Merge pull request #45 from imsweb/cleanup

Cleanup tests and update dependencies

Author: ctmay4

.github/workflows/integration.yml

@@ -20,7 +20,7 @@ jobs:
           distribution: 'adopt'
           java-version: '17'
       - name: Cache Gradle packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: |
             ~/.gradle/caches

build.gradle

@@ -2,14 +2,14 @@ plugins {
     id 'java-library'
     id 'checkstyle'
     id 'jacoco'
-    id "com.github.spotbugs" version "6.0.25"
+    id "com.github.spotbugs" version "6.1.11"
     id 'maven-publish'
     id 'signing'
     id "io.codearte.nexus-staging" version "0.30.0"
     id 'com.adarshr.test-logger' version '4.0.0'
-    id "com.github.ben-manes.versions" version "0.51.0"
-    id 'org.sonatype.gradle.plugins.scan' version '2.8.3'
-    id "org.sonarqube" version "5.1.0.4882"
+    id "com.github.ben-manes.versions" version "0.52.0"
+    id 'org.sonatype.gradle.plugins.scan' version '3.1.1'
+    id "org.sonarqube" version "6.1.0.5360"
 }
 
 group = 'com.imsweb'
@@ -18,7 +18,7 @@ description = 'Java client library for SEER*API'
 
 tasks.withType(JavaCompile).configureEach {
     options.encoding = 'UTF-8'
-    options.compilerArgs << "-Werror"
+    options.compilerArgs << "-Werror" << "-Xlint:-options"
 }
 
 java {
@@ -34,19 +34,22 @@ repositories {
 }
 
 dependencies {
-    spotbugs 'com.github.spotbugs:spotbugs:4.8.6'
+    spotbugs 'com.github.spotbugs:spotbugs:4.9.3'
 
     api 'com.squareup.retrofit2:retrofit:2.11.0'
     api 'com.squareup.retrofit2:converter-jackson:2.11.0'
 
     // retrofit will not update these dependencies to fix vulnerabilities
     api 'com.squareup.okhttp3:okhttp:4.12.0'
-    api 'com.squareup.okio:okio:3.9.1'
+    api 'com.squareup.okio:okio:3.11.0'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.11.3'
-    testImplementation 'org.junit.jupiter:junit-jupiter-params:5.11.3'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.11.3'
-    testImplementation 'org.assertj:assertj-core:3.26.3'
+    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 'com.google.code.bean-matchers:bean-matchers:0.14'
 }
 
@@ -122,7 +125,7 @@ tasks.named("dependencyUpdates").configure {
 }
 
 wrapper {
-    gradleVersion = '8.8'
+    gradleVersion = '8.14'
     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-8.8-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-all.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradle/wrapper/gradle-wrapper.properties

@@ -15,6 +15,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+# SPDX-License-Identifier: Apache-2.0
+#
 
 ##############################################################################
 #
@@ -84,7 +86,7 @@ done
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
 # Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
+APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s\n' "$PWD" ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -112,7 +114,7 @@ case "$( uname )" in                #(
   NONSTOP* )        nonstop=true ;;
 esac
 
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+CLASSPATH="\\\"\\\""
 
 
 # Determine the Java command to use to start the JVM.
@@ -203,15 +205,15 @@ fi
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Collect all arguments for the java command:
-#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
 #     and any embedded shellness will be escaped.
 #   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
 #     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \
         -classpath "$CLASSPATH" \
-        org.gradle.wrapper.GradleWrapperMain \
+        -jar "$APP_HOME/gradle/wrapper/gradle-wrapper.jar" \
         "$@"
 
 # Stop when "xargs" is not available.

gradlew

@@ -13,6 +13,8 @@
 @rem See the License for the specific language governing permissions and
 @rem limitations under the License.
 @rem
+@rem SPDX-License-Identifier: Apache-2.0
+@rem
 
 @if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
@@ -68,11 +70,11 @@ goto fail
 :execute
 @rem Setup the command line
 
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+set CLASSPATH=
 
 
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" -jar "%APP_HOME%\gradle\wrapper\gradle-wrapper.jar" %*
 
 :end
 @rem End local scope for the variables with windows NT shell

gradlew.bat

@@ -28,7 +28,7 @@ class DiseaseTest {
     private static DiseaseService _DISEASE;
 
     @BeforeAll
-    public static void setup() {
+    static void setup() {
         _DISEASE = new SeerApi.Builder().connect().disease();
     }
 
@@ -117,7 +117,7 @@ void testDiseaseById() throws IOException {
         assertEquals(2, disease.getTreatment().size());
         assertNull(disease.getGenetics());
         assertFalse(disease.getAlternateName().isEmpty());
-        assertEquals("Acute erythremia", disease.getAlternateName().get(0).getValue());
+        assertEquals("Acute erythemia [OBS]", disease.getAlternateName().get(0).getValue());
         assertTrue(disease.getIcdO2Morphology().contains("9840/3"));
         assertTrue(disease.getIcdO1Morphology().contains("9840/3"));
         assertEquals("C94.0 Acute erythroid leukemia", disease.getIcd10CmCode().get(0).getValue());

src/test/java/com/imsweb/seerapi/client/disease/DiseaseTest.java

@@ -21,6 +21,7 @@
 import static com.google.code.beanmatchers.BeanMatchers.hasValidBeanConstructor;
 import static com.google.code.beanmatchers.BeanMatchers.hasValidGettersAndSetters;
 import static com.imsweb.seerapi.client.glossary.Glossary.Category.GENERAL;
+import static com.imsweb.seerapi.client.glossary.Glossary.Category.HEMATO;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -32,7 +33,7 @@ class GlossaryTest {
     private static GlossaryService _GLOSSARY;
 
     @BeforeAll
-    public static void setup() {
+    static void setup() {
         _GLOSSARY = new SeerApi.Builder().connect().glossary();
     }
 
@@ -49,7 +50,7 @@ void testGlossaryVersions() throws IOException {
         assertEquals(1, versions.size());
         GlossaryVersion version = versions.get(0);
         assertEquals("latest", version.getName());
-        assertNull(version.getType());  // type not returned when no permisisons
+        assertNull(version.getType());  // type isn't returned when no permisisons
         assertNotNull(version.getFirstPublished());
         assertNotNull(version.getCount());
     }
@@ -68,7 +69,7 @@ void testGlossaryById() throws IOException {
         assertNull(glossary.getPrimarySite());
 
         assertNull(glossary.getHistology());
-        assertTrue(glossary.getDefinition().startsWith("An x-ray of the lymphatic system."));
+        assertTrue(glossary.getDefinition().startsWith("An x-ray or computer image of the lymphatic system."));
         assertNull(glossary.getAlternateName());
         assertNull(glossary.getHistory());
     }
@@ -87,15 +88,15 @@ void testGlossarySearch() throws IOException {
         assertEquals(Collections.singletonList(term), results.getTerms());
 
         // add the category and verify there are no results
-        results = _GLOSSARY.search("latest", search.paramMap(), EnumSet.of(Glossary.Category.SOLID_TUMOR)).execute().body();
+        results = _GLOSSARY.search("latest", search.paramMap(), EnumSet.of(GENERAL)).execute().body();
 
         assertNotNull(results);
         assertEquals(25, results.getCount().longValue());
-        assertEquals(0, results.getTotal().longValue());
-        assertNull(results.getResults());
+        assertTrue(results.getTotal().longValue() > 0);
+        assertFalse(results.getResults().isEmpty());
 
         // add a second category and verify there are we get the results again
-        results = _GLOSSARY.search("latest", search.paramMap(), EnumSet.of(Glossary.Category.SOLID_TUMOR, Glossary.Category.HEMATO)).execute().body();
+        results = _GLOSSARY.search("latest", search.paramMap(), EnumSet.of(GENERAL, Glossary.Category.HEMATO)).execute().body();
 
         assertNotNull(results);
         assertEquals(25, results.getCount().longValue());
@@ -126,19 +127,23 @@ void testGlossarySearchIterate() throws IOException {
             search.setOffset(search.getOffset() + results.getResults().size());
         }
 
-        assertTrue(total > 100);
+        assertTrue(total > 0);
     }
 
     @Test
     void testGlossaryMatch() throws IOException {
-        String text = "This text contains summary stage which should be found.";
+        String text = "white blood cells that produce antibodies";
 
         Set<KeywordMatch> matches = _GLOSSARY.match(text, null, true).execute().body();
         assertNotNull(matches);
-        assertEquals(1, matches.size());
+        assertEquals(2, matches.size());
 
         matches = _GLOSSARY.match(text, EnumSet.of(GENERAL), true).execute().body();
         assertNotNull(matches);
+        assertEquals(2, matches.size());
+
+        matches = _GLOSSARY.match(text, EnumSet.of(HEMATO), true).execute().body();
+        assertNotNull(matches);
         assertEquals(0, matches.size());
     }
 

src/test/java/com/imsweb/seerapi/client/glossary/GlossaryTest.java

@@ -30,7 +30,7 @@ class RxTest {
     private static RxService _RX;
 
     @BeforeAll
-    public static void setup() {
+    static void setup() {
         _RX = new SeerApi.Builder().connect().rx();
     }
 
@@ -123,8 +123,8 @@ void testRxSearch() throws IOException {
 
         assertNotNull(results);
         assertEquals(25, results.getCount().longValue());
-        assertEquals(7, results.getTotal().longValue());
-        assertEquals(7, results.getResults().size());
+        assertEquals(8, results.getTotal().longValue());
+        assertEquals(8, results.getResults().size());
         assertEquals(Collections.singletonList("abt"), results.getTerms());
 
         search.setMode(PublishableSearch.SearchMode.OR);

src/test/java/com/imsweb/seerapi/client/rx/RxTest.java

@@ -95,7 +95,7 @@ class StagingTest {
     private static StagingService _STAGING;
 
     @BeforeAll
-    public static void setup() {
+    static void setup() {
         _STAGING = new SeerApi.Builder().connect().staging();
     }
 
@@ -538,11 +538,11 @@ void testStagingWithErrors() throws IOException {
     void testStagingGlossary() throws IOException {
         Set<KeywordMatch> matches = _STAGING.schemaGlossary("eod_public", "2.0", "breast", null, true).execute().body();
         assertThat(matches).hasSize(26);
-        matches = _STAGING.schemaGlossary("eod_public", "2.0", "breast", EnumSet.of(Category.STAGING), true).execute().body();
-        assertThat(matches).hasSize(1);
+        matches = _STAGING.schemaGlossary("eod_public", "2.0", "breast", EnumSet.of(Category.GENERAL), true).execute().body();
+        assertThat(matches).hasSize(26);
 
         matches = _STAGING.tableGlossary("eod_public", "2.0", "cea_pretx_lab_value_33864", null, true).execute().body();
-        assertThat(matches).hasSize(24);
+        assertThat(matches).hasSize(23);
         matches = _STAGING.tableGlossary("eod_public", "2.0", "cea_pretx_lab_value_33864", EnumSet.of(Category.STAGING), true).execute().body();
         assertThat(matches).isEmpty();
     }