Implement FHIR Types in Java

Author: alexanderkiel

.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
@@ -2693,6 +2726,7 @@ 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-1.2.0-standalone.jar"]
+CMD ["sh", "-c", "JAVA_TOOL_OPTIONS=\"${BASE_JAVA_TOOL_OPTIONS} ${JAVA_TOOL_OPTIONS}\" exec java -jar blaze-1.2.0-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]]

modules/admin-api/src/blaze/admin_api.clj

@@ -188,12 +188,12 @@
    :wrap link-headers/wrap-link-headers})
 
 (def ^:private allowed-profiles
-  #{#fhir/canonical "https://samply.github.io/blaze/fhir/StructureDefinition/AsyncInteractionJob"
-    #fhir/canonical "https://samply.github.io/blaze/fhir/StructureDefinition/CompactJob"
-    #fhir/canonical "https://samply.github.io/blaze/fhir/StructureDefinition/ReIndexJob"})
+  #{"https://samply.github.io/blaze/fhir/StructureDefinition/AsyncInteractionJob"
+    "https://samply.github.io/blaze/fhir/StructureDefinition/CompactJob"
+    "https://samply.github.io/blaze/fhir/StructureDefinition/ReIndexJob"})
 
 (defn- check-profile [resource]
-  (if (some allowed-profiles (-> resource :meta :profile))
+  (if (some allowed-profiles (map :value (-> resource :meta :profile)))
     resource
     (ba/incorrect
      "No allowed profile found."
@@ -213,7 +213,7 @@
        (datafy/datafy)))
 
 (defn- error-issues [outcome]
-  (update outcome :issue (partial filterv (comp #{#fhir/code "error"} :severity))))
+  (update outcome :issue (partial filterv (comp #{"error"} :value :severity))))
 
 (def ^:private wrap-validate-job
   {:name :wrap-validate-job

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

@@ -735,7 +735,7 @@
              {: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
@@ -756,7 +756,7 @@
              {: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"]}))

modules/cql/src/blaze/elm/compiler/external_data.clj

@@ -61,13 +61,12 @@
   (reify-expr core/Expression
     (-eval [_ {:keys [db]} resource _]
       (prom/inc! retrieve-total)
-      (let [{{:keys [reference]} :subject} resource]
-        (when reference
-          (when-let [[type id] (fsr/split-literal-ref reference)]
-            (when (and (= "Patient" type) (string? id))
-              (when-let [handle (d/resource-handle db "Patient" id)]
-                (when-not (d/deleted? handle)
-                  [(cr/mk-resource db handle)])))))))
+      (when-let [reference (-> resource :subject :reference :value)]
+        (when-let [[type id] (fsr/split-literal-ref reference)]
+          (when (and (= "Patient" type) (string? id))
+            (when-let [handle (d/resource-handle db "Patient" id)]
+              (when-not (d/deleted? handle)
+                [(cr/mk-resource db handle)]))))))
     (-form [_]
       '(retrieve (Specimen) "Patient"))))
 

modules/cql/src/blaze/elm/compiler/reusing_logic.clj

@@ -13,10 +13,10 @@
    [blaze.elm.interval :as interval]
    [blaze.elm.protocols :as p]
    [blaze.elm.quantity :as quantity]
+   [blaze.fhir.spec :as fhir-spec]
    [blaze.fhir.spec.type :as type])
   (:import
-   [blaze.fhir.spec.type Period]
-   [java.util Map]))
+   [blaze.fhir.spec.type Period Quantity]))
 
 (set! *warn-on-reflection* true)
 
@@ -84,10 +84,10 @@
   (-to-quantity [x]))
 
 (extend-protocol ToQuantity
-  Map
-  (-to-quantity [m]
-    (when-let [value (:value m)]
-      (quantity/quantity value (or (-> m :code type/value) "1"))))
+  Quantity
+  (-to-quantity [fhir-quantity]
+    (when-let [decimal (-> fhir-quantity :value :value)]
+      (quantity/quantity decimal (or (-> fhir-quantity :code :value) "1"))))
 
   Object
   (-to-quantity [x]
@@ -112,7 +112,7 @@
       `(~'call "ToQuantity" ~(core/-form operand)))))
 
 (defn- to-code [{:keys [system version code]}]
-  (code/code (type/value system) (type/value version) (type/value code)))
+  (code/code (:value system) (:value version) (:value code)))
 
 (defn- to-code-function-expr [operand]
   (reify-expr core/Expression
@@ -129,6 +129,21 @@
     (-form [_]
       `(~'call "ToCode" ~(core/-form operand)))))
 
+(defn- to-decimal-function-expr [operand]
+  (reify-expr core/Expression
+    (-attach-cache [_ cache]
+      (core/attach-cache-helper to-decimal-function-expr cache operand))
+    (-resolve-refs [_ expression-defs]
+      (to-decimal-function-expr (core/-resolve-refs operand expression-defs)))
+    (-resolve-params [_ parameters]
+      (core/resolve-params-helper to-decimal-function-expr parameters operand))
+    (-optimize [_ db]
+      (core/optimize-helper to-decimal-function-expr db operand))
+    (-eval [_ context resource scope]
+      (:value (core/-eval operand context resource scope)))
+    (-form [_]
+      `(~'call "ToDecimal" ~(core/-form operand)))))
+
 (defn- to-date-function-expr [operand]
   (reify-expr core/Expression
     (-attach-cache [_ cache]
@@ -140,7 +155,7 @@
     (-optimize [_ db]
       (core/optimize-helper to-date-function-expr db operand))
     (-eval [_ context resource scope]
-      (type/value (core/-eval operand context resource scope)))
+      (:value (core/-eval operand context resource scope)))
     (-form [_]
       `(~'call "ToDate" ~(core/-form operand)))))
 
@@ -155,7 +170,7 @@
     (-optimize [_ parameters]
       (to-date-time-function-expr (core/-optimize operand parameters)))
     (-eval [_ {:keys [now] :as context} resource scope]
-      (p/to-date-time (type/value (core/-eval operand context resource scope)) now))
+      (p/to-date-time (:value (core/-eval operand context resource scope)) now))
     (-form [_]
       `(~'call "ToDateTime" ~(core/-form operand)))))
 
@@ -170,7 +185,11 @@
     (-optimize [_ db]
       (core/optimize-helper to-string-function-expr db operand))
     (-eval [_ context resource scope]
-      (some-> (type/value (core/-eval operand context resource scope)) str))
+      (let [value (core/-eval operand context resource scope)]
+        (cond
+          (or (string? value) (nil? value)) value
+          (fhir-spec/primitive-val? value) (:value value)
+          :else (str value))))
     (-form [_]
       `(~'call "ToString" ~(core/-form operand)))))
 
@@ -181,8 +200,8 @@
   Period
   (-to-interval [{:keys [start end]} {:keys [now]}]
     (interval/interval
-     (p/to-date-time (type/value start) now)
-     (p/to-date-time (type/value end) now)))
+     (p/to-date-time (:value start) now)
+     (p/to-date-time (:value end) now)))
 
   nil
   (-to-interval [_ _]))
@@ -250,7 +269,7 @@
       (to-code-function-expr (first operands))
 
       "ToDecimal"
-      (first operands)
+      (to-decimal-function-expr (first operands))
 
       "ToInterval"
       (to-interval-function-expr (first operands))

modules/cql/src/blaze/elm/compiler/structured_values.clj

@@ -10,12 +10,9 @@
    [blaze.elm.compiler.core :as core]
    [blaze.elm.compiler.macros :refer [reify-expr]]
    [blaze.elm.protocols :as p]
-   [blaze.fhir.spec.type :as type]
    [clojure.string :as str])
   (:import
-   [clojure.lang ILookup IReduceInit]
-   [java.time Instant LocalDateTime LocalTime OffsetDateTime]
-   [java.util UUID]))
+   [clojure.lang ILookup IReduceInit]))
 
 (set! *warn-on-reflection* true)
 
@@ -35,43 +32,7 @@
     (throw-anom (invalid-structured-type-access-anom coll key)))
   ILookup
   (get [m key]
-    (.valAt m key))
-  Boolean
-  (get [boolean key]
-    (when (identical? :value key)
-      boolean))
-  Integer
-  (get [int key]
-    (when (identical? :value key)
-      int))
-  String
-  (get [s key]
-    (when (identical? :value key)
-      s))
-  BigDecimal
-  (get [decimal key]
-    (when (identical? :value key)
-      decimal))
-  Instant
-  (get [instant key]
-    (when (identical? :value key)
-      instant))
-  LocalDateTime
-  (get [date-time key]
-    (when (identical? :value key)
-      date-time))
-  OffsetDateTime
-  (get [date-time key]
-    (when (identical? :value key)
-      date-time))
-  LocalTime
-  (get [time key]
-    (when (identical? :value key)
-      time))
-  UUID
-  (get [uuid key]
-    (when (identical? :value key)
-      uuid)))
+    (.valAt m key)))
 
 (defn- compile-elements [context elements]
   (reduce
@@ -143,7 +104,7 @@
     (-resolve-params [_ parameters]
       (source-property-value-expr (core/-resolve-params source parameters) key))
     (-eval [_ context resource scope]
-      (type/value (p/get (core/-eval source context resource scope) key)))
+      (:value (key (core/-eval source context resource scope))))
     (-form [_]
       `(:value (~key ~(core/-form source))))))
 
@@ -157,7 +118,7 @@
 (defn- scope-property-value-expr [scope-key key]
   (reify-expr core/Expression
     (-eval [_ _ _ scope]
-      (type/value (p/get (get scope scope-key) key)))
+      (:value (key (get scope scope-key))))
     (-form [_]
       `(:value (~key ~(symbol (name scope-key)))))))