Added jProcesses for report tool

Addressed PR comments

community/dbms/pom.xml

@@ -164,6 +164,11 @@
       <version>${project.version}</version>
     </dependency>
 
+    <dependency>
+      <groupId>org.jprocesses</groupId>
+      <artifactId>jProcesses</artifactId>
+    </dependency>
+
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-compress</artifactId>

community/dbms/src/main/java/org/neo4j/commandline/dbms/DiagnosticsReportCommand.java

@@ -19,6 +19,9 @@
  */
 package org.neo4j.commandline.dbms;
 
+import org.jutils.jprocesses.JProcesses;
+import org.jutils.jprocesses.model.ProcessInfo;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
@@ -30,6 +33,7 @@
 import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 
@@ -43,9 +47,10 @@
 import org.neo4j.commandline.arguments.OptionalNamedArg;
 import org.neo4j.commandline.arguments.PositionalArgument;
 import org.neo4j.commandline.arguments.common.OptionalCanonicalPath;
-import org.neo4j.dbms.report.jmx.JmxDump;
-import org.neo4j.dbms.report.jmx.LocalVirtualMachine;
+import org.neo4j.dbms.diagnostics.jmx.JmxDump;
+import org.neo4j.dbms.diagnostics.jmx.LocalVirtualMachine;
 import org.neo4j.diagnostics.DiagnosticsOfflineReportProvider;
+import org.neo4j.diagnostics.DiagnosticsReportSource;
 import org.neo4j.diagnostics.DiagnosticsReportSources;
 import org.neo4j.diagnostics.DiagnosticsReporter;
 import org.neo4j.helpers.Args;
@@ -57,7 +62,7 @@
 
 public class DiagnosticsReportCommand implements AdminCommand
 {
-    private static OptionalNamedArg destinationArgument =
+    private static final OptionalNamedArg destinationArgument =
             new OptionalCanonicalPath( "to", "/tmp/", "reports/", "Destination directory for reports" );
     private static final Arguments arguments = new Arguments()
             .withArgument( new OptionalListArgument() )
@@ -67,18 +72,16 @@ public class DiagnosticsReportCommand implements AdminCommand
 
     private final Path homeDir;
     private final Path configDir;
-    private final OutsideWorld outsideWorld;
     static final String[] DEFAULT_CLASSIFIERS = new String[]{"logs", "config"};
     private boolean verbose;
-    private PrintStream err;
-    private PrintStream out;
-    private FileSystemAbstraction fs;
+    private final PrintStream err;
+    private final PrintStream out;
+    private final FileSystemAbstraction fs;
 
     DiagnosticsReportCommand( Path homeDir, Path configDir, OutsideWorld outsideWorld )
     {
         this.homeDir = homeDir;
         this.configDir = configDir;
-        this.outsideWorld = outsideWorld;
         this.fs = outsideWorld.fileSystem();
         this.out = outsideWorld.outStream();
         this.err = outsideWorld.errorStream();
@@ -103,31 +106,7 @@ public void execute( String[] stringArgs ) throws IncorrectUsage, CommandFailed
         }
         Config config = Config.fromFile( configFile ).withHome( homeDir ).withConnectorsDisabled().build();
 
-        File storeDirectory = config.get( database_path );
-
-        DiagnosticsReporter reporter = new DiagnosticsReporter( out );
-
-        // Find all offline providers and register them
-        for ( DiagnosticsOfflineReportProvider provider : Service.load( DiagnosticsOfflineReportProvider.class ) )
-        {
-            provider.init( fs, config, storeDirectory );
-            reporter.registerOfflineProvider( provider );
-        }
-
-        // Register sources provided by this tool
-        reporter.registerSource( "config",
-                DiagnosticsReportSources.newDiagnosticsFile( "neo4j.conf", fs, configFile ) );
-
-        // Online connection
-        JmxDump jmxDump = connectToNeo4jInstance();
-        if ( jmxDump != null )
-        {
-            reporter.registerSource( "threads", jmxDump.threadDump() );
-            reporter.registerSource( "heap", jmxDump.heapDump() );
-            reporter.registerSource( "sysprop", jmxDump.systemProperties() );
-            //reporter.registerSource( "env", null );
-        }
-
+        DiagnosticsReporter reporter = createAndRegisterSources( config, configFile );
         Set<String> availableClassifiers = reporter.getAvailableClassifiers();
 
         // Passing '--list' should print list and end execution
@@ -188,9 +167,73 @@ public void execute( String[] stringArgs ) throws IncorrectUsage, CommandFailed
         }
     }
 
-    private JmxDump connectToNeo4jInstance()
+    private DiagnosticsReporter createAndRegisterSources( Config config, File configFile )
+    {
+        DiagnosticsReporter reporter = new DiagnosticsReporter( out );
+        File storeDirectory = config.get( database_path );
+
+        // Find all offline providers and register them
+        for ( DiagnosticsOfflineReportProvider provider : Service.load( DiagnosticsOfflineReportProvider.class ) )
+        {
+            provider.init( fs, config, storeDirectory );
+            reporter.registerOfflineProvider( provider );
+        }
+
+        // Register sources provided by this tool
+        reporter.registerSource( "config", DiagnosticsReportSources.newDiagnosticsFile( "neo4j.conf", fs, configFile ) );
+        reporter.registerSource( "ps", runningProcesses() );
+
+        // Online connection
+        Optional<JmxDump> jmxDump = connectToNeo4jInstance();
+        if ( jmxDump.isPresent() )
+        {
+            JmxDump jmx = jmxDump.get();
+            reporter.registerSource( "threads", jmx.threadDump() );
+            reporter.registerSource( "heap", jmx.heapDump() );
+            reporter.registerSource( "sysprop", jmx.systemProperties() );
+            //reporter.registerSource( "env", null ); // TODO:
+        }
+        return reporter;
+    }
+
+    private Optional<JmxDump> connectToNeo4jInstance()
     {
         out.println( "Trying to find running instance of neo4j" );
+
+        Optional<Long> pid = getPid();
+        if ( pid.isPresent() )
+        {
+            try
+            {
+                LocalVirtualMachine vm = LocalVirtualMachine.from( pid.get() );
+                out.println( "Attached to running process with process id " + pid );
+                try
+                {
+                    JmxDump jmxDump = JmxDump.connectTo( vm.getJmxAddress() );
+                    jmxDump.attachSystemProperties( vm.getSystemProperties() );
+                    out.println( "Connected to JMX endpoint" );
+                    return Optional.of( jmxDump );
+                }
+                catch ( IOException e )
+                {
+                    printError( "Unable to communicate with JMX endpoint. Reason: " + e.getMessage(), e );
+                }
+            }
+            catch ( IOException e )
+            {
+                printError( "Unable to connect to process. Reason: " + e.getMessage(), e );
+            }
+        }
+        else
+        {
+            out.println( "No running instance of neo4j was found. Online reports will be omitted." );
+        }
+
+        return Optional.empty();
+    }
+
+    private Optional<Long> getPid()
+    {
         Path pidFile = homeDir.resolve( "run/neo4j.pid" );
         if ( fs.fileExists( pidFile.toFile() ) )
         {
@@ -199,29 +242,9 @@ private JmxDump connectToNeo4jInstance()
                 String pidFileContent = reader.readLine();
                 try
                 {
-                    long pid = Long.parseLong( pidFileContent );
-
-                    try
-                    {
-                        LocalVirtualMachine vm = LocalVirtualMachine.from( pid );
-                        out.println( "Attached to running process with process id " + pid );
-                        try
-                        {
-                            JmxDump jmxDump = JmxDump.connectTo( vm.getJmxAddress() );
-                            jmxDump.attachSystemProperties( vm.getSystemProperties() );
-                            out.println( "Connected to JMX endpoint" );
-                            return jmxDump;
-                        }
-                        catch ( IOException e )
-                        {
-                            printError( "Unable to communicate with JMX endpoint. Reason: " + e.getMessage(), e );
-                        }
-                    }
-                    catch ( IOException e )
-                    {
-                        printError( "Unable to connect to process. Reason: " + e.getMessage(), e );
-                    }
+                    return Optional.of( Long.parseLong( pidFileContent ) );
                 }
+
                 catch ( NumberFormatException e )
                 {
                     printError( pidFile.toString() + " does not contain a valid id. Found: " + pidFileContent );
@@ -232,12 +255,7 @@ private JmxDump connectToNeo4jInstance()
                 printError( "Error reading the .pid file. Reason: " + e.getMessage(), e );
             }
         }
-        else
-        {
-            out.println( "No running instance of neo4j was found. Online reports will be omitted." );
-        }
-
-        return null;
+        return Optional.empty();
     }
 
     private void printError( String message )
@@ -282,11 +300,37 @@ static String describeClassifier( String classifier )
             return "include the raft log";
         case "queries":
             return "include the output of dbms.listQueries()";
+        case "ps":
+            return "include a list of running processes";
         default:
         }
         throw new IllegalArgumentException( "Unknown classifier: " + classifier );
     }
 
+    private static DiagnosticsReportSource runningProcesses()
+    {
+        return DiagnosticsReportSources.newDiagnosticsString( "ps.txt", () ->
+        {
+            List<ProcessInfo> processesList = JProcesses.getProcessList();
+
+            StringBuilder sb = new StringBuilder();
+            for (final ProcessInfo processInfo : processesList) {
+                sb.append( "Process PID: " ).append( processInfo.getPid() ).append( '\n' )
+                        .append( "Process Name: " ).append( processInfo.getName() ).append( '\n' )
+                        .append( "Process Time: " ).append( processInfo.getTime() ).append( '\n' )
+                        .append( "User: " ).append( processInfo.getUser() ).append( '\n' )
+                        .append( "Virtual Memory: " ).append( processInfo.getVirtualMemory() ).append( '\n' )
+                        .append( "Physical Memory: " ).append( processInfo.getPhysicalMemory() ).append( '\n' )
+                        .append( "CPU usage: " ).append( processInfo.getCpuUsage() ).append( '\n' )
+                        .append( "Start Time: " ).append( processInfo.getStartTime() ).append( '\n' )
+                        .append( "Priority: " ).append( processInfo.getPriority() ).append( '\n' )
+                        .append( "Full command: " ).append( processInfo.getCommand() ).append( '\n' )
+                        .append("------------------").append( '\n' );
+            }
+            return sb.toString();
+        });
+    }
+
     /**
      * Helper class to format output of {@link Usage}. Parsing is done manually in this command module.
      */

community/dbms/src/main/java/org/neo4j/dbms/report/jmx/JmxDump.java → community/dbms/src/main/java/org/neo4j/dbms/diagnostics/jmx/JmxDump.java

@@ -17,7 +17,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package org.neo4j.dbms.report.jmx;
+package org.neo4j.dbms.diagnostics.jmx;
 
 import com.sun.management.HotSpotDiagnosticMXBean;
 
@@ -193,8 +193,10 @@ public void addToArchive( Path archiveDestination, DiagnosticsReporterProgressCa
                 monitor.info( "archiving..." );
                 long size = Files.size( tempFile );
                 InputStream in = Files.newInputStream( tempFile );
-                ProgressAwareInputStream inStream = new ProgressAwareInputStream( in, size, monitor::percentChanged );
-                Files.copy( inStream, archiveDestination );
+                try ( ProgressAwareInputStream inStream = new ProgressAwareInputStream( in, size, monitor::percentChanged ) )
+                {
+                    Files.copy( inStream, archiveDestination );
+                }
 
                 Files.delete( tempFile );
             }

community/dbms/src/main/java/org/neo4j/dbms/report/jmx/LocalVirtualMachine.java → community/dbms/src/main/java/org/neo4j/dbms/diagnostics/jmx/LocalVirtualMachine.java

@@ -17,7 +17,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package org.neo4j.dbms.report.jmx;
+package org.neo4j.dbms.diagnostics.jmx;
 
 import com.sun.tools.attach.AttachNotSupportedException;
 import com.sun.tools.attach.VirtualMachine;

community/dbms/src/test/java/org/neo4j/commandline/dbms/DiagnosticsReportCommandIT.java

@@ -20,7 +20,6 @@
 package org.neo4j.commandline.dbms;
 
 import org.junit.After;
-import org.junit.Assume;
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
@@ -45,6 +44,7 @@
 
 import static org.hamcrest.CoreMatchers.containsString;
 import static org.hamcrest.CoreMatchers.is;
+import static org.hamcrest.CoreMatchers.not;
 import static org.hamcrest.CoreMatchers.notNullValue;
 import static org.junit.Assert.assertThat;
 
@@ -74,7 +74,7 @@ public void tearDown()
     public void shouldBeAbleToAttachToPidAndRunThreadDump() throws IOException, CommandFailed, IncorrectUsage
     {
         long pid = getPID();
-        Assume.assumeTrue( pid != 0 );
+        assertThat( pid, is( not( 0 ) ) );
 
         // Write config file
         Files.createFile( testDirectory.file( "neo4j.conf" ).toPath() );

community/dbms/src/test/java/org/neo4j/commandline/dbms/DiagnosticsReportCommandTest.java

@@ -19,6 +19,7 @@
  */
 package org.neo4j.commandline.dbms;
 
+import org.junit.After;
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
@@ -69,6 +70,7 @@ public class DiagnosticsReportCommandTest
     private Path homeDir;
     private Path configDir;
     private Path configFile;
+    private String originalUserDir;
 
     public static class MyDiagnosticsOfflineReportProvider extends DiagnosticsOfflineReportProvider
     {
@@ -101,7 +103,14 @@ public void setUp() throws Exception
         Files.createFile( configFile );
 
         // To make sure files are resolved from the working directory
-        System.setProperty( "user.dir", testDirectory.absolutePath().getAbsolutePath() );
+        originalUserDir = System.setProperty( "user.dir", testDirectory.absolutePath().getAbsolutePath() );
+    }
+
+    @After
+    public void tearDown()
+    {
+        // Restore directory
+        System.setProperty( "user.dir", originalUserDir );
     }
 
     @Test

community/kernel/src/main/java/org/neo4j/diagnostics/DiagnosticsReportSources.java

@@ -22,7 +22,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
-import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
@@ -126,8 +126,10 @@ public void addToArchive( Path archiveDestination, DiagnosticsReporterProgressCa
             InputStream in = fs.openAsInputStream( source );
 
             // Track progress of the file reading, source might be a very large file
-            ProgressAwareInputStream inStream = new ProgressAwareInputStream( in, size, monitor::percentChanged );
-            Files.copy( inStream, archiveDestination );
+            try ( ProgressAwareInputStream inStream = new ProgressAwareInputStream( in, size, monitor::percentChanged ) )
+            {
+                Files.copy( inStream, archiveDestination );
+            }
         }
     }
 
@@ -153,7 +155,7 @@ public void addToArchive( Path archiveDestination, DiagnosticsReporterProgressCa
                 throws IOException
         {
             String message = messageSupplier.get();
-            Files.write( archiveDestination, message.getBytes( Charset.forName( "UTF8" ) ), StandardOpenOption.CREATE,
+            Files.write( archiveDestination, message.getBytes( StandardCharsets.UTF_8 ), StandardOpenOption.CREATE,
                     StandardOpenOption.APPEND );
         }
     }

community/kernel/src/main/java/org/neo4j/diagnostics/DiagnosticsReporter.java

@@ -110,6 +110,7 @@ public Set<String> getAvailableClassifiers()
         return availableClassifiers;
     }
 
+    // TODO:
     private static class Mon implements DiagnosticsReporterProgressCallback
     {
         private final String prefix;