[CORE-69]: bump to avro 1.12.2 with compatibility fixes

library/build.gradle

@@ -19,7 +19,7 @@ repositories {
 }
 
 dependencies {
-    api "org.apache.avro:avro:1.12.1"
+    api "org.apache.avro:avro:1.12.2"
     implementation 'ch.qos.logback:logback-classic:1.5.32'
     testImplementation 'org.json:json:20260522'
     testImplementation 'com.fasterxml.jackson.core:jackson-databind:2.21.3'

library/src/main/java/bio/terra/pfb/PfbClassSecurity.java

@@ -0,0 +1,50 @@
+package bio.terra.pfb;
+
+import org.apache.avro.Schema;
+import org.apache.avro.specific.SpecificData;
+import org.apache.avro.util.ClassSecurityValidator;
+
+/**
+ * Marks the classes generated from {@code PfbSchema} as trusted for Avro deserialization.
+ *
+ * <p>As of Avro 1.12.2 (<a href="https://issues.apache.org/jira/browse/AVRO-4189">AVRO-4189</a>),
+ * {@code SpecificDatumReader} refuses to instantiate any class that has not been explicitly
+ * allowlisted, failing with {@code SecurityException: Forbidden bio.terra.pfb.Entity! This class is
+ * not trusted to be included in Avro schemas.} The generated PFB types - {@code Entity}, {@code
+ * Metadata}, {@code Node} and friends - are the only classes this library asks Avro to instantiate,
+ * so we trust exactly those rather than a broad wildcard via {@code
+ * org.apache.avro.SERIALIZABLE_PACKAGES=*}.
+ *
+ * <p>{@link PfbReader} registers them automatically. Callers that read PFB files with their own
+ * {@code SpecificDatumReader} over these generated classes should call {@link #register()} first.
+ */
+public final class PfbClassSecurity {
+
+  private static boolean registered = false;
+
+  private PfbClassSecurity() {}
+
+  /**
+   * Adds the generated PFB types to Avro's global allowlist. Idempotent, and safe to call from any
+   * thread.
+   */
+  public static synchronized void register() {
+    if (registered) {
+      return;
+    }
+
+    ClassSecurityValidator.Builder trustedPfbTypes = ClassSecurityValidator.builder();
+    for (Schema type : PfbSchema.PROTOCOL.getTypes()) {
+      trustedPfbTypes.add(SpecificData.getClassName(type));
+    }
+
+    // Compose with the current validator instead of replacing it, so we don't overwrite
+    // Avro's own defaults or anything already allowed through the
+    // org.apache.avro.SERIALIZABLE_CLASSES / SERIALIZABLE_PACKAGES properties
+    ClassSecurityValidator.setGlobal(
+        ClassSecurityValidator.composite(
+            ClassSecurityValidator.getGlobal(), trustedPfbTypes.build()));
+
+    registered = true;
+  }
+}

library/src/main/java/bio/terra/pfb/PfbReader.java

@@ -23,6 +23,12 @@ public class PfbReader {
   // regex for decoding enums. See convertEnum().
   private static final Pattern ENUM_PATTERN = Pattern.compile("_([A-Fa-f0-9]{2,3})_");
 
+  static {
+    // Avro will not instantiate our generated types until they are allowlisted.
+    // See PfbClassSecurity.
+    PfbClassSecurity.register();
+  }
+
   public static String showSchema(String fileLocation) throws IOException {
     // TODO AJ-1288: the use of convertEnum here is incorrect. It performs decoding on the entire
     //     string output of the schema. Instead, it should only perform decoding on the individual

library/src/test/java/bio/terra/pfb/PfbClassSecurityTest.java

@@ -0,0 +1,46 @@
+package bio.terra.pfb;
+
+import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+import java.util.stream.Stream;
+import org.apache.avro.Schema;
+import org.apache.avro.specific.SpecificData;
+import org.apache.avro.util.ClassSecurityValidator;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.MethodSource;
+
+class PfbClassSecurityTest {
+
+  @BeforeAll
+  static void register() {
+    PfbClassSecurity.register();
+  }
+
+  public static Stream<Class<?>> provideGeneratedTypes() {
+    return PfbSchema.PROTOCOL.getTypes().stream().map(PfbClassSecurityTest::loadGeneratedClass);
+  }
+
+  /** Every type in pfbSchema.avdl must be instantiable by Avro's SpecificDatumReader. */
+  @ParameterizedTest
+  @MethodSource("provideGeneratedTypes")
+  void generatedTypesAreTrusted(Class<?> generatedType) {
+    assertDoesNotThrow(() -> ClassSecurityValidator.validate(generatedType));
+  }
+
+  /** Registering our types must not trust everything else along with them. */
+  @Test
+  void otherClassesRemainForbidden() {
+    assertThrows(SecurityException.class, () -> ClassSecurityValidator.validate(PfbReader.class));
+  }
+
+  private static Class<?> loadGeneratedClass(Schema type) {
+    try {
+      return Class.forName(SpecificData.getClassName(type));
+    } catch (ClassNotFoundException e) {
+      throw new IllegalStateException("No generated class for schema " + type.getFullName(), e);
+    }
+  }
+}