Merge pull request #142 from medizininformatik-initiative/release-v0.4.0

Release v0.4.0

pom.xml

@@ -4,7 +4,7 @@
 
     <groupId>de.medizininformatik-initiative</groupId>
     <artifactId>sq2cql</artifactId>
-    <version>0.3.0</version>
+    <version>0.4.0</version>
 
     <name>sq2cql</name>
 
@@ -28,9 +28,9 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <maven.compiler.release>17</maven.compiler.release>
-        <junit-jupiter.version>5.10.2</junit-jupiter.version>
+        <junit-jupiter.version>5.10.3</junit-jupiter.version>
         <hapi-fhir.version>7.2.1</hapi-fhir.version>
-        <testcontainers.version>1.19.8</testcontainers.version>
+        <testcontainers.version>1.20.0</testcontainers.version>
         <slf4j.version>2.0.13</slf4j.version>
         <ontology.version>2.2.0</ontology.version>
     </properties>
@@ -40,7 +40,7 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.17.1</version>
+            <version>2.17.2</version>
         </dependency>
 
         <dependency>
@@ -73,7 +73,7 @@
         <dependency>
             <groupId>org.assertj</groupId>
             <artifactId>assertj-core</artifactId>
-            <version>3.26.0</version>
+            <version>3.26.3</version>
             <scope>test</scope>
         </dependency>
 
@@ -128,13 +128,13 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>3.3.0</version>
+                <version>3.3.1</version>
             </plugin>
 
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>
-                <version>3.3.0</version>
+                <version>3.3.1</version>
                 <executions>
                     <execution>
                         <goals>

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

@@ -29,7 +29,7 @@ public Container<QueryExpression> updateQuery(MappingContext mappingContext, Con
                     var referenceExpr = InvocationExpression.of(query.sourceAlias(), path);
                     var alias = StandardIdentifierExpression.of(targetType.substring(0, 1));
                     var ref = AdditionExpressionTerm.of(StringLiteralExpression.of(targetType + "/"), InvocationExpression.of(alias, "id"));
-                    var comparatorExpr = ComparatorExpression.equal(referenceExpr, ref);
+                    var comparatorExpr = MembershipExpression.contains(referenceExpr, ref);
                     return query.appendQueryInclusionClause(WithClause.of(AliasedQuerySource.of(referencesExprName, alias), comparatorExpr));
                 }));
     }

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

@@ -13,6 +13,7 @@
 import org.junit.jupiter.api.TestInstance;
 import org.junit.jupiter.api.TestInstance.Lifecycle;
 import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.CsvSource;
 import org.junit.jupiter.params.provider.MethodSource;
 import org.junit.jupiter.params.provider.ValueSource;
 import org.slf4j.Logger;
@@ -49,7 +50,7 @@ public class AcceptanceTest {
     private static final Logger logger = LoggerFactory.getLogger(AcceptanceTest.class);
 
     private final GenericContainer<?> blaze = new GenericContainer<>(
-            DockerImageName.parse("samply/blaze:0.27"))
+            DockerImageName.parse("samply/blaze:0.28"))
             .withImagePullPolicy(PullPolicy.alwaysPull())
             .withEnv("LOG_LEVEL", "debug")
             .withExposedPorts(8080)
@@ -158,7 +159,8 @@ public void consent() throws Exception {
     }
 
     @ParameterizedTest
-    @ValueSource(strings = {"large-query-worst-case-with-time-constraints.json", "test-large-query-more-crit-time-rest-1.json"})
+    @ValueSource(strings = {"large-query-worst-case-with-time-constraints.json",
+            "test-large-query-more-crit-time-rest-1.json"})
     public void largeQuery(String filename) throws Exception {
         var structuredQuery = new ObjectMapper().readValue(slurp(filename), StructuredQuery.class);
         var cql = translator.toCql(structuredQuery).print();
@@ -168,6 +170,23 @@ public void largeQuery(String filename) throws Exception {
         assertEquals(0, report.getGroupFirstRep().getPopulationFirstRep().getCount());
     }
 
+    @ParameterizedTest
+    @CsvSource({
+            "SpecimenSQ.json, 0",
+            "SpecimenSQExclusion.json, 159",
+            "SpecimenSQTwoInclusion.json, 0",
+            "SpecimenSQTwoReferenceCriteria.json, 0",
+            "SpecimenSQAndBodySite.json, 0"
+    })
+    public void specimenQuery(String filename, int count) throws Exception {
+        var structuredQuery = new ObjectMapper().readValue(slurp(filename), StructuredQuery.class);
+        var cql = translator.toCql(structuredQuery).print();
+        var measureUri = createMeasureAndLibrary(cql);
+        var report = evaluateMeasure(measureUri);
+
+        assertEquals(count, report.getGroupFirstRep().getPopulationFirstRep().getCount());
+    }
+
     private String createMeasureAndLibrary(String cql) throws Exception {
         var libraryUri = "urn:uuid" + UUID.randomUUID();
         var library = appendCql(parseResource(Library.class, slurp("Library.json")).setUrl(libraryUri), cql);

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:0.27"))
+    private final GenericContainer<?> blaze = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.28"))
             .withImagePullPolicy(PullPolicy.alwaysPull())
             .withExposedPorts(8080)
             .waitingFor(Wait.forHttp("/health").forStatusCode(200))