From 222161fb1c47225f81d1cfd22c2ec507c9350c01 Mon Sep 17 00:00:00 2001
From: ahmadsebak <radio_frequency@hotmail.com>
Date: Sat, 20 Jun 2015 17:58:06 -0400
Subject: [PATCH 1/4] smarter deployment algorithm implementation

---
 META-INF/plugin.xml                           |  3 ++
 .../commandline/AppCommandLineState.java      | 43 ++++++++++++++--
 .../deploy/DeployedLibrary.java               | 13 +++++
 .../protocol/ssh/SSHHandlerTarget.java        | 50 ++++++++++++++++++-
 .../embeddedlinuxjvm/utils/FileUtilities.java | 18 +++++--
 5 files changed, 118 insertions(+), 9 deletions(-)
 create mode 100644 src/com/atsebak/embeddedlinuxjvm/deploy/DeployedLibrary.java

diff --git a/META-INF/plugin.xml b/META-INF/plugin.xml
index 4ab193a..1932462 100644
--- a/META-INF/plugin.xml
+++ b/META-INF/plugin.xml
@@ -14,6 +14,9 @@
             <li>
                 Fixed Null pointer exception on startup after adding run configuration.
             </li>
+            <li>
+                Smarter deployment algorithm to not deploy libs that already exist on target device.
+            </li>
         </ul>
         <b>Version 0.41</b>
         <ul>
diff --git a/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java b/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java
index 9ba335d..86259c3 100644
--- a/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java
+++ b/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java
@@ -2,6 +2,7 @@
 
 import com.atsebak.embeddedlinuxjvm.console.EmbeddedLinuxJVMConsoleView;
 import com.atsebak.embeddedlinuxjvm.console.EmbeddedLinuxJVMOutputForwarder;
+import com.atsebak.embeddedlinuxjvm.deploy.DeployedLibrary;
 import com.atsebak.embeddedlinuxjvm.deploy.DeploymentTarget;
 import com.atsebak.embeddedlinuxjvm.localization.EmbeddedLinuxJVMBundle;
 import com.atsebak.embeddedlinuxjvm.protocol.ssh.SSH;
@@ -47,9 +48,7 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
 
 public class AppCommandLineState extends JavaCommandLineState {
     @NonNls
@@ -203,8 +202,28 @@ public void run() {
                     @Override
                     public void run() {
                         try {
-                            List<File> files = invokeClassPathResolver(classPath.getPathList(), manager.getProjectSdk());
-                            File classpathArchive = FileUtilities.createClasspathArchive(files, project);
+                            List<File> hostLibraries = invokeClassPathResolver(classPath.getPathList(), manager.getProjectSdk());
+                            List<DeployedLibrary> targetLibraries = invokeFindDeployedJars();
+                            Set<String> filesToDeploy = new HashSet<String>(); //hash what files exist
+                            //todo improve based on last modified date, size, and the name of the file
+                            for (DeployedLibrary deployedLibrary : targetLibraries) {
+                                for (File hostFile : hostLibraries) {
+                                    if (deployedLibrary.getJarName().equals(hostFile.getName())) {
+                                        filesToDeploy.add(hostFile.getName());
+                                        break;
+                                    }
+                                }
+                            }
+
+                            //add files that do not exist on target
+                            List<File> newLibraries = new ArrayList<File>();
+                            for (File hostFile : hostLibraries) {
+                                if (!filesToDeploy.contains(hostFile.getName())) {
+                                    newLibraries.add(hostFile);
+                                }
+                            }
+
+                            File classpathArchive = FileUtilities.createClasspathArchive(newLibraries, project);
                             invokeDeployment(classpathArchive.getPath(), commandLineTarget);
                         } catch (Exception e) {
                             EmbeddedLinuxJVMConsoleView.getInstance(project).print(EmbeddedLinuxJVMBundle.message("pi.connection.failed", e.getLocalizedMessage()),
@@ -270,6 +289,20 @@ private void invokeDeployment(String projectOutput, CommandLineTarget commandLin
         target.upload(new File(projectOutput), commandLineTarget.toString());
     }
 
+    /**
+     * Gets deployed jars
+     */
+    private List<DeployedLibrary> invokeFindDeployedJars() throws IOException, RuntimeConfigurationException {
+        EmbeddedLinuxJVMRunConfigurationRunnerParameters runnerParameters = configuration.getRunnerParameters();
+        SSHHandlerTarget target = SSHHandlerTarget.builder().piRunnerParameters(runnerParameters)
+                .consoleView(EmbeddedLinuxJVMConsoleView.getInstance(project))
+                .ssh(SSH.builder()
+                        .connectionTimeout(30000)
+                        .timeout(30000)
+                        .build()).build();
+        return target.listAlreadyUploadedJars();
+    }
+
     /**
      * Creates debugging settings for server
      *
diff --git a/src/com/atsebak/embeddedlinuxjvm/deploy/DeployedLibrary.java b/src/com/atsebak/embeddedlinuxjvm/deploy/DeployedLibrary.java
new file mode 100644
index 0000000..48be83a
--- /dev/null
+++ b/src/com/atsebak/embeddedlinuxjvm/deploy/DeployedLibrary.java
@@ -0,0 +1,13 @@
+package com.atsebak.embeddedlinuxjvm.deploy;
+
+import lombok.Builder;
+import lombok.Getter;
+
+
+@Builder
+@Getter
+public class DeployedLibrary {
+    private String jarName;
+    private String size;
+    private String lastModified;
+}
diff --git a/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java b/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java
index f53181b..cd0dfad 100644
--- a/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java
+++ b/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java
@@ -2,6 +2,7 @@
 
 import com.atsebak.embeddedlinuxjvm.commandline.LinuxCommand;
 import com.atsebak.embeddedlinuxjvm.console.EmbeddedLinuxJVMConsoleView;
+import com.atsebak.embeddedlinuxjvm.deploy.DeployedLibrary;
 import com.atsebak.embeddedlinuxjvm.localization.EmbeddedLinuxJVMBundle;
 import com.atsebak.embeddedlinuxjvm.runner.data.EmbeddedLinuxJVMRunConfigurationRunnerParameters;
 import com.atsebak.embeddedlinuxjvm.utils.FileUtilities;
@@ -11,16 +12,21 @@
 import com.intellij.notification.NotificationType;
 import com.intellij.notification.Notifications;
 import lombok.Builder;
+import lombok.SneakyThrows;
 import net.schmizz.sshj.SSHClient;
+import net.schmizz.sshj.common.IOUtils;
 import net.schmizz.sshj.common.StreamCopier;
 import net.schmizz.sshj.connection.channel.direct.Session;
 import net.schmizz.sshj.sftp.SFTPClient;
 import net.schmizz.sshj.xfer.FileSystemFile;
+import org.apache.commons.lang.StringUtils;
 import org.jetbrains.annotations.NotNull;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.List;
 
 @Builder
 public class SSHHandlerTarget {
@@ -30,6 +36,44 @@ public class SSHHandlerTarget {
     private EmbeddedLinuxJVMConsoleView consoleView;
     private SSH ssh;
 
+    public List<DeployedLibrary> listAlreadyUploadedJars() throws IOException, RuntimeConfigurationException {
+        final String remoteDir = FileUtilities.separator + "home" + FileUtilities.separator
+                + piRunnerParameters.getUsername() + FileUtilities.separator + OUTPUT_LOCATION;
+        String path = remoteDir + FileUtilities.separator + consoleView.getProject().getName();
+        String deploymentPathJars = path + FileUtilities.separator + FileUtilities.LIB;
+        SSHClient ssh = this.ssh.toClient();
+        connect(ssh);
+        Session session = ssh.startSession();
+        String cmd = LinuxCommand.builder().commands(
+                Arrays.asList(
+                        String.format("cd %s", deploymentPathJars),
+                        "du -h --max-depth=0 * --time"
+                ))
+                .build()
+                .toString();
+        List<DeployedLibrary> libraries = new ArrayList<DeployedLibrary>();
+        try {
+            Session.Command exec = session.exec(cmd);
+            String files = IOUtils.readFully(exec.getInputStream()).toString();
+            if (StringUtils.isNotBlank(files)) {
+                String[] unparsedFiles = files.split("\\r?\\n");
+                for (int i = 0; i < unparsedFiles.length; i++) {
+                    String[] splitDescription = unparsedFiles[i].split("\t");
+                    libraries.add(DeployedLibrary.builder()
+                            .size(splitDescription[0])
+                            .lastModified(splitDescription[1])
+                            .jarName(splitDescription[2])
+                            .build());
+                }
+            }
+        } finally {
+            session.close();
+            ssh.disconnect();
+        }
+
+        return libraries;
+    }
+
     /** Uploads Java application output folders
      * @param compileOutput Output directory folder where to store the java application
      * @param cmd         The command to execute on the java files
@@ -62,6 +106,9 @@ private void forceCreateDirectories(String path) throws IOException, RuntimeConf
                 Arrays.asList(
                         String.format("mkdir -p %s", path),
                         String.format("cd %s", path),
+                        String.format("mkdir -p %s", FileUtilities.CLASSES),
+                        String.format("mkdir -p %s", FileUtilities.LIB),
+                        String.format("cd %s", path + FileUtilities.separator + FileUtilities.CLASSES),
                         "rm -rf *"
                 ))
                 .build()
@@ -127,7 +174,8 @@ private void runJavaApp(String path, String cmd) throws IOException, RuntimeConf
      * @throws IOException
      * @throws RuntimeConfigurationException
      */
-    private void connect(SSHClient client) throws IOException, RuntimeConfigurationException {
+    @SneakyThrows({IOException.class, RuntimeConfigurationException.class})
+    private void connect(SSHClient client) {
         if (!client.isAuthenticated()) {
             client.connect(piRunnerParameters.getHostname());
             client.authPassword(piRunnerParameters.getUsername(), piRunnerParameters.getPassword());
diff --git a/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java b/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java
index 5fdd176..021971a 100644
--- a/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java
+++ b/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java
@@ -15,7 +15,9 @@
 
 public class FileUtilities {
 
-    public static String separator = "/";
+    public static final String LIB = "lib";
+    public static final String CLASSES = "classes";
+    public static final String separator = "/";
 
     /**
      * Unzips a file all into one directory
@@ -83,10 +85,10 @@ public static File createClasspathArchive(Collection<File> classpathEntries, Pro
             LinkedList<String> pathElements = new LinkedList<String>();
             for (File f : classpathEntries) {
                 if (f.isFile()) { //is a jar file
-                    pathElements.addLast("lib");
+                    pathElements.addLast(LIB);
                     writeClassPath(pathElements, f, archiveOutputStream);
                 } else {
-                    pathElements.addLast("classes");  // is output of the project
+                    pathElements.addLast(CLASSES);  // is output of the project
                     for (File child : f.listFiles()) {
                         writeClassPath(pathElements, child, archiveOutputStream);
                     }
@@ -160,4 +162,14 @@ public static String getPath(LinkedList<String> pathElements) {
         }
         return buf.toString();
     }
+
+    public static String toNumInUnits(long bytes) {
+        int u = 0;
+        for (; bytes > 1024 * 1024; bytes >>= 10) {
+            u++;
+        }
+        if (bytes > 1024)
+            u++;
+        return String.format("%.1f %cB", bytes / 1024f, " kMGTPE".charAt(u));
+    }
 }

From dfc0c3973214dfff39ea106d0e8d06b8bc98ce98 Mon Sep 17 00:00:00 2001
From: ahmadsebak <radio_frequency@hotmail.com>
Date: Sat, 20 Jun 2015 18:11:38 -0400
Subject: [PATCH 2/4] more refactoring

---
 META-INF/plugin.xml                           |  4 +-
 .../commandline/AppCommandLineState.java      | 51 +++++++++++--------
 .../project/RPiJavaModuleBuilder.java         |  9 ++--
 .../protocol/ssh/SSHHandlerTarget.java        | 16 +++---
 .../embeddedlinuxjvm/utils/FileUtilities.java | 17 ++-----
 .../protocol/ssh/SSHHandlerTargetTest.java    |  6 +--
 6 files changed, 50 insertions(+), 53 deletions(-)

diff --git a/META-INF/plugin.xml b/META-INF/plugin.xml
index 1932462..9bcf969 100644
--- a/META-INF/plugin.xml
+++ b/META-INF/plugin.xml
@@ -1,7 +1,7 @@
 <idea-plugin version="2">
   <id>com.atsebak.raspberrypi</id>
     <name>Embedded Linux JVM Debugger (Raspberry Pi, Intel x86, ARM processors)</name>
-    <version>0.42</version>
+    <version>0.45</version>
   <vendor email="ahmad@atsebak.com" url="http://www.atsebak.com">At Sebak</vendor>
 
   <description><![CDATA[
@@ -9,7 +9,7 @@
     ]]></description>
 
   <change-notes><![CDATA[
-        <b>Version 0.42</b>
+        <b>Version 0.45</b>
         <ul>
             <li>
                 Fixed Null pointer exception on startup after adding run configuration.
diff --git a/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java b/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java
index 86259c3..656be89 100644
--- a/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java
+++ b/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java
@@ -203,27 +203,7 @@ public void run() {
                     public void run() {
                         try {
                             List<File> hostLibraries = invokeClassPathResolver(classPath.getPathList(), manager.getProjectSdk());
-                            List<DeployedLibrary> targetLibraries = invokeFindDeployedJars();
-                            Set<String> filesToDeploy = new HashSet<String>(); //hash what files exist
-                            //todo improve based on last modified date, size, and the name of the file
-                            for (DeployedLibrary deployedLibrary : targetLibraries) {
-                                for (File hostFile : hostLibraries) {
-                                    if (deployedLibrary.getJarName().equals(hostFile.getName())) {
-                                        filesToDeploy.add(hostFile.getName());
-                                        break;
-                                    }
-                                }
-                            }
-
-                            //add files that do not exist on target
-                            List<File> newLibraries = new ArrayList<File>();
-                            for (File hostFile : hostLibraries) {
-                                if (!filesToDeploy.contains(hostFile.getName())) {
-                                    newLibraries.add(hostFile);
-                                }
-                            }
-
-                            File classpathArchive = FileUtilities.createClasspathArchive(newLibraries, project);
+                            File classpathArchive = FileUtilities.createClasspathArchive(deltaOfDeployedJars(hostLibraries), project);
                             invokeDeployment(classpathArchive.getPath(), commandLineTarget);
                         } catch (Exception e) {
                             EmbeddedLinuxJVMConsoleView.getInstance(project).print(EmbeddedLinuxJVMBundle.message("pi.connection.failed", e.getLocalizedMessage()),
@@ -303,6 +283,35 @@ private List<DeployedLibrary> invokeFindDeployedJars() throws IOException, Runti
         return target.listAlreadyUploadedJars();
     }
 
+    /**
+     * Gets the delta of jars between host and target machines
+     *
+     * @param hostLibraries
+     * @return targetLibraries
+     */
+    private List<File> deltaOfDeployedJars(List<File> hostLibraries) throws IOException, RuntimeConfigurationException {
+        List<DeployedLibrary> targetLibraries = invokeFindDeployedJars();
+        Set<String> filesToDeploy = new HashSet<String>(); //hash what files exist
+        //todo improve based on last modified date, size, and the name of the file and not just the filename
+        for (DeployedLibrary deployedLibrary : targetLibraries) {
+            for (File hostFile : hostLibraries) {
+                if (deployedLibrary.getJarName().equals(hostFile.getName())) {
+                    filesToDeploy.add(hostFile.getName());
+                    break;
+                }
+            }
+        }
+
+        //add files that do not exist on target
+        List<File> newLibraries = new ArrayList<File>();
+        for (File hostFile : hostLibraries) {
+            if (!filesToDeploy.contains(hostFile.getName())) {
+                newLibraries.add(hostFile);
+            }
+        }
+        return newLibraries;
+    }
+
     /**
      * Creates debugging settings for server
      *
diff --git a/src/com/atsebak/embeddedlinuxjvm/project/RPiJavaModuleBuilder.java b/src/com/atsebak/embeddedlinuxjvm/project/RPiJavaModuleBuilder.java
index 152c276..da11026 100644
--- a/src/com/atsebak/embeddedlinuxjvm/project/RPiJavaModuleBuilder.java
+++ b/src/com/atsebak/embeddedlinuxjvm/project/RPiJavaModuleBuilder.java
@@ -1,11 +1,10 @@
 package com.atsebak.embeddedlinuxjvm.project;
 
 import com.atsebak.embeddedlinuxjvm.localization.EmbeddedLinuxJVMBundle;
+import com.atsebak.embeddedlinuxjvm.ui.PIJavaModuleStep;
 import com.atsebak.embeddedlinuxjvm.utils.FileUtilities;
 import com.atsebak.embeddedlinuxjvm.utils.ProjectUtils;
 import com.atsebak.embeddedlinuxjvm.utils.Template;
-import com.atsebak.embeddedlinuxjvm.utils.UrlDownloader;
-import com.atsebak.embeddedlinuxjvm.ui.PIJavaModuleStep;
 import com.google.common.io.Files;
 import com.intellij.icons.AllIcons;
 import com.intellij.ide.util.projectWizard.JavaModuleBuilder;
@@ -90,15 +89,15 @@ public void run() {
                 String[] directoriesToMake = packageName.split(Pattern.quote("."));
                 for (String directory : directoriesToMake) {
                     try {
-                        VfsUtil.createDirectories(srcPath + FileUtilities.separator + directory);
+                        VfsUtil.createDirectories(srcPath + FileUtilities.SEPARATOR + directory);
                     } catch (IOException e) {
 
                     }
-                    srcPath += FileUtilities.separator + directory;
+                    srcPath += FileUtilities.SEPARATOR + directory;
                 }
                 Template.builder().name("main.ftl")
                         .classContext(this.getClass())
-                        .outputFile(srcPath + FileUtilities.separator + "Main.java")
+                        .outputFile(srcPath + FileUtilities.SEPARATOR + "Main.java")
                         .data(new HashMap<String, Object>() {{
                             put("packagename", packageName);
                         }}).build()
diff --git a/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java b/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java
index cd0dfad..9ba5b5d 100644
--- a/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java
+++ b/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java
@@ -37,10 +37,10 @@ public class SSHHandlerTarget {
     private SSH ssh;
 
     public List<DeployedLibrary> listAlreadyUploadedJars() throws IOException, RuntimeConfigurationException {
-        final String remoteDir = FileUtilities.separator + "home" + FileUtilities.separator
-                + piRunnerParameters.getUsername() + FileUtilities.separator + OUTPUT_LOCATION;
-        String path = remoteDir + FileUtilities.separator + consoleView.getProject().getName();
-        String deploymentPathJars = path + FileUtilities.separator + FileUtilities.LIB;
+        final String remoteDir = FileUtilities.SEPARATOR + "home" + FileUtilities.SEPARATOR
+                + piRunnerParameters.getUsername() + FileUtilities.SEPARATOR + OUTPUT_LOCATION;
+        String path = remoteDir + FileUtilities.SEPARATOR + consoleView.getProject().getName();
+        String deploymentPathJars = path + FileUtilities.SEPARATOR + FileUtilities.LIB;
         SSHClient ssh = this.ssh.toClient();
         connect(ssh);
         Session session = ssh.startSession();
@@ -83,9 +83,9 @@ public List<DeployedLibrary> listAlreadyUploadedJars() throws IOException, Runti
      */
     public void uploadAndRunJavaApp(@NotNull final File compileOutput, @NotNull final String cmd)
             throws IOException, ClassNotFoundException, RuntimeConfigurationException {
-        final String remoteDir = FileUtilities.separator + "home" + FileUtilities.separator
-                + piRunnerParameters.getUsername() + FileUtilities.separator + OUTPUT_LOCATION;
-        String deploymentPath = remoteDir + FileUtilities.separator + consoleView.getProject().getName();
+        final String remoteDir = FileUtilities.SEPARATOR + "home" + FileUtilities.SEPARATOR
+                + piRunnerParameters.getUsername() + FileUtilities.SEPARATOR + OUTPUT_LOCATION;
+        String deploymentPath = remoteDir + FileUtilities.SEPARATOR + consoleView.getProject().getName();
         genericUpload(deploymentPath, compileOutput);
         consoleView.print(EmbeddedLinuxJVMBundle.getString("pi.deployment.finished") + NEW_LINE, ConsoleViewContentType.SYSTEM_OUTPUT);
         runJavaApp(deploymentPath, cmd);
@@ -108,7 +108,7 @@ private void forceCreateDirectories(String path) throws IOException, RuntimeConf
                         String.format("cd %s", path),
                         String.format("mkdir -p %s", FileUtilities.CLASSES),
                         String.format("mkdir -p %s", FileUtilities.LIB),
-                        String.format("cd %s", path + FileUtilities.separator + FileUtilities.CLASSES),
+                        String.format("cd %s", path + FileUtilities.SEPARATOR + FileUtilities.CLASSES),
                         "rm -rf *"
                 ))
                 .build()
diff --git a/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java b/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java
index 021971a..70cc271 100644
--- a/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java
+++ b/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java
@@ -17,7 +17,7 @@ public class FileUtilities {
 
     public static final String LIB = "lib";
     public static final String CLASSES = "classes";
-    public static final String separator = "/";
+    public static final String SEPARATOR = "/";
 
     /**
      * Unzips a file all into one directory
@@ -42,7 +42,7 @@ public static void unzip(InputStream inputStream, String outputFolder) {
                     continue;
                 }
                 fileName = new File(fileName).getName();
-                File newFile = new File(outputFolder + FileUtilities.separator + fileName);
+                File newFile = new File(outputFolder + FileUtilities.SEPARATOR + fileName);
                 new File(newFile.getParent()).mkdirs();
 
                 FileOutputStream fos = new FileOutputStream(newFile);
@@ -115,7 +115,7 @@ public static File createClasspathArchive(Collection<File> classpathEntries, Pro
     private static void writeClassPath(LinkedList<String> pathElements, File entry, TarArchiveOutputStream archiveOutputStream) throws IOException {
         if (entry.isFile()) {
             archiveOutputStream.setLongFileMode(TarArchiveOutputStream.LONGFILE_GNU);
-            archiveOutputStream.putArchiveEntry(new TarArchiveEntry(entry, getPath(pathElements) + FileUtilities.separator + entry.getName()));
+            archiveOutputStream.putArchiveEntry(new TarArchiveEntry(entry, getPath(pathElements) + FileUtilities.SEPARATOR + entry.getName()));
             copy(entry, archiveOutputStream);
             archiveOutputStream.closeArchiveEntry();
         } else {
@@ -156,20 +156,11 @@ public static String getPath(LinkedList<String> pathElements) {
         StringBuilder buf = new StringBuilder();
         for (int i = 0; i < pathElements.size(); i++) {
             if (i != 0) {
-                buf.append(FileUtilities.separator);
+                buf.append(FileUtilities.SEPARATOR);
             }
             buf.append(pathElements.get(i));
         }
         return buf.toString();
     }
 
-    public static String toNumInUnits(long bytes) {
-        int u = 0;
-        for (; bytes > 1024 * 1024; bytes >>= 10) {
-            u++;
-        }
-        if (bytes > 1024)
-            u++;
-        return String.format("%.1f %cB", bytes / 1024f, " kMGTPE".charAt(u));
-    }
 }
diff --git a/test/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTargetTest.java b/test/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTargetTest.java
index 3450213..ca50534 100644
--- a/test/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTargetTest.java
+++ b/test/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTargetTest.java
@@ -5,7 +5,6 @@
 import com.atsebak.embeddedlinuxjvm.utils.FileUtilities;
 import com.intellij.execution.configurations.RuntimeConfigurationException;
 import com.intellij.notification.Notifications;
-import com.intellij.openapi.components.ServiceManager;
 import com.intellij.openapi.project.Project;
 import net.schmizz.sshj.SSHClient;
 import net.schmizz.sshj.connection.channel.direct.Session;
@@ -26,7 +25,6 @@
 
 import static org.mockito.Matchers.*;
 import static org.mockito.Mockito.times;
-import static org.powermock.api.mockito.PowerMockito.when;
 
 @RunWith(PowerMockRunner.class)
 public class SSHHandlerTargetTest {
@@ -103,7 +101,7 @@ public void verifyUploadToTarget() throws RuntimeConfigurationException, IOExcep
         Mockito.when(project.getName()).thenReturn("untitled");
         target.uploadAndRunJavaApp(sampleFile, "java -jar");
         Mockito.verify(sftpClient).put(any(FileSystemFile.class),
-                eq(FileUtilities.separator + "home" + FileUtilities.separator + "ahmad" + FileUtilities.separator + "IdeaProjects" + FileUtilities.separator + "untitled"));
+                eq(FileUtilities.SEPARATOR + "home" + FileUtilities.SEPARATOR + "ahmad" + FileUtilities.SEPARATOR + "IdeaProjects" + FileUtilities.SEPARATOR + "untitled"));
         Mockito.verify(sshClient).disconnect();
         Mockito.verify(sshClient, times(2)).startSession();
 
@@ -115,7 +113,7 @@ public void verifyUploadToTarget() throws RuntimeConfigurationException, IOExcep
 
     @Test
     public void verifyJavaCommands() throws IOException, RuntimeConfigurationException, ClassNotFoundException {
-        final String path = FileUtilities.separator + "home" + FileUtilities.separator + "ahmad" + FileUtilities.separator + "IdeaProjects" + FileUtilities.separator + "untitled";
+        final String path = FileUtilities.SEPARATOR + "home" + FileUtilities.SEPARATOR + "ahmad" + FileUtilities.SEPARATOR + "IdeaProjects" + FileUtilities.SEPARATOR + "untitled";
         final String commandToBeExecuted = "mkdir -p " + path + "; " + "cd " + path + "; rm -rf *;";
         Mockito.when(sshClient.isAuthenticated()).thenReturn(true);
         Mockito.when(project.getName()).thenReturn("untitled");

From 02978f1e6098c4818f98a6348209e6472df2e814 Mon Sep 17 00:00:00 2001
From: ahmadsebak <radio_frequency@hotmail.com>
Date: Sun, 21 Jun 2015 08:41:00 -0400
Subject: [PATCH 3/4] update to include classpath service, to check between
 previous runs

---
 META-INF/plugin.xml                           |  3 +
 embeddedlinux-jvmdebugger.iml                 |  2 +-
 .../commandline/AppCommandLineState.java      | 52 ++------------
 .../protocol/ssh/SSHHandlerTarget.java        |  7 ++
 .../services/ClasspathService.java            | 70 +++++++++++++++++++
 .../embeddedlinuxjvm/utils/FileUtilities.java |  6 +-
 .../embeddedlinuxjvm/utils/Notifications.java |  2 +-
 7 files changed, 92 insertions(+), 50 deletions(-)
 create mode 100644 src/com/atsebak/embeddedlinuxjvm/services/ClasspathService.java

diff --git a/META-INF/plugin.xml b/META-INF/plugin.xml
index 9bcf969..04ee9bc 100644
--- a/META-INF/plugin.xml
+++ b/META-INF/plugin.xml
@@ -83,6 +83,9 @@
       <configurationType implementation="com.atsebak.embeddedlinuxjvm.runner.conf.EmbeddedLinuxJVMConfigurationType"/>
       <projectService serviceImplementation="com.atsebak.embeddedlinuxjvm.console.EmbeddedLinuxJVMConsoleView"/>
       <moduleBuilder builderClass="com.atsebak.embeddedlinuxjvm.project.RPiJavaModuleBuilder"/>
+
+      <projectService serviceImplementation="com.atsebak.embeddedlinuxjvm.services.ClasspathService"
+                      serviceInterface="com.atsebak.embeddedlinuxjvm.services.ClasspathService"/>
   </extensions>
 
 </idea-plugin>
diff --git a/embeddedlinux-jvmdebugger.iml b/embeddedlinux-jvmdebugger.iml
index d905056..a274004 100644
--- a/embeddedlinux-jvmdebugger.iml
+++ b/embeddedlinux-jvmdebugger.iml
@@ -9,7 +9,7 @@
       <sourceFolder url="file://$MODULE_DIR$/Resources" type="java-resource" />
       <sourceFolder url="file://$MODULE_DIR$/test" isTestSource="true" />
     </content>
-    <orderEntry type="jdk" jdkName="IntelliJ IDEA Community Edition IC-141.178.9 (1)" jdkType="IDEA JDK" />
+    <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />
     <orderEntry type="library" name="lombok" level="project" />
     <orderEntry type="library" name="bcprov-ext-jdk15on-1.47" level="project" />
diff --git a/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java b/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java
index 656be89..ef7ebb5 100644
--- a/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java
+++ b/src/com/atsebak/embeddedlinuxjvm/commandline/AppCommandLineState.java
@@ -2,13 +2,13 @@
 
 import com.atsebak.embeddedlinuxjvm.console.EmbeddedLinuxJVMConsoleView;
 import com.atsebak.embeddedlinuxjvm.console.EmbeddedLinuxJVMOutputForwarder;
-import com.atsebak.embeddedlinuxjvm.deploy.DeployedLibrary;
 import com.atsebak.embeddedlinuxjvm.deploy.DeploymentTarget;
 import com.atsebak.embeddedlinuxjvm.localization.EmbeddedLinuxJVMBundle;
 import com.atsebak.embeddedlinuxjvm.protocol.ssh.SSH;
 import com.atsebak.embeddedlinuxjvm.protocol.ssh.SSHHandlerTarget;
 import com.atsebak.embeddedlinuxjvm.runner.conf.EmbeddedLinuxJVMRunConfiguration;
 import com.atsebak.embeddedlinuxjvm.runner.data.EmbeddedLinuxJVMRunConfigurationRunnerParameters;
+import com.atsebak.embeddedlinuxjvm.services.ClasspathService;
 import com.atsebak.embeddedlinuxjvm.utils.FileUtilities;
 import com.atsebak.embeddedlinuxjvm.utils.RemoteCommandLineBuilder;
 import com.intellij.execution.*;
@@ -25,6 +25,7 @@
 import com.intellij.openapi.actionSystem.CommonDataKeys;
 import com.intellij.openapi.application.Application;
 import com.intellij.openapi.application.ApplicationManager;
+import com.intellij.openapi.components.ServiceManager;
 import com.intellij.openapi.module.Module;
 import com.intellij.openapi.module.ModuleManager;
 import com.intellij.openapi.progress.ProgressIndicator;
@@ -48,7 +49,9 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
 
 public class AppCommandLineState extends JavaCommandLineState {
     @NonNls
@@ -202,8 +205,9 @@ public void run() {
                     @Override
                     public void run() {
                         try {
+                            ClasspathService service = ServiceManager.getService(project, ClasspathService.class);
                             List<File> hostLibraries = invokeClassPathResolver(classPath.getPathList(), manager.getProjectSdk());
-                            File classpathArchive = FileUtilities.createClasspathArchive(deltaOfDeployedJars(hostLibraries), project);
+                            File classpathArchive = FileUtilities.createClasspathArchive(service.deltaOfDeployedJars(hostLibraries), project);
                             invokeDeployment(classpathArchive.getPath(), commandLineTarget);
                         } catch (Exception e) {
                             EmbeddedLinuxJVMConsoleView.getInstance(project).print(EmbeddedLinuxJVMBundle.message("pi.connection.failed", e.getLocalizedMessage()),
@@ -269,48 +273,6 @@ private void invokeDeployment(String projectOutput, CommandLineTarget commandLin
         target.upload(new File(projectOutput), commandLineTarget.toString());
     }
 
-    /**
-     * Gets deployed jars
-     */
-    private List<DeployedLibrary> invokeFindDeployedJars() throws IOException, RuntimeConfigurationException {
-        EmbeddedLinuxJVMRunConfigurationRunnerParameters runnerParameters = configuration.getRunnerParameters();
-        SSHHandlerTarget target = SSHHandlerTarget.builder().piRunnerParameters(runnerParameters)
-                .consoleView(EmbeddedLinuxJVMConsoleView.getInstance(project))
-                .ssh(SSH.builder()
-                        .connectionTimeout(30000)
-                        .timeout(30000)
-                        .build()).build();
-        return target.listAlreadyUploadedJars();
-    }
-
-    /**
-     * Gets the delta of jars between host and target machines
-     *
-     * @param hostLibraries
-     * @return targetLibraries
-     */
-    private List<File> deltaOfDeployedJars(List<File> hostLibraries) throws IOException, RuntimeConfigurationException {
-        List<DeployedLibrary> targetLibraries = invokeFindDeployedJars();
-        Set<String> filesToDeploy = new HashSet<String>(); //hash what files exist
-        //todo improve based on last modified date, size, and the name of the file and not just the filename
-        for (DeployedLibrary deployedLibrary : targetLibraries) {
-            for (File hostFile : hostLibraries) {
-                if (deployedLibrary.getJarName().equals(hostFile.getName())) {
-                    filesToDeploy.add(hostFile.getName());
-                    break;
-                }
-            }
-        }
-
-        //add files that do not exist on target
-        List<File> newLibraries = new ArrayList<File>();
-        for (File hostFile : hostLibraries) {
-            if (!filesToDeploy.contains(hostFile.getName())) {
-                newLibraries.add(hostFile);
-            }
-        }
-        return newLibraries;
-    }
 
     /**
      * Creates debugging settings for server
diff --git a/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java b/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java
index 9ba5b5d..c470d16 100644
--- a/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java
+++ b/src/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTarget.java
@@ -36,6 +36,13 @@ public class SSHHandlerTarget {
     private EmbeddedLinuxJVMConsoleView consoleView;
     private SSH ssh;
 
+    /**
+     * Can get this information from the IDE
+     *
+     * @return
+     * @throws IOException
+     * @throws RuntimeConfigurationException
+     */
     public List<DeployedLibrary> listAlreadyUploadedJars() throws IOException, RuntimeConfigurationException {
         final String remoteDir = FileUtilities.SEPARATOR + "home" + FileUtilities.SEPARATOR
                 + piRunnerParameters.getUsername() + FileUtilities.SEPARATOR + OUTPUT_LOCATION;
diff --git a/src/com/atsebak/embeddedlinuxjvm/services/ClasspathService.java b/src/com/atsebak/embeddedlinuxjvm/services/ClasspathService.java
new file mode 100644
index 0000000..7c9d986
--- /dev/null
+++ b/src/com/atsebak/embeddedlinuxjvm/services/ClasspathService.java
@@ -0,0 +1,70 @@
+package com.atsebak.embeddedlinuxjvm.services;
+
+
+import com.atsebak.embeddedlinuxjvm.console.EmbeddedLinuxJVMConsoleView;
+import com.atsebak.embeddedlinuxjvm.deploy.DeployedLibrary;
+import com.atsebak.embeddedlinuxjvm.protocol.ssh.SSH;
+import com.atsebak.embeddedlinuxjvm.protocol.ssh.SSHHandlerTarget;
+import com.atsebak.embeddedlinuxjvm.runner.data.EmbeddedLinuxJVMRunConfigurationRunnerParameters;
+import com.intellij.execution.configurations.RuntimeConfigurationException;
+import com.intellij.openapi.project.Project;
+import org.jetbrains.annotations.NotNull;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+public class ClasspathService {
+    @NotNull
+    private final Project project;
+    private List<File> previousDeployFiles;
+
+    /**
+     * Clear up static file list of deployments
+     */
+    public ClasspathService(@NotNull Project project) {
+        this.project = project;
+        previousDeployFiles = new ArrayList<File>();
+    }
+
+    /**
+     * Gets the delta of jars between host and target machines.  It will always add the normal project output path but not necessarily the external libs
+     * Some potential problems can be that the user stops it midway while deploying so the jars don't go on the target.
+     *
+     * @param hostLibraries
+     * @return targetLibraries
+     */
+    public List<File> deltaOfDeployedJars(List<File> hostLibraries) throws IOException, RuntimeConfigurationException {
+        List<File> newLibraries = new ArrayList<File>();
+        for (File hostFile : hostLibraries) {
+            if (!hostFile.getName().contains("jar")) {
+                newLibraries.add(hostFile);
+            } else if (!previousDeployFiles.contains(hostFile)) {
+                newLibraries.add(hostFile);
+            }
+        }
+        previousDeployFiles = hostLibraries;
+        return newLibraries;
+    }
+
+    /**
+     * Gets the deployed jars on target machine
+     *
+     * @return
+     * @throws IOException
+     * @throws RuntimeConfigurationException
+     * @deprecated use deltaOfDeployedJars instead
+     */
+    @Deprecated
+    public List<DeployedLibrary> invokeFindDeployedJars(EmbeddedLinuxJVMRunConfigurationRunnerParameters runnerParameters)
+            throws IOException, RuntimeConfigurationException {
+        SSHHandlerTarget target = SSHHandlerTarget.builder().piRunnerParameters(runnerParameters)
+                .consoleView(EmbeddedLinuxJVMConsoleView.getInstance(project))
+                .ssh(SSH.builder()
+                        .connectionTimeout(30000)
+                        .timeout(30000)
+                        .build()).build();
+        return target.listAlreadyUploadedJars();
+    }
+}
diff --git a/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java b/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java
index 70cc271..eed335b 100644
--- a/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java
+++ b/src/com/atsebak/embeddedlinuxjvm/utils/FileUtilities.java
@@ -42,7 +42,7 @@ public static void unzip(InputStream inputStream, String outputFolder) {
                     continue;
                 }
                 fileName = new File(fileName).getName();
-                File newFile = new File(outputFolder + FileUtilities.SEPARATOR + fileName);
+                File newFile = new File(outputFolder + SEPARATOR + fileName);
                 new File(newFile.getParent()).mkdirs();
 
                 FileOutputStream fos = new FileOutputStream(newFile);
@@ -115,7 +115,7 @@ public static File createClasspathArchive(Collection<File> classpathEntries, Pro
     private static void writeClassPath(LinkedList<String> pathElements, File entry, TarArchiveOutputStream archiveOutputStream) throws IOException {
         if (entry.isFile()) {
             archiveOutputStream.setLongFileMode(TarArchiveOutputStream.LONGFILE_GNU);
-            archiveOutputStream.putArchiveEntry(new TarArchiveEntry(entry, getPath(pathElements) + FileUtilities.SEPARATOR + entry.getName()));
+            archiveOutputStream.putArchiveEntry(new TarArchiveEntry(entry, getPath(pathElements) + SEPARATOR + entry.getName()));
             copy(entry, archiveOutputStream);
             archiveOutputStream.closeArchiveEntry();
         } else {
@@ -156,7 +156,7 @@ public static String getPath(LinkedList<String> pathElements) {
         StringBuilder buf = new StringBuilder();
         for (int i = 0; i < pathElements.size(); i++) {
             if (i != 0) {
-                buf.append(FileUtilities.SEPARATOR);
+                buf.append(SEPARATOR);
             }
             buf.append(pathElements.get(i));
         }
diff --git a/src/com/atsebak/embeddedlinuxjvm/utils/Notifications.java b/src/com/atsebak/embeddedlinuxjvm/utils/Notifications.java
index d6b1121..7c93662 100644
--- a/src/com/atsebak/embeddedlinuxjvm/utils/Notifications.java
+++ b/src/com/atsebak/embeddedlinuxjvm/utils/Notifications.java
@@ -5,5 +5,5 @@ public class Notifications {
     /**
      * ID for notifications
      */
-    public static final String GROUPDISPLAY_ID = "Raspbery PI Notifications";
+    public static final String GROUPDISPLAY_ID = "EmbeddedLinux JVM Notifications";
 }

From a15109362f889e32eb13933f3b8c3c6a44be5e26 Mon Sep 17 00:00:00 2001
From: ahmadsebak <radio_frequency@hotmail.com>
Date: Sun, 21 Jun 2015 08:54:51 -0400
Subject: [PATCH 4/4] added tests for class path service

---
 .../services/ClasspathService.java            |  2 +-
 .../protocol/ssh/SSHHandlerTargetTest.java    |  2 +-
 .../services/ClasspathServiceTest.java        | 45 +++++++++++++++++++
 3 files changed, 47 insertions(+), 2 deletions(-)
 create mode 100644 test/com/atsebak/embeddedlinuxjvm/services/ClasspathServiceTest.java

diff --git a/src/com/atsebak/embeddedlinuxjvm/services/ClasspathService.java b/src/com/atsebak/embeddedlinuxjvm/services/ClasspathService.java
index 7c9d986..3af5090 100644
--- a/src/com/atsebak/embeddedlinuxjvm/services/ClasspathService.java
+++ b/src/com/atsebak/embeddedlinuxjvm/services/ClasspathService.java
@@ -35,7 +35,7 @@ public ClasspathService(@NotNull Project project) {
      * @param hostLibraries
      * @return targetLibraries
      */
-    public List<File> deltaOfDeployedJars(List<File> hostLibraries) throws IOException, RuntimeConfigurationException {
+    public List<File> deltaOfDeployedJars(List<File> hostLibraries) {
         List<File> newLibraries = new ArrayList<File>();
         for (File hostFile : hostLibraries) {
             if (!hostFile.getName().contains("jar")) {
diff --git a/test/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTargetTest.java b/test/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTargetTest.java
index ca50534..16fddd0 100644
--- a/test/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTargetTest.java
+++ b/test/com/atsebak/embeddedlinuxjvm/protocol/ssh/SSHHandlerTargetTest.java
@@ -114,7 +114,7 @@ public void verifyUploadToTarget() throws RuntimeConfigurationException, IOExcep
     @Test
     public void verifyJavaCommands() throws IOException, RuntimeConfigurationException, ClassNotFoundException {
         final String path = FileUtilities.SEPARATOR + "home" + FileUtilities.SEPARATOR + "ahmad" + FileUtilities.SEPARATOR + "IdeaProjects" + FileUtilities.SEPARATOR + "untitled";
-        final String commandToBeExecuted = "mkdir -p " + path + "; " + "cd " + path + "; rm -rf *;";
+        final String commandToBeExecuted = "mkdir -p " + path + "; " + "cd " + path + "; mkdir -p classes; mkdir -p lib; " + "cd " + path + FileUtilities.SEPARATOR + FileUtilities.CLASSES + "; rm -rf *;";
         Mockito.when(sshClient.isAuthenticated()).thenReturn(true);
         Mockito.when(project.getName()).thenReturn("untitled");
         Mockito.when(sshClient.isConnected()).thenReturn(true);
diff --git a/test/com/atsebak/embeddedlinuxjvm/services/ClasspathServiceTest.java b/test/com/atsebak/embeddedlinuxjvm/services/ClasspathServiceTest.java
new file mode 100644
index 0000000..148065d
--- /dev/null
+++ b/test/com/atsebak/embeddedlinuxjvm/services/ClasspathServiceTest.java
@@ -0,0 +1,45 @@
+package com.atsebak.embeddedlinuxjvm.services;
+
+import com.intellij.openapi.project.Project;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+public class ClasspathServiceTest {
+    private final Project project = mock(Project.class);
+    private ClasspathService classpathService;
+    private File jar1 = mock(File.class);
+    private File jar2 = mock(File.class);
+    private File output = mock(File.class);
+    private List<File> hostFiles;
+
+    @Before
+    public void setUp() throws Exception {
+        classpathService = new ClasspathService(project);
+        hostFiles = Arrays.asList(jar1, jar2, output);
+        when(jar1.getName()).thenReturn("randomjar1.jar");
+        when(jar2.getName()).thenReturn("randomjar2.jar");
+        when(output.getName()).thenReturn("untitledproject");
+    }
+
+    @Test
+    public void testFirstDeployment() {
+        List<File> filesToDeploy = classpathService.deltaOfDeployedJars(hostFiles);
+        assertEquals(filesToDeploy, hostFiles);
+    }
+
+    @Test
+    public void testSecondDeployment() {
+        List<File> filesToDeploy = classpathService.deltaOfDeployedJars(hostFiles);
+        assertEquals(filesToDeploy, hostFiles);
+        filesToDeploy = classpathService.deltaOfDeployedJars(hostFiles);
+        assertEquals(filesToDeploy, Arrays.asList(output));
+    }
+}
\ No newline at end of file