pubmed-mcp-server/.env.example at main · cyanheads/pubmed-mcp-server · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
# -----------------------------------------------------------------
# Environment
# -----------------------------------------------------------------

# Environment: "development", "production", or "testing"
NODE_ENV=development

# -----------------------------------------------------------------
# MCP Server Configuration
# -----------------------------------------------------------------

# Transport type: "stdio" or "http"
MCP_TRANSPORT_TYPE=http

# Session mode: "stateless", "stateful", or "auto" (only used if MCP_TRANSPORT_TYPE=http)
MCP_SESSION_MODE=auto

# Log level: "debug", "info", "notice", "warning", "error", "crit", "alert", "emerg"
MCP_LOG_LEVEL=debug

# Directory for log files
LOGS_DIR=logs/

# -----------------------------------------------------------------
# HTTP Transport Configuration (only used if MCP_TRANSPORT_TYPE=http)
# -----------------------------------------------------------------

MCP_HTTP_HOST=127.0.0.1
MCP_HTTP_PORT=3017

# Comma-separated list of allowed origins for CORS
MCP_ALLOWED_ORIGINS=http://localhost:8080

# -----------------------------------------------------------------
# Authentication Configuration
# -----------------------------------------------------------------

# Authentication mode: "none", "jwt", or "oauth"
MCP_AUTH_MODE=none

# --- JWT Auth (required when MCP_AUTH_MODE=jwt) ---
# MCP_AUTH_SECRET_KEY=your-super-secret-key-that-is-at-least-32-characters-long
# DEV_MCP_AUTH_BYPASS=false

# --- OAuth Auth (required when MCP_AUTH_MODE=oauth) ---
# OAUTH_ISSUER_URL=https://your-idp.example.com
# OAUTH_AUDIENCE=your-api-audience

# -----------------------------------------------------------------
# NCBI / PubMed Configuration
# -----------------------------------------------------------------

# NCBI API key — increases rate limit from 3 req/s to 10 req/s
# Get one free at: https://www.ncbi.nlm.nih.gov/account/settings/
# NCBI_API_KEY=

# Contact email sent with NCBI requests (recommended by NCBI policy)
# NCBI_ADMIN_EMAIL=

# Delay between NCBI requests in ms (default: 334 without key, set to 100 with key)
# NCBI_REQUEST_DELAY_MS=334

# Max retry attempts for failed NCBI requests
# NCBI_MAX_RETRIES=3

# -----------------------------------------------------------------
# Storage Configuration
# -----------------------------------------------------------------

# Storage backend: "in-memory", "filesystem", "supabase", "cloudflare-r2", "cloudflare-kv", "cloudflare-d1"
STORAGE_PROVIDER_TYPE="filesystem"
STORAGE_FILESYSTEM_PATH="./.storage"

# -----------------------------------------------------------------
# Database Configuration (required if STORAGE_PROVIDER_TYPE=supabase)
# -----------------------------------------------------------------

# SUPABASE_URL=
# SUPABASE_ANON_KEY=
# SUPABASE_SERVICE_ROLE_KEY=

# -----------------------------------------------------------------
# OpenTelemetry Configuration (optional)
# -----------------------------------------------------------------

# OTEL_ENABLED=false
# OTEL_EXPORTER_OTLP_TRACES_ENDPOINT=http://localhost:4318/v1/traces
# OTEL_EXPORTER_OTLP_METRICS_ENDPOINT=http://localhost:4318/v1/metrics