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Implement FHIR Types in Java
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‎.github/distributed-test/docker-compose.yml‎

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

‎.github/scripts/age-test.sh‎

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#!/bin/bash -e
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#
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# This script test that the complex data type Age works as expected
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#
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script_dir="$(dirname "$(readlink -f "$0")")"
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. "$script_dir/util.sh"
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base="http://localhost:8080/fhir"
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echo "ℹ️ Age as polymorph data element in Condition"
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condition() {
15+
cat <<END
16+
{
17+
"resourceType": "Condition",
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"onsetAge": {
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"value": 42,
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"unit": "year",
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"system": "http://unitsofmeasure.org",
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"code": "a"
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}
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}
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END
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}
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response="$(condition | create "$base/Condition")"
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test "age value" "$(echo "$response" | jq -r .onsetAge.value)" "42"
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test "age unit" "$(echo "$response" | jq -r .onsetAge.unit)" "year"
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echo "ℹ️ Age as extension value"
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patient() {
36+
cat <<END
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{
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"resourceType": "Patient",
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"extension": [
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{
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"url": "foo",
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"valueAge": {
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"value": 42,
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"unit": "year",
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"system": "http://unitsofmeasure.org",
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"code": "a"
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}
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}
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]
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}
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END
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}
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response="$(patient | create "$base/Patient")"
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test "age value" "$(echo "$response" | jq -r .extension[0].valueAge.value)" "42"
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test "age unit" "$(echo "$response" | jq -r .extension[0].valueAge.unit)" "year"

‎.github/scripts/count-test.sh‎

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

‎.github/scripts/distance-test.sh‎

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

‎.github/scripts/duration-test.sh‎

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#!/bin/bash -e
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#
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# This script test that the complex data type Duration works as expected
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#
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script_dir="$(dirname "$(readlink -f "$0")")"
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. "$script_dir/util.sh"
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base="http://localhost:8080/fhir"
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echo "ℹ️ Duration as polymorph data element in ActivityDefinition"
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activity_definition() {
15+
cat <<END
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{
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"resourceType": "ActivityDefinition",
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"timingDuration": {
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"value": 23,
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"unit": "second",
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"system": "http://unitsofmeasure.org",
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"code": "s"
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}
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}
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END
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}
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response="$(activity_definition | create "$base/ActivityDefinition")"
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test "duration value" "$(echo "$response" | jq -r .timingDuration.value)" "23"
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test "duration unit" "$(echo "$response" | jq -r .timingDuration.unit)" "second"
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echo "ℹ️ Duration as extension value"
34+
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patient() {
36+
cat <<END
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{
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"resourceType": "Patient",
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"extension": [
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{
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"url": "foo",
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"valueDuration": {
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"value": 23,
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"unit": "second",
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"system": "http://unitsofmeasure.org",
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"code": "s"
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}
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}
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]
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}
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END
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}
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response="$(patient | create "$base/Patient")"
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test "duration value" "$(echo "$response" | jq -r .extension[0].valueDuration.value)" "23"
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test "duration unit" "$(echo "$response" | jq -r .extension[0].valueDuration.unit)" "second"

‎.github/workflows/build.yml‎

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- name: Test
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run: make -C modules/${{ matrix.module }} test-slow
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test-mem-size:
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runs-on: ubuntu-24.04
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steps:
263+
- name: Setup Java
264+
uses: actions/setup-java@dded0888837ed1f317902acf8a20df0ad188d165 # v5
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with:
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distribution: 'temurin'
267+
java-version: '25'
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- name: Setup Clojure
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uses: DeLaGuardo/setup-clojure@3fe9b3ae632c6758d0b7757b0838606ef4287b08 # 13.4
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with:
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cli: '1.12.3.1577'
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- name: Check out Git repository
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uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
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- name: Cache Local Maven Repo
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uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4
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with:
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path: ~/.m2/repository
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key: ${{ runner.os }}-temurin-25-maven-fhir-structure-${{ hashFiles('modules/fhir-structure/deps.edn') }}
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- name: Cache Clojure GitLibs
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uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4
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with:
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path: ~/.gitlibs
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key: ${{ runner.os }}-gitlibs-fhir-structure-${{ hashFiles('modules/fhir-structure/deps.edn') }}
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- name: Test
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run: make -C modules/fhir-structure test-mem-size
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# Special treatment, because it runs much longer as the other modules.
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test-coverage-db:
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strategy:
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run: .github/scripts/evaluate-measure.sh q36-parameter 86
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- name: Check Bloom Filter
659-
run: .github/scripts/check-bloom-filter.sh fbb79d85457069c8e1926c949690deecd60d751942d5b0cd0b61c08e6029224c 86
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run: .github/scripts/check-bloom-filter.sh 017a0f079c2a76a731db3cdf68637afc8e4fac34409b032b5ac93958923e0501 86
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- name: Evaluate CQL Query 36 - Subject List
662695
run: .github/scripts/evaluate-measure-subject-list.sh q36-parameter 86
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run: .github/scripts/evaluate-measure.sh q37-overlaps 24
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- name: Check Bloom Filter
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run: .github/scripts/check-bloom-filter.sh 9fe779d821d7647831331b490939aa0cdf314d76c9b2a9518ffaf559353db043 24
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run: .github/scripts/check-bloom-filter.sh e7d79fd90bce0a8c5abad06027e3b6d57b448076ff41fa36827e5e3b65ca10c2 24
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673706
- name: Evaluate CQL Query 37 - Blazectl
674707
run: .github/scripts/evaluate-measure-blazectl.sh q37-overlaps 24
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- name: Control Character Handling
13191352
run: .github/scripts/control-character-handling.sh
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1354+
- name: Age Test
1355+
run: .github/scripts/age-test.sh
1356+
1357+
- name: Count Test
1358+
run: .github/scripts/count-test.sh
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- name: Distance Test
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run: .github/scripts/distance-test.sh
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- name: Duration Test
1364+
run: .github/scripts/duration-test.sh
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13211366
- name: Prometheus Metrics
13221367
run: .github/scripts/test-metrics.sh
13231368
if: ${{ matrix.variant == 'standalone' }}
@@ -2439,7 +2484,7 @@ jobs:
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run: docker load --input /tmp/blaze.tar
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24412486
- name: Run Blaze
2442-
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
2487+
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
24432488

24442489
- name: Wait for Blaze
24452490
run: .github/scripts/wait-for-url.sh http://localhost:8080/health
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- lint
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- test
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- test-slow
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- test-mem-size
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- test-root
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- image-scan
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- cql-expr-cache-test

‎Dockerfile‎

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1-
FROM eclipse-temurin:21.0.8_9-jre-noble@sha256:20e7f7288e1c18eebe8f06a442c9f7183342d9b022d3b9a9677cae2b558ddddd
1+
FROM eclipse-temurin:25-jre-noble
22

33
ENV DEBIAN_FRONTEND=noninteractive
44

@@ -15,11 +15,12 @@ WORKDIR /app
1515
USER 1001
1616

1717
ENV LD_PRELOAD="libjemalloc.so.2"
18+
ENV BASE_JAVA_TOOL_OPTIONS="-XX:+UseCompactObjectHeaders --enable-native-access=ALL-UNNAMED"
1819
ENV STORAGE="standalone"
1920
ENV INDEX_DB_DIR="/app/data/index"
2021
ENV TRANSACTION_DB_DIR="/app/data/transaction"
2122
ENV RESOURCE_DB_DIR="/app/data/resource"
2223
ENV ADMIN_INDEX_DB_DIR="/app/data/admin-index"
2324
ENV ADMIN_TRANSACTION_DB_DIR="/app/data/admin-transaction"
2425

25-
CMD ["java", "-jar", "blaze-1.3.1-standalone.jar"]
26+
CMD ["sh", "-c", "JAVA_TOOL_OPTIONS=\"${BASE_JAVA_TOOL_OPTIONS} ${JAVA_TOOL_OPTIONS}\" exec java -jar blaze-1.3.1-standalone.jar"]

‎cljfmt.edn‎

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reg-collector [[:block 1]]
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deftests [[:block 1]]
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satisfies-prop [[:block 1]]
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mem-size-test [[:block 1]]
1920
clojure.test.check.properties/for-all [[:block 1]]
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blaze.metrics.core/collector [[:block 0]]
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reify-expr [[:inner 0] [:inner 1]]

‎docs/deployment/distributed-backend.md‎

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DB_CASSANDRA_CONTACT_POINTS: "cassandra-1:9042,cassandra-2:9042"
161161
DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
162162
DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
163-
DB_RESOURCE_CACHE_SIZE: "100000"
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ENABLE_ADMIN_API: "true"
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LOG_LEVEL: "debug"
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ports:

‎docs/deployment/distributed/docker-compose.yml‎

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DB_CASSANDRA_CONTACT_POINTS: "cassandra-1:9042,cassandra-2:9042"
122122
DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
123123
DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
124-
DB_RESOURCE_CACHE_SIZE: "100000"
125124
ENABLE_ADMIN_API: "true"
126125
LOG_LEVEL: "debug"
127126
ports:
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151150
DB_CASSANDRA_CONTACT_POINTS: "cassandra-1:9042,cassandra-2:9042"
152151
DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
153152
DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
154-
DB_RESOURCE_CACHE_SIZE: "100000"
155153
ENABLE_ADMIN_API: "true"
156154
LOG_LEVEL: "debug"
157155
ports:

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