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API key and environment configuration management.
Keys are stored in session state only — never written to disk.
"""
import os
from dotenv import load_dotenv
# All supported API keys with metadata
API_KEYS = {
"NCBI_API_KEY": {
"label": "NCBI API Key",
"description": "Improves PubTator/PMC OA rate limits (3→10 req/sec)",
"url": "https://www.ncbi.nlm.nih.gov/account/settings/",
"required": False,
},
"S2_API_KEY": {
"label": "Semantic Scholar API Key",
"description": "Dedicated S2 quota (1 req/sec) for article search/TLDR/citations",
"url": "https://www.semanticscholar.org/product/api",
"required": False,
},
"ONCOKB_TOKEN": {
"label": "OncoKB Token",
"description": "Production OncoKB variant therapy & level evidence",
"url": "https://www.oncokb.org/account/register",
"required": False,
},
"OPENFDA_API_KEY": {
"label": "OpenFDA API Key",
"description": "Better OpenFDA rate limits for drug safety/adverse event lookups",
"url": "https://open.fda.gov/apis/authentication/",
"required": False,
},
"NCI_API_KEY": {
"label": "NCI CTS API Key",
"description": "NCI Clinical Trials Search (--source nci)",
"url": "https://clinicaltrialsapi.cancer.gov/",
"required": False,
},
"DISGENET_API_KEY": {
"label": "DisGeNET API Key",
"description": "Scored gene-disease associations in gene/disease lookups",
"url": "https://www.disgenet.com/",
"required": False,
},
"UMLS_API_KEY": {
"label": "UMLS API Key",
"description": "Clinical crosswalk enrichment in discover command",
"url": "https://uts.nlm.nih.gov/uts/signup-login",
"required": False,
},
"ALPHAGENOME_API_KEY": {
"label": "AlphaGenome API Key",
"description": "Variant effect prediction (get variant ... predict)",
"url": "https://deepmind.google/science/alphagenome/",
"required": False,
},
}
# Additional config env vars
CONFIG_VARS = {
"BIOMCP_STUDY_DIR": {
"label": "Study Directory",
"description": "Local study root for cBioPortal datasets (leave blank for default)",
},
}
def load_env_keys() -> dict[str, str]:
"""Load API keys from .env file and environment, return as dict."""
load_dotenv()
keys = {}
for key_name in API_KEYS:
keys[key_name] = os.environ.get(key_name, "")
for key_name in CONFIG_VARS:
keys[key_name] = os.environ.get(key_name, "")
return keys
def build_env_overrides(session_keys: dict[str, str]) -> dict[str, str]:
"""
Build env overrides dict from session keys.
Only includes non-empty values.
"""
return {k: v for k, v in session_keys.items() if v}
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