Fix JarAnalyzer warnings on Payara

instrumentation/runtime-telemetry/runtime-telemetry-java8/javaagent/src/main/java/io/opentelemetry/instrumentation/javaagent/runtimemetrics/java8/JarAnalyzer.java

@@ -8,6 +8,9 @@
 import static io.opentelemetry.instrumentation.javaagent.runtimemetrics.java8.JarDetails.EAR_EXTENSION;
 import static io.opentelemetry.instrumentation.javaagent.runtimemetrics.java8.JarDetails.JAR_EXTENSION;
 import static io.opentelemetry.instrumentation.javaagent.runtimemetrics.java8.JarDetails.WAR_EXTENSION;
+import static java.util.logging.Level.FINE;
+import static java.util.logging.Level.INFO;
+import static java.util.logging.Level.WARNING;
 
 import io.opentelemetry.api.OpenTelemetry;
 import io.opentelemetry.api.common.AttributeKey;
@@ -18,6 +21,7 @@
 import io.opentelemetry.instrumentation.runtimemetrics.java8.internal.JmxRuntimeMetricsUtil;
 import io.opentelemetry.sdk.common.Clock;
 import io.opentelemetry.sdk.internal.DaemonThreadFactory;
+import java.io.File;
 import java.io.IOException;
 import java.lang.instrument.ClassFileTransformer;
 import java.net.URI;
@@ -54,27 +58,29 @@ final class JarAnalyzer implements ClassFileTransformer {
       AttributeKey.stringKey("package.checksum_algorithm");
   static final AttributeKey<String> PACKAGE_PATH = AttributeKey.stringKey("package.path");
 
+  private final boolean debug;
   private final Set<URI> seenUris = new HashSet<>();
   private final BlockingQueue<URL> toProcess = new LinkedBlockingDeque<>();
 
-  private JarAnalyzer(OpenTelemetry unused, int jarsPerSecond) {
+  private JarAnalyzer(OpenTelemetry unused, int jarsPerSecond, boolean debug) {
+    this.debug = debug;
     // TODO(jack-berg): Use OpenTelemetry to obtain EventEmitter when event API is stable
     EventEmitter eventEmitter =
         GlobalEventEmitterProvider.get()
             .eventEmitterBuilder(JmxRuntimeMetricsUtil.getInstrumentationName())
             .setInstrumentationVersion(JmxRuntimeMetricsUtil.getInstrumentationVersion())
             .setEventDomain(EVENT_DOMAIN_PACKAGE)
             .build();
-    Worker worker = new Worker(eventEmitter, toProcess, jarsPerSecond);
+    Worker worker = new Worker(eventEmitter, toProcess, jarsPerSecond, debug);
     Thread workerThread =
         new DaemonThreadFactory(JarAnalyzer.class.getSimpleName() + "_WorkerThread")
             .newThread(worker);
     workerThread.start();
   }
 
   /** Create {@link JarAnalyzer} and start the worker thread. */
-  public static JarAnalyzer create(OpenTelemetry unused, int jarsPerSecond) {
-    return new JarAnalyzer(unused, jarsPerSecond);
+  public static JarAnalyzer create(OpenTelemetry unused, int jarsPerSecond, boolean debug) {
+    return new JarAnalyzer(unused, jarsPerSecond, debug);
   }
 
   /**
@@ -108,7 +114,8 @@ private void handle(ProtectionDomain protectionDomain) {
     try {
       locationUri = archiveUrl.toURI();
     } catch (URISyntaxException e) {
-      logger.log(Level.WARNING, "Unable to get URI for code location URL: " + archiveUrl, e);
+      logger.log(
+          debug ? WARNING : FINE, "Unable to get URI for code location URL: " + archiveUrl, e);
       return;
     }
 
@@ -127,10 +134,27 @@ private void handle(ProtectionDomain protectionDomain) {
     if (!file.endsWith(JAR_EXTENSION)
         && !file.endsWith(WAR_EXTENSION)
         && !file.endsWith(EAR_EXTENSION)) {
-      logger.log(Level.INFO, "Skipping processing unrecognized code location: {0}", archiveUrl);
+      logger.log(
+          debug ? INFO : FINE, "Skipping processing unrecognized code location: {0}", archiveUrl);
       return;
     }
 
+    // Payara 5 and 6 have url with file protocol that fail on openStream with
+    // java.io.IOException: no entry name specified
+    //   at
+    // java.base/sun.net.www.protocol.jar.JarURLConnection.getInputStream(JarURLConnection.java:160)
+    // To avoid this here we recreate the URL when it points to a file.
+    if ("file".equals(archiveUrl.getProtocol())) {
+      try {
+        File archiveFile = new File(archiveUrl.toURI().getSchemeSpecificPart());
+        if (archiveFile.exists() && archiveFile.isFile()) {
+          archiveUrl = archiveFile.toURI().toURL();
+        }
+      } catch (Exception e) {
+        logger.log(debug ? WARNING : FINE, "Unable to normalize location URL: " + archiveUrl, e);
+      }
+    }
+
     // Only code locations with .jar and .war extension should make it here
     toProcess.add(archiveUrl);
   }
@@ -140,18 +164,21 @@ private static final class Worker implements Runnable {
     private final EventEmitter eventEmitter;
     private final BlockingQueue<URL> toProcess;
     private final io.opentelemetry.sdk.internal.RateLimiter rateLimiter;
+    private final boolean debug;
 
-    private Worker(EventEmitter eventEmitter, BlockingQueue<URL> toProcess, int jarsPerSecond) {
+    private Worker(
+        EventEmitter eventEmitter, BlockingQueue<URL> toProcess, int jarsPerSecond, boolean debug) {
       this.eventEmitter = eventEmitter;
       this.toProcess = toProcess;
       this.rateLimiter =
           new io.opentelemetry.sdk.internal.RateLimiter(
               jarsPerSecond, jarsPerSecond, Clock.getDefault());
+      this.debug = debug;
     }
 
     /**
      * Continuously poll the {@link #toProcess} for archive {@link URL}s, and process each wit
-     * {@link #processUrl(EventEmitter, URL)}.
+     * {@link #processUrl(EventEmitter, URL, boolean)}.
      */
     @Override
     public void run() {
@@ -172,25 +199,26 @@ public void run() {
         try {
           // TODO(jack-berg): add ability to optionally re-process urls periodically to re-emit
           // events
-          processUrl(eventEmitter, archiveUrl);
+          processUrl(eventEmitter, archiveUrl, debug);
         } catch (Throwable e) {
-          logger.log(Level.WARNING, "Unexpected error processing archive URL: " + archiveUrl, e);
+          logger.log(
+              debug ? WARNING : FINE, "Unexpected error processing archive URL: " + archiveUrl, e);
         }
       }
-      logger.warning("JarAnalyzer stopped");
+      logger.log(debug ? WARNING : FINE, "JarAnalyzer stopped");
     }
   }
 
   /**
    * Process the {@code archiveUrl}, extracting metadata from it and emitting an event with the
    * content.
    */
-  static void processUrl(EventEmitter eventEmitter, URL archiveUrl) {
+  static void processUrl(EventEmitter eventEmitter, URL archiveUrl, boolean debug) {
     JarDetails jarDetails;
     try {
       jarDetails = JarDetails.forUrl(archiveUrl);
     } catch (IOException e) {
-      logger.log(Level.WARNING, "Error reading package for archive URL: " + archiveUrl, e);
+      logger.log(debug ? WARNING : FINE, "Error reading package for archive URL: " + archiveUrl, e);
       return;
     }
     AttributesBuilder builder = Attributes.builder();

instrumentation/runtime-telemetry/runtime-telemetry-java8/javaagent/src/main/java/io/opentelemetry/instrumentation/javaagent/runtimemetrics/java8/JarAnalyzerInstaller.java

@@ -8,6 +8,7 @@
 import com.google.auto.service.AutoService;
 import io.opentelemetry.javaagent.bootstrap.InstrumentationHolder;
 import io.opentelemetry.javaagent.tooling.BeforeAgentListener;
+import io.opentelemetry.javaagent.tooling.config.AgentConfig;
 import io.opentelemetry.sdk.autoconfigure.AutoConfiguredOpenTelemetrySdk;
 import io.opentelemetry.sdk.autoconfigure.internal.AutoConfigureUtil;
 import io.opentelemetry.sdk.autoconfigure.spi.ConfigProperties;
@@ -32,7 +33,10 @@ public void beforeAgent(AutoConfiguredOpenTelemetrySdk autoConfiguredOpenTelemet
     int jarsPerSecond =
         config.getInt("otel.instrumentation.runtime-telemetry.package-emitter.jars-per-second", 10);
     JarAnalyzer jarAnalyzer =
-        JarAnalyzer.create(autoConfiguredOpenTelemetrySdk.getOpenTelemetrySdk(), jarsPerSecond);
+        JarAnalyzer.create(
+            autoConfiguredOpenTelemetrySdk.getOpenTelemetrySdk(),
+            jarsPerSecond,
+            AgentConfig.isDebugModeEnabled(config));
     inst.addTransformer(jarAnalyzer);
   }
 }

instrumentation/runtime-telemetry/runtime-telemetry-java8/testing/src/test/java/io/opentelemetry/instrumentation/javaagent/runtimemetrics/java8/JarAnalyzerTest.java

@@ -40,7 +40,7 @@ class JarAnalyzerTest {
   @MethodSource("processUrlArguments")
   void processUrl_EmitsEvents(URL archiveUrl, Consumer<AttributesAssert> attributesConsumer) {
     EventEmitter eventEmitter = mock(EventEmitter.class);
-    JarAnalyzer.processUrl(eventEmitter, archiveUrl);
+    JarAnalyzer.processUrl(eventEmitter, archiveUrl, false);
 
     ArgumentCaptor<Attributes> attributesArgumentCaptor = ArgumentCaptor.forClass(Attributes.class);
     verify(eventEmitter).emit(eq("info"), attributesArgumentCaptor.capture());