Adjust to transaction behavior change in Alpine

The biggest impact is that some tests now require eviction of the L1 cache to see changes made in the functionality they're testing.

stevespringett/Alpine#552
Signed-off-by: nscuro <[email protected]>

pom.xml

@@ -24,7 +24,7 @@
     <parent>
         <groupId>us.springett</groupId>
         <artifactId>alpine-parent</artifactId>
-        <version>2.2.5</version>
+        <version>2.2.6-SNAPSHOT</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>

src/main/java/org/dependencytrack/model/ProjectProperty.java

@@ -56,6 +56,7 @@ public class ProjectProperty implements IConfigProperty, Serializable {
 
     @Persistent
     @Column(name = "PROJECT_ID", allowsNull = "false")
+    @JsonIgnore
     private Project project;
 
     @Persistent

src/main/java/org/dependencytrack/persistence/QueryManager.java

@@ -92,9 +92,6 @@
 import java.util.Map;
 import java.util.Set;
 import java.util.UUID;
-import java.util.function.Consumer;
-import java.util.function.Function;
-import java.util.function.Supplier;
 
 /**
  * This QueryManager provides a concrete extension of {@link AlpineQueryManager} by
@@ -1380,59 +1377,6 @@ public <T> Query<T> getObjectsByUuidsQuery(final Class<T> clazz, final List<UUID
         return query;
     }
 
-    /**
-     * Convenience method to execute a given {@link Runnable} within the context of a {@link Transaction}.
-     * <p>
-     * Eventually, this may be moved to {@link alpine.persistence.AbstractAlpineQueryManager}.
-     *
-     * @param runnable The {@link Runnable} to execute
-     * @since 4.6.0
-     */
-    public void runInTransaction(final Runnable runnable) {
-        runInTransaction((Function<Transaction, Void>) trx -> {
-            runnable.run();
-            return null;
-        });
-    }
-
-    public void runInTransaction(final Consumer<Transaction> consumer) {
-        runInTransaction((Function<Transaction, Void>) trx -> {
-            consumer.accept(trx);
-            return null;
-        });
-    }
-
-    /**
-     * Convenience method to execute a given {@link Supplier} within the context of a {@link Transaction}.
-     * <p>
-     * Eventually, this may be moved to {@link alpine.persistence.AbstractAlpineQueryManager}.
-     *
-     * @param supplier The {@link Supplier} to execute
-     * @since 4.9.0
-     */
-    public <T> T runInTransaction(final Supplier<T> supplier) {
-        return runInTransaction((Function<Transaction, T>) trx -> supplier.get());
-    }
-
-    public <T> T runInTransaction(final Function<Transaction, T> function) {
-        final Transaction trx = pm.currentTransaction();
-        final boolean isJoiningExisting = trx.isActive();
-        try {
-            if (!isJoiningExisting) {
-                trx.begin();
-            }
-            final T result = function.apply(trx);
-            if (!isJoiningExisting) {
-                trx.commit();
-            }
-            return result;
-        } finally {
-            if (!isJoiningExisting && trx.isActive()) {
-                trx.rollback();
-            }
-        }
-    }
-
     /**
      * Convenience method to ensure that any active transaction is rolled back.
      * <p>

src/main/java/org/dependencytrack/persistence/VulnerabilityQueryManager.java

@@ -530,7 +530,7 @@ public List<AffectedProject> getAffectedProjects(Vulnerability vulnerability) {
     }
 
     public synchronized VulnerabilityAlias synchronizeVulnerabilityAlias(final VulnerabilityAlias alias) {
-        return runInTransaction(() -> {
+        return callInTransaction(() -> {
             // Query existing aliases that match AT LEAST ONE identifier of the given alias.
             //
             // For each data source, we want to know the existing aliases where the respective identifier either:

src/main/java/org/dependencytrack/resources/v1/TeamResource.java

@@ -272,7 +272,7 @@ public Response updateApiKeyComment(@PathParam("key") final String key,
         try (final var qm = new QueryManager()) {
             qm.getPersistenceManager().setProperty(PROPERTY_RETAIN_VALUES, "true");
 
-            return qm.runInTransaction(() -> {
+            return qm.callInTransaction(() -> {
                 final ApiKey apiKey = qm.getApiKey(key);
                 if (apiKey == null) {
                     return Response

src/main/java/org/dependencytrack/tasks/NistApiMirrorTask.java

@@ -25,6 +25,7 @@
 import alpine.event.framework.LoggableUncaughtExceptionHandler;
 import alpine.event.framework.Subscriber;
 import alpine.model.ConfigProperty;
+import alpine.persistence.Transaction;
 import alpine.security.crypto.DataEncryption;
 import io.github.jeremylong.openvulnerability.client.HttpAsyncClientSupplier;
 import io.github.jeremylong.openvulnerability.client.nvd.CveItem;
@@ -232,9 +233,8 @@ public void inform(final Event e) {
     }
 
     private static Vulnerability synchronizeVulnerability(final QueryManager qm, final Vulnerability vuln) {
-        final Pair<Vulnerability, IndexEvent> vulnIndexEventPair = qm.runInTransaction(trx -> {
-            trx.setSerializeRead(true); // SELECT ... FOR UPDATE
-
+        final Transaction.Options trxOptions = Transaction.defaultOptions().withSerializeRead(true);
+        final Pair<Vulnerability, IndexEvent> vulnIndexEventPair = qm.callInTransaction(trxOptions, () -> {
             Vulnerability persistentVuln = getVulnerabilityByCveId(qm, vuln.getVulnId());
             if (persistentVuln == null) {
                 persistentVuln = qm.getPersistenceManager().makePersistent(vuln);
@@ -262,9 +262,7 @@ private static Vulnerability synchronizeVulnerability(final QueryManager qm, fin
     }
 
     private static void synchronizeVulnerableSoftware(final QueryManager qm, final Vulnerability persistentVuln, final List<VulnerableSoftware> vsList) {
-        qm.runInTransaction(tx -> {
-            tx.setSerializeRead(false);
-
+        qm.runInTransaction(() -> {
             // Get all VulnerableSoftware records that are currently associated with the vulnerability.
             // Note: For SOME ODD REASON, duplicate (as in, same database ID and all) VulnerableSoftware
             // records are returned, when operating on data that was originally created by the feed-based

src/main/resources/logback.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <configuration scan="true">
-
+    <statusListener class="ch.qos.logback.core.status.NopStatusListener" />
     <appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
         <file>${user.home}/.dependency-track/dependency-track.log</file>
         <rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">

src/test/java/org/dependencytrack/persistence/DefaultObjectGeneratorTest.java

@@ -68,7 +68,7 @@ public void testLoadDefaultLicensesUpdatesExistingLicenses() throws Exception {
         method.setAccessible(true);
         method.invoke(generator);
 
-        qm.getPersistenceManager().refresh(license);
+        qm.getPersistenceManager().evictAll();
         assertThat(license.getLicenseId()).isEqualTo("LGPL-2.1+");
         assertThat(license.getName()).isEqualTo("GNU Lesser General Public License v2.1 or later");
         assertThat(license.getComment()).isNotEqualTo("comment");

src/test/java/org/dependencytrack/resources/v1/ProjectResourceTest.java

@@ -746,7 +746,7 @@ public void patchProjectParentTest() {
                         """);
 
         // Ensure the parent was updated.
-        qm.getPersistenceManager().refresh(project);
+        qm.getPersistenceManager().evictAll();
         assertThat(project.getParent()).isNotNull();
         assertThat(project.getParent().getUuid()).isEqualTo(newParent.getUuid());
     }

src/test/java/org/dependencytrack/tasks/BomUploadProcessingTaskTest.java

@@ -427,6 +427,9 @@ public void informWithExistingDuplicateComponentsTest() {
         componentB.setVersion("2.0.0");
         qm.persist(componentB);
 
+        final Component transientComponentA = qm.makeTransient(componentA);
+        final Component transientComponentB = qm.makeTransient(componentB);
+
         final byte[] bomBytes = """
                 {
                   "bomFormat": "CycloneDX",
@@ -466,15 +469,15 @@ public void informWithExistingDuplicateComponentsTest() {
                     assertThat(indexEvent.getIndexableClass()).isEqualTo(Component.class);
                     assertThat(indexEvent.getAction()).isEqualTo(IndexEvent.Action.UPDATE);
                     final var searchDoc = (ComponentDocument) indexEvent.getDocument();
-                    assertThat(searchDoc.uuid()).isEqualTo(componentA.getUuid());
+                    assertThat(searchDoc.uuid()).isEqualTo(transientComponentA.getUuid());
                 },
                 event -> {
                     assertThat(event).isInstanceOf(IndexEvent.class);
                     final var indexEvent = (IndexEvent) event;
                     assertThat(indexEvent.getIndexableClass()).isEqualTo(Component.class);
                     assertThat(indexEvent.getAction()).isEqualTo(IndexEvent.Action.DELETE);
                     final var searchDoc = (ComponentDocument) indexEvent.getDocument();
-                    assertThat(searchDoc.uuid()).isEqualTo(componentB.getUuid());
+                    assertThat(searchDoc.uuid()).isEqualTo(transientComponentB.getUuid());
                 },
                 event -> {
                     assertThat(event).isInstanceOf(IndexEvent.class);

src/test/java/org/dependencytrack/tasks/GitHubAdvisoryMirrorTaskTest.java

@@ -188,6 +188,7 @@ public void testUpdateDatasourceVulnerableVersionRanges() {
         final var task = new GitHubAdvisoryMirrorTask();
         task.updateDatasource(List.of(ghAdvisory));
 
+        qm.getPersistenceManager().evictAll();
         final Vulnerability vuln = qm.getVulnerabilityByVulnId(Source.GITHUB, "GHSA-57j2-w4cx-62h2");
         assertThat(vuln).isNotNull();
 

src/test/java/org/dependencytrack/tasks/OsvDownloadTaskTest.java

@@ -285,6 +285,7 @@ public void testUpdateDatasourceVulnerableVersionRanges() {
                  }
                 """)));
 
+        qm.getPersistenceManager().evictAll();
         final Vulnerability vuln = qm.getVulnerabilityByVulnId(Vulnerability.Source.GITHUB, "GHSA-57j2-w4cx-62h2");
         assertThat(vuln).isNotNull();