Update dependencies and clean up unit tests

Author: ctmay4

build.gradle

@@ -2,14 +2,14 @@ plugins {
     id 'java-library'
     id 'checkstyle'
     id 'jacoco'
-    id "com.github.spotbugs" version "5.0.12"
+    id "com.github.spotbugs" version "5.0.14"
     id 'maven-publish'
     id 'signing'
     id "io.codearte.nexus-staging" version "0.30.0"
     id 'com.adarshr.test-logger' version '3.2.0'
-    id "com.github.ben-manes.versions" version "0.42.0"
-    id 'org.sonatype.gradle.plugins.scan' version '2.4.1'
-    id "org.sonarqube" version "3.4.0.2513"
+    id "com.github.ben-manes.versions" version "0.47.0"
+    id 'org.sonatype.gradle.plugins.scan' version '2.6.0'
+    id "org.sonarqube" version "4.2.1.3168"
 }
 
 group = 'com.imsweb'
@@ -34,22 +34,22 @@ repositories {
 }
 
 dependencies {
-    spotbugs 'com.github.spotbugs:spotbugs:4.7.2'
+    spotbugs 'com.github.spotbugs:spotbugs:4.7.3'
 
     api 'com.squareup.retrofit2:retrofit:2.9.0'
     api 'com.squareup.retrofit2:converter-jackson:2.9.0'
 
     // retrofit will not update these dependencies to fix vulnerabilities
-    api 'com.squareup.okhttp3:okhttp:4.10.0'
-    api 'com.squareup.okio:okio:3.2.0'
+    api 'com.squareup.okhttp3:okhttp:4.11.0'
+    api 'com.squareup.okio:okio:3.4.0'
 
     // newer version of dependency to fix vulnerability until converter-jackson is updated
-    api 'com.fasterxml.jackson.core:jackson-databind:2.13.4'
+    api 'com.fasterxml.jackson.core:jackson-databind:2.15.2'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.9.1'
-    testImplementation 'org.junit.jupiter:junit-jupiter-params:5.9.1'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.9.1'
-    testImplementation 'org.assertj:assertj-core:3.23.1'
+    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.9.3'
+    testImplementation 'org.junit.jupiter:junit-jupiter-params:5.9.3'
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.9.3'
+    testImplementation 'org.assertj:assertj-core:3.24.2'
     testImplementation 'com.google.code.bean-matchers:bean-matchers:0.14'
 }
 
@@ -111,8 +111,21 @@ ossIndexAudit {
     printBanner = false
 }
 
+def isNonStable = { String version ->
+    def stableKeyword = ['RELEASE', 'FINAL', 'GA'].any { it -> version.toUpperCase().contains(it) }
+    def regex = /^[0-9,.v-]+(-r)?$/
+    return !stableKeyword && !(version ==~ regex)
+}
+
+// https://github.com/ben-manes/gradle-versions-plugin
+tasks.named("dependencyUpdates").configure {
+    rejectVersionIf {
+        isNonStable(it.candidate.version)
+    }
+}
+
 wrapper {
-    gradleVersion = '7.5.1'
+    gradleVersion = '8.2.1'
     distributionType = Wrapper.DistributionType.ALL
 }
 

gradle/wrapper/gradle-wrapper.jar

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-all.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradle/wrapper/gradle-wrapper.properties

@@ -79,7 +79,7 @@ void testResults() throws IOException {
         MphOutput result = _MPH.mph(new MphInputPair(input1, input2)).execute().body();
         assertNotNull(result);
         assertEquals(MphOutput.Result.SINGLE_PRIMARY, result.getResult());
-        assertEquals("mp_2007_breast", result.getGroupId());
+        assertEquals("mph_2007_to_2017_breast", result.getGroupId());
         assertEquals("M13", result.getStep());
         assertEquals("Tumors that do not meet any of the criteria are abstracted as a single primary.", result.getReason());
         assertEquals(10, result.getAppliedRules().size());
@@ -90,9 +90,9 @@ void testResults() throws IOException {
         result = _MPH.mph(new MphInputPair(input1, input2)).execute().body();
         assertNotNull(result);
         assertEquals(MphOutput.Result.QUESTIONABLE, result.getResult());
-        assertEquals("mp_2007_breast", result.getGroupId());
+        assertEquals("mph_2007_to_2017_breast", result.getGroupId());
         assertEquals("M7", result.getStep());
-        assertEquals("Unable to apply Rule M7 of mp_2007_breast. Valid and known laterality should be provided.", result.getReason());
+        assertEquals("Unable to apply Rule M7 of MPH 2007-2017 Breast. Valid and known laterality should be provided.", result.getReason());
         assertEquals(4, result.getAppliedRules().size());
         assertEquals("Is there a tumor(s) in each breast?", result.getAppliedRules().get(3).getQuestion());
 
@@ -110,7 +110,7 @@ void testResults() throws IOException {
         result = _MPH.mph(new MphInputPair(input1, input2)).execute().body();
         assertNotNull(result);
         assertEquals(MphOutput.Result.MULTIPLE_PRIMARIES, result.getResult());
-        assertEquals("mp_2007_breast", result.getGroupId());
+        assertEquals("mph_2007_to_2017_breast", result.getGroupId());
         assertEquals("M5", result.getStep());
         assertEquals("Tumors diagnosed more than five (5) years apart are multiple primaries.", result.getReason());
         assertEquals(2, result.getAppliedRules().size());

gradlew

@@ -48,19 +48,19 @@ void testRxVersions() throws IOException {
 
     @Test
     void testRxById() throws IOException {
-        Rx rx = _RX.getById("latest", "53c44afe102c1290262dc672").execute().body();
+        Rx rx = _RX.getById("latest", "53c44b0a102c1290262dce76").execute().body();
 
         assertNotNull(rx);
-        assertEquals("ABT-751", rx.getName());
+        assertEquals("Imatinib mesylate", rx.getName());
         assertTrue(rx.getAlternateName().size() > 1);
         assertEquals(Rx.Type.DRUG, rx.getType());
         assertNull(rx.getHistology());
-        assertTrue(rx.getRemarks().startsWith("Phase II ALL"));
+        assertTrue(rx.getRemarks().startsWith("January 31, 2012"));
         assertNull(rx.getEvsId());
         assertNull(rx.getAbbreviation());
         assertEquals(Collections.singletonList("Chemotherapy"), rx.getCategory());
         assertTrue(rx.getSubcategory().size() > 0);
-        assertNull(rx.getNscNumber());
+        assertEquals(1, rx.getNscNumber().size());
         assertNull(rx.getDrugs());
         assertNull(rx.getRadiation());
         assertNull(rx.getHidden());
@@ -72,7 +72,17 @@ void testRxById() throws IOException {
         assertNull(rx.getNote());
         assertNull(rx.getFieldNotes());
         assertNull(rx.getScore());
-        assertEquals(Arrays.asList("neuroblastoma", "Pediatric ALL"), rx.getPrimarySite());
+        assertEquals(Arrays.asList("aggressive mastocytosis",
+                "chronic eosinophilic leukemia",
+                "Colorectal",
+                "dermatofibrosarcoma protuberans",
+                "gastric",
+                "GIST",
+                "hypereosinophilic syndrome",
+                "leukemia",
+                "lung",
+                "other cancer",
+                "Ph+ALL"), rx.getPrimarySite());
         assertNull(rx.getHistory());
     }
 
@@ -112,8 +122,8 @@ void testRxSearch() throws IOException {
 
         assertNotNull(results);
         assertEquals(25, results.getCount().longValue());
-        assertEquals(12, results.getTotal().longValue());
-        assertEquals(12, results.getResults().size());
+        assertEquals(8, results.getTotal().longValue());
+        assertEquals(8, results.getResults().size());
         assertEquals(Collections.singletonList("abt"), results.getTerms());
 
         search.setMode(PublishableSearch.SearchMode.OR);

gradlew.bat

@@ -51,7 +51,7 @@ void testExceptionMessages() throws IOException {
 
         // the API call works out to:
         //     https://api.seer.cancer.gov/rest/recode/sitegroup?site=C379
-        assertEquals("Required request parameter 'hist' for method parameter type String is not present", message);
+        assertEquals("Required parameter 'hist' is not present.", message);
     }
 
     @Test