @@ __all__ = [
     "get_xesmf_info",
     "get_xgboost_info",
     "get_zarr_info",
+    "gnomAD_query_variant",
     "gwas_get_association_by_id",
     "gwas_get_associations_for_snp",
     "gwas_get_associations_for_study",

tooluniverse/tools/convert_to_markdown.py

@@ -0,0 +1,59 @@
+"""
+convert_to_markdown
+
+Convert a resource described by an http:, https:, file: or data: URI to markdown.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def convert_to_markdown(
+    uri: str,
+    output_path: Optional[str] = None,
+    enable_plugins: Optional[bool] = False,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Convert a resource described by an http:, https:, file: or data: URI to markdown.
+
+    Parameters
+    ----------
+    uri : str
+        URI of the resource to convert (supports http:, https:, file:, data: URIs)
+    output_path : str
+        Optional output file path
+    enable_plugins : bool
+        Enable 3rd-party plugins
+    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": "convert_to_markdown",
+            "arguments": {
+                "uri": uri,
+                "output_path": output_path,
+                "enable_plugins": enable_plugins,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["convert_to_markdown"]

tooluniverse/tools/dbSNP_get_variant_by_rsid.py

@@ -0,0 +1,46 @@
+"""
+dbSNP_get_variant_by_rsid
+
+Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def dbSNP_get_variant_by_rsid(
+    rsid: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).
+
+    Parameters
+    ----------
+    rsid : str
+        rsID without 'rs' prefix or with (e.g., rs699 or 699).
+    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": "dbSNP_get_variant_by_rsid", "arguments": {"rsid": rsid}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["dbSNP_get_variant_by_rsid"]

tooluniverse/tools/gnomAD_query_variant.py

@@ -0,0 +1,52 @@
+"""
+gnomAD_query_variant
+
+Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gnomAD_query_variant(
+    variant_id: str,
+    dataset: Optional[str] = "gnomad_r4",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).
+
+    Parameters
+    ----------
+    variant_id : str
+        Variant ID like '1-230710048-A-G'.
+    dataset : str
+        Dataset ID (e.g., gnomad_r4).
+    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": "gnomAD_query_variant",
+            "arguments": {"variant_id": variant_id, "dataset": dataset},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gnomAD_query_variant"]

tooluniverse/tools/openalex_literature_search.py

@@ -10,10 +10,10 @@ from ._shared_client import get_shared_client
 
 def openalex_literature_search(
     search_keywords: str,
-    max_results: int,
-    year_from: int,
-    year_to: int,
-    open_access: bool,
+    max_results: Optional[int] = 10,
+    year_from: Optional[int] = None,
+    year_to: Optional[int] = None,
+    open_access: Optional[bool] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/ucsc_tool.py

@@ -0,0 +1,60 @@
+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,
+        }