HTS

Use this when working on the hts binary or terminology server behavior.

Running

# Default: SQLite, port 8090
cargo run --bin hts

# Custom database path and port
HTS_DATABASE_URL=./my-terminology.db HTS_SERVER_PORT=9090 cargo run --bin hts

Environment

Variable	Default	Description
HTS_SERVER_PORT	8090	Server port
HTS_SERVER_HOST	127.0.0.1	Host to bind
HTS_LOG_LEVEL	info	Log level: error, warn, info, debug, trace
HTS_DATABASE_URL	./data/hts.db	SQLite file path or PostgreSQL connection URL
HTS_STORAGE_BACKEND	sqlite	Storage backend; postgres when built with --features postgres
HTS_BOOTSTRAP_DIR	none	Directory of terminology files imported on startup
HTS_MAX_BODY_SIZE	10485760	Max request body size in bytes, applied after decompression
HTS_ENABLE_CORS	true	Enable CORS
HTS_CORS_ORIGINS	*	Allowed CORS origins

Bootstrap Directory Sync

When HTS_BOOTSTRAP_DIR points at a directory, HTS synchronizes recognized files into the database on every startup. Each recognized file is hashed with SHA-256 and recorded in a bootstrap_imports ledger keyed by file name. A file imports only when the hash is absent or changed.

• Adding a new file imports it on the next restart.
• Replacing a file with a newer terminology release re-imports it. Imports upsert on canonical (url, version), so a new version coexists with the old and a same-version re-import refreshes in place.
• Unchanged files are skipped without reparsing.
• RxNorm RRF directory signatures are derived from immediate children's (name, size) instead of full content hashing to avoid rereading multi-gigabyte folders on every boot.

API Endpoints

Operation	Method	URL
health	GET	/health
capabilities	GET	/metadata
lookup	POST	/CodeSystem/$lookup
validate code, CodeSystem	POST	/CodeSystem/$validate-code
subsumes	POST	/CodeSystem/$subsumes
expand	POST	/ValueSet/$expand
validate code, ValueSet	POST	/ValueSet/$validate-code
translate	POST	/ConceptMap/$translate
closure	POST	/ConceptMap/$closure
import bundle	POST	/import
CRUD	GET/POST/PUT/DELETE	/CodeSystem/:id, /ValueSet/:id, /ConceptMap/:id

Quick Examples

# Import a FHIR Bundle containing CodeSystem, ValueSet, or ConceptMap resources
curl -X POST http://localhost:8090/import \
  -H "Content-Type: application/fhir+json" \
  -d @bundle.json

# Lookup a concept
curl -X POST http://localhost:8090/CodeSystem/\$lookup \
  -H "Content-Type: application/fhir+json" \
  -d '{"resourceType":"Parameters","parameter":[{"name":"url","valueUri":"http://example.org/cs"},{"name":"code","valueCode":"ABC"}]}'

# Expand a value set
curl -X POST http://localhost:8090/ValueSet/\$expand \
  -H "Content-Type: application/fhir+json" \
  -d '{"resourceType":"Parameters","parameter":[{"name":"url","valueUri":"http://example.org/vs"}]}'

HFS Integration

Set HFS_TERMINOLOGY_SERVER=http://localhost:8090 on HFS to enable:

• FHIR search :in modifier, using ValueSet expansion to filter by code.
• FHIRPath memberOf() and subsumes() delegation through FHIRPATH_TERMINOLOGY_SERVER.

Bulk Import CLI

Load terminology packages directly from the filesystem:

# HL7 FHIR NPM package
cargo run --bin hts -- import ./hl7.terminology.r4-6.0.0.tgz

# SNOMED CT RF2 ZIP, requires NRC license
cargo run --bin hts -- import ./SnomedCT_InternationalRF2_*.zip --format snomed-rf2

# LOINC CSV ZIP, requires free Regenstrief registration
cargo run --bin hts -- import ./Loinc_*.zip --format loinc

# ICD-10-CM tabular XML
cargo run --bin hts -- import ./icd10cm_tabular_2025.xml

# RxNorm RRF folder, requires free NLM terms of service
cargo run --bin hts -- import ./RxNorm_full_current/rrf/

# Common flags
cargo run --bin hts -- import ./package.tgz \
  --database-url ./data/hts.db \
  --batch-size 1000 \
  --dry-run \
  --verbose

LOINC language translations under AccessoryFiles/LinguisticVariants/, such as frFR28LinguisticVariant.csv, are imported automatically as FHIR concept.designation entries tagged with BCP-47 language values such as fr-FR and de-DE.

SNOMED CT descriptions in all languages — including per-language Description files from national extensions — are imported as concept.designation entries tagged with the RF2 language code. Every language refset marks its preferred synonyms with preferredForLanguage designations (a bare language tag plus a dialect tag like en-US/da-DK/fr-CA for published national refsets), and en-US→en-GB preference picks the display. Select language via the displayLanguage parameter or the Accept-Language header on $lookup / $expand / $validate-code; matching is BCP-47-aware (de-DE finds de, fr accepts fr-CA).

Format Auto-detection

Extension or pattern	Detected format
.tgz or .tar.gz	hl7-npm
*_tabular*.xml	icd10-cm
.rrf or directory	rxnorm
.zip containing RF2 files	snomed-rf2
.zip containing LoincTable.csv	loinc
.zip containing RXNCONSO.RRF	rxnorm

Zip files that cannot be auto-detected require --format.

Exit Codes

Code	Meaning
0	Success; all resources imported
1	Fatal error; import aborted
2	Success with non-fatal errors; some records skipped