Update hades to v2.0.280

servers/hades/Dockerfile

@@ -10,7 +10,7 @@ RUN mkdir -p /opt/hades /opt/scripts /var/hades
 
 # Hades 2.x: single uberjar covering import / index / compact / serve for
 # SNOMED, LOINC and FHIR packages.
-ADD https://github.com/wardle/hades/releases/download/v2.0.206/hades.jar /opt/hades/hades.jar
+ADD https://github.com/wardle/hades/releases/download/v2.0.282/hades.jar /opt/hades/hades.jar
 
 COPY build-databases.sh /opt/scripts/build-databases.sh
 RUN chmod +x /opt/scripts/build-databases.sh

servers/hades/README.md

@@ -26,7 +26,7 @@ The builder service consumes everything under `../../.tx-content/`:
 | ------------------------------------- | ------------------------------------ |
 | `SnomedCT_*.zip`                      | `/var/hades/snomed.db` (Hermes)      |
 | `Loinc_*.zip` / `loinc-*.zip`         | `/var/hades/loinc.db` (FTRM SQLite)  |
-| `*.tgz` (FHIR NPM packages)           | `/var/hades/packages/<id>-<ver>/`    |
+| `*.tgz` (FHIR NPM packages)           | `/var/hades/fhir.db` (FTRM SQLite)   |
 
 Multiple SNOMED zips (intl, US, UK) are imported into the same Hermes DB —
 the composite serves each module/version distinctly.
@@ -40,20 +40,21 @@ path passed to `serve`:
 java -Xmx8g -jar hades.jar serve --port 8080 \
   /var/hades/snomed.db \
   /var/hades/loinc.db \
-  /var/hades/packages/hl7.fhir.r4.core-4.0.1/package \
-  /var/hades/packages/hl7.terminology.r4-7.0.1/package \
-  ...
+  /var/hades/fhir.db
 ```
 
-FHIR packages are loaded **in-memory** rather than into SQLite — boot
-takes ~15 s longer, but every CodeSystem / ValueSet / ConceptMap
-lookup becomes a hashmap hit. With six standard HL7 packages this is
-~600 MB of resident heap; the `-Xmx8g` ceiling gives comfortable
-headroom for the in-memory data + Hermes' Lucene mmap caches +
-transient `$expand` working sets. On RAM-constrained hosts, `hades
-import fhir.db <pkg-dirs…>` and `serve … fhir.db` (instead of the
-package directories) keeps the resident footprint to ~80 MB at the
-cost of small per-request JDBC overhead — see the
+FHIR packages are built into a single **FTRM SQLite container**
+(`fhir.db`) rather than served in-memory. SQLite is mmap'd, so the
+*corpus at rest* lives off-heap, and the indexed/FTS query paths are
+faster than scanning an in-memory corpus on search and intensional
+`$expand`. Heap is still sized at `-Xmx8g`, though: `$expand` builds
+each result set in heap to serialize it, so concurrent large
+expansions (e.g. 200k-member VSAC/PHINVADS value sets) need multiple
+GB regardless of where the corpus is stored — a measured ~6 GB working
+set for 30 concurrent large expansions. The in-memory alternative —
+serving the unpacked package directories instead of `fhir.db` — trades
+that for hashmap-hit lookups and is the right choice only on large-RAM
+hosts or for request-scoped overlays; see the
 [in-memory vs SQLite section](https://github.com/wardle/hades#in-memory-vs-sqlite-container)
 in hades' README.
 
@@ -67,9 +68,9 @@ hades compact <dest-db>
 
 ## Loading Terminologies
 
-Place each artefact in `tx-benchmark/.tx-content/`. The builder is
-idempotent — it skips packages already extracted and rebuilds the
-SNOMED/LOINC DBs only when `REBUILD_DB=1` or the destination is empty.
+Place each artefact in `tx-benchmark/.tx-content/`. Set `REBUILD_DB=1`
+to drop and rebuild `snomed.db` / `loinc.db` / `fhir.db` from scratch;
+otherwise the builder imports into whatever containers already exist.
 
 ## Known limitations
 

servers/hades/build-databases.sh

@@ -4,16 +4,16 @@ set -eu
 DB_ROOT="${DB_ROOT:-/var/hades}"
 SNOMED_DB="${DB_ROOT}/snomed.db"
 LOINC_DB="${DB_ROOT}/loinc.db"
-PKG_DIR="${DB_ROOT}/packages"
+FHIR_DB="${DB_ROOT}/fhir.db"
 
 SOURCE="${SOURCE_DIR:-/source-data}"
 HADES="${HADES:-java -jar /opt/hades/hades.jar}"
 
 if [ "${REBUILD_DB:-0}" = "1" ]; then
-  rm -rf "${SNOMED_DB}" "${LOINC_DB}" "${PKG_DIR}"
+  rm -rf "${SNOMED_DB}" "${LOINC_DB}" "${FHIR_DB}"
 fi
 
-mkdir -p "${DB_ROOT}" "${PKG_DIR}"
+mkdir -p "${DB_ROOT}"
 
 EXTRACT_DIR="$(mktemp -d)"
 trap 'rm -rf "${EXTRACT_DIR}"' EXIT
@@ -61,16 +61,28 @@ if [ "${found_loinc}" = "1" ]; then
   ${HADES} compact "${LOINC_DB}"
 fi
 
-# FHIR packages are loaded in-memory at serve time, not pre-built into a DB.
+# FHIR packages are built into a single FTRM SQLite container (fhir.db)
+# rather than served in-memory: lower memory footprint and faster on the
+# search / intensional-expand paths. `import` auto-indexes after each
+# call, so pass `--no-index` while importing each package sequentially,
+# then `index` + `compact` once at the end (compact vacuums only — it
+# does not index).
+found_fhir=0
 for tgz in "${SOURCE}"/*.tgz; do
   [ -f "${tgz}" ] || continue
   name="$(basename "${tgz}" .tgz)"
-  dest="${PKG_DIR}/${name}"
-  if [ ! -d "${dest}" ]; then
-    mkdir -p "${dest}"
-    echo "Extracting FHIR package ${tgz} -> ${dest}"
-    tar xzf "${tgz}" -C "${dest}"
-  fi
+  dest="${EXTRACT_DIR}/pkg-${name}"
+  mkdir -p "${dest}"
+  echo "Extracting FHIR package ${tgz} -> ${dest}"
+  tar xzf "${tgz}" -C "${dest}"
+  echo "Importing FHIR package ${name} -> ${FHIR_DB}"
+  ${HADES} import --no-index "${FHIR_DB}" "${dest}"
+  found_fhir=1
 done
 
+if [ "${found_fhir}" = "1" ]; then
+  ${HADES} index   "${FHIR_DB}"
+  ${HADES} compact "${FHIR_DB}"
+fi
+
 ls -la "${DB_ROOT}"

servers/hades/docker-compose.yaml

@@ -21,12 +21,9 @@ services:
       - >
         test -d /var/hades/snomed.db || { echo 'snomed.db missing — run builder first'; exit 1; };
         set --;
-        for d in /var/hades/snomed.db /var/hades/loinc.db; do
+        for d in /var/hades/snomed.db /var/hades/loinc.db /var/hades/fhir.db; do
           [ -e "$$d" ] && set -- "$$@" "$$d";
         done;
-        for d in /var/hades/packages/*; do
-          [ -d "$$d" ] && set -- "$$@" "$$d/package";
-        done;
         exec java -Xmx8g -jar /opt/hades/hades.jar serve --port 8080 "$$@"
     ports:
       - "7006:8080"