.env.example

# ============================================================================
# Environment Variables for research-workflow-assistant
# ============================================================================
# Copy this file to .env and fill in your credentials.
# See docs/api-setup-guide.md for instructions on obtaining each key.
# ============================================================================

# PubMed / NCBI E-utilities
# Get your key at: https://www.ncbi.nlm.nih.gov/account/settings/
# Without key: 3 requests/sec. With key: 10 requests/sec.
NCBI_API_KEY=

# OpenAlex (free API key required)
# Create account at: https://openalex.org/
# Get your key at: https://openalex.org/settings/api-key
OPENALEX_API_KEY=

# Semantic Scholar (optional, for authenticated access)
# Request at: https://www.semanticscholar.org/product/api
S2_API_KEY=

# CrossRef (email for polite pool, no API key needed)
CROSSREF_EMAIL=

# Zotero (required for reference management features)
# Create key at: https://www.zotero.org/settings/keys
ZOTERO_API_KEY=
# Your numeric User ID (NOT your username). Find it at the top of:
# https://www.zotero.org/settings/keys — it will be a number like 12345678.
ZOTERO_USER_ID=

# Optional: Zotero group library (leave blank for personal library)
# ZOTERO_GROUP_ID=

# Zotero Local (optional — needed for PDF text extraction, annotation reading, and keyword search)
# Path to your Zotero data directory (the folder containing zotero.sqlite and storage/).
# If blank, auto-detection is attempted using platform defaults:
#   Windows:  %APPDATA%\Zotero\Zotero\Profiles\*  or  %USERPROFILE%\Zotero
#   macOS:    ~/Zotero
#   Linux:    ~/Zotero
ZOTERO_DATA_DIR=

# Projects root directory
# Default: ./my_projects (relative to the assistant workspace)
# Can be an absolute path to store projects elsewhere, e.g.:
#   PROJECTS_ROOT=C:\Users\you\Documents\research-projects
#   PROJECTS_ROOT=/home/you/research-projects
PROJECTS_ROOT=./my_projects

# Optional readiness mirror (fallback only)
# Primary source of truth remains .rwa-user-config.yaml in the workspace root.
# These keys can be used by runtime checks if YAML is temporarily unavailable.
# RWA_DISCLAIMER_ACCEPTED=true
# RWA_DISCLAIMER_ACCEPTED_DATE=2026-03-10

# Tracking directories (optional, defaults shown)
# These are legacy single-project settings. For multi-project workflows,
# use PROJECTS_ROOT instead — each project gets its own tracking dirs.
# PRISMA_PROJECT_DIR=./review-tracking
# PROJECT_TRACKER_DIR=./project-tracking