Merge pull request #423 from medizininformatik-initiative/release/v6.0.4

Release v6.0.4

.github/integration-test/docker-compose.yml

@@ -87,7 +87,7 @@ services:
       POSTGRES_DB: "dataportal"
 
   dataportal-elastic:
-    image: docker.elastic.co/elasticsearch/elasticsearch:8.16.0
+    image: docker.elastic.co/elasticsearch/elasticsearch:8.16.1
     container_name: dataportal-elastic
     ports:
       - '9200:9200'

CHANGELOG.md

@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
+## [6.0.4] - 2025-01-10
+
+### Fixed
+- Time Restriction validation was broken when only one of beforeDate or afterDate was set ([#421](https://github.com/medizininformatik-initiative/feasibility-backend/issues/421))
+- ### Security
+- Update Spring Boot to 3.4.1
+
 ## [6.0.3] - 2024-12-10
 
 ### Changed

docker-compose.yml

@@ -111,7 +111,7 @@ services:
         source: dataportal-postgres-data
         target: /var/lib/postgresql/data
   dataportal-elastic:
-    image: docker.elastic.co/elasticsearch/elasticsearch:8.16.0
+    image: docker.elastic.co/elasticsearch/elasticsearch:8.16.1
     container_name: dataportal-elastic
     ports:
       - '9200:9200'

pom.xml

@@ -6,13 +6,13 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.4.0</version>
+    <version>3.4.1</version>
     <relativePath /> <!-- lookup parent from repository -->
   </parent>
 
   <groupId>de.medizininformatik-initiative</groupId>
   <artifactId>DataportalBackend</artifactId>
-  <version>6.0.3</version>
+  <version>6.0.4</version>
 
   <name>Dataportal Backend</name>
   <description>Backend of the Dataportal</description>

src/main/java/de/numcodex/feasibility_gui_backend/terminology/validation/StructuredQueryValidation.java

@@ -129,8 +129,8 @@ private boolean containsInvalidCriteria(List<Criterion> criteria) {
   }
 
   private boolean isTimeRestrictionInvalid(TimeRestriction timeRestriction) {
-    // If no timeRestriction is set, it is not invalid
-    if (timeRestriction == null) {
+    // If no timeRestriction is set or only on of both dates is set, it is not invalid
+    if (timeRestriction == null || timeRestriction.beforeDate() == null || timeRestriction.afterDate() == null) {
       return false;
     }
     return LocalDate.parse(timeRestriction.beforeDate()).isBefore(LocalDate.parse(timeRestriction.afterDate()));

src/test/java/de/numcodex/feasibility_gui_backend/terminology/es/CodeableConceptServiceIT.java

@@ -25,7 +25,6 @@
 import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 
-@Disabled("There seems to be a concurrency issue with TerminologyServiceIT. Disable this for now until it is fixed.")
 @Tag("terminology")
 @Tag("elasticsearch")
 @Import({CodeableConceptService.class})
@@ -46,7 +45,7 @@ public class CodeableConceptServiceIT {
 
   @Container
   @ServiceConnection
-  public static ElasticsearchContainer ELASTICSEARCH_CONTAINER = new ElasticsearchContainer("docker.elastic.co/elasticsearch/elasticsearch:8.16.0")
+  public static ElasticsearchContainer ELASTICSEARCH_CONTAINER = new ElasticsearchContainer("docker.elastic.co/elasticsearch/elasticsearch:8.16.1")
       .withEnv("discovery.type", "single-node")
       .withEnv("xpack.security.enabled", "false")
       .withReuse(false)
@@ -56,7 +55,7 @@ public class CodeableConceptServiceIT {
       .waitingFor(Wait.forHttp("/health").forStatusCodeMatching(c -> c >= 200 && c <= 500));
 
   @BeforeAll
-  static void setUp() {
+  static void setUp() throws InterruptedException {
     ELASTICSEARCH_CONTAINER.start();
     WebClient webClient = WebClient.builder().baseUrl("http://" + ELASTICSEARCH_CONTAINER.getHttpHostAddress()).build();
     webClient.put()
@@ -72,6 +71,9 @@ static void setUp() {
         .retrieve()
         .toBodilessEntity()
         .block();
+
+    // When running in github actions without a slight delay, the data might not be complete in the elastic search container (although a blocking call is used)
+    Thread.sleep(1000);
   }
 
   @AfterAll

src/test/java/de/numcodex/feasibility_gui_backend/terminology/es/TerminologyEsServiceIT.java

@@ -51,7 +51,7 @@ public class TerminologyEsServiceIT {
 
   @Container
   @ServiceConnection
-  public static ElasticsearchContainer ELASTICSEARCH_CONTAINER = new ElasticsearchContainer("docker.elastic.co/elasticsearch/elasticsearch:8.16.0")
+  public static ElasticsearchContainer ELASTICSEARCH_CONTAINER = new ElasticsearchContainer("docker.elastic.co/elasticsearch/elasticsearch:8.16.1")
       .withEnv("discovery.type", "single-node")
       .withEnv("xpack.security.enabled", "false")
       .withReuse(false)

src/test/java/de/numcodex/feasibility_gui_backend/terminology/validation/StructuredQueryValidationTest.java

@@ -70,6 +70,22 @@ void testIsValid_falseOnInvalidTimeRestriction() {
         assertFalse(isValid);
     }
 
+    @Test
+    void testIsValid_trueOnOnlyBeforeDateTimeRestriction() {
+        doReturn(true).when(terminologyService).isExistingTermCode(any(String.class), any(String.class));
+        var isValid = structuredQueryValidation.isValid(createStructuredQueryWithOnlyBeforeDate());
+
+        assertTrue(isValid);
+    }
+
+    @Test
+    void testIsValid_trueOnOnlyAfterDateTimeRestriction() {
+        doReturn(true).when(terminologyService).isExistingTermCode(any(String.class), any(String.class));
+        var isValid = structuredQueryValidation.isValid(createStructuredQueryWithOnlyAfterDate());
+
+        assertTrue(isValid);
+    }
+
     @ParameterizedTest
     @CsvSource({"true,true", "true,false", "false,true", "false,false"})
     void testAnnotateStructuredQuery_emptyIssuesOnValidCriteriaOrSkippedValidation(String withExclusionCriteriaString, String skipValidationString) {
@@ -201,4 +217,64 @@ private static StructuredQuery createStructuredQueryWithInvalidTimeRestriction()
             .display("foo")
             .build();
     }
+
+    @NotNull
+    private static StructuredQuery createStructuredQueryWithOnlyBeforeDate() {
+        var context = TermCode.builder()
+            .code("Laboruntersuchung")
+            .system("fdpg.mii.cds")
+            .display("Laboruntersuchung")
+            .version("1.0.0")
+            .build();
+        var termCode = TermCode.builder()
+            .code("19113-0")
+            .system("http://loinc.org")
+            .display("IgE")
+            .build();
+        var timeRestriction = TimeRestriction.builder()
+            .beforeDate("1991-06-15")
+            .build();
+        var criterion = Criterion.builder()
+            .termCodes(List.of(termCode))
+            .context(context)
+            .attributeFilters(List.of())
+            .timeRestriction(timeRestriction)
+            .build();
+        return StructuredQuery.builder()
+            .version(URI.create("http://to_be_decided.com/draft-2/schema#"))
+            .inclusionCriteria(List.of(List.of(criterion)))
+            .exclusionCriteria(List.of())
+            .display("foo")
+            .build();
+    }
+
+    @NotNull
+    private static StructuredQuery createStructuredQueryWithOnlyAfterDate() {
+        var context = TermCode.builder()
+            .code("Laboruntersuchung")
+            .system("fdpg.mii.cds")
+            .display("Laboruntersuchung")
+            .version("1.0.0")
+            .build();
+        var termCode = TermCode.builder()
+            .code("19113-0")
+            .system("http://loinc.org")
+            .display("IgE")
+            .build();
+        var timeRestriction = TimeRestriction.builder()
+            .afterDate("1998-05-09")
+            .build();
+        var criterion = Criterion.builder()
+            .termCodes(List.of(termCode))
+            .context(context)
+            .attributeFilters(List.of())
+            .timeRestriction(timeRestriction)
+            .build();
+        return StructuredQuery.builder()
+            .version(URI.create("http://to_be_decided.com/draft-2/schema#"))
+            .inclusionCriteria(List.of(List.of(criterion)))
+            .exclusionCriteria(List.of())
+            .display("foo")
+            .build();
+    }
 }