Implement FHIR Types in Java

.github/distributed-test/docker-compose.yml

@@ -122,7 +122,6 @@ services:
       DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
       DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
       DB_BLOCK_CACHE_SIZE: "128"
-      DB_RESOURCE_CACHE_SIZE: "100000"
       DB_RESOURCE_INDEXER_THREADS: "8"
       ALLOW_MULTIPLE_DELETE: "true"
       ENABLE_INTERACTION_DELETE_HISTORY: "true"
@@ -156,7 +155,6 @@ services:
       DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
       DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
       DB_BLOCK_CACHE_SIZE: "128"
-      DB_RESOURCE_CACHE_SIZE: "100000"
       DB_RESOURCE_INDEXER_THREADS: "8"
       ALLOW_MULTIPLE_DELETE: "true"
       ENABLE_INTERACTION_DELETE_HISTORY: "true"

.github/scripts/age-test.sh

@@ -0,0 +1,57 @@
+#!/bin/bash -e
+
+#
+# This script test that the complex data type Age works as expected
+#
+
+script_dir="$(dirname "$(readlink -f "$0")")"
+. "$script_dir/util.sh"
+
+base="http://localhost:8080/fhir"
+
+echo "ℹ️ Age as polymorph data element in Condition"
+
+condition() {
+cat <<END
+{
+  "resourceType": "Condition",
+  "onsetAge": {
+    "value": 42,
+    "unit": "year",
+    "system": "http://unitsofmeasure.org",
+    "code": "a"
+  }
+}
+END
+}
+
+response="$(condition | create "$base/Condition")"
+
+test "age value" "$(echo "$response" | jq -r .onsetAge.value)" "42"
+test "age unit" "$(echo "$response" | jq -r .onsetAge.unit)" "year"
+
+echo "ℹ️ Age as extension value"
+
+patient() {
+cat <<END
+{
+  "resourceType": "Patient",
+  "extension": [
+    {
+      "url": "foo",
+      "valueAge": {
+        "value": 42,
+        "unit": "year",
+        "system": "http://unitsofmeasure.org",
+        "code": "a"
+      }
+    }
+  ]
+}
+END
+}
+
+response="$(patient | create "$base/Patient")"
+
+test "age value" "$(echo "$response" | jq -r .extension[0].valueAge.value)" "42"
+test "age unit" "$(echo "$response" | jq -r .extension[0].valueAge.unit)" "year"

.github/scripts/count-test.sh

@@ -0,0 +1,35 @@
+#!/bin/bash -e
+
+#
+# This script test that the complex data type Count works as expected
+#
+
+script_dir="$(dirname "$(readlink -f "$0")")"
+. "$script_dir/util.sh"
+
+base="http://localhost:8080/fhir"
+
+echo "ℹ️ Count as extension value"
+
+patient() {
+cat <<END
+{
+  "resourceType": "Patient",
+  "extension": [
+    {
+      "url": "foo",
+      "valueCount": {
+        "value": 23,
+        "system": "http://unitsofmeasure.org",
+        "code": "1"
+      }
+    }
+  ]
+}
+END
+}
+
+response="$(patient | create "$base/Patient")"
+
+test "count value" "$(echo "$response" | jq -r .extension[0].valueCount.value)" "23"
+test "count code" "$(echo "$response" | jq -r .extension[0].valueCount.code)" "1"

.github/scripts/distance-test.sh

@@ -0,0 +1,36 @@
+#!/bin/bash -e
+
+#
+# This script test that the complex data type Distance works as expected
+#
+
+script_dir="$(dirname "$(readlink -f "$0")")"
+. "$script_dir/util.sh"
+
+base="http://localhost:8080/fhir"
+
+echo "ℹ️ Distance as extension value"
+
+patient() {
+cat <<END
+{
+  "resourceType": "Patient",
+  "extension": [
+    {
+      "url": "foo",
+      "valueDistance": {
+        "value": 23,
+        "unit": "km",
+        "system": "http://unitsofmeasure.org",
+        "code": "km"
+      }
+    }
+  ]
+}
+END
+}
+
+response="$(patient | create "$base/Patient")"
+
+test "distance value" "$(echo "$response" | jq -r .extension[0].valueDistance.value)" "23"
+test "distance unit" "$(echo "$response" | jq -r .extension[0].valueDistance.unit)" "km"

.github/scripts/duration-test.sh

@@ -0,0 +1,57 @@
+#!/bin/bash -e
+
+#
+# This script test that the complex data type Duration works as expected
+#
+
+script_dir="$(dirname "$(readlink -f "$0")")"
+. "$script_dir/util.sh"
+
+base="http://localhost:8080/fhir"
+
+echo "ℹ️ Duration as polymorph data element in ActivityDefinition"
+
+activity_definition() {
+cat <<END
+{
+  "resourceType": "ActivityDefinition",
+  "timingDuration": {
+    "value": 23,
+    "unit": "second",
+    "system": "http://unitsofmeasure.org",
+    "code": "s"
+  }
+}
+END
+}
+
+response="$(activity_definition | create "$base/ActivityDefinition")"
+
+test "duration value" "$(echo "$response" | jq -r .timingDuration.value)" "23"
+test "duration unit" "$(echo "$response" | jq -r .timingDuration.unit)" "second"
+
+echo "ℹ️ Duration as extension value"
+
+patient() {
+cat <<END
+{
+  "resourceType": "Patient",
+  "extension": [
+    {
+      "url": "foo",
+      "valueDuration": {
+        "value": 23,
+        "unit": "second",
+        "system": "http://unitsofmeasure.org",
+        "code": "s"
+      }
+    }
+  ]
+}
+END
+}
+
+response="$(patient | create "$base/Patient")"
+
+test "duration value" "$(echo "$response" | jq -r .extension[0].valueDuration.value)" "23"
+test "duration unit" "$(echo "$response" | jq -r .extension[0].valueDuration.unit)" "second"

.github/workflows/build.yml

@@ -256,6 +256,39 @@ jobs:
     - name: Test
       run: make -C modules/${{ matrix.module }} test-slow
 
+  test-mem-size:
+    runs-on: ubuntu-24.04
+
+    steps:
+    - name: Setup Java
+      uses: actions/setup-java@dded0888837ed1f317902acf8a20df0ad188d165 # v5
+      with:
+        distribution: 'temurin'
+        java-version: '25'
+
+    - name: Setup Clojure
+      uses: DeLaGuardo/setup-clojure@3fe9b3ae632c6758d0b7757b0838606ef4287b08 # 13.4
+      with:
+        cli: '1.12.3.1577'
+
+    - name: Check out Git repository
+      uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+
+    - name: Cache Local Maven Repo
+      uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4
+      with:
+        path: ~/.m2/repository
+        key: ${{ runner.os }}-temurin-25-maven-fhir-structure-${{ hashFiles('modules/fhir-structure/deps.edn') }}
+
+    - name: Cache Clojure GitLibs
+      uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4
+      with:
+        path: ~/.gitlibs
+        key: ${{ runner.os }}-gitlibs-fhir-structure-${{ hashFiles('modules/fhir-structure/deps.edn') }}
+
+    - name: Test
+      run: make -C modules/fhir-structure test-mem-size
+
   # Special treatment, because it runs much longer as the other modules.
   test-coverage-db:
     strategy:
@@ -656,7 +689,7 @@ jobs:
       run: .github/scripts/evaluate-measure.sh q36-parameter 86
 
     - name: Check Bloom Filter
-      run: .github/scripts/check-bloom-filter.sh fbb79d85457069c8e1926c949690deecd60d751942d5b0cd0b61c08e6029224c 86
+      run: .github/scripts/check-bloom-filter.sh 017a0f079c2a76a731db3cdf68637afc8e4fac34409b032b5ac93958923e0501 86
 
     - name: Evaluate CQL Query 36 - Subject List
       run: .github/scripts/evaluate-measure-subject-list.sh q36-parameter 86
@@ -668,7 +701,7 @@ jobs:
       run: .github/scripts/evaluate-measure.sh q37-overlaps 24
 
     - name: Check Bloom Filter
-      run: .github/scripts/check-bloom-filter.sh 9fe779d821d7647831331b490939aa0cdf314d76c9b2a9518ffaf559353db043 24
+      run: .github/scripts/check-bloom-filter.sh e7d79fd90bce0a8c5abad06027e3b6d57b448076ff41fa36827e5e3b65ca10c2 24
 
     - name: Evaluate CQL Query 37 - Blazectl
       run: .github/scripts/evaluate-measure-blazectl.sh q37-overlaps 24
@@ -1321,6 +1354,18 @@ jobs:
     - name: Search for Location using near Search Param
       run: .github/scripts/search-location-near.sh
 
+    - name: Age Test
+      run: .github/scripts/age-test.sh
+
+    - name: Count Test
+      run: .github/scripts/count-test.sh
+
+    - name: Distance Test
+      run: .github/scripts/distance-test.sh
+
+    - name: Duration Test
+      run: .github/scripts/duration-test.sh
+
     - name: Prometheus Metrics
       run: .github/scripts/test-metrics.sh
       if: ${{ matrix.variant == 'standalone' }}
@@ -2442,7 +2487,7 @@ jobs:
       run: docker load --input /tmp/blaze.tar
 
     - name: Run Blaze
-      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e DB_RESOURCE_CACHE_SIZE=0 -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
+      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
 
     - name: Wait for Blaze
       run: .github/scripts/wait-for-url.sh http://localhost:8080/health
@@ -2738,6 +2783,7 @@ jobs:
     - lint
     - test
     - test-slow
+    - test-mem-size
     - test-root
     - image-scan
     - cql-expr-cache-test

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:21.0.9_10-jre-noble@sha256:67fc762eabacb56e5444b367889e04ce8c839b8f4b3d8ef3e459c5579fbefd8a
+FROM eclipse-temurin:25-jre-noble
 
 ENV DEBIAN_FRONTEND=noninteractive
 
@@ -15,11 +15,12 @@ WORKDIR /app
 USER 1001
 
 ENV LD_PRELOAD="libjemalloc.so.2"
+ENV BASE_JAVA_TOOL_OPTIONS="-XX:+UseCompactObjectHeaders --enable-native-access=ALL-UNNAMED --sun-misc-unsafe-memory-access=allow"
 ENV STORAGE="standalone"
 ENV INDEX_DB_DIR="/app/data/index"
 ENV TRANSACTION_DB_DIR="/app/data/transaction"
 ENV RESOURCE_DB_DIR="/app/data/resource"
 ENV ADMIN_INDEX_DB_DIR="/app/data/admin-index"
 ENV ADMIN_TRANSACTION_DB_DIR="/app/data/admin-transaction"
 
-CMD ["java", "-jar",  "blaze-1.4.1-standalone.jar"]
+CMD ["sh", "-c", "JAVA_TOOL_OPTIONS=\"${BASE_JAVA_TOOL_OPTIONS} ${JAVA_TOOL_OPTIONS}\" exec java -jar blaze-1.4.1-standalone.jar"]

cljfmt.edn

@@ -16,6 +16,7 @@
   reg-collector [[:block 1]]
   deftests [[:block 1]]
   satisfies-prop [[:block 1]]
+  mem-size-test [[:block 1]]
   clojure.test.check.properties/for-all [[:block 1]]
   blaze.metrics.core/collector [[:block 0]]
   reify-expr [[:inner 0] [:inner 1]]

docs/deployment/distributed-backend.md

@@ -160,7 +160,6 @@ blaze-1:
     DB_CASSANDRA_CONTACT_POINTS: "cassandra-1:9042,cassandra-2:9042"
     DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
     DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
-    DB_RESOURCE_CACHE_SIZE: "100000"
     ENABLE_ADMIN_API: "true"
     LOG_LEVEL: "debug"
   ports:

docs/deployment/distributed/docker-compose.yml

@@ -121,7 +121,6 @@ services:
       DB_CASSANDRA_CONTACT_POINTS: "cassandra-1:9042,cassandra-2:9042"
       DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
       DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
-      DB_RESOURCE_CACHE_SIZE: "100000"
       ENABLE_ADMIN_API: "true"
       LOG_LEVEL: "debug"
     ports:
@@ -151,7 +150,6 @@ services:
       DB_CASSANDRA_CONTACT_POINTS: "cassandra-1:9042,cassandra-2:9042"
       DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
       DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
-      DB_RESOURCE_CACHE_SIZE: "100000"
       ENABLE_ADMIN_API: "true"
       LOG_LEVEL: "debug"
     ports:

docs/deployment/environment-variables.md

@@ -92,12 +92,18 @@ The size of the [block cache][2] of the DB in MiB. This cache is outside of the
 
 **Default:** 128
 
-#### `DB_RESOURCE_CACHE_SIZE` <Badge type="warning" text="Since 0.8"/>
+#### `DB_RESOURCE_CACHE_SIZE` <Badge type="warning" text="Since 0.8"/> <Badge type="danger" text="unreleased"/>
 
-The size of the resource cache of the DB in number of resources.
+The size of the resource cache of the DB in number of resources. (Deprecated)
 
 **Default:** 100000
 
+#### `DB_RESOURCE_CACHE_SIZE_RATIO` <Badge type="warning" text="unreleased"/>
+
+The ratio of JVM heap size that is allocated to the resource cache. A value of 0 disables the resource cache and a value of 0.8 is the maximum. 
+
+**Default:** 0.25
+
 #### `DB_SCALE_FACTOR` <Badge type="warning" text="Since 1.4"/>
 
 Scales sizes of DB in-memory buffers and SST files. See also: [Production Configuration](../production-configuration.md#db-scale-factor).
@@ -166,12 +172,18 @@ The size of the [block cache][2] of the DB in MiB. This cache is outside of the
 
 **Default:** 128
 
-#### `DB_RESOURCE_CACHE_SIZE` <Badge type="warning" text="Since 0.8"/>
+#### `DB_RESOURCE_CACHE_SIZE` <Badge type="warning" text="Since 0.8"/> <Badge type="danger" text="unreleased"/>
 
-The size of the resource cache of the DB in number of resources.
+The size of the resource cache of the DB in number of resources. (Deprecated)
 
 **Default:** 100000
 
+#### `DB_RESOURCE_CACHE_SIZE_RATIO` <Badge type="warning" text="unreleased"/>
+
+The ratio of JVM heap size that is allocated to the resource cache. A value of 0 disables the resource cache and a value of 0.8 is the maximum.
+
+**Default:** 0.25
+
 #### `DB_MAX_BACKGROUND_JOBS` <Badge type="warning" text="Since 0.8"/>
 
 The maximum number of the [background jobs][3] used for DB compactions.