"""
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
# 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"
),
"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
"arxiv": os.path.join(current_dir, "data", "arxiv_tools.json"),
"crossref": os.path.join(current_dir, "data", "crossref_tools.json"),
"dblp": os.path.join(current_dir, "data", "dblp_tools.json"),
"pubmed": os.path.join(current_dir, "data", "pubmed_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"),
"agents": os.path.join(current_dir, "data", "agentic_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"),
"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"),
"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"
),
"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"),
"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_tools.json"),
"url": os.path.join(current_dir, "data", "url_fetch_tools.json"),
# 'langchain': os.path.join(current_dir, 'data', 'langchain_tools.json'),
"rcsb_pdb": os.path.join(current_dir, "data", "rcsb_pdb_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"),
"markitdown": os.path.join(current_dir, "data", "markitdown_tools.json"),
# Genomics tools
"genomics": os.path.join(current_dir, "data", "genomics_tools.json"),
# Guideline and health policy tools
"guidelines": os.path.join(current_dir, "data", "unified_guideline_tools.json"),
}
[docs]
def get_default_hook_config():
"""
Get default hook configuration.
Returns:
dict: Default hook configuration with basic settings
"""
return {
"global_settings": {
"default_timeout": 30,
"max_hook_depth": 3,
"enable_hook_caching": True,
"hook_execution_order": "priority_desc",
},
"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": {},
}
