Merge pull request #44 from imsweb/recode-updates

Recode updates

Author: ctmay4

.github/workflows/integration.yml

@@ -34,4 +34,4 @@ jobs:
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         run: |
           chmod +x gradlew
-          ./gradlew --continue build sonarqube
+          ./gradlew --continue build sonar

build.gradle

@@ -2,21 +2,21 @@ plugins {
     id 'java-library'
     id 'checkstyle'
     id 'jacoco'
-    id "com.github.spotbugs" version "5.0.14"
+    id "com.github.spotbugs" version "6.0.25"
     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 "0.47.0"
-    id 'org.sonatype.gradle.plugins.scan' version '2.6.0'
-    id "org.sonarqube" version "4.2.1.3168"
+    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"
 }
 
 group = 'com.imsweb'
 version = '5.6'
 description = 'Java client library for SEER*API'
 
-tasks.withType(JavaCompile) {
+tasks.withType(JavaCompile).configureEach {
     options.encoding = 'UTF-8'
     options.compilerArgs << "-Werror"
 }
@@ -34,22 +34,19 @@ repositories {
 }
 
 dependencies {
-    spotbugs 'com.github.spotbugs:spotbugs:4.7.3'
+    spotbugs 'com.github.spotbugs:spotbugs:4.8.6'
 
-    api 'com.squareup.retrofit2:retrofit:2.9.0'
-    api 'com.squareup.retrofit2:converter-jackson:2.9.0'
+    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:4.11.0'
-    api 'com.squareup.okio:okio:3.4.0'
+    api 'com.squareup.okhttp3:okhttp:4.12.0'
+    api 'com.squareup.okio:okio:3.9.1'
 
-    // newer version of dependency to fix vulnerability until converter-jackson is updated
-    api 'com.fasterxml.jackson.core:jackson-databind:2.15.2'
-
-    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 '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 'com.google.code.bean-matchers:bean-matchers:0.14'
 }
 
@@ -70,7 +67,7 @@ jar {
     }
 }
 
-tasks.withType(Javadoc) {
+tasks.withType(Javadoc).configureEach {
     failOnError false
     options.addStringOption('Xdoclint:none', '-quiet')
     options.addStringOption('encoding', 'UTF-8')

config/spotbugs/spotbugs-exclude.xml

@@ -36,6 +36,10 @@
         <Bug pattern="DM_DEFAULT_ENCODING" />
     </Match>
 
+    <Match>
+        <Bug pattern="CT_CONSTRUCTOR_THROW"/>
+    </Match>
+
     <Match>
         <Class name="com.imsweb.seerutils.SeerUtils" />
         <Bug pattern="OS_OPEN_STREAM" />

src/main/java/com/imsweb/seerapi/client/siterecode/SiteGroupAlgorithm.java

@@ -0,0 +1,50 @@
+/*
+ * Copyright (C) 2024 Information Management Services, Inc.
+ */
+package com.imsweb.seerapi.client.siterecode;
+
+import java.util.List;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+public class SiteGroupAlgorithm {
+
+    private String id;
+    private String name;
+    private String version;
+    @JsonProperty("required_input")
+    private List<String> requiredInput;
+
+    public String getId() {
+        return id;
+    }
+
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getVersion() {
+        return version;
+    }
+
+    public void setVersion(String version) {
+        this.version = version;
+    }
+
+    public List<String> getRequiredInput() {
+        return requiredInput;
+    }
+
+    public void setRequiredInput(List<String> requiredInput) {
+        this.requiredInput = requiredInput;
+    }
+
+}

src/main/java/com/imsweb/seerapi/client/siterecode/SiteRecode.java

@@ -11,6 +11,8 @@ public class SiteRecode {
     protected String _site;
     @JsonProperty("hist")
     protected String _hist;
+    @JsonProperty("behavior")
+    protected String _behavior;
     @JsonProperty("site_group")
     protected String _siteGroup;
 
@@ -30,6 +32,14 @@ public void setHist(String hist) {
         _hist = hist;
     }
 
+    public String getBehavior() {
+        return _behavior;
+    }
+
+    public void setBehavior(String behavior) {
+        _behavior = behavior;
+    }
+
     public String getSiteGroup() {
         return _siteGroup;
     }

src/main/java/com/imsweb/seerapi/client/siterecode/SiteRecodeService.java

@@ -3,28 +3,31 @@
  */
 package com.imsweb.seerapi.client.siterecode;
 
+import java.util.List;
+
 import retrofit2.Call;
 import retrofit2.http.GET;
+import retrofit2.http.Path;
 import retrofit2.http.Query;
 
-import com.imsweb.seerapi.client.shared.Version;
-
 public interface SiteRecodeService {
 
     /**
-     * Return the version of the SEER Site Recode database.
-     * @return a String representing the database version
+     * Return the supported algorithms and versions
+     * @return a list of information about the algorithms
      */
-    @GET("recode/version")
-    Call<Version> version();
+    @GET("recode/sitegroup/algorithms")
+    Call<List<SiteGroupAlgorithm>> algorithms();
 
     /**
-     * Return the SEER Site Group for the site/histology combination, or 99999 if the combination is unknown.
+     * Return the specified algorithm site group for the site/histology/behavior combination, or 99999 if the combination is unknown.
+     * @param algorithm site group algorithm
      * @param site Primary Site O3
      * @param hist Histology O3
+     * @param behavior Behavior O3
      * @return a SiteRecode object based on the site and histology
      */
-    @GET("recode/sitegroup")
-    Call<SiteRecode> siteGroup(@Query("site") String site, @Query("hist") String hist);
+    @GET("recode/sitegroup/{algorithm}")
+    Call<SiteRecode> siteGroup(@Path("algorithm") String algorithm, @Query("site") String site, @Query("hist") String hist, @Query("behavior") String behavior);
 
 }

src/test/java/com/imsweb/seerapi/client/SeerApiTest.java

@@ -3,27 +3,27 @@
  */
 package com.imsweb.seerapi.client;
 
-import java.io.IOException;
+import java.util.List;
 
 import org.junit.jupiter.api.Test;
 
 import retrofit2.Call;
 
-import com.imsweb.seerapi.client.shared.Version;
+import com.imsweb.seerapi.client.siterecode.SiteGroupAlgorithm;
 
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
 class SeerApiTest {
 
     @Test
     void testBadApiKeyAndURL() {
-        Call<Version> call = new SeerApi.Builder().url("https://api.seer.cancer.gov/rest/").apiKey("BAD KEY").connect().siteRecode().version();
+        Call<List<SiteGroupAlgorithm>> call = new SeerApi.Builder().url("https://api.seer.cancer.gov/rest/").apiKey("BAD KEY").connect().siteRecode().algorithms();
         assertThrows(NotAuthorizedException.class, call::execute);
     }
 
     @Test
-    void testBadApiKey() throws IOException {
-        Call<Version> call = new SeerApi.Builder().apiKey("BAD KEY").connect().siteRecode().version();
+    void testBadApiKey() {
+        Call<List<SiteGroupAlgorithm>> call = new SeerApi.Builder().apiKey("BAD KEY").connect().siteRecode().algorithms();
         assertThrows(NotAuthorizedException.class, call::execute);
     }
 

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

@@ -18,6 +18,7 @@
 import static com.google.code.beanmatchers.BeanMatchers.hasValidBeanConstructor;
 import static com.google.code.beanmatchers.BeanMatchers.hasValidGettersAndSetters;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
@@ -54,7 +55,7 @@ void testDiseasePrimarySites() throws IOException {
         List<PrimarySite> sites = _DISEASE.primarySites().execute().body();
 
         assertNotNull(sites);
-        assertTrue(sites.size() > 0);
+        assertFalse(sites.isEmpty());
         assertEquals("C000", sites.get(0).getValue());
         assertEquals("External upper lip", sites.get(0).getLabel());
     }
@@ -64,7 +65,7 @@ void testDiseasePrimarySiteCode() throws IOException {
         List<PrimarySite> sites = _DISEASE.primarySiteCode("C021").execute().body();
 
         assertNotNull(sites);
-        assertTrue(sites.size() > 0);
+        assertFalse(sites.isEmpty());
         assertEquals("C021", sites.get(0).getValue());
         assertEquals("Border of tongue", sites.get(0).getLabel());
     }
@@ -74,7 +75,7 @@ void testDiseaseSiteCateogires() throws IOException {
         List<SiteCategory> categories = _DISEASE.siteCategories().execute().body();
 
         assertNotNull(categories);
-        assertTrue(categories.size() > 0);
+        assertFalse(categories.isEmpty());
         assertEquals("head-and-neck", categories.get(0).getId());
         assertEquals("Head and Neck", categories.get(0).getLabel());
         assertEquals(2, categories.get(0).getSites().size());
@@ -91,7 +92,7 @@ void testDiseaseById() throws IOException {
         assertEquals("Pure erythroid leukemia", disease.getName());
         assertEquals(Disease.Type.HEMATO, disease.getType());
         assertEquals("9840/3", disease.getIcdO3Morphology());
-        assertTrue(disease.getSamePrimaries().size() > 0);
+        assertFalse(disease.getSamePrimaries().isEmpty());
 
         assertNotNull(disease.getId());
         assertEquals("latest", disease.getVersion());
@@ -115,7 +116,7 @@ void testDiseaseById() throws IOException {
         assertEquals(1, disease.getAbstractorNote().size());
         assertEquals(2, disease.getTreatment().size());
         assertNull(disease.getGenetics());
-        assertTrue(disease.getAlternateName().size() > 0);
+        assertFalse(disease.getAlternateName().isEmpty());
         assertEquals("Acute erythremia", disease.getAlternateName().get(0).getValue());
         assertTrue(disease.getIcdO2Morphology().contains("9840/3"));
         assertTrue(disease.getIcdO1Morphology().contains("9840/3"));
@@ -228,7 +229,7 @@ void testDiseaseSearchIterate() throws IOException {
             DiseaseSearchResults results = _DISEASE.search("latest", search.paramMap()).execute().body();
             assertNotNull(results);
             assertTrue(results.getTotal() > 0);
-            assertTrue(results.getResults().size() > 0);
+            assertFalse(results.getResults().isEmpty());
 
             // the first time through, set the total
             if (total == null)
@@ -276,8 +277,8 @@ void testDiseaseChangelog() throws IOException {
         assertEquals("Initial migration", changelog.getDescription());
 
         DiseaseChangelogEntry entry = changelog.getAdds().get(0);
-        assertTrue(entry.getId().length() > 0);
-        assertTrue(entry.getName().length() > 0);
+        assertFalse(entry.getId().isEmpty());
+        assertFalse(entry.getName().isEmpty());
         assertNull(entry.getOldVersion());
         assertNull(entry.getNewVersion());
     }

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

@@ -22,6 +22,7 @@
 import static com.google.code.beanmatchers.BeanMatchers.hasValidGettersAndSetters;
 import static com.imsweb.seerapi.client.glossary.Glossary.Category.GENERAL;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
@@ -72,37 +73,6 @@ void testGlossaryById() throws IOException {
         assertNull(glossary.getHistory());
     }
 
-    @Test
-    void testGlossaryChangelog() throws IOException {
-        GlossaryChangelogResults results = _GLOSSARY.changelogs("latest", null, null, 1).execute().body();
-
-        assertNotNull(results);
-
-        // TODO since all the glossary items were removed from the production database, this needs to be commented out; it will return when they are published again
-
-            /*
-            Assert.assertEquals(1, changes.size());
-
-            GlossaryChangelog changelog = changes.get(0);
-
-            Assert.assertNotNull(changelog.getUser());
-            Assert.assertEquals("latest_dev", changelog.getVersion());
-            Assert.assertTrue(changelog.getId().length() > 0);
-            Assert.assertTrue(changelog.getAdds().size() > 0);
-
-            GlossaryChangelogEntry entry = changelog.getAdds().get(0);
-            Assert.assertTrue(entry.getId().length() > 0);
-            Assert.assertTrue(entry.getName().length() > 0);
-            Assert.assertNull(entry.getOldVersion());
-            Assert.assertNull(entry.getNewVersion());
-
-            Assert.assertNull(changelog.getMods());
-            Assert.assertNull(changelog.getDeletes());
-            Assert.assertNotNull(changelog.getDate());
-            Assert.assertEquals("Initial migration", changelog.getDescription());
-            */
-    }
-
     @Test
     void testGlossarySearch() throws IOException {
         String term = "killer";
@@ -113,7 +83,7 @@ void testGlossarySearch() throws IOException {
         assertNotNull(results);
         assertEquals(25, results.getCount().longValue());
         assertTrue(results.getTotal().longValue() > 0);
-        assertTrue(results.getResults().size() > 0);
+        assertFalse(results.getResults().isEmpty());
         assertEquals(Collections.singletonList(term), results.getTerms());
 
         // add the category and verify there are no results
@@ -130,7 +100,7 @@ void testGlossarySearch() throws IOException {
         assertNotNull(results);
         assertEquals(25, results.getCount().longValue());
         assertTrue(results.getTotal().longValue() > 0);
-        assertTrue(results.getResults().size() > 0);
+        assertFalse(results.getResults().isEmpty());
         assertEquals(Collections.singletonList(term), results.getTerms());
     }
 
@@ -147,7 +117,7 @@ void testGlossarySearchIterate() throws IOException {
             GlossarySearchResults results = _GLOSSARY.search("latest", search.paramMap(), EnumSet.of(Glossary.Category.HEMATO)).execute().body();
             assertNotNull(results);
             assertTrue(results.getTotal() > 0);
-            assertTrue(results.getResults().size() > 0);
+            assertFalse(results.getResults().isEmpty());
 
             // the first time through, set the total
             if (total == null)

src/test/java/com/imsweb/seerapi/client/hcpcs/HcpcsServiceTest.java

@@ -93,8 +93,7 @@ void testSearch() throws IOException {
         assertThat(results).hasSize(2);
         assertThat(results).extracting("hcpcsCode").contains("J9207", "C9240");
 
-        // TODO the scores should be coming back from the API but are not; waiting on API fix
-        //assertThat(Objects.requireNonNull(results).get(0).getScore()).isGreaterThan(0);
+        assertThat(Objects.requireNonNull(results).get(0).getScore()).isPositive();
 
         // test categories
         params.put("category", Category.CHEMOTHERAPY.toString());