Update deps

Author: ctmay4

build.gradle

@@ -6,11 +6,11 @@ plugins {
     id 'java-library'
     id 'checkstyle'
     id 'jacoco'
-    id "com.github.spotbugs" version "6.1.11"
+    id "com.github.spotbugs" version "6.4.8"
     id 'com.adarshr.test-logger' version '4.0.0'
-    id "com.github.ben-manes.versions" version "0.52.0"
-    id 'org.sonatype.gradle.plugins.scan' version '3.1.1'
-    id "org.sonarqube" version "6.2.0.5505"
+    id "com.github.ben-manes.versions" version "0.53.0"
+    id 'org.sonatype.gradle.plugins.scan' version '3.1.4'
+    id "org.sonarqube" version "7.2.3.7755"
     id 'com.vanniktech.maven.publish' version '0.31.0'
 }
 
@@ -33,23 +33,23 @@ repositories {
 }
 
 dependencies {
-    spotbugs 'com.github.spotbugs:spotbugs:4.9.3'
+    spotbugs 'com.github.spotbugs:spotbugs:4.9.8'
 
-    api 'com.squareup.retrofit2:retrofit:2.11.0'
-    api 'com.squareup.retrofit2:converter-jackson:2.11.0'
-    api 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.19.1'
+    api 'com.squareup.retrofit2:retrofit:3.0.0'
+    api 'com.squareup.retrofit2:converter-jackson:3.0.0'
+    api 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.21.1'
 
     // retrofit will not update these dependencies to fix vulnerabilities
     api 'com.squareup.okhttp3:okhttp:4.12.0'
-    api 'com.squareup.okio:okio:3.11.0'
+    api 'com.squareup.okio:okio:3.16.4'
 
     testImplementation platform('org.junit:junit-bom:5.12.2')
     testImplementation 'org.junit.jupiter:junit-jupiter-api'
     testImplementation 'org.junit.jupiter:junit-jupiter-params'
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine'
     testRuntimeOnly 'org.junit.platform:junit-platform-launcher:1.12.2'
 
-    testImplementation 'org.assertj:assertj-core:3.27.3'
+    testImplementation 'org.assertj:assertj-core:3.27.7'
     testImplementation 'com.google.code.bean-matchers:bean-matchers:0.14'
 }
 
@@ -157,6 +157,6 @@ mavenPublishing {
 }
 
 wrapper {
-    gradleVersion = '8.14'
+    gradleVersion = '9.4.0'
     distributionType = Wrapper.DistributionType.ALL
 }

gradle/wrapper/gradle-wrapper.jar

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.4.0-all.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradle/wrapper/gradle-wrapper.properties

@@ -97,6 +97,7 @@ private SeerApi(String baseUrl, final String apiKey) {
      * Return the internal ObjectMapper
      * @return an Objectmapper
      */
+    @SuppressWarnings("deprecation")
     static ObjectMapper getMapper() {
         ObjectMapper mapper = new ObjectMapper();
 

gradlew

@@ -89,7 +89,7 @@ void testDiseaseById() throws IOException {
         Disease disease = _DISEASE.getById("latest", "51f6cf58e3e27c3994bd5408").execute().body();
 
         assertNotNull(disease);
-        assertEquals("Pure erythroid leukemia", disease.getName());
+        assertEquals("Acute erythroid leukemia (AEL)", disease.getName());
         assertEquals(Disease.Type.HEMATO, disease.getType());
         assertEquals("9840/3", disease.getIcdO3Morphology());
         assertFalse(disease.getSamePrimaries().isEmpty());
@@ -115,7 +115,7 @@ void testDiseaseById() throws IOException {
         assertNull(disease.getObsoleteNewCode());
         assertEquals(1, disease.getAbstractorNote().size());
         assertEquals(2, disease.getTreatment().size());
-        assertNull(disease.getGenetics());
+        assertNotNull(disease.getGenetics());
         assertFalse(disease.getAlternateName().isEmpty());
         assertEquals("Acute erythemia [OBS]", disease.getAlternateName().get(0).getValue());
         assertTrue(disease.getIcdO2Morphology().contains("9840/3"));
@@ -138,7 +138,7 @@ void testDiseaseById() throws IOException {
         assertNotNull(disease.getTransformFrom());
         assertNull(disease.getTransformTo());
         assertNotNull(disease.getImmunophenotype());
-        assertEquals("Bone marrow biopsy", disease.getDiagnosisMethod().get(0).getValue());
+        assertEquals("Cytogenetics", disease.getDiagnosisMethod().get(0).getValue());
         assertEquals("See abstractor notes", disease.getModuleId().get(0).getValue());
         assertNull(disease.getBiomarkers());
         assertNull(disease.getTreatmentText());
@@ -175,8 +175,8 @@ void testDiseaseSearch() throws IOException {
 
         assertNotNull(results);
         assertEquals(25, results.getCount().longValue());
-        assertEquals(5, results.getTotal().longValue());
-        assertEquals(5, results.getResults().size());
+        assertEquals(7, results.getTotal().longValue());
+        assertEquals(7, results.getResults().size());
         assertEquals(Collections.singletonList("basophilic"), results.getTerms());
 
         search.setSiteCategory("BAD_VALUE");
@@ -211,8 +211,8 @@ void testDiseaseSearch() throws IOException {
 
         assertNotNull(results);
         assertEquals(25, results.getCount().longValue());
-        assertEquals(6, results.getTotal().longValue());
-        assertEquals(6, results.getResults().size());
+        assertEquals(8, results.getTotal().longValue());
+        assertEquals(8, results.getResults().size());
         assertEquals(Collections.singletonList("basophilic"), results.getTerms());
     }
 

gradlew.bat

@@ -43,7 +43,7 @@ void testNdcByCode() throws IOException {
         assertThat(product.getDosageFormName()).isEqualTo("CAPSULE");
         assertThat(product.getRouteName()).containsExactly("ORAL");
         assertThat(product.getStartMarketingDate()).isEqualTo("20021126");
-        assertThat(product.getEndMarketingDate()).isNull();
+        assertThat(product.getEndMarketingDate()).isEqualTo("20270731");
         assertThat(product.getMarketingCategoryName()).isEqualTo("NDA");
         assertThat(product.getApplicationNumber()).isEqualTo("NDA021411");
         assertThat(product.getLabelerName()).isEqualTo("Eli Lilly and Company");