Release v0.6.0

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
     - name: Check out Git repository
@@ -42,7 +42,7 @@ jobs:
       run: mvn -B verify
 
   deploy:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     needs: build
     if: startsWith(github.ref, 'refs/tags/')
 
@@ -63,7 +63,7 @@ jobs:
         key: maven-${{ hashFiles('pom.xml') }}
 
     - name: Maven Settings
-      uses: s4u/maven-settings-action@v3.0.0
+      uses: s4u/maven-settings-action@v3.1.0
       with:
         servers: |
           [{"id": "github", "username": "${{ github.actor }}", "password": "${{ secrets.GITHUB_TOKEN }}"}]

pom.xml

@@ -4,7 +4,7 @@
 
     <groupId>de.medizininformatik-initiative</groupId>
     <artifactId>sq2cql</artifactId>
-    <version>0.5.0</version>
+    <version>0.6.0</version>
 
     <name>sq2cql</name>
 
@@ -28,10 +28,10 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <maven.compiler.release>17</maven.compiler.release>
-        <junit-jupiter.version>5.10.3</junit-jupiter.version>
-        <hapi-fhir.version>7.2.1</hapi-fhir.version>
-        <testcontainers.version>1.20.0</testcontainers.version>
-        <slf4j.version>2.0.13</slf4j.version>
+        <junit-jupiter.version>5.11.3</junit-jupiter.version>
+        <hapi-fhir.version>7.6.0</hapi-fhir.version>
+        <testcontainers.version>1.20.4</testcontainers.version>
+        <slf4j.version>2.0.16</slf4j.version>
         <ontology.version>3.0.0</ontology.version>
     </properties>
 
@@ -94,7 +94,7 @@
         <dependency>
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
-            <version>1.5.6</version>
+            <version>1.5.12</version>
             <scope>test</scope>
         </dependency>
 
@@ -128,13 +128,13 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>3.3.1</version>
+                <version>3.5.2</version>
             </plugin>
 
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>
-                <version>3.3.1</version>
+                <version>3.5.2</version>
                 <executions>
                     <execution>
                         <goals>
@@ -148,7 +148,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-deploy-plugin</artifactId>
-                <version>3.1.2</version>
+                <version>3.1.3</version>
             </plugin>
 
             <plugin>

src/main/java/de/numcodex/sq2cql/model/structured_query/AbstractCriterion.java

@@ -76,6 +76,11 @@ private static String referenceName(TermCode termCode) {
 
     public abstract T appendAttributeFilter(AttributeFilter attributeFilter);
 
+    @Override
+    public List<AttributeFilter> attributeFilters() {
+        return attributeFilters;
+    }
+
     @Override
     public ContextualConcept getConcept() {
         return concept;

src/main/java/de/numcodex/sq2cql/model/structured_query/Criterion.java

@@ -48,6 +48,11 @@ public Container<DefaultExpression> toReferencesCql(MappingContext mappingContex
             throw new UnsupportedOperationException();
         }
 
+        @Override
+        public List<AttributeFilter> attributeFilters() {
+            return List.of();
+        }
+
         @Override
         public TimeRestriction timeRestriction() {
             return null;
@@ -74,6 +79,11 @@ public Container<DefaultExpression> toReferencesCql(MappingContext mappingContex
             throw new UnsupportedOperationException();
         }
 
+        @Override
+        public List<AttributeFilter> attributeFilters() {
+            return List.of();
+        }
+
         @Override
         public TimeRestriction timeRestriction() {
             return null;
@@ -172,5 +182,7 @@ private static <T> T getAndMap(JsonNode node, String name, Function<JsonNode, T>
 
     Container<DefaultExpression> toReferencesCql(MappingContext mappingContext);
 
+    List<AttributeFilter> attributeFilters();
+
     TimeRestriction timeRestriction();
 }

src/main/java/de/numcodex/sq2cql/model/structured_query/TimeRestriction.java

@@ -5,24 +5,41 @@
 import com.fasterxml.jackson.databind.JsonNode;
 import de.numcodex.sq2cql.model.Mapping;
 
-public record TimeRestriction(String afterDate, String beforeDate) {
+import java.time.LocalDate;
 
-    public static TimeRestriction of(String afterDate, String beforeDate) {
+import static java.util.Objects.requireNonNull;
+
+public record TimeRestriction(LocalDate afterDate, LocalDate beforeDate) {
+
+    public TimeRestriction {
+        requireNonNull(afterDate);
+        requireNonNull(beforeDate);
+        if (beforeDate.isBefore(afterDate)) {
+            throw new IllegalArgumentException("Invalid time restriction: beforeDate `%s` is before afterDate `%s` but should not be."
+                    .formatted(beforeDate, afterDate));
+        }
+    }
+
+    public static TimeRestriction of(LocalDate afterDate, LocalDate beforeDate) {
         return new TimeRestriction(afterDate, beforeDate);
     }
 
     @JsonCreator
     public static TimeRestriction create(@JsonProperty("afterDate") String afterDate,
                                          @JsonProperty("beforeDate") String beforeDate) {
-        //FIXME: quick and dirty for empty timeRestriction
         if (afterDate == null && beforeDate == null) {
             return null;
+        } else if (afterDate == null) {
+            return TimeRestriction.of(LocalDate.of(1900, 1, 1), LocalDate.parse(beforeDate));
+        } else if (beforeDate == null) {
+            return TimeRestriction.of(LocalDate.parse(afterDate), LocalDate.of(2040, 1, 1));
+        } else {
+            return TimeRestriction.of(LocalDate.parse(afterDate), LocalDate.parse(beforeDate));
         }
-        return TimeRestriction.of(afterDate, beforeDate);
     }
 
     public static TimeRestriction fromJsonNode(JsonNode node) {
-        return TimeRestriction.of(node.get("afterDate").asText(), node.get("beforeDate").asText());
+        return TimeRestriction.create(node.get("afterDate").asText(), node.get("beforeDate").asText());
     }
 
     public Modifier toModifier(Mapping mapping) {

src/main/java/de/numcodex/sq2cql/model/structured_query/TimeRestrictionModifier.java

@@ -3,19 +3,20 @@
 import de.numcodex.sq2cql.model.MappingContext;
 import de.numcodex.sq2cql.model.cql.*;
 
+import java.time.LocalDate;
 import java.util.List;
 
 import static java.util.Objects.requireNonNull;
 
-public record TimeRestrictionModifier(String path, String afterDate, String beforeDate) implements SimpleModifier {
+public record TimeRestrictionModifier(String path, LocalDate afterDate, LocalDate beforeDate) implements SimpleModifier {
 
     public TimeRestrictionModifier {
         requireNonNull(path);
-        afterDate = afterDate == null ? "1900-01-01T" : afterDate;
-        beforeDate = beforeDate == null ? "2040-01-01T" : beforeDate;
+        requireNonNull(afterDate);
+        requireNonNull(beforeDate);
     }
 
-    public static TimeRestrictionModifier of(String path, String afterDate, String beforeDate) {
+    public static TimeRestrictionModifier of(String path, LocalDate afterDate, LocalDate beforeDate) {
         return new TimeRestrictionModifier(path, afterDate, beforeDate);
     }
 
@@ -24,8 +25,13 @@ public Container<DefaultExpression> expression(MappingContext mappingContext, Id
         var invocationExpr = InvocationExpression.of(sourceAlias, path);
         var castExp = TypeExpression.of(invocationExpr, "dateTime");
         var toDateFunction = FunctionInvocation.of("ToDate", List.of(castExp));
-        var intervalSelector = IntervalSelector.of(DateTimeExpression.of(afterDate), DateTimeExpression.of(beforeDate));
+        var intervalSelector = IntervalSelector.of(DateTimeExpression.of(afterDate.toString()), DateTimeExpression.of(beforeDate.toString()));
         var dateTimeInExpr = MembershipExpression.in(toDateFunction, intervalSelector);
+
+        if ("recordedDate".equals(path)) {
+            return Container.of(dateTimeInExpr);
+        }
+
         var intervalOverlapExpr = OverlapsIntervalOperatorPhrase.of(invocationExpr, intervalSelector);
         return Container.of(OrExpression.of(dateTimeInExpr, intervalOverlapExpr));
     }

src/test/java/de/numcodex/sq2cql/AcceptanceTest.java

@@ -34,7 +34,6 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.List;
 import java.util.Objects;
 import java.util.UUID;
 import java.util.stream.Stream;
@@ -53,7 +52,7 @@ public class AcceptanceTest {
     private static final Logger logger = LoggerFactory.getLogger(AcceptanceTest.class);
 
     private final GenericContainer<?> blaze = new GenericContainer<>(
-            DockerImageName.parse("samply/blaze:0.28"))
+            DockerImageName.parse("samply/blaze:0.30"))
             .withImagePullPolicy(PullPolicy.alwaysPull())
             .withEnv("LOG_LEVEL", "debug")
             .withExposedPorts(8080)
@@ -80,16 +79,8 @@ private static Bundle createBundle(Library library, Measure measure) {
         return bundle;
     }
 
-    public static List<StructuredQuery> getTestQueriesReturningOnePatient() throws URISyntaxException, IOException {
-        try (Stream<Path> paths = Files.list(resourcePath("returningOnePatient"))) {
-            return paths.map(path -> {
-                try {
-                    return new ObjectMapper().readValue(Files.readString(path), StructuredQuery.class);
-                } catch (IOException e) {
-                    throw new RuntimeException(e);
-                }
-            }).toList();
-        }
+    public static Stream<Path> getTestQueriesReturningOnePatient() throws IOException, URISyntaxException {
+        return Files.list(resourcePath("returningOnePatient"));
     }
 
     @BeforeAll
@@ -106,7 +97,8 @@ public void setUp() throws Exception {
 
     @ParameterizedTest
     @MethodSource("de.numcodex.sq2cql.AcceptanceTest#getTestQueriesReturningOnePatient")
-    public void runTestCase(StructuredQuery structuredQuery) throws Exception {
+    public void runTestCase(Path path) throws Exception {
+        var structuredQuery = new ObjectMapper().readValue(Files.readString(path), StructuredQuery.class);
         var cql = translator.toCql(structuredQuery).print();
         var measureUri = createMeasureAndLibrary(cql);
         var report = evaluateMeasure(measureUri);

src/test/java/de/numcodex/sq2cql/EvaluationIT.java

@@ -50,7 +50,7 @@ public class EvaluationIT {
     static final Map<String, String> CODE_SYSTEM_ALIASES = Map.of("http://loinc.org", "loinc");
 
     @Container
-    private final GenericContainer<?> blaze = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.28"))
+    private final GenericContainer<?> blaze = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.30"))
             .withImagePullPolicy(PullPolicy.alwaysPull())
             .withExposedPorts(8080)
             .waitingFor(Wait.forHttp("/health").forStatusCode(200))