Merge branch 'master' into master

openEHR · Apr 1, 2024 · da70a65 · da70a65
2 parents ca42c1a + f5d640e
commit da70a65
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diff --git a/.github/workflows/pull-request.yaml b/.github/workflows/pull-request.yaml
@@ -0,0 +1,29 @@
+name: Gradle Build & Test
+
+on:
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up GraalVM JDK 17
+        uses: graalvm/setup-graalvm@v1
+        with:
+          java-version: '17'
+          distribution: 'graalvm-community'
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Gradle Build
+        uses: gradle/[email protected]
+        with:
+          arguments: build
+        env:
+          ORG_GRADLE_PROJECT_mavenUser: ${{ github.actor }}
+          ORG_GRADLE_PROJECT_mavenPassword: ${{ secrets.GITHUB_TOKEN }}
+          ORG_GRADLE_PROJECT_snapshotsRepoURL: https://maven.pkg.github.com/${{ github.repository }}
+          ORG_GRADLE_PROJECT_releasesRepoURL: https://maven.pkg.github.com/${{ github.repository }}
diff --git a/.github/workflows/push.yaml b/.github/workflows/push.yaml
@@ -0,0 +1,30 @@
+name: Build & Release
+
+on:
+  push:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up GraalVM JDK 17
+        uses: graalvm/setup-graalvm@v1
+        with:
+          java-version: '17'
+          distribution: 'graalvm-community'
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Gradle Build
+        uses: gradle/[email protected]
+        with:
+          arguments: build publish
+        env:
+          ORG_GRADLE_PROJECT_mavenUser: ${{ github.actor }}
+          ORG_GRADLE_PROJECT_mavenPassword: ${{ secrets.GITHUB_TOKEN }}
+          ORG_GRADLE_PROJECT_snapshotsRepoURL: https://maven.pkg.github.com/${{ github.repository }}
+          ORG_GRADLE_PROJECT_releasesRepoURL: https://maven.pkg.github.com/${{ github.repository }}
diff --git a/aom/src/main/java/com/nedap/archie/rminfo/ArchieModelNamingStrategy.java b/aom/src/main/java/com/nedap/archie/rminfo/ArchieModelNamingStrategy.java
@@ -27,15 +27,15 @@ public ArchieModelNamingStrategy(boolean standardCompliantExpressionNames) {
         this.standardsCompliantExpressionNames = standardCompliantExpressionNames;
     }
 
-    private static HashMap<String, String> rulesArchieToStandardTypeNamesMap = new HashMap<>();
-    {
+    private static final HashMap<String, String> rulesArchieToStandardTypeNamesMap = new HashMap<>();
+    static {
         rulesArchieToStandardTypeNamesMap.put("Operator", "EXPR_OPERATOR");
         rulesArchieToStandardTypeNamesMap.put("UnaryOperator", "EXPR_UNARY_OPERATOR");
         rulesArchieToStandardTypeNamesMap.put("BinaryOperator", "EXPR_BINARY_OPERATOR");
-        rulesArchieToStandardTypeNamesMap.put("Leaf", "EXPR_LITERAL");
+        rulesArchieToStandardTypeNamesMap.put("Leaf", "EXPR_LEAF");
         rulesArchieToStandardTypeNamesMap.put("Function", "EXPR_FUNCTION");
         rulesArchieToStandardTypeNamesMap.put("VariableReference", "EXPR_VARIABLE_REF");
-        rulesArchieToStandardTypeNamesMap.put("Constant", "EXPR_CONSTANT");
+        rulesArchieToStandardTypeNamesMap.put("Constant", "EXPR_LITERAL");
         rulesArchieToStandardTypeNamesMap.put("Constraint", "EXPR_CONSTRAINT");
         rulesArchieToStandardTypeNamesMap.put("ArchetypeIdConstraint", "EXPR_ARCHETYPE_ID_CONSTRAINT");
         rulesArchieToStandardTypeNamesMap.put("ModelReference", "EXPR_ARCHETYPE_REF");

diff --git a/aom/src/main/java/com/nedap/archie/rules/ExpressionType.java b/aom/src/main/java/com/nedap/archie/rules/ExpressionType.java
@@ -5,7 +5,7 @@
  * Created by pieter.bos on 27/10/15.
  */
 public enum ExpressionType {
-     BOOLEAN, STRING, INTEGER, REAL, DATE, TIME, DATETIME, DURATION;
+     BOOLEAN, STRING, INTEGER, REAL, DATE, TIME, DATETIME, DURATION, C_STRING;
 
     public static ExpressionType fromString(String string) {
         switch(string) {
@@ -25,6 +25,8 @@ public static ExpressionType fromString(String string) {
                 return DATETIME;
             case "Duration":
                 return DURATION;
+            case "CString":
+                return C_STRING;
         }
         return null;
     }
@@ -47,6 +49,8 @@ public String toString() {
                 return "DateTime";
             case DURATION:
                 return "Duration";
+            case C_STRING:
+                return "CString";
         }
         return null;
     }

diff --git a/archie-utils/src/main/java/com/nedap/archie/json/JacksonUtil.java b/archie-utils/src/main/java/com/nedap/archie/json/JacksonUtil.java
@@ -83,6 +83,7 @@ public static void configureObjectMapper(ObjectMapper objectMapper, ArchieJackso
         objectMapper.setPropertyNamingStrategy(PropertyNamingStrategy.SNAKE_CASE);
         objectMapper.enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY);
         objectMapper.enable(DeserializationFeature.UNWRAP_SINGLE_VALUE_ARRAYS);
+        objectMapper.configure(MapperFeature.ACCEPT_CASE_INSENSITIVE_ENUMS, true);
         if(!configuration.isSerializeEmptyCollections()) {
             objectMapper.setDefaultPropertyInclusion(
                     JsonInclude.Value.construct(

diff --git a/base/src/main/java/com/nedap/archie/base/MultiplicityInterval.java b/base/src/main/java/com/nedap/archie/base/MultiplicityInterval.java
@@ -45,13 +45,16 @@ public MultiplicityInterval(Integer lower, Boolean lowerIncluded, Boolean lowerU
 
     @JsonCreator
     public static MultiplicityInterval createFromString(String interval) {
-        Pattern pattern = Pattern.compile("(?<lower>[0-9]+)\\.\\.(?<upper>[0-9]+|\\*)");
+        Pattern pattern = Pattern.compile("(?<lower>[0-9]+)(\\.\\.(?<upper>[0-9]+|\\*))?");
         Matcher matcher = pattern.matcher(interval);
         if(!matcher.matches()) {
             throw new IllegalArgumentException("Cannot parse interval " + interval);
         }
         String lower = matcher.group("lower");
         String upper = matcher.group("upper");
+        if (upper == null) {
+            upper = lower;
+        }
         MultiplicityInterval result = new MultiplicityInterval();
         if(upper.equalsIgnoreCase("*")) {
             result.setUpperUnbounded(true);

diff --git a/build.gradle b/build.gradle
@@ -9,7 +9,8 @@ wrapper {
 
 allprojects {
   version = '3.9.1'
-  group = 'com.nedap.healthcare.archie'
+  group =  'io.graphitehealth.archie'
+
   ext.gradleScriptDir = "${rootProject.projectDir}/gradle"
   //archivesBaseName = 'archie'
 

diff --git a/gradle/publish-maven.gradle b/gradle/publish-maven.gradle
@@ -12,16 +12,12 @@ if(gradle.ext.shouldSign) {
 publishing {
   repositories {
     maven {
-      name = "ossrh"
-      // OSSRH URLS
-      def releasesRepoUrl = 'https://oss.sonatype.org/service/local/staging/deploy/maven2/'
-      def snapshotsRepoUrl = 'ttps://oss.sonatype.org/content/repositories/snapshots/'
-      url = version.endsWith('SNAPSHOT') ? snapshotsRepoUrl : releasesRepoUrl
-
       credentials {
-        username = project.hasProperty('ossrhUsername') ? ossrhUsername : "Unknown user"
-        password = project.hasProperty('ossrhPassword') ? ossrhPassword : "Unknown password"
+        username mavenUser
+        password mavenPassword
       }
+
+      url = version.endsWith('SNAPSHOT') ? snapshotsRepoURL : releasesRepoURL
     }
   }
 }

diff --git a/tools/src/test/java/com/nedap/archie/json/AOMJacksonTest.java b/tools/src/test/java/com/nedap/archie/json/AOMJacksonTest.java
@@ -20,11 +20,14 @@
 import com.nedap.archie.rules.OperatorKind;
 import com.nedap.archie.serializer.adl.ADLArchetypeSerializer;
 import com.nedap.archie.testutil.TestUtil;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.openehr.referencemodels.BuiltinReferenceModels;
 import org.threeten.extra.PeriodDuration;
 
+import java.io.File;
 import java.io.InputStream;
+import java.nio.file.Files;
 import java.time.Duration;
 import java.time.Period;
 import java.time.temporal.ChronoUnit;
@@ -269,4 +272,34 @@ public void rmOverlay() throws Exception {
                 "    }\n" +
                 "  },"));
     }
+
+    @Test
+    public void parseS2AomJson() throws Exception {
+        try(InputStream stream = getClass().getResourceAsStream( "/S2/json/flat/s2-EHR-Action.medication.v1.2.2.json")) {
+
+            Archetype parsed = JacksonUtil.getObjectMapper(ArchieJacksonConfiguration.createStandardsCompliant()).readValue(stream, Archetype.class);
+            assertNotNull(parsed);
+        }
+    }
+
+    @Ignore // for local testing
+    @Test
+    public void parseS2AomJsonAll() throws Exception {
+
+        ObjectMapper mapper = JacksonUtil.getObjectMapper(ArchieJacksonConfiguration.createStandardsCompliant());
+
+        Files.find(new File("../../ADL-exported/S2-S2_demo/json/flat").toPath(),
+                        1,
+                        (file, att) -> file.toString().endsWith(".json"))
+                .forEach(file -> {
+                    try (InputStream stream = Files.newInputStream(file)) {
+                        Archetype parsed = mapper.readValue(stream, Archetype.class);
+                        assertNotNull(parsed);
+                    } catch (Exception e) {
+                        System.out.println("Error parsing " + file.toString());
+                        throw new RuntimeException(e);
+                    }
+                });
+    }
+
 }