"""
Default tool configuration files mapping.
This module contains the default mapping of tool categories to their JSON configuration files.
It's separated from __init__.py to avoid circular imports.
"""
import os
import json
from pathlib import Path
# Get the current directory where this file is located
current_dir = os.path.dirname(os.path.abspath(__file__))
default_tool_files = {
"special_tools": os.path.join(current_dir, "data", "special_tools.json"),
"tool_finder": os.path.join(current_dir, "data", "finder_tools.json"),
# 'tool_finder_llm': os.path.join(current_dir, 'data', 'tool_finder_llm_config.json'),
"opentarget": os.path.join(current_dir, "data", "opentarget_tools.json"),
"fda_drug_label": os.path.join(current_dir, "data", "fda_drug_labeling_tools.json"),
"monarch": os.path.join(current_dir, "data", "monarch_tools.json"),
"clinical_trials": os.path.join(
current_dir, "data", "clinicaltrials_gov_tools.json"
),
"fda_drug_adverse_event": os.path.join(
current_dir, "data", "fda_drug_adverse_event_tools.json"
),
"fda_drug_adverse_event_detail": os.path.join(
current_dir, "data", "fda_drug_adverse_event_detail_tools.json"
),
"ChEMBL": os.path.join(current_dir, "data", "chembl_tools.json"),
"EuropePMC": os.path.join(current_dir, "data", "europe_pmc_tools.json"),
"semantic_scholar": os.path.join(
current_dir, "data", "semantic_scholar_tools.json"
),
"pubtator": os.path.join(current_dir, "data", "pubtator_tools.json"),
"EFO": os.path.join(current_dir, "data", "efo_tools.json"),
"Enrichr": os.path.join(current_dir, "data", "enrichr_tools.json"),
"HumanBase": os.path.join(current_dir, "data", "humanbase_tools.json"),
"OpenAlex": os.path.join(current_dir, "data", "openalex_tools.json"),
# Literature search tools
"literature_search": os.path.join(
current_dir, "data", "literature_search_tools.json"
),
"arxiv": os.path.join(current_dir, "data", "arxiv_tools.json"),
"crossref": os.path.join(current_dir, "data", "crossref_tools.json"),
"simbad": os.path.join(current_dir, "data", "simbad_tools.json"),
"dblp": os.path.join(current_dir, "data", "dblp_tools.json"),
"pubmed": os.path.join(current_dir, "data", "pubmed_tools.json"),
"ncbi_nucleotide": os.path.join(current_dir, "data", "ncbi_nucleotide_tools.json"),
"doaj": os.path.join(current_dir, "data", "doaj_tools.json"),
"unpaywall": os.path.join(current_dir, "data", "unpaywall_tools.json"),
"biorxiv": os.path.join(current_dir, "data", "biorxiv_tools.json"),
"medrxiv": os.path.join(current_dir, "data", "medrxiv_tools.json"),
"hal": os.path.join(current_dir, "data", "hal_tools.json"),
"core": os.path.join(current_dir, "data", "core_tools.json"),
"pmc": os.path.join(current_dir, "data", "pmc_tools.json"),
"zenodo": os.path.join(current_dir, "data", "zenodo_tools.json"),
"openaire": os.path.join(current_dir, "data", "openaire_tools.json"),
"osf_preprints": os.path.join(current_dir, "data", "osf_preprints_tools.json"),
"fatcat": os.path.join(current_dir, "data", "fatcat_tools.json"),
"wikidata_sparql": os.path.join(current_dir, "data", "wikidata_sparql_tools.json"),
"wikipedia": os.path.join(current_dir, "data", "wikipedia_tools.json"),
"dbpedia": os.path.join(current_dir, "data", "dbpedia_tools.json"),
"agents": os.path.join(current_dir, "data", "agentic_tools.json"),
# Smolagents tool wrapper configs
"smolagents": os.path.join(current_dir, "data", "smolagent_tools.json"),
"tool_discovery_agents": os.path.join(
current_dir, "data", "tool_discovery_agents.json"
),
"web_search_tools": os.path.join(current_dir, "data", "web_search_tools.json"),
"package_discovery_tools": os.path.join(
current_dir, "data", "package_discovery_tools.json"
),
"pypi_package_inspector_tools": os.path.join(
current_dir, "data", "pypi_package_inspector_tools.json"
),
"drug_discovery_agents": os.path.join(
current_dir, "data", "drug_discovery_agents.json"
),
"dataset": os.path.join(current_dir, "data", "dataset_tools.json"),
# 'mcp_clients': os.path.join(current_dir, 'data', 'mcp_client_tools_example.json'),
"mcp_auto_loader_txagent": os.path.join(
current_dir, "data", "txagent_client_tools.json"
),
"mcp_auto_loader_expert_feedback": os.path.join(
current_dir, "data", "expert_feedback_tools.json"
),
"adverse_event": os.path.join(current_dir, "data", "adverse_event_tools.json"),
"dailymed": os.path.join(current_dir, "data", "dailymed_tools.json"),
"cdc": os.path.join(current_dir, "data", "cdc_tools.json"),
"nhanes": os.path.join(current_dir, "data", "nhanes_tools.json"),
"health_disparities": os.path.join(
current_dir, "data", "health_disparities_tools.json"
),
"hpa": os.path.join(current_dir, "data", "hpa_tools.json"),
"reactome": os.path.join(current_dir, "data", "reactome_tools.json"),
"pubchem": os.path.join(current_dir, "data", "pubchem_tools.json"),
"medlineplus": os.path.join(current_dir, "data", "medlineplus_tools.json"),
"rxnorm": os.path.join(current_dir, "data", "rxnorm_tools.json"),
"uniprot": os.path.join(current_dir, "data", "uniprot_tools.json"),
"cellosaurus": os.path.join(current_dir, "data", "cellosaurus_tools.json"),
# 'software': os.path.join(current_dir, 'data', 'software_tools.json'),
# Package tools - categorized software tools
"software_bioinformatics": os.path.join(
current_dir, "data", "packages", "bioinformatics_core_tools.json"
),
"software_genomics": os.path.join(
current_dir, "data", "packages", "genomics_tools.json"
),
"software_single_cell": os.path.join(
current_dir, "data", "packages", "single_cell_tools.json"
),
"software_structural_biology": os.path.join(
current_dir, "data", "packages", "structural_biology_tools.json"
),
"software_cheminformatics": os.path.join(
current_dir, "data", "packages", "cheminformatics_tools.json"
),
"software_machine_learning": os.path.join(
current_dir, "data", "packages", "machine_learning_tools.json"
),
"software_visualization": os.path.join(
current_dir, "data", "packages", "visualization_tools.json"
),
# Scientific visualization tools
"visualization_protein_3d": os.path.join(
current_dir, "data", "protein_structure_3d_tools.json"
),
"visualization_molecule_2d": os.path.join(
current_dir, "data", "molecule_2d_tools.json"
),
# New database tools
"interpro": os.path.join(current_dir, "data", "interpro_tools.json"),
"ebi_search": os.path.join(current_dir, "data", "ebi_search_tools.json"),
"intact": os.path.join(current_dir, "data", "intact_tools.json"),
"metabolights": os.path.join(current_dir, "data", "metabolights_tools.json"),
"proteins_api": os.path.join(current_dir, "data", "proteins_api_tools.json"),
"arrayexpress": os.path.join(current_dir, "data", "arrayexpress_tools.json"),
"biostudies": os.path.join(current_dir, "data", "biostudies_tools.json"),
"dbfetch": os.path.join(current_dir, "data", "dbfetch_tools.json"),
"pdbe_api": os.path.join(current_dir, "data", "pdbe_api_tools.json"),
"ena_browser": os.path.join(current_dir, "data", "ena_browser_tools.json"),
"blast": os.path.join(current_dir, "data", "blast_tools.json"),
"cbioportal": os.path.join(current_dir, "data", "cbioportal_tools.json"),
"regulomedb": os.path.join(current_dir, "data", "regulomedb_tools.json"),
"jaspar": os.path.join(current_dir, "data", "jaspar_tools.json"),
"remap": os.path.join(current_dir, "data", "remap_tools.json"),
"screen": os.path.join(current_dir, "data", "screen_tools.json"),
"pride": os.path.join(current_dir, "data", "pride_tools.json"),
"emdb": os.path.join(current_dir, "data", "emdb_tools.json"),
"gtopdb": os.path.join(current_dir, "data", "gtopdb_tools.json"),
"mpd": os.path.join(current_dir, "data", "mpd_tools.json"),
"worms": os.path.join(current_dir, "data", "worms_tools.json"),
"paleobiology": os.path.join(current_dir, "data", "paleobiology_tools.json"),
"visualization_molecule_3d": os.path.join(
current_dir, "data", "molecule_3d_tools.json"
),
"software_scientific_computing": os.path.join(
current_dir, "data", "packages", "scientific_computing_tools.json"
),
"software_physics_astronomy": os.path.join(
current_dir, "data", "packages", "physics_astronomy_tools.json"
),
"software_earth_sciences": os.path.join(
current_dir, "data", "packages", "earth_sciences_tools.json"
),
"software_image_processing": os.path.join(
current_dir, "data", "packages", "image_processing_tools.json"
),
"software_neuroscience": os.path.join(
current_dir, "data", "packages", "neuroscience_tools.json"
),
"go": os.path.join(current_dir, "data", "gene_ontology_tools.json"),
"compose": os.path.join(current_dir, "data", "compose_tools.json"),
"python_executor": os.path.join(current_dir, "data", "python_executor_tools.json"),
"idmap": os.path.join(current_dir, "data", "idmap_tools.json"),
"disease_target_score": os.path.join(
current_dir, "data", "disease_target_score_tools.json"
),
"mcp_auto_loader_uspto_downloader": os.path.join(
current_dir, "data", "uspto_downloader_tools.json"
),
"uspto": os.path.join(current_dir, "data", "uspto_tools.json"),
"xml": os.path.join(current_dir, "data", "xml_tools.json"),
"mcp_auto_loader_boltz": os.path.join(
current_dir, "data", "boltz_mcp_loader_tools.json"
),
"url": os.path.join(current_dir, "data", "url_fetch_tools.json"),
"file_download": os.path.join(current_dir, "data", "file_download_tools.json"),
# 'langchain': os.path.join(current_dir, 'data', 'langchain_tools.json'),
"rcsb_pdb": os.path.join(current_dir, "data", "rcsb_pdb_tools.json"),
"rcsb_search": os.path.join(current_dir, "data", "rcsb_search_tools.json"),
"tool_composition": os.path.join(
current_dir, "data", "tool_composition_tools.json"
),
"embedding": os.path.join(current_dir, "data", "embedding_tools.json"),
"gwas": os.path.join(current_dir, "data", "gwas_tools.json"),
"admetai": os.path.join(current_dir, "data", "admetai_tools.json"),
# duplicate key removed
"alphafold": os.path.join(current_dir, "data", "alphafold_tools.json"),
"output_summarization": os.path.join(
current_dir, "data", "output_summarization_tools.json"
),
"odphp": os.path.join(current_dir, "data", "odphp_tools.json"),
"who_gho": os.path.join(current_dir, "data", "who_gho_tools.json"),
"umls": os.path.join(current_dir, "data", "umls_tools.json"),
"euhealth": os.path.join(current_dir, "data", "euhealth_tools.json"),
"markitdown": os.path.join(current_dir, "data", "markitdown_tools.json"),
# Guideline and health policy tools
"guidelines": os.path.join(current_dir, "data", "unified_guideline_tools.json"),
# Database tools
"kegg": os.path.join(current_dir, "data", "kegg_tools.json"),
"ensembl": os.path.join(current_dir, "data", "ensembl_tools.json"),
"clinvar": os.path.join(current_dir, "data", "clinvar_tools.json"),
"geo": os.path.join(current_dir, "data", "geo_tools.json"),
"dbsnp": os.path.join(current_dir, "data", "dbsnp_tools.json"),
"gnomad": os.path.join(current_dir, "data", "gnomad_tools.json"),
# Newly added database tools
"gbif": os.path.join(current_dir, "data", "gbif_tools.json"),
"obis": os.path.join(current_dir, "data", "obis_tools.json"),
"wikipathways": os.path.join(current_dir, "data", "wikipathways_tools.json"),
"rnacentral": os.path.join(current_dir, "data", "rnacentral_tools.json"),
"encode": os.path.join(current_dir, "data", "encode_tools.json"),
"gtex": os.path.join(current_dir, "data", "gtex_tools.json"),
"mgnify": os.path.join(current_dir, "data", "mgnify_tools.json"),
"gdc": os.path.join(current_dir, "data", "gdc_tools.json"),
# Ontology tools
"ols": os.path.join(current_dir, "data", "ols_tools.json"),
"optimizer": os.path.join(current_dir, "data", "optimizer_tools.json"),
# Compact mode core tools
"compact_mode": os.path.join(current_dir, "data", "compact_mode_tools.json"),
# New Life Science Tools
"hca_tools": os.path.join(current_dir, "data", "hca_tools.json"),
"clinical_trials_tools": os.path.join(
current_dir, "data", "clinical_trials_tools.json"
),
"iedb_tools": os.path.join(current_dir, "data", "iedb_tools.json"),
"pathway_commons_tools": os.path.join(
current_dir, "data", "pathway_commons_tools.json"
),
"biomodels_tools": os.path.join(current_dir, "data", "biomodels_tools.json"),
# BioThings APIs (MyGene, MyVariant, MyChem)
"biothings": os.path.join(current_dir, "data", "biothings_tools.json"),
# FDA Pharmacogenomic Biomarkers
"fda_pharmacogenomic_biomarkers": os.path.join(
current_dir, "data", "fda_pharmacogenomic_biomarkers_tools.json"
),
# Metabolomics Workbench
"metabolomics_workbench": os.path.join(
current_dir, "data", "metabolomics_workbench_tools.json"
),
# PharmGKB - Pharmacogenomics
"pharmgkb": os.path.join(current_dir, "data", "pharmgkb_tools.json"),
# DisGeNET - Gene-Disease Associations
# DGIdb - Drug Gene Interactions
"dgidb": os.path.join(current_dir, "data", "dgidb_tools.json"),
# STITCH - Chemical-Protein Interactions
"stitch": os.path.join(current_dir, "data", "stitch_tools.json"),
# CIViC - Clinical Interpretation of Variants in Cancer
"civic": os.path.join(current_dir, "data", "civic_tools.json"),
# Single-cell RNA-seq data
"cellxgene_census": os.path.join(
current_dir, "data", "cellxgene_census_tools.json"
),
# Chromatin and epigenetics data
"chipatlas": os.path.join(current_dir, "data", "chipatlas_tools.json"),
# 4DN Data Portal - 3D genome organization
"fourdn": os.path.join(current_dir, "data", "fourdn_tools.json"),
# GTEx Portal API V2 - Tissue-specific gene expression and eQTLs
"gtex_v2": os.path.join(current_dir, "data", "gtex_v2_tools.json"),
# Rfam Database API - RNA families (v15.1, January 2026)
"rfam": os.path.join(current_dir, "data", "rfam_tools.json"),
# BiGG Models API - Genome-scale metabolic models
"bigg_models": os.path.join(current_dir, "data", "bigg_models_tools.json"),
# Protein-Protein Interaction (PPI) tools - STRING and BioGRID
"ppi": os.path.join(current_dir, "data", "ppi_tools.json"),
# NVIDIA NIM Healthcare APIs - Structure prediction, molecular docking, genomics
"nvidia_nim": os.path.join(current_dir, "data", "nvidia_nim_tools.json"),
# COSMIC - Catalogue of Somatic Mutations in Cancer
"cosmic": os.path.join(current_dir, "data", "cosmic_tools.json"),
# OncoKB - Precision Oncology Knowledge Base
"oncokb": os.path.join(current_dir, "data", "oncokb_tools.json"),
# OMIM - Online Mendelian Inheritance in Man
"omim": os.path.join(current_dir, "data", "omim_tools.json"),
# Orphanet - Rare Disease Encyclopedia
"orphanet": os.path.join(current_dir, "data", "orphanet_tools.json"),
# DisGeNET - Gene-Disease Associations
"disgenet": os.path.join(current_dir, "data", "disgenet_tools.json"),
# BindingDB - Protein-Ligand Binding Affinities
"bindingdb": os.path.join(current_dir, "data", "bindingdb_tools.json"),
# GPCRdb - G Protein-Coupled Receptor Database
"gpcrdb": os.path.join(current_dir, "data", "gpcrdb_tools.json"),
# BRENDA - Enzyme Kinetics Database
"brenda": os.path.join(current_dir, "data", "brenda_tools.json"),
# SAbDab - Structural Antibody Database
"sabdab": os.path.join(current_dir, "data", "sabdab_tools.json"),
# IMGT - International ImMunoGeneTics Information System
"imgt": os.path.join(current_dir, "data", "imgt_tools.json"),
# HMDB - Human Metabolome Database
"hmdb": os.path.join(current_dir, "data", "hmdb_tools.json"),
# MetaCyc - Metabolic Pathway Database
"metacyc": os.path.join(current_dir, "data", "metacyc_tools.json"),
# ZINC - Virtual Screening Library
"zinc": os.path.join(current_dir, "data", "zinc_tools.json"),
# Enamine - Make-on-Demand Compounds
"enamine": os.path.join(current_dir, "data", "enamine_tools.json"),
# eMolecules - Vendor Aggregator
"emolecules": os.path.join(current_dir, "data", "emolecules_tools.json"),
# Pharos/TCRD - NIH IDG Understudied Proteins Database
"pharos": os.path.join(current_dir, "data", "pharos_tools.json"),
# AlphaMissense - DeepMind Pathogenicity Predictions
"alphamissense": os.path.join(current_dir, "data", "alphamissense_tools.json"),
# CADD - Combined Annotation Dependent Depletion
"cadd": os.path.join(current_dir, "data", "cadd_tools.json"),
# DepMap - Cancer Dependency Map (Sanger Cell Model Passports)
"depmap": os.path.join(current_dir, "data", "depmap_tools.json"),
# InterProScan - Protein Domain/Family Prediction
"interproscan": os.path.join(current_dir, "data", "interproscan_tools.json"),
# EVE - Evolutionary Variant Effect Predictions
"eve": os.path.join(current_dir, "data", "eve_tools.json"),
# Thera-SAbDab - Therapeutic Structural Antibody Database
"therasabdab": os.path.join(current_dir, "data", "therasabdab_tools.json"),
# DeepGO - Protein Function Prediction
"deepgo": os.path.join(current_dir, "data", "deepgo_tools.json"),
# ClinGen - Gene-Disease Validity, Dosage Sensitivity, Actionability
"clingen": os.path.join(current_dir, "data", "clingen_tools.json"),
# SpliceAI - Deep Learning Splice Prediction
"spliceai": os.path.join(current_dir, "data", "spliceai_tools.json"),
}
# Auto-load any user-provided tools from ~/.tooluniverse/user_tools/
user_tools_dir = os.path.expanduser("~/.tooluniverse/data/user_tools")
if os.path.exists(user_tools_dir):
for filename in os.listdir(user_tools_dir):
if filename.endswith(".json"):
key = f"user_{filename.replace('.json', '')}"
default_tool_files[key] = os.path.join(user_tools_dir, filename)
def _get_hook_config_file_path():
"""
Get the path to the hook configuration file.
This function uses the same logic as HookManager._get_config_file_path()
to ensure consistent path resolution across different installation scenarios.
Returns
Path: Path to the hook_config.json file
"""
try:
import importlib.resources as pkg_resources
except ImportError:
import importlib_resources as pkg_resources
try:
data_files = pkg_resources.files("tooluniverse.template")
return data_files / "hook_config.json"
except Exception:
return Path(__file__).parent / "template" / "hook_config.json"
[docs]
def get_default_hook_config():
"""
Get default hook configuration from hook_config.json.
This function loads the default hook configuration from the hook_config.json
template file, providing a single source of truth for default hook settings.
If the file cannot be loaded, it falls back to a minimal configuration.
Returns
dict: Default hook configuration with basic settings
"""
try:
config_file = _get_hook_config_file_path()
content = (
config_file.read_text(encoding="utf-8")
if hasattr(config_file, "read_text")
else Path(config_file).read_text(encoding="utf-8")
)
return json.loads(content)
except Exception:
# Fallback to minimal configuration if file cannot be loaded
# This ensures the system continues to work even if the config file
# is missing or corrupted
return {
"global_settings": {
"default_timeout": 30,
"max_hook_depth": 3,
"enable_hook_caching": True,
"hook_execution_order": "priority_desc",
},
"exclude_tools": [
"Tool_RAG",
"ToolFinderEmbedding",
"ToolFinderLLM",
],
"hook_type_defaults": {
"SummarizationHook": {
"default_output_length_threshold": 5000,
"default_chunk_size": 32000,
"default_focus_areas": "key_findings_and_results",
"default_max_summary_length": 3000,
},
"FileSaveHook": {
"default_temp_dir": None,
"default_file_prefix": "tool_output",
"default_include_metadata": True,
"default_auto_cleanup": False,
"default_cleanup_age_hours": 24,
},
},
"hooks": [
{
"name": "default_summarization_hook",
"type": "SummarizationHook",
"enabled": True,
"priority": 1,
"conditions": {
"output_length": {"operator": ">", "threshold": 5000}
},
"hook_config": {
"composer_tool": "OutputSummarizationComposer",
"chunk_size": 32000,
"focus_areas": "key_findings_and_results",
"max_summary_length": 3000,
},
}
],
"tool_specific_hooks": {},
"category_hooks": {},
}
