Merge release

.travis.yml

@@ -42,7 +42,7 @@ jobs:
     - sudo apt-get install sshpass xml-twig-tools
     script:
     - sshpass -p $PROD_MACHINE_PASSWORD ssh -o StrictHostKeyChecking=no $PROD_MACHINE_USERNAME@$PROD_MACHINE_IP
-      "service iofog-agent stop"
+      "service iofog-agent stop; sudo apt-get install --only-upgrade -y iofog-agent"
     - sshpass -p $PROD_MACHINE_PASSWORD scp -o StrictHostKeyChecking=no daemon/target/iofog-agent-daemon-jar-with-dependencies.jar
       $PROD_MACHINE_USERNAME@$PROD_MACHINE_IP:/usr/bin/iofog-agentd.jar
     - sshpass -p $PROD_MACHINE_PASSWORD scp -o StrictHostKeyChecking=no client/target/iofog-agent-client-jar-with-dependencies.jar

client/pom.xml

@@ -16,7 +16,7 @@
 	<parent>
 		<groupId>org.eclipse</groupId>
 		<artifactId>iofog-agent</artifactId>
-		<version>1.0.8</version>
+		<version>1.0.9</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

daemon/pom.xml

@@ -16,7 +16,7 @@
 	<parent>
 		<groupId>org.eclipse</groupId>
 		<artifactId>iofog-agent</artifactId>
-		<version>1.0.8</version>
+		<version>1.0.9</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

daemon/src/org/eclipse/iofog/command_line/util/CommandShellExecutor.java

@@ -34,116 +34,135 @@
  * on 2/7/18.
  */
 public class CommandShellExecutor {
-	private static final String MODULE_NAME = "CommandShellExecutor";
-	private static final String CMD = "/bin/sh";
-	private static final String CMD_WIN = "powershell";
-
-
-	public static CommandShellResultSet<List<String>, List<String>> executeCommand(String command) {
-		String[] fullCommand = computeCommand(command);
-		return execute(fullCommand);
-	}
-
-	public static CommandShellResultSet<List<String>, List<String>> executeScript(String script, String... args) {
-		String[] fullCommand = computeScript(script, args);
-		return execute(fullCommand);
-	}
-
-	public static void executeDynamicCommand(String command, CommandShellResultSet<List<String>, List<String>> resultSet, AtomicBoolean isRun) {
-		String[] fullCommand = computeCommand(command);
-		executeDynamic(fullCommand, resultSet, isRun);
-	}
-
-	private static CommandShellResultSet<List<String>, List<String>> execute( String[] fullCommand) {
-		CommandShellResultSet<List<String>, List<String>> resultSet = null;
-		try {
-			Process process = Runtime.getRuntime().exec(fullCommand);
-			List<String> value = readOutput(process, Process::getInputStream);
-			List<String> errors = readOutput(process, Process::getErrorStream);
-			resultSet = new CommandShellResultSet<>(value, errors);
-		} catch (IOException e) {
-			LoggingService.logWarning(MODULE_NAME, e.getMessage());
-		}
-		return resultSet;
-	}
-
-	private static void executeDynamic( String[] fullCommand, CommandShellResultSet<List<String>, List<String>> resultSet, AtomicBoolean isRun) {
-		try {
-			Process process = Runtime.getRuntime().exec(fullCommand);
-
-			Runnable readVal = () -> {
-				readOutputDynamic(process, Process::getInputStream, resultSet.getValue(), isRun);
-			};
-			new Thread(readVal).start();
-
-			Runnable readErr = () -> {
-				readOutputDynamic(process, Process::getErrorStream, resultSet.getError(), isRun);
-			};
-			new Thread(readErr).start();
-
-		} catch (IOException e) {
-			LoggingService.logWarning(MODULE_NAME, e.getMessage());
-		}
-	}
-
-
-	public static <V, E> CommandShellResultSet<V, E> executeCommand(String command, Function<CommandShellResultSet<List<String>, List<String>>, CommandShellResultSet<V, E>> mapper) {
-		return executeCommand(command).map(mapper);
-	}
-
-	private static String[] computeCommand(String command) {
-		return new String[]{
-				SystemUtils.IS_OS_WINDOWS ? CMD_WIN : CMD,
-				"-c",
-				command
-		};
-	}
-
-	private static String[] computeScript(String script, String... args) {
-		String[] command = {
-				SystemUtils.IS_OS_WINDOWS ? CMD_WIN : CMD,
-				script
-		};
-
-		Stream<String> s1 = Arrays.stream(command);
-		Stream<String> s2 = Arrays.stream(args);
-		return Stream.concat(s1, s2).toArray(String[]::new);
-	}
-
-	private static List<String> readOutput(Process process, Function<Process, InputStream> streamExtractor) throws IOException {
-		List<String> result = new ArrayList<>();
-		String line;
-		try (BufferedReader stdInput = new BufferedReader(new
-				InputStreamReader(streamExtractor.apply(process), UTF_8))) {
-			while ((line = stdInput.readLine()) != null) {
-				result.add(line);
-			}
-		}
-		return result;
-	}
-
-	private static void readOutputDynamic(Process process, Function<Process,
-	                                      InputStream> streamExtractor, List<String> result,
-	                                      AtomicBoolean isRun) {
-		String line;
-		if (result == null) {
-			return;
-		}
-		try (BufferedReader stdInput = new BufferedReader(new
-				InputStreamReader(streamExtractor.apply(process)))) {
-
-			while (isRun != null && isRun.get()) {
-				line = stdInput.readLine();
-				if (line != null) {
-					result.add(line);
-				} else {
-					Thread.sleep(3000);
-				}
-			}
-		} catch (InterruptedException | IOException e) {
-			LoggingService.logWarning(MODULE_NAME, e.getMessage());
-		} finally {
-			process.destroy();
-		}
-	}
+    private static final String MODULE_NAME = "CommandShellExecutor";
+    private static final String CMD = "/bin/sh";
+    private static final String CMD_WIN = "powershell";
+
+
+    public static CommandShellResultSet<List<String>, List<String>> executeCommand(String command) {
+        String[] fullCommand = computeCommand(command);
+        return execute(fullCommand);
+    }
+
+    public static CommandShellResultSet<List<String>, List<String>> executeScript(String script, String... args) {
+        String[] fullCommand = computeScript(script, args);
+        return execute(fullCommand);
+    }
+
+    public static void executeDynamicCommand(String command,
+                                             CommandShellResultSet<List<String>, List<String>> resultSet,
+                                             AtomicBoolean isRun,
+                                             Runnable killOrphanedProcessesRunnable) {
+        String[] fullCommand = computeCommand(command);
+        executeDynamic(fullCommand, resultSet, isRun, killOrphanedProcessesRunnable);
+    }
+
+    private static CommandShellResultSet<List<String>, List<String>> execute(String[] fullCommand) {
+        CommandShellResultSet<List<String>, List<String>> resultSet = null;
+        try {
+            Process process = Runtime.getRuntime().exec(fullCommand);
+            List<String> value = readOutput(process, Process::getInputStream);
+            List<String> errors = readOutput(process, Process::getErrorStream);
+            resultSet = new CommandShellResultSet<>(value, errors);
+        } catch (IOException e) {
+            LoggingService.logWarning(MODULE_NAME, e.getMessage());
+        }
+        return resultSet;
+    }
+
+    private static void executeDynamic(String[] fullCommand,
+                                       CommandShellResultSet<List<String>, List<String>> resultSet,
+                                       AtomicBoolean isRun,
+                                       Runnable killOrphanedProcessesRunnable) {
+        try {
+            Process process = Runtime.getRuntime().exec(fullCommand);
+
+            Runnable readVal = () -> {
+                readOutputDynamic(process, Process::getInputStream, resultSet.getValue(), isRun, killOrphanedProcessesRunnable);
+            };
+            new Thread(readVal).start();
+
+            Runnable readErr = () -> {
+                readOutputDynamic(process, Process::getErrorStream, resultSet.getError(), isRun, killOrphanedProcessesRunnable);
+            };
+            new Thread(readErr).start();
+
+        } catch (IOException e) {
+            LoggingService.logWarning(MODULE_NAME, e.getMessage());
+        }
+    }
+
+
+    public static <V, E> CommandShellResultSet<V, E> executeCommand(String command, Function<CommandShellResultSet<List<String>, List<String>>, CommandShellResultSet<V, E>> mapper) {
+        return executeCommand(command).map(mapper);
+    }
+
+    private static String[] computeCommand(String command) {
+        return new String[]{
+            SystemUtils.IS_OS_WINDOWS ? CMD_WIN : CMD,
+            "-c",
+            command
+        };
+    }
+
+    private static String[] computeScript(String script, String... args) {
+        String[] command = {
+            SystemUtils.IS_OS_WINDOWS ? CMD_WIN : CMD,
+            script
+        };
+
+        Stream<String> s1 = Arrays.stream(command);
+        Stream<String> s2 = Arrays.stream(args);
+        return Stream.concat(s1, s2).toArray(String[]::new);
+    }
+
+    private static List<String> readOutput(Process process, Function<Process, InputStream> streamExtractor) throws IOException {
+        List<String> result = new ArrayList<>();
+        String line;
+        try (BufferedReader stdInput = new BufferedReader(new
+            InputStreamReader(streamExtractor.apply(process), UTF_8))) {
+            while ((line = stdInput.readLine()) != null) {
+                result.add(line);
+            }
+        }
+        return result;
+    }
+
+    private static void readOutputDynamic(Process process,
+                                          Function<Process, InputStream> streamExtractor,
+                                          List<String> result,
+                                          AtomicBoolean isRun,
+                                          Runnable killOrphanedProcessesRunnable) {
+        StringBuilder line = new StringBuilder();
+        if (result == null) {
+            return;
+        }
+        try (BufferedReader reader = new BufferedReader(new
+            InputStreamReader(streamExtractor.apply(process)))) {
+
+            while (isRun != null && isRun.get()) {
+                if (reader.ready()) {
+                    int c = reader.read();
+                    if (c == -1) {
+                        break;
+                    }
+                    if (System.lineSeparator().contains(Character.toString((char)c)) && line.length() != 0) {
+                        result.add(line.toString());
+                        line.setLength(0);
+                    } else {
+                        line.append((char)c);
+                    }
+                } else {
+                    Thread.sleep(3000);
+                }
+            }
+        } catch (InterruptedException | IOException e) {
+            LoggingService.logWarning(MODULE_NAME, e.getMessage());
+        } finally {
+            process.destroy();
+            if (killOrphanedProcessesRunnable != null) {
+                killOrphanedProcessesRunnable.run();
+            }
+        }
+    }
 }

daemon/src/org/eclipse/iofog/diagnostics/strace/StraceDiagnosticManger.java

@@ -15,9 +15,12 @@
 
 import org.eclipse.iofog.command_line.util.CommandShellExecutor;
 import org.eclipse.iofog.command_line.util.CommandShellResultSet;
+import org.eclipse.iofog.process_manager.DockerUtil;
 import org.eclipse.iofog.utils.logging.LoggingService;
 
-import javax.json.*;
+import javax.json.JsonArray;
+import javax.json.JsonObject;
+import javax.json.JsonValue;
 import java.util.List;
 import java.util.Optional;
 import java.util.concurrent.CopyOnWriteArrayList;
@@ -81,7 +84,7 @@ private Optional<MicroserviceStraceData> getStraceDataByMicroserviceUuid(String
 
 	public void enableMicroserviceStraceDiagnostics(String microserviceUuid) {
 		try {
-			int pid = getPidByMicroserviceUuid(microserviceUuid);
+			int pid = getPidByMicroserviceUuid(DockerUtil.getContainerName(microserviceUuid));
 			MicroserviceStraceData newMicroserviceStraceData = new MicroserviceStraceData(microserviceUuid, pid, true);
 			this.monitoringMicroservices.removeIf(
 				oldMicroserviceStraceData -> oldMicroserviceStraceData.getMicroserviceUuid().equals(microserviceUuid)
@@ -114,7 +117,21 @@ private int getPidByMicroserviceUuid(String microserviceUuid) throws IllegalArgu
 	private void runStrace(MicroserviceStraceData microserviceStraceData) {
 		String straceCommand = "strace -p " + microserviceStraceData.getPid();
 		CommandShellResultSet<List<String>, List<String>> resultSet = new CommandShellResultSet<>(null, microserviceStraceData.getResultBuffer());
-		CommandShellExecutor.executeDynamicCommand(straceCommand, resultSet, microserviceStraceData.getStraceRun());
+		CommandShellExecutor.executeDynamicCommand(
+			straceCommand,
+			resultSet,
+			microserviceStraceData.getStraceRun(),
+			killOrphanedStraceProcessesRunnable()
+		);
+	}
+
+	private Runnable killOrphanedStraceProcessesRunnable() {
+		return () -> {
+			CommandShellResultSet<List<String>, List<String>> resultSet = CommandShellExecutor.executeCommand("pgrep strace");
+			if (resultSet.getValue() != null) {
+				resultSet.getValue().forEach(value -> CommandShellExecutor.executeCommand(String.format("kill -9 %s", value)));
+			}
+		};
 	}
 
 }

daemon/src/org/eclipse/iofog/field_agent/VersionHandler.java

@@ -35,7 +35,7 @@ public class VersionHandler {
 	private static final String MODULE_NAME = "Version Handler";
 
 	private final static String PACKAGE_NAME = "iofog-agent";
-	private final static String BACKUPS_DIR = SystemUtils.IS_OS_WINDOWS ? SNAP_COMMON + "./var/backups/iofog-agent" : SNAP_COMMON + "/var/backups/iofog";
+	private final static String BACKUPS_DIR = SystemUtils.IS_OS_WINDOWS ? SNAP_COMMON + "./var/backups/iofog-agent" : SNAP_COMMON + "/var/backups/iofog-agent";
 	private final static String MAX_RESTARTING_TIMEOUT = "60";
 
 	private final static String GET_LINUX_DISTRIBUTION_NAME = "grep = /etc/os-release | awk -F\"[=]\" '{print $2}' | sed -n 1p";

daemon/src/org/eclipse/iofog/microservice/Microservice.java

@@ -21,6 +21,7 @@
  */
 public class Microservice {
 
+    public static final Object deleteLock = new Object();
     private final String microserviceUuid; //container name
     private final String imageName;
     private List<PortMapping> portMappings;
@@ -34,6 +35,7 @@ public class Microservice {
     private long logSize;
     private List<VolumeMapping> volumeMappings;
     private boolean isUpdating;
+
     private boolean delete;
     private boolean deleteWithCleanup;
 
@@ -123,11 +125,11 @@ public void setVolumeMappings(List<VolumeMapping> volumeMappings) {
         this.volumeMappings = volumeMappings;
     }
 
-	public boolean isUpdating() {
+	public synchronized boolean isUpdating() {
 		return isUpdating;
 	}
 
-	public void setUpdating(boolean updating) {
+	public synchronized void setUpdating(boolean updating) {
 		isUpdating = updating;
 	}