Implement FHIR Types in Java

Author: alexanderkiel

.github/scripts/check-bloom-filter.sh

@@ -7,4 +7,9 @@ BASE="http://localhost:8080/fhir"
 HASH="$1"
 PATIENT_COUNT="$2"
 
-test "patient count" "$(curl -s "$BASE/__admin/cql/bloom-filters" | jq -r ".[] | select(.hash == \"$HASH\") | .patientCount")" "$PATIENT_COUNT"
+BLOOM_FILTERS="$(curl -s "$BASE/__admin/cql/bloom-filters")"
+
+echo "All Bloom filters:"
+echo "$BLOOM_FILTERS" | jq -r '.[]'
+
+test "patient count" "$(echo "$BLOOM_FILTERS" | jq -r ".[] | select(.hash == \"$HASH\") | .patientCount")" "$PATIENT_COUNT"

.github/workflows/build.yml

@@ -252,6 +252,39 @@ 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:
@@ -652,7 +685,7 @@ 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
@@ -664,7 +697,7 @@ 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
@@ -2686,6 +2719,7 @@ jobs:
     - lint
     - test
     - test-slow
+    - test-mem-size
     - test-root
     - image-scan
     - cql-expr-cache-test

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:21.0.8_9-jre-noble@sha256:20e7f7288e1c18eebe8f06a442c9f7183342d9b022d3b9a9677cae2b558ddddd
+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"
 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-1.1.2-standalone.jar"]
+CMD ["sh", "-c", "JAVA_TOOL_OPTIONS=\"${BASE_JAVA_TOOL_OPTIONS} ${JAVA_TOOL_OPTIONS}\" exec java -jar blaze-1.1.2-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/performance/cql.md

@@ -422,7 +422,7 @@ cql/search.sh medication-7
 |---------|--------|-------:|---------:|-------:|-------:|
 | 100k    | LEA58  |  5.2 M |    12.79 |  0.325 |  7.8 k |
 | 1M      | LEA58  | 52.3 M |   399.64 | 11.966 |  2.5 k |
-| 1M      | A5N46  | 52.3 M |   267.65 |  4.829 |  3.7 k |
+| 1M      | A5N46  | 52.3 M |   252.74 |  1.111 |  4.0 k |
 
 ### CQL Queries
 

docs/performance/fhir-search.md

@@ -63,9 +63,9 @@ curl -s "http://localhost:8080/fhir/Observation?code=http://loinc.org|$CODE&_sum
 | LEA58  | 1M      | 8310-5  |  1.1 M |     0.39 |  0.009 |   3.0 M |
 | LEA58  | 1M      | 55758-7 | 10.1 M |     2.84 |  0.026 |   3.6 M |
 | LEA58  | 1M      | 72514-3 | 27.3 M |     7.52 |  0.138 |   3.6 M |
-| A5N46  | 1M      | 8310-5  |  1.1 M |     0.20 |  0.008 |   5.8 M |
-| A5N46  | 1M      | 55758-7 | 10.1 M |     2.35 |  0.016 |   4.3 M |
-| A5N46  | 1M      | 72514-3 | 27.3 M |     4.75 |  0.074 |   5.8 M |
+| A5N46  | 1M      | 8310-5  |  1.1 M |     0.17 |  0.010 |   6.7 M |
+| A5N46  | 1M      | 55758-7 | 10.1 M |     1.99 |  0.029 |   5.1 M |
+| A5N46  | 1M      | 72514-3 | 27.3 M |     4.02 |  0.017 |   6.8 M |
 
 ¹ resources per second
 
@@ -81,26 +81,26 @@ Downloads were performed using the following `blazectl` command:
 blazectl download --server http://localhost:8080/fhir Observation -q "code=http://loinc.org|$CODE&_count=1000" > /dev/null
 ```
 
-| System | Dataset | Code    | # Hits | Time (s) | StdDev |  Res/s ¹ |
-|--------|---------|---------|-------:|---------:|-------:|---------:|
-| LEA36  | 100k    | 8310-5  |  115 k |     1.90 |  0.016 |  60.53 k |  
-| LEA36  | 100k    | 55758-7 |  1.0 M |    15.45 |  0.121 |  64.72 k |
-| LEA36  | 100k    | 72514-3 |  2.7 M |    41.09 |  0.530 |  65.71 k |
-| LEA47  | 100k    | 8310-5  |  115 k |     2.00 |  0.021 |  57.50 k |  
-| LEA47  | 100k    | 55758-7 |  1.0 M |    15.99 |  0.147 |  62.54 k |
-| LEA47  | 100k    | 72514-3 |  2.7 M |    43.48 |  0.128 |  62.10 k |
-| LEA58  | 100k    | 8310-5  |  115 k |     1.96 |  0.039 |  58.67 k |  
-| LEA58  | 100k    | 55758-7 |  1.0 M |    16.61 |  0.161 |  60.20 k |
-| LEA58  | 100k    | 72514-3 |  2.7 M |    43.84 |  0.124 |  61.59 k |         
-| LEA47  | 1M      | 8310-5  |  1.1 M |    15.43 |  0.034 |   75.1 k |         
-| LEA47  | 1M      | 55758-7 | 10.1 M |   155.78 |  0.976 | 65.1 k ² |         
-| LEA47  | 1M      | 72514-3 | 10.1 M |   114.41 |  0.438 | 88.6 k ² |
-| LEA58  | 1M      | 8310-5  |  1.1 M |    15.35 |  0.135 |   75.5 k |         
-| LEA58  | 1M      | 55758-7 | 10.1 M |   136.48 |  0.236 |   74.3 k |         
-| LEA58  | 1M      | 72514-3 | 27.3 M |   416.05 | 22.655 | 65.7 k ² |
-| A5N46  | 1M      | 8310-5  |  1.1 M |     7.78 |  0.040 |  148.9 k |         
-| A5N46  | 1M      | 55758-7 | 10.1 M |   148.39 |  1.776 | 68.3 k ² |        
-| A5N46  | 1M      | 72514-3 | 27.3 M |   413.87 |  0.165 | 66.1 k ² |
+| System | Dataset | Code    | # Hits | Time (s) | StdDev |   Res/s ¹ |
+|--------|---------|---------|-------:|---------:|-------:|----------:|
+| LEA36  | 100k    | 8310-5  |  115 k |     1.90 |  0.016 |   60.53 k |  
+| LEA36  | 100k    | 55758-7 |  1.0 M |    15.45 |  0.121 |   64.72 k |
+| LEA36  | 100k    | 72514-3 |  2.7 M |    41.09 |  0.530 |   65.71 k |
+| LEA47  | 100k    | 8310-5  |  115 k |     2.00 |  0.021 |   57.50 k |  
+| LEA47  | 100k    | 55758-7 |  1.0 M |    15.99 |  0.147 |   62.54 k |
+| LEA47  | 100k    | 72514-3 |  2.7 M |    43.48 |  0.128 |   62.10 k |
+| LEA58  | 100k    | 8310-5  |  115 k |     1.96 |  0.039 |   58.67 k |  
+| LEA58  | 100k    | 55758-7 |  1.0 M |    16.61 |  0.161 |   60.20 k |
+| LEA58  | 100k    | 72514-3 |  2.7 M |    43.84 |  0.124 |   61.59 k |         
+| LEA47  | 1M      | 8310-5  |  1.1 M |    15.43 |  0.034 |    75.1 k |         
+| LEA47  | 1M      | 55758-7 | 10.1 M |   155.78 |  0.976 |  65.1 k ² |         
+| LEA47  | 1M      | 72514-3 | 10.1 M |   114.41 |  0.438 |  88.6 k ² |
+| LEA58  | 1M      | 8310-5  |  1.1 M |    15.35 |  0.135 |    75.5 k |         
+| LEA58  | 1M      | 55758-7 | 10.1 M |   136.48 |  0.236 |    74.3 k |         
+| LEA58  | 1M      | 72514-3 | 27.3 M |   416.05 | 22.655 |  65.7 k ² |
+| A5N46  | 1M      | 8310-5  |  1.1 M |     7.03 |  0.021 |   164.8 k |         
+| A5N46  | 1M      | 55758-7 | 10.1 M |   116.01 |  9.946 |  87.4 k ² |        
+| A5N46  | 1M      | 72514-3 | 27.3 M |   254.89 |  4.042 | 107.3 k ² |
 
 ¹ resources per second, ² resource cache size is smaller than the number of resources returned
 
@@ -133,9 +133,9 @@ blazectl download --server http://localhost:8080/fhir Observation -q "code=http:
 | LEA58  | 1M      | 8310-5  |  1.1 M |    10.61 |  0.120 |   109.2 k |          
 | LEA58  | 1M      | 55758-7 | 10.1 M |    88.05 |  1.587 |   115.2 k |          
 | LEA58  | 1M      | 72514-3 | 27.3 M |   259.91 |  2.506 | 105.2 k ² |
-| A5N46  | 1M      | 8310-5  |  1.1 M |     5.08 |  0.054 |   228.3 k |          
-| A5N46  | 1M      | 55758-7 | 10.1 M |   105.87 |  0.544 |  95.8 k ² |          
-| A5N46  | 1M      | 72514-3 | 27.3 M |   318.80 |  7.558 |  85.8 k ² |          
+| A5N46  | 1M      | 8310-5  |  1.1 M |     4.60 |  0.019 |   251.8 k |          
+| A5N46  | 1M      | 55758-7 | 10.1 M |    78.03 |  1.621 | 129.9 k ² |          
+| A5N46  | 1M      | 72514-3 | 27.3 M |   209.98 |  4.923 | 130.2 k ² |          
 
 ¹ resources per second, ² resource cache size is smaller than the number of resources returned
 

docs/tuning-guide.md

@@ -23,12 +23,12 @@ As a general rule of thumb, 1/4 of the available memory should be assigned to th
 
 The list of all environment variables can be found in the [Environment Variables Section](deployment/environment-variables.md) under [Deployment](deployment.md). The variables important here are:
 
-| Name                   | Use for        | Default | Description                                               |
-|:-----------------------|----------------|:--------|:----------------------------------------------------------|
-| JAVA_TOOL_OPTIONS      | Heap Mem       | —       | eg. -Xmx2g, -Xmx4g, -Xmx8g, -Xmx16g, -Xmx32g or -Xmx64g   |
-| DB_BLOCK_CACHE_SIZE    | Block Cache    | 128     | eg. 2048, 4096, 8192, 16384, 32768 or 65536               |
-| DB_RESOURCE_CACHE_SIZE | Resource Cache | 100000  | eg. 50000, 100000, 2500000, 5000000, 10000000 or 20000000 |
-| CQL_EXPR_CACHE_SIZE    | Resource Cache | —       | eg. 128, 512, 1024                                        |
+| Name                   | Use for              | Default | Description                                               |
+|:-----------------------|----------------------|:--------|:----------------------------------------------------------|
+| JAVA_TOOL_OPTIONS      | Heap Mem             | —       | eg. -Xmx2g, -Xmx4g, -Xmx8g, -Xmx16g, -Xmx32g or -Xmx64g   |
+| DB_BLOCK_CACHE_SIZE    | Block Cache          | 128     | eg. 2048, 4096, 8192, 16384, 32768 or 65536 (in megabyte) |
+| DB_RESOURCE_CACHE_SIZE | Resource Cache       | 100000  | eg. 50000, 100000, 2500000, 5000000, 10000000 or 20000000 |
+| CQL_EXPR_CACHE_SIZE    | CQL Expression Cache | —       | eg. 128, 512, 1024 (in megabyte)                          |
 
 ### Other Tuning Options
 

modules/admin-api/test/blaze/admin_api_test.clj

@@ -729,7 +729,7 @@
              {:system #fhir/uri "https://samply.github.io/blaze/fhir/CodeSystem/JobType"
               :code #fhir/code "re-index"
               :display #fhir/string "(Re)Index a Search Parameter"}]}
-   :authoredOn #fhir/dateTime "2024-04-13T10:05:20.927Z"
+   :authoredOn #fhir/dateTime #system/date-time "2024-04-13T10:05:20.927Z"
    :input
    [{:fhir/type :fhir.Task/input
      :type #fhir/CodeableConcept
@@ -750,7 +750,7 @@
              {:system #fhir/uri "https://samply.github.io/blaze/fhir/CodeSystem/JobType"
               :code #fhir/code "compact"
               :display #fhir/string "Compact a Database Column Family"}]}
-   :authoredOn #fhir/dateTime "2024-04-13T10:05:20.927Z"
+   :authoredOn #fhir/dateTime #system/date-time "2024-04-13T10:05:20.927Z"
    :input
    [{:fhir/type :fhir.Task/input
      :type #fhir/CodeableConcept

modules/byte-buffer/build.clj

@@ -7,4 +7,4 @@
    {:basis (b/create-basis {:project "deps.edn"})
     :src-dirs ["java"]
     :class-dir "target/classes"
-    :javac-opts ["-Xlint:all" "-proc:none" "--release" "17"]}))
+    :javac-opts ["-Xlint:all" "-proc:none" "--release" "21"]}))

modules/coll/build.clj

@@ -7,4 +7,4 @@
    {:basis (b/create-basis {:project "deps.edn"})
     :src-dirs ["java"]
     :class-dir "target/classes"
-    :javac-opts ["-Xlint:all" "-proc:none" "--release" "17"]}))
+    :javac-opts ["-Xlint:all" "-proc:none" "--release" "21"]}))