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Environment Variables Reference¶

BioRemPP uses environment variables to configure runtime behavior, security, resume flow, and observability.

Use the tracked files below as reference:

.env/env.example (template)
.env/env.production (production baseline)

Runtime Core¶

Variable	Purpose	Default
`BIOREMPP_ENV`	Environment profile (`development` or `production`)	`development`
`BIOREMPP_DEBUG`	Dash/Flask debug mode	`True` in dev, forced `False` in prod
`BIOREMPP_HOT_RELOAD`	Dash hot reload	`True` in dev, forced `False` in prod
`BIOREMPP_HOST`	Bind host	`127.0.0.1` (forced `0.0.0.0` in prod)
`BIOREMPP_PORT`	Bind port	`8050`
`BIOREMPP_URL_BASE_PATH`	Base path prefix (`/`, `/biorempp/`, `/app/biorempp/`)	`/`

Gunicorn¶

Variable	Purpose	Default
`BIOREMPP_WORKERS`	Worker count	`4`
`BIOREMPP_WORKER_CLASS`	Worker class (`sync`, `gevent`, `eventlet`)	`sync`
`BIOREMPP_WORKER_CONNECTIONS`	Connections per worker (async classes)	`1000`
`BIOREMPP_TIMEOUT`	Request timeout (seconds)	`60`
`BIOREMPP_KEEPALIVE`	Keepalive timeout (seconds)	`5`
`BIOREMPP_MAX_REQUESTS`	Worker recycle threshold	`1000`
`BIOREMPP_MAX_REQUESTS_JITTER`	Worker recycle jitter	`100`

Upload and Parsing Limits¶

Variable	Purpose	Default
`BIOREMPP_UPLOAD_MAX_SIZE_MB`	Max upload size (MB)	`5`
`BIOREMPP_UPLOAD_SAMPLE_LIMIT`	Max samples in uploaded file	`100`
`BIOREMPP_UPLOAD_KO_LIMIT`	Max KO identifiers in uploaded file	`500000`
`BIOREMPP_UPLOAD_ENCODING`	Expected file encoding	`utf-8`
`BIOREMPP_PARSING_MAX_SAMPLES`	Max samples during parsing	`1000`
`BIOREMPP_PARSING_MAX_KOS_PER_SAMPLE`	Max KOs per sample	`10000`
`BIOREMPP_PARSING_MAX_TOTAL_KOS`	Max KOs during parsing	`100000`

Resume by Job ID¶

Variable	Purpose	Default
`BIOREMPP_RESUME_BACKEND`	Resume storage backend (`diskcache`, `redis`)	`diskcache`
`BIOREMPP_RESUME_SECURITY_MODE`	Error exposure mode (`normal`, `strict`)	`normal`
`BIOREMPP_RESUME_TTL_SECONDS`	Resume TTL in seconds	`14400` (4h)
`BIOREMPP_RESUME_CACHE_SIZE_MB`	Resume cache max size	`512`
`BIOREMPP_RESUME_MAX_PAYLOAD_MB`	Max payload size per job	`64`
`BIOREMPP_RESUME_REDIS_HOST`	Resume Redis host	`redis`
`BIOREMPP_RESUME_REDIS_PORT`	Resume Redis port	`6379`
`BIOREMPP_RESUME_REDIS_DB`	Resume Redis DB index	`0`
`BIOREMPP_RESUME_REDIS_PASSWORD`	Resume Redis password	inherits `REDIS_PASSWORD` if unset
`BIOREMPP_RESUME_REDIS_KEY_PREFIX`	Resume key prefix in Redis	`biorempp:resume:`
`BIOREMPP_RESUME_REDIS_COMPRESSION_LEVEL`	Redis payload compression level (1..9)	`6`
`BIOREMPP_RESUME_REDIS_SOCKET_TIMEOUT_SECONDS`	Redis socket timeout	`3`
`BIOREMPP_RESUME_REDIS_HEALTHCHECK`	Startup Redis health gate for resume	`false`

Resume Rate-Limit¶

Variable	Purpose	Default
`BIOREMPP_RESUME_RATE_LIMIT_ATTEMPTS`	Attempts per window	`10`
`BIOREMPP_RESUME_RATE_LIMIT_WINDOW_SECONDS`	Rate-limit window	`60`
`BIOREMPP_RESUME_RATE_LIMIT_BACKOFF_BASE_SECONDS`	Base backoff	`5`
`BIOREMPP_RESUME_RATE_LIMIT_BACKOFF_MAX_SECONDS`	Max backoff	`300`
`BIOREMPP_RESUME_RATE_LIMIT_CACHE_SIZE_MB`	Local limiter cache size	`64`
`BIOREMPP_RESUME_RATE_LIMIT_BACKEND`	Backend (`auto`, `diskcache`, `redis`)	`auto`
`BIOREMPP_RESUME_RATE_LIMIT_REDIS_KEY_PREFIX`	Redis limiter key prefix	`biorempp:resume:ratelimit:`

Resume Alert Thresholds¶

Variable	Purpose	Default
`BIOREMPP_RESUME_ALERT_WINDOW_SECONDS`	Alert window	`300`
`BIOREMPP_RESUME_ALERT_NOT_FOUND_THRESHOLD`	Not-found threshold	`30`
`BIOREMPP_RESUME_ALERT_TOKEN_MISMATCH_THRESHOLD`	Token mismatch threshold	`10`
`BIOREMPP_RESUME_ALERT_SAVE_FAILED_THRESHOLD`	Save failed threshold	`5`

Security and Proxy Trust¶

Variable	Purpose	Default
`SECRET_KEY`	Required secret in production	empty (must be set securely in prod)
`BIOREMPP_TRUST_PROXY_HEADERS`	Trust `X-Forwarded-*` headers	`false`
`BIOREMPP_TRUSTED_PROXY_CIDRS`	Trusted ingress/proxy CIDRs	`127.0.0.1/32,::1/128`
`BIOREMPP_PUBLIC_DATA_ALLOWED_FILES`	Allowlist for `/data/<filename>`	`exemple_dataset.txt`
`BIOREMPP_LOG_REF_SALT`	Salt for HMAC log references	falls back to `SECRET_KEY`
`BIOREMPP_LOG_REF_LENGTH`	Redacted reference length	`12` (clamped 8..24)

Production fail-fast notes¶

Startup aborts in production when:

SECRET_KEY is missing, placeholder, or weak;
Redis backend is selected without secure Redis password;
BIOREMPP_TRUST_PROXY_HEADERS=true with invalid/missing trusted CIDRs.

Observability¶

Variable	Purpose	Default
`BIOREMPP_OBSERVABILITY_ENABLED`	Enable app metrics instrumentation	`false`
`BIOREMPP_OBSERVABILITY_METRICS_PATH`	Metrics endpoint path	`/metrics`
`BIOREMPP_OBSERVABILITY_FAIL_FAST`	Fail startup when observability prerequisites fail	`false`
`PROMETHEUS_MULTIPROC_DIR`	Prometheus multiprocess directory	`/tmp/prometheus_multiproc`
`BIOREMPP_OBSERVABILITY_MULTIPROC_TMPFS_SIZE_BYTES`	tmpfs size for multiprocess files	`67108864`

Redis Cache (Optional)¶

Variable	Purpose	Default
`ENABLE_CACHE`	Enable application Redis cache usage	`False`
`REDIS_HOST`	Redis host	`redis`
`REDIS_PORT`	Redis port	`6379`
`REDIS_DB`	Redis DB index	`0`
`REDIS_PASSWORD`	Redis password	empty (must be secure in prod use)
`CACHE_DEFAULT_TIMEOUT`	Cache TTL (seconds)	`300`
`CACHE_THRESHOLD`	Cache entry threshold	`1000`

Minimal Production Example¶

# .env/env.production
BIOREMPP_ENV=production
BIOREMPP_URL_BASE_PATH=/
SECRET_KEY=<secure-secret>
BIOREMPP_TRUST_PROXY_HEADERS=true
BIOREMPP_TRUSTED_PROXY_CIDRS=<institution-cidrs>
BIOREMPP_RESUME_BACKEND=diskcache
BIOREMPP_OBSERVABILITY_ENABLED=false

To enable Redis-backed resume and full observability, adjust values in .env/env.production and activate cache/observability profiles in Docker Compose.

See Also¶