CLI reference

Hades owns the full lifecycle for SNOMED CT and FHIR conformance packages — discovery, download, import, indexing, compaction and serving — through a single binary. Examples below use java -jar hades.jar; from a source checkout, replace with clj -M:run.

Commands

Command	Purpose
serve <paths…> [--port N] [--bind-address A] [--default URL=VERSION]… [--locale LOCALE]	Start the FHIR server. Each path opens a Hermes SNOMED store, a Hades SQLite container, or a directory of FHIR JSON resources (auto-detected). Use --default URL=VERSION (repeatable) when multiple providers claim the same canonical URL — bare-URL requests resolve to the chosen version. --locale sets the server default locale (e.g. en-GB) for terminologies that support it, such as SNOMED CT.
mcp <paths…> [--default URL=VERSION]… [--locale LOCALE]	Start a Model Context Protocol server over stdio, exposing FHIR terminology operations as MCP tools. Source paths and --default / --locale work identically to serve. See MCP server.
install <dest-db> --dist <id>… [--no-index] [--cache-dir DIR]	Download and import one or more distributions (SNOMED CT or FHIR package) into the destination database. Auto-indexes when done; pass --no-index to skip (for layered loads). Distribution ids may carry @<version>.
import <dest-db> <sources…> [--no-index]	Import sources into a destination database. Auto-detects RF2 (SNOMED), LOINC release archive, or FHIR JSON / NPM-package directory. Auto-indexes when done.
list <paths…>	List importable files under given paths.
available [--dist <id>…]	List installable terminologies, or releases/versions for the given ids.
index <paths…>	Rebuild search indices on each database. Useful for explicit recovery or to finish a layered load. Release sources are silently skipped.
compact <paths…>	Compact the underlying store (LMDB compact for Hermes, VACUUM for SQLite). Optional space optimisation.
status <paths…> [--format json|edn] [--modules] [--refsets]	Show database status. --modules and --refsets add SNOMED-specific detail to the report.

Commands can be chained on a single command line and execute in the order given, sharing positional paths and flags — for example install compact snomed.db --dist ihtsdo.mlds/167 --username you@example.com --password ./pw.txt. index and compact silently skip release source paths so they're safe to chain after import.

Per-command help is available with --help:

java -jar hades.jar --help install

Examples

# Run a FHIR server on port 8080 across SNOMED, LOINC and FHIR packages
java -jar hades.jar serve snomed.db loinc.db fhir.db --port 8080

# Download, import and index SNOMED CT International edition (MLDS, latest)
java -jar hades.jar install snomed.db \
    --dist ihtsdo.mlds/167 \
    --username 'you@example.com' --password ./mlds-password.txt

# UK alternative: SNOMED CT UK monolith edition (TRUD)
java -jar hades.jar install snomed.db \
    --dist uk.nhs/sct-monolith \
    --api-key ./trud-api-key.txt

# Install one or more FHIR packages from packages.fhir.org (no auth)
java -jar hades.jar install fhir.db --dist hl7.fhir.r4.core@4.0.1

# Import an unzipped RF2 release into a destination database
java -jar hades.jar import snomed.db /path/to/RF2

# Preview the importable files under a path
java -jar hades.jar list /path/to/RF2

# Discover available terminologies and versions
java -jar hades.jar available
java -jar hades.jar available --dist ihtsdo.mlds/167 \
    --username 'you@example.com' --password ./mlds-password.txt
java -jar hades.jar available --dist hl7.fhir.r4.core

# Maintenance
java -jar hades.jar index   snomed.db
java -jar hades.jar compact snomed.db
java -jar hades.jar status  snomed.db --format json

# Start an MCP server over stdio for AI assistants
java -jar hades.jar mcp snomed.db loinc.db

See Installation for full setup recipes covering SNOMED CT, LOINC and FHIR packages.