[ARQ-1931] Fixes NPE when directory named after Java archive

When the directory has a suffix of `[.jar, .war, .ear, .rar]` NPE is thrown when recursively processing subarchives, as the directory matches the pattern,  but has no content (`null` asset).

src/main/java/org/jboss/arquillian/extension/jacoco/client/ArchiveInstrumenter.java

@@ -0,0 +1,58 @@
+package org.jboss.arquillian.extension.jacoco.client;
+
+import org.jboss.shrinkwrap.api.Archive;
+import org.jboss.shrinkwrap.api.ArchivePath;
+import org.jboss.shrinkwrap.api.Filter;
+import org.jboss.shrinkwrap.api.Filters;
+import org.jboss.shrinkwrap.api.Node;
+import org.jboss.shrinkwrap.api.asset.Asset;
+import org.jboss.shrinkwrap.api.spec.JavaArchive;
+
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+public class ArchiveInstrumenter
+{
+
+   private static final Logger LOGGER = Logger.getLogger(JaCoCoApplicationArchiveProcessor.class.getName());
+
+   private final SignatureRemover signatureRemover;
+
+   public ArchiveInstrumenter(SignatureRemover signatureRemover)
+   {
+      this.signatureRemover = signatureRemover;
+   }
+
+   public void processArchive(Archive<?> archive, Filter<ArchivePath> filter)
+   {
+      instrument(archive, archive.getContent(filter));
+      signatureRemover.removeSignatures(archive);
+
+      final Map<ArchivePath, Node> jars = archive.getContent(Filters.include(".*\\.(jar|war|rar|ear)$"));
+      for (Map.Entry<ArchivePath, Node> entry : jars.entrySet())
+      {
+         // Should have used genericArchive, but with GenericArchive we need
+         // to specify a ArchiveFormat and that trigger this SHRINKWRAP-474
+         final JavaArchive subArchive = archive.getAsType(JavaArchive.class, entry.getKey());
+         if (subArchive == null) // [ARQ-1931] Asset is null which means we are dealing with the directory
+         {
+            LOGGER.log(Level.WARNING, String.format("directory path %s  ends one of the suffixes: [.ear, .war, .rar, .jar]", entry.getValue()));
+         }
+         else
+         {
+            processArchive(subArchive, filter);
+         }
+      }
+   }
+
+   private void instrument(Archive<?> archive, Map<ArchivePath, Node> classes)
+   {
+      for (Map.Entry<ArchivePath, Node> entry : classes.entrySet())
+      {
+         final Asset original = entry.getValue().getAsset();
+         archive.delete(entry.getKey());
+         archive.add(new InstrumentedAsset(original), entry.getKey());
+      }
+   }
+}

src/main/java/org/jboss/arquillian/extension/jacoco/client/CoverageDataReceiver.java

@@ -1,12 +1,5 @@
 package org.jboss.arquillian.extension.jacoco.client;
 
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.Field;
-import java.lang.reflect.Method;
-import java.util.UUID;
-
 import org.jacoco.core.data.ExecutionData;
 import org.jacoco.core.data.ExecutionDataReader;
 import org.jacoco.core.data.ExecutionDataStore;
@@ -16,6 +9,13 @@
 import org.jboss.arquillian.core.api.annotation.Observes;
 import org.jboss.arquillian.extension.jacoco.CoverageDataCommand;
 
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.lang.reflect.Field;
+import java.lang.reflect.Method;
+import java.util.UUID;
+
 public class CoverageDataReceiver
 {
    public void storeCoverageData(@Observes CoverageDataCommand coverageDataCommandEvent)
@@ -43,7 +43,7 @@ private void copyToAgentExecutionStore(ExecutionDataStore dataStore) throws Exce
       Field f = UUID.class.getDeclaredField("$jacocoAccess");
       Object executor = f.get(null);
 
-      Method m = executor.getClass().getDeclaredMethod("getProbes", new Class[] {Object[].class});
+      Method m = executor.getClass().getDeclaredMethod("getProbes", Object[].class);
       m.setAccessible(true);
       for (ExecutionData data : dataStore.getContents())
       {
@@ -62,7 +62,6 @@ private void copyToAgentExecutionStore(ExecutionDataStore dataStore) throws Exce
 
 
    private void read(InputStream stream, IExecutionDataVisitor executionDataVisitor, ISessionInfoVisitor sessionVisitor)
-         throws IOException
    {
       ExecutionDataReader reader = new ExecutionDataReader(stream);
 

src/main/java/org/jboss/arquillian/extension/jacoco/client/InstrumenterAsset.java → src/main/java/org/jboss/arquillian/extension/jacoco/client/InstrumentedAsset.java

@@ -16,14 +16,14 @@
  */
 package org.jboss.arquillian.extension.jacoco.client;
 
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-
 import org.jacoco.core.instr.Instrumenter;
 import org.jacoco.core.runtime.IRuntime;
 import org.jboss.arquillian.extension.jacoco.container.ArquillianRuntime;
 import org.jboss.shrinkwrap.api.asset.Asset;
 
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+
 /**
  * Instrument the underlying Class using the Jacoco Runtime.
  * 
@@ -32,13 +32,13 @@
  * @author <a href="mailto:aslak@redhat.com">Aslak Knutsen</a>
  * @version $Revision: $
  */
-public class InstrumenterAsset implements Asset
+public class InstrumentedAsset implements Asset
 {
-   private Asset asset;
+   private final Asset asset;
 
    public static final String EX_STRING = "arquillian";
 
-   public InstrumenterAsset(Asset asset)
+   public InstrumentedAsset(Asset asset)
    {
       this.asset = asset;
    }
@@ -50,10 +50,9 @@ public InputStream openStream()
    {
       try
       {
-         IRuntime runtime = ArquillianRuntime.getInstance();
-         Instrumenter instrumenter = new Instrumenter(runtime);
-         byte[] instrumented = instrumenter.instrument(asset.openStream(), EX_STRING);
-
+         final IRuntime runtime = ArquillianRuntime.getInstance();
+         final Instrumenter instrumenter = new Instrumenter(runtime);
+         final byte[] instrumented = instrumenter.instrument(asset.openStream(), EX_STRING);
          return new ByteArrayInputStream(instrumented);
       }
       catch (Exception e) 

src/main/java/org/jboss/arquillian/extension/jacoco/client/ApplicationArchiveInstrumenter.java → src/main/java/org/jboss/arquillian/extension/jacoco/client/JaCoCoApplicationArchiveProcessor.java

@@ -16,63 +16,29 @@
  */
 package org.jboss.arquillian.extension.jacoco.client;
 
-import java.util.Map;
-import java.util.Map.Entry;
-
 import org.jboss.arquillian.container.test.spi.client.deployment.ApplicationArchiveProcessor;
 import org.jboss.arquillian.core.api.Instance;
 import org.jboss.arquillian.core.api.annotation.Inject;
 import org.jboss.arquillian.test.spi.TestClass;
 import org.jboss.shrinkwrap.api.Archive;
-import org.jboss.shrinkwrap.api.ArchivePath;
-import org.jboss.shrinkwrap.api.Filter;
-import org.jboss.shrinkwrap.api.Filters;
-import org.jboss.shrinkwrap.api.Node;
-import org.jboss.shrinkwrap.api.asset.Asset;
-import org.jboss.shrinkwrap.api.spec.JavaArchive;
 
 /**
  * Instrument all Classes (or their subset if found in the User defined
- * 
- * @Deployment.
- * 
+ *
  * @author <a href="mailto:aslak@redhat.com">Aslak Knutsen</a>
  * @author <a href="mailto:lkrejci@redhat.com">Lukas Krejci</a>
- * 
  * @version $Revision: $
+ * @Deployment.
  */
-public class ApplicationArchiveInstrumenter implements
-      ApplicationArchiveProcessor
+public class JaCoCoApplicationArchiveProcessor implements ApplicationArchiveProcessor
 {
+
    @Inject
    private Instance<JacocoConfiguration> config;
 
-   private void processArchive(Archive<?> archive, Filter<ArchivePath> filter)
-   {
-      SignatureRemover signatureRemover = new SignatureRemover();
-
-      Map<ArchivePath, Node> classes = archive.getContent(filter);
-
-      for (Entry<ArchivePath, Node> entry : classes.entrySet())
-      {
-         Asset original = entry.getValue().getAsset();
-         archive.delete(entry.getKey());
-         archive.add(new InstrumenterAsset(original), entry.getKey());
-      }
-      signatureRemover.removeSignatures(archive);
-      // Process sub-archives recursively
-      Map<ArchivePath, Node> jars = archive.getContent(Filters.include(".*\\.(jar|war|rar|ear)$"));
-      for (Entry<ArchivePath, Node> entry : jars.entrySet())
-      {
-         // Should have used genericArchive, but with GenericArchive we need
-         // to specify a ArchiveFormat and that trigger this SHRINKWRAP-474
-         JavaArchive subArchive = archive.getAsType(JavaArchive.class, entry.getKey());
-         processArchive(subArchive, filter);
-      }
-   }
-
    public void process(Archive<?> applicationArchive, TestClass testClass)
    {
-      processArchive(applicationArchive, config.get().getClassFilter());
+      new ArchiveInstrumenter(new SignatureRemover()).processArchive(applicationArchive, config.get().getClassFilter());
    }
+
 }

src/main/java/org/jboss/arquillian/extension/jacoco/client/JacocoConfiguration.java

@@ -18,6 +18,10 @@
 
 package org.jboss.arquillian.extension.jacoco.client;
 
+import org.jboss.shrinkwrap.api.ArchivePath;
+import org.jboss.shrinkwrap.api.Filter;
+import org.jboss.shrinkwrap.api.Filters;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -26,23 +30,21 @@
 import java.util.Map;
 import java.util.UUID;
 
-import org.jboss.shrinkwrap.api.ArchivePath;
-import org.jboss.shrinkwrap.api.Filter;
-import org.jboss.shrinkwrap.api.Filters;
-
 /**
  * @author Lukas Krejci
  */
 public class JacocoConfiguration
 {
 
+   public static final Filter<ArchivePath> ALL_CLASSES = Filters.include(".*\\.class");
+
    private static final String INCLUDES_PROPERTY = "includes";
    public static final String INCLUDES_DEFAULT_VALUE = null;
    private static final String EXCLUDES_PROPERTY = "excludes";
    public static final String EXCLUDES_DEFAULT_VALUE = null;
    private static final String APPEND_ASM_LIBRARY_PROPERTY = "appendAsmLibrary";
-   private static final String APPEND_ASM_LIBRARY_DEFAULT = "true";
 
+   private static final String APPEND_ASM_LIBRARY_DEFAULT = "true";
    private static final String SEPARATOR = "\\s*;\\s*";
 
    private List<String> includes;
@@ -98,11 +100,11 @@ public static JacocoConfiguration fromMap(Map<String, String> map)
       ConfigMap c = new ConfigMap(map);
 
       String incls = c.get(INCLUDES_PROPERTY, INCLUDES_DEFAULT_VALUE);
-      ret.includes = incls == null ? Collections.<String> emptyList() : Arrays
+      ret.includes = incls == null ? Collections.<String>emptyList() : Arrays
             .asList(incls.split(SEPARATOR));
 
       String excls = c.get(EXCLUDES_PROPERTY, EXCLUDES_DEFAULT_VALUE);
-      ret.excludes = excls == null ? Collections.<String> emptyList() : Arrays
+      ret.excludes = excls == null ? Collections.<String>emptyList() : Arrays
             .asList(excls.split(SEPARATOR));
 
       ret.composedFilter = ret.composeFilter();
@@ -130,13 +132,13 @@ public Filter<ArchivePath> getClassFilter()
 
    public boolean isAppendAsmLibrary()
    {
-    return appendAsmLibrary;
+      return appendAsmLibrary;
    }
 
    private Filter<ArchivePath> composeFilter()
    {
       List<Filter<ArchivePath>> filters = new ArrayList<Filter<ArchivePath>>();
-      filters.add(Filters.include(".*\\.class"));
+      filters.add(ALL_CLASSES);
 
       for (String include : getIncludeRegexps())
       {
@@ -166,9 +168,10 @@ private List<String> convertToRegexps(List<String> patterns)
       if (patterns.isEmpty())
       {
          return patterns;
-      } else
+      }
+      else
       {
-         ArrayList<String> ret = new ArrayList<String>(patterns.size());
+         final List<String> ret = new ArrayList<String>(patterns.size());
          for (String regexp : patterns)
          {
             regexp = regexp.replace(".", "\\/").replace("*", ".*")
@@ -186,8 +189,7 @@ public static boolean isJacocoAgentActive()
       try
       {
          UUID.class.getDeclaredField("$jacocoAccess");
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
          return false;
       }

src/main/java/org/jboss/arquillian/extension/jacoco/client/JacocoExtension.java

@@ -35,7 +35,7 @@ public void register(ExtensionBuilder builder)
       if(JacocoConfiguration.isJacocoAgentActive())
       {
          builder.service(AuxiliaryArchiveAppender.class, JacocoArchiveAppender.class)
-               .service(ApplicationArchiveProcessor.class, ApplicationArchiveInstrumenter.class);
+               .service(ApplicationArchiveProcessor.class, JaCoCoApplicationArchiveProcessor.class);
 
          builder.observer(CoverageDataReceiver.class)
                 .observer(JacocoConfigurator.class);

src/main/java/org/jboss/arquillian/extension/jacoco/client/SignatureRemover.java

@@ -15,7 +15,7 @@
 import org.jboss.shrinkwrap.api.asset.Asset;
 
 /**
- * Signed jars must have their signatures removed. Since {@link InstrumenterAsset} only deals with classes we must actually
+ * Signed jars must have their signatures removed. Since {@link InstrumentedAsset} only deals with classes we must actually
  * perform the duties of {@link org.jacoco.core.internal.instr.SignatureRemover} ourselves
  *
  * @see org.jacoco.core.internal.instr.SignatureRemover