Example usage for java.io File canExecute

List of usage examples for java.io File canExecute

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Introduction

In this page you can find the example usage for java.io File canExecute.

Prototype

public boolean canExecute()

Source Link

Document

Tests whether the application can execute the file denoted by this abstract pathname.

Usage

From source file:eu.scape_project.tool.toolwrapper.toolwrapper_bash_debian_generator.DebianBashWrapperGenerator.java

private void verifyExecutionPermissionsOfFilesBeingInstalled(File file) {
    String absolutePath = file.getAbsolutePath();
    String relativePath = absolutePath
            .replaceFirst(new File(inputDir, Constants.BASHGENERATOR_INSTALL_OUTDIRNAME).getAbsolutePath(), "");
    if (file.isFile()) {

        // if the original has execution permission, then add the same
        // permission to the copied version
        if (file.canExecute()) {
            new File(tempDebianDir, relativePath).setExecutable(true);
        }//from  w  w  w.j a  v a2s  . c  om
    } else if (file.isDirectory()) {
        for (File f : file.listFiles()) {
            verifyExecutionPermissionsOfFilesBeingInstalled(f);
        }
    }
}

From source file:com.cws.esolutions.agent.processors.impl.ServiceCheckProcessorImpl.java

public ServiceCheckResponse runSystemCheck(final ServiceCheckRequest request) throws ServiceCheckException {
    final String methodName = IServiceCheckProcessor.CNAME
            + "#runSystemCheck(final ServiceCheckRequest request) throws ServiceCheckException";

    if (DEBUG) {/*from  ww  w.  j  a  v  a2s .  c  o m*/
        DEBUGGER.debug(methodName);
        DEBUGGER.debug("ServiceCheckRequest: {}", request);
    }

    int exitCode = -1;
    Socket socket = null;
    File sourceFile = null;
    CommandLine command = null;
    BufferedWriter writer = null;
    ExecuteStreamHandler streamHandler = null;
    ByteArrayOutputStream outputStream = null;
    ServiceCheckResponse response = new ServiceCheckResponse();

    final DefaultExecutor executor = new DefaultExecutor();
    final ExecuteWatchdog watchdog = new ExecuteWatchdog(CONNECT_TIMEOUT * 1000);
    final DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler();

    try {
        switch (request.getRequestType()) {
        case NETSTAT:
            sourceFile = scriptConfig.getScripts().get("netstat");

            if (DEBUG) {
                DEBUGGER.debug("sourceFile: {}", sourceFile);
            }

            if (!(sourceFile.canExecute())) {
                throw new ServiceCheckException(
                        "Script file either does not exist or cannot be executed. Cannot continue.");
            }

            command = CommandLine.parse(sourceFile.getAbsolutePath());

            if (request.getPortNumber() != 0) {
                command.addArgument(String.valueOf(request.getPortNumber()), true);
            }

            if (DEBUG) {
                DEBUGGER.debug("CommandLine: {}", command);
            }

            outputStream = new ByteArrayOutputStream();
            streamHandler = new PumpStreamHandler(outputStream);

            executor.setWatchdog(watchdog);
            executor.setStreamHandler(streamHandler);

            if (DEBUG) {
                DEBUGGER.debug("ExecuteStreamHandler: {}", streamHandler);
                DEBUGGER.debug("ExecuteWatchdog: {}", watchdog);
                DEBUGGER.debug("DefaultExecuteResultHandler: {}", resultHandler);
                DEBUGGER.debug("DefaultExecutor: {}", executor);
            }

            executor.execute(command, resultHandler);

            resultHandler.waitFor();
            exitCode = resultHandler.getExitValue();

            if (DEBUG) {
                DEBUGGER.debug("exitCode: {}", exitCode);
            }

            writer = new BufferedWriter(new FileWriter(LOGS_DIRECTORY + "/" + sourceFile.getName() + ".log"));
            writer.write(outputStream.toString());
            writer.flush();

            response.setResponseData(outputStream.toString());

            if (executor.isFailure(exitCode)) {
                response.setRequestStatus(AgentStatus.FAILURE);
            } else {
                response.setRequestStatus(AgentStatus.SUCCESS);
            }

            break;
        case REMOTEDATE:
            response.setRequestStatus(AgentStatus.SUCCESS);
            response.setResponseData(System.currentTimeMillis());

            break;
        case TELNET:
            response = new ServiceCheckResponse();

            int targetPort = request.getPortNumber();
            String targetServer = request.getTargetHost();

            if (DEBUG) {
                DEBUGGER.debug("Target port: {}", targetPort);
                DEBUGGER.debug("Target server: {}", targetServer);
            }

            if (targetPort == 0) {
                throw new ServiceCheckException("Target port number was not assigned. Cannot action request.");
            }

            final String CRLF = "\r\n";
            final String TERMINATE_TELNET = "^]";

            synchronized (new Object()) {
                InetSocketAddress socketAddress = new InetSocketAddress(targetServer, targetPort);

                socket = new Socket();
                socket.setSoTimeout(IServiceCheckProcessor.CONNECT_TIMEOUT);
                socket.setSoLinger(false, 0);
                socket.setKeepAlive(false);

                try {
                    socket.connect(socketAddress, IServiceCheckProcessor.CONNECT_TIMEOUT);

                    if (!(socket.isConnected())) {
                        throw new ConnectException("Failed to connect to host " + targetServer + " on port "
                                + request.getPortNumber());
                    }

                    PrintWriter pWriter = new PrintWriter(socket.getOutputStream(), true);
                    pWriter.println(TERMINATE_TELNET + CRLF);
                    pWriter.flush();
                    pWriter.close();

                    response.setRequestStatus(AgentStatus.SUCCESS);
                    response.setResponseData("Telnet connection to " + targetServer + " on port "
                            + request.getPortNumber() + " successful.");
                } catch (ConnectException cx) {
                    response.setRequestStatus(AgentStatus.FAILURE);
                    response.setResponseData("Telnet connection to " + targetServer + " on port "
                            + request.getPortNumber() + " failed with message: " + cx.getMessage());
                }
            }

            break;
        case PROCESSLIST:
            sourceFile = scriptConfig.getScripts().get("processList");

            if (DEBUG) {
                DEBUGGER.debug("sourceFile: {}", sourceFile);
            }

            if (!(sourceFile.canExecute())) {
                throw new ServiceCheckException(
                        "Script file either does not exist or cannot be executed. Cannot continue.");
            }

            command = CommandLine.parse(sourceFile.getAbsolutePath());

            if (request.getPortNumber() != 0) {
                command.addArgument(String.valueOf(request.getPortNumber()), true);
            }

            if (DEBUG) {
                DEBUGGER.debug("CommandLine: {}", command);
            }

            outputStream = new ByteArrayOutputStream();
            streamHandler = new PumpStreamHandler(outputStream);

            executor.setWatchdog(watchdog);
            executor.setStreamHandler(streamHandler);

            if (DEBUG) {
                DEBUGGER.debug("ExecuteStreamHandler: {}", streamHandler);
                DEBUGGER.debug("ExecuteWatchdog: {}", watchdog);
                DEBUGGER.debug("DefaultExecuteResultHandler: {}", resultHandler);
                DEBUGGER.debug("DefaultExecutor: {}", executor);
            }

            executor.execute(command, resultHandler);

            resultHandler.waitFor();
            exitCode = resultHandler.getExitValue();

            if (DEBUG) {
                DEBUGGER.debug("exitCode: {}", exitCode);
            }

            writer = new BufferedWriter(new FileWriter(LOGS_DIRECTORY + "/" + sourceFile.getName() + ".log"));
            writer.write(outputStream.toString());
            writer.flush();

            response.setResponseData(outputStream.toString());

            if (executor.isFailure(exitCode)) {
                response.setRequestStatus(AgentStatus.FAILURE);
            } else {
                response.setRequestStatus(AgentStatus.SUCCESS);
            }

            break;
        default:
            // unknown operation
            throw new ServiceCheckException("No valid operation was specified");
        }
    } catch (UnknownHostException uhx) {
        ERROR_RECORDER.error(uhx.getMessage(), uhx);

        throw new ServiceCheckException(uhx.getMessage(), uhx);
    } catch (SocketException sx) {
        ERROR_RECORDER.error(sx.getMessage(), sx);

        throw new ServiceCheckException(sx.getMessage(), sx);
    } catch (IOException iox) {
        ERROR_RECORDER.error(iox.getMessage(), iox);

        throw new ServiceCheckException(iox.getMessage(), iox);
    } catch (InterruptedException ix) {
        ERROR_RECORDER.error(ix.getMessage(), ix);

        throw new ServiceCheckException(ix.getMessage(), ix);
    } finally {
        try {
            if (writer != null) {
                writer.close();
            }

            if ((socket != null) && (!(socket.isClosed()))) {
                socket.close();
            }
        } catch (IOException iox) {
            ERROR_RECORDER.error(iox.getMessage(), iox);
        }
    }

    return response;
}

From source file:edu.ucsd.crbs.cws.cluster.submission.TestJobCmdScriptCreatorImpl.java

@Test
public void testCreateWithErrorEmailsSet() throws Exception {
    File tempDirectory = Folder.newFolder();
    File outputsDir = new File(tempDirectory + File.separator + Constants.OUTPUTS_DIR_NAME);
    assertTrue(outputsDir.mkdirs());/*  w w  w . j  a  v a 2  s.c o  m*/

    JobEmailNotificationData emailNotifyData = createJobEmailNotificationData();
    emailNotifyData.setErrorEmail("error@error.com");
    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript("kepler.sh");
    jb.setRegisterUpdateJar("register.jar");
    jb.setRetryCount(1);

    JobCmdScriptCreatorImpl scriptCreator = new JobCmdScriptCreatorImpl("/workflowsdir", jb, emailNotifyData);

    Job j = new Job();
    Workflow w = new Workflow();
    w.setId(new Long(5));
    j.setWorkflow(w);
    Parameter emailParam = new Parameter();
    emailParam.setName(Constants.CWS_NOTIFYEMAIL);
    emailParam.setValue("bob@bob.com");
    ArrayList<Parameter> params = new ArrayList<>();
    params.add(emailParam);
    j.setParameters(params);

    String jobCmd = scriptCreator.create(tempDirectory.getAbsolutePath(), j, new Long(10));

    assertTrue(jobCmd != null);
    assertTrue(
            jobCmd.equals(outputsDir.getAbsolutePath() + File.separator + JobCmdScriptCreatorImpl.JOB_CMD_SH));
    File checkCmdFile = new File(jobCmd);
    assertTrue(checkCmdFile.canExecute());

    List<String> lines = IOUtils.readLines(new FileReader(jobCmd));
    assertTrue(lines != null);
    boolean emailFound = false;
    boolean errorEmailFound = false;
    for (String line : lines) {
        if (line.startsWith("EMAIL_ADDR=")) {
            assertTrue(line.equals("EMAIL_ADDR=\"bob@bob.com\""));
            emailFound = true;
        }
        if (line.startsWith("ERROR_EMAIL_ADDR")) {
            assertTrue(line.equals("ERROR_EMAIL_ADDR=\"error@error.com\""));
            errorEmailFound = true;
        }
    }
    assertTrue(emailFound);
    assertTrue(errorEmailFound);
}

From source file:edu.ucsd.crbs.cws.cluster.submission.TestJobCmdScriptCreatorImpl.java

@Test
public void testCreateAndRunScriptWhereUpdateFailsOnceAndThenWorks() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//from w w  w  .  java2s. c o m
    File baseDirectory = Folder.newFolder();
    File tempDirectory = new File(baseDirectory + File.separator + "subdir");
    File outputsDir = new File(tempDirectory + File.separator + Constants.OUTPUTS_DIR_NAME);
    assertTrue(outputsDir.mkdirs());

    JobEmailNotificationData emailNotifyData = createJobEmailNotificationData();

    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript(getAndCheckForTrueBinaryFile().getAbsolutePath());
    jb.setRegisterUpdateJar("register.jar");
    jb.setMailCommand("cat > email.${finishedMessage};/bin/echo");
    jb.setJavaCommand("if [ $cntr -eq 0 ] ; then " + getAndCheckForFalseBinaryFile().getAbsolutePath()
            + "; else " + getAndCheckForTrueBinaryFile().getAbsolutePath() + "; fi #");
    jb.setRetryCount(3);

    JobCmdScriptCreatorImpl scriptCreator = new JobCmdScriptCreatorImpl("/workflowsdir", jb, emailNotifyData);

    Job j = new Job();
    Workflow w = new Workflow();
    w.setId(new Long(5));
    j.setWorkflow(w);

    String jobCmd = scriptCreator.create(tempDirectory.getAbsolutePath(), j, new Long(10));

    assertTrue(jobCmd != null);
    assertTrue(
            jobCmd.equals(outputsDir.getAbsolutePath() + File.separator + JobCmdScriptCreatorImpl.JOB_CMD_SH));
    File checkCmdFile = new File(jobCmd);
    assertTrue(checkCmdFile.canExecute());

    RunCommandLineProcessImpl rclpi = new RunCommandLineProcessImpl();
    rclpi.setWorkingDirectory(outputsDir.getAbsolutePath());

    String result = rclpi.runCommandLineProcess(jobCmd);
    assertTrue(result.contains("Update of workspace path try 1 of 3 failed.  Sleeping 0 seconds and retrying"));

    String logFile = tempDirectory.getAbsoluteFile() + File.separator + "job...log";
    File checkLogFile = new File(logFile);
    assertTrue(logFile + " and we ran " + jobCmd, checkLogFile.exists());
    List<String> lines = IOUtils.readLines(new FileReader(logFile));
    boolean exitFound = false;
    for (String line : lines) {
        if (line.startsWith("exitcode: ")) {
            assertTrue(line, line.equals("exitcode: 0"));
            exitFound = true;
        }
    }
    assertTrue(exitFound);
}

From source file:edu.ucsd.crbs.cws.cluster.submission.TestJobCmdScriptCreatorImpl.java

@Test
public void testCreateAndRunScriptWithFakeKeplerThatSimulatesUSR2Signal() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);/*from  w w  w.  j a v a 2 s . co  m*/
    File baseDirectory = Folder.newFolder();
    File tempDirectory = new File(baseDirectory + File.separator + "subdir");
    File outputsDir = new File(tempDirectory + File.separator + Constants.OUTPUTS_DIR_NAME);
    assertTrue(outputsDir.mkdirs());

    JobEmailNotificationData emailNotifyData = createJobEmailNotificationData();

    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript("kill -s USR2 $$;sleep 100");
    jb.setRegisterUpdateJar("register.jar");
    jb.setJavaCommand("/bin/echo");
    jb.setRetryCount(1);

    JobCmdScriptCreatorImpl scriptCreator = new JobCmdScriptCreatorImpl("/workflowsdir", jb, emailNotifyData);

    Job j = new Job();
    Workflow w = new Workflow();
    w.setId(new Long(5));
    j.setWorkflow(w);

    String jobCmd = scriptCreator.create(tempDirectory.getAbsolutePath(), j, new Long(10));

    assertTrue(jobCmd != null);
    assertTrue(
            jobCmd.equals(outputsDir.getAbsolutePath() + File.separator + JobCmdScriptCreatorImpl.JOB_CMD_SH));
    File checkCmdFile = new File(jobCmd);
    assertTrue(checkCmdFile.canExecute());

    RunCommandLineProcessImpl rclpi = new RunCommandLineProcessImpl();
    rclpi.setWorkingDirectory(outputsDir.getAbsolutePath());
    String result;
    try {
        result = rclpi.runCommandLineProcess(jobCmd);
    } catch (Exception ex) {
        assertTrue(ex.getMessage(), ex.getMessage().startsWith("Non zero exit code (100)"));
    }

    String logFile = tempDirectory.getAbsoluteFile() + File.separator + "job...log";
    File checkLogFile = new File(logFile);
    assertTrue(logFile + " and we ran " + jobCmd, checkLogFile.exists());
    List<String> lines = IOUtils.readLines(new FileReader(logFile));
    for (String line : lines) {
        if (line.startsWith("exitcode: ")) {
            assertTrue(line, line.equals("exitcode: 100"));
        }
    }

    checkWorkflowFailed(outputsDir.getAbsolutePath(), "Job killed by scheduler",
            "Job received USR2 signal which is the signal to exit");
}

From source file:edu.ucsd.crbs.cws.cluster.submission.TestJobCmdScriptCreatorImpl.java

@Test
public void testCreateAndRunScriptWithFakeKeplerThatFailsAndNoEmailsSet() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//from w ww .  j a  v a  2 s  .  c  o  m
    File baseDirectory = Folder.newFolder();
    File tempDirectory = new File(baseDirectory + File.separator + "subdir");
    File outputsDir = new File(tempDirectory + File.separator + Constants.OUTPUTS_DIR_NAME);
    assertTrue(outputsDir.mkdirs());

    JobEmailNotificationData emailNotifyData = createJobEmailNotificationData();

    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript(getAndCheckForFalseBinaryFile().getAbsolutePath());
    jb.setRegisterUpdateJar("register.jar");
    jb.setJavaCommand("/bin/echo");
    jb.setRetryCount(1);

    JobCmdScriptCreatorImpl scriptCreator = new JobCmdScriptCreatorImpl("/workflowsdir", jb, emailNotifyData);

    File checkForTrue = getAndCheckForTrueBinaryFile();

    scriptCreator.setJavaBinaryPath(checkForTrue.getAbsolutePath());

    Job j = new Job();
    Workflow w = new Workflow();
    w.setId(new Long(5));
    j.setWorkflow(w);

    String jobCmd = scriptCreator.create(tempDirectory.getAbsolutePath(), j, new Long(10));

    assertTrue(jobCmd != null);
    assertTrue(
            jobCmd.equals(outputsDir.getAbsolutePath() + File.separator + JobCmdScriptCreatorImpl.JOB_CMD_SH));
    File checkCmdFile = new File(jobCmd);
    assertTrue(checkCmdFile.canExecute());

    RunCommandLineProcessImpl rclpi = new RunCommandLineProcessImpl();
    rclpi.setWorkingDirectory(tempDirectory.getAbsolutePath());

    try {
        String result = rclpi.runCommandLineProcess(jobCmd);
    } catch (Exception ex) {
        assertTrue(ex.getMessage().startsWith("Non zero exit code (1)"));
    }

    String logFile = baseDirectory.getAbsoluteFile() + File.separator + "job...log";
    File checkLogFile = new File(logFile);
    assertTrue(logFile + " and we ran " + jobCmd, checkLogFile.exists());
    List<String> lines = IOUtils.readLines(new FileReader(logFile));
    for (String line : lines) {
        if (line.startsWith("exitcode: ")) {
            assertTrue(line, line.equals("exitcode: 1"));
        }
    }

}

From source file:edu.ucsd.crbs.cws.cluster.submission.TestJobCmdScriptCreatorImpl.java

@Test
public void testCreateWithJobWithNoArgs() throws Exception {
    File tempDirectory = Folder.newFolder();
    File outputsDir = new File(tempDirectory + File.separator + Constants.OUTPUTS_DIR_NAME);
    assertTrue(outputsDir.mkdirs());/*  w ww  .  ja v  a 2s .  c o m*/

    JobEmailNotificationData emailNotifyData = createJobEmailNotificationData();
    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript("kepler.sh");
    jb.setRegisterUpdateJar("register.jar");
    jb.setRetryCount(1);

    JobCmdScriptCreatorImpl scriptCreator = new JobCmdScriptCreatorImpl("/workflowsdir", jb, emailNotifyData);

    Job j = new Job();
    Workflow w = new Workflow();
    w.setId(new Long(5));
    j.setWorkflow(w);

    String jobCmd = scriptCreator.create(tempDirectory.getAbsolutePath(), j, new Long(10));

    assertTrue(jobCmd != null);
    assertTrue(
            jobCmd.equals(outputsDir.getAbsolutePath() + File.separator + JobCmdScriptCreatorImpl.JOB_CMD_SH));
    File checkCmdFile = new File(jobCmd);
    assertTrue(checkCmdFile.canExecute());

    List<String> lines = IOUtils.readLines(new FileReader(jobCmd));
    assertTrue(lines != null);
    boolean emailFound = false;
    boolean errorEmailFound = false;
    boolean javaFound = false;
    boolean keplerFound = false;
    for (String line : lines) {
        if (line.startsWith("kepler.sh")) {
            assertTrue(":" + line + ":", line.equals("kepler.sh  -runwf -redirectgui "
                    + outputsDir.getAbsolutePath() + " /workflowsdir/5/5.kar &"));
            keplerFound = true;
        }
        if (line.startsWith("EMAIL_ADDR=")) {
            assertTrue(line.equals("EMAIL_ADDR=\"\""));
            emailFound = true;
        }
        if (line.startsWith("ERROR_EMAIL_ADDR")) {
            assertTrue(line.equals("ERROR_EMAIL_ADDR=\"\""));
            errorEmailFound = true;
        }
        if (line.startsWith("  java")) {
            assertTrue(line,
                    line.equals("  java  -jar register.jar --updatepath \"10\" --path \""
                            + outputsDir.getAbsolutePath() + "\" --size `du " + outputsDir.getAbsolutePath()
                            + " -bs | sed \"s/\\W*\\/.*//\"` $workspaceStatusFlag >> "
                            + tempDirectory.getAbsolutePath() + "/updateworkspacefile.out 2>&1"));
            javaFound = true;
        }
    }
    assertTrue(emailFound);
    assertTrue(errorEmailFound);
    assertTrue(javaFound);
    assertTrue(keplerFound);
}

From source file:edu.ucsd.crbs.cws.cluster.submission.TestJobCmdScriptCreatorImpl.java

@Test
public void testCreateAndRunScriptWithFakeKeplerThatSucceedsWithNoEmailSet() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);/*ww  w . j  a va 2  s .c o m*/
    File baseDirectory = Folder.newFolder();
    File tempDirectory = new File(baseDirectory + File.separator + "subdir");
    File outputsDir = new File(tempDirectory + File.separator + Constants.OUTPUTS_DIR_NAME);
    assertTrue(outputsDir.mkdirs());

    JobEmailNotificationData emailNotifyData = createJobEmailNotificationData();

    File stderrFile = new File(outputsDir.getAbsolutePath() + File.separator + "stderr");
    assertTrue(stderrFile.createNewFile());

    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript(getAndCheckForTrueBinaryFile().getAbsolutePath());
    jb.setRegisterUpdateJar("register.jar");
    jb.setJavaCommand("/bin/echo");
    jb.setRetryCount(1);

    JobCmdScriptCreatorImpl scriptCreator = new JobCmdScriptCreatorImpl("/workflowsdir", jb, emailNotifyData);

    Job j = new Job();
    Workflow w = new Workflow();
    w.setId(new Long(5));
    j.setWorkflow(w);

    String jobCmd = scriptCreator.create(tempDirectory.getAbsolutePath(), j, new Long(2345));

    assertTrue(jobCmd != null);
    assertTrue(
            jobCmd.equals(outputsDir.getAbsolutePath() + File.separator + JobCmdScriptCreatorImpl.JOB_CMD_SH));
    File checkCmdFile = new File(jobCmd);
    assertTrue(checkCmdFile.canExecute());

    RunCommandLineProcessImpl rclpi = new RunCommandLineProcessImpl();
    rclpi.setWorkingDirectory(tempDirectory.getAbsolutePath());

    String result = rclpi.runCommandLineProcess(jobCmd);

    String logFile = baseDirectory.getAbsoluteFile() + File.separator + "job...log";
    File checkLogFile = new File(logFile);
    assertTrue(logFile + " and we ran " + jobCmd, checkLogFile.exists());
    List<String> lines = IOUtils.readLines(new FileReader(logFile));
    for (String line : lines) {
        if (line.startsWith("exitcode: ")) {
            assertTrue(line, line.equals("exitcode: 0"));
        }
    }

    String updateFile = tempDirectory.getAbsoluteFile() + File.separator + "updateworkspacefile.out";

    lines = IOUtils.readLines(new FileReader(updateFile));
    for (String line : lines) {
        if (line.startsWith("-jar")) {
            assertTrue(line, line.startsWith(
                    "-jar register.jar --updatepath 2345 --path " + outputsDir.getAbsolutePath() + " --size "));
            assertTrue(line, line.endsWith(" --workspacefilefailed false"));
        }
    }

}

From source file:edu.ucsd.crbs.cws.cluster.submission.TestJobCmdScriptCreatorImpl.java

@Test
public void testCreateAndRunScriptWithFakeKeplerThatGeneratesWorkflowFailedFile() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//from ww  w . j  a v  a  2  s.c  o m
    File baseDirectory = Folder.newFolder();
    File tempDirectory = new File(baseDirectory + File.separator + "subdir");
    File outputsDir = new File(tempDirectory + File.separator + Constants.OUTPUTS_DIR_NAME);
    assertTrue(outputsDir.mkdirs());

    JobEmailNotificationData emailNotifyData = createJobEmailNotificationData();

    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript(
            "/bin/echo -e \"simple.error.message=fake fail\\\\n" + "detailed.error.message=fake fail detailed"
                    + "\\\\n\" > " + outputsDir.getAbsolutePath() + File.separator + "WORKFLOW.FAILED.txt");
    jb.setRegisterUpdateJar("register.jar");
    jb.setJavaCommand("/bin/echo");
    jb.setRetryCount(1);

    JobCmdScriptCreatorImpl scriptCreator = new JobCmdScriptCreatorImpl("/workflowsdir", jb, emailNotifyData);

    Job j = new Job();
    Workflow w = new Workflow();
    w.setId(new Long(5));
    j.setWorkflow(w);

    String jobCmd = scriptCreator.create(tempDirectory.getAbsolutePath(), j, new Long(10));

    assertTrue(jobCmd != null);
    assertTrue(
            jobCmd.equals(outputsDir.getAbsolutePath() + File.separator + JobCmdScriptCreatorImpl.JOB_CMD_SH));
    File checkCmdFile = new File(jobCmd);
    assertTrue(checkCmdFile.canExecute());

    RunCommandLineProcessImpl rclpi = new RunCommandLineProcessImpl();
    rclpi.setWorkingDirectory(outputsDir.getAbsolutePath());
    String result;
    try {
        result = rclpi.runCommandLineProcess(jobCmd);
    } catch (Exception ex) {
        assertTrue(ex.getMessage().startsWith("Non zero exit code (101)"));
    }

    String logFile = tempDirectory.getAbsoluteFile() + File.separator + "job...log";
    File checkLogFile = new File(logFile);
    assertTrue(logFile + " and we ran " + jobCmd, checkLogFile.exists());
    List<String> lines = IOUtils.readLines(new FileReader(logFile));
    for (String line : lines) {
        if (line.startsWith("exitcode: ")) {
            assertTrue(line, line.equals("exitcode: 101"));
        }
    }

    String updateFile = tempDirectory.getAbsoluteFile() + File.separator + "updateworkspacefile.out";

    lines = IOUtils.readLines(new FileReader(updateFile));
    for (String line : lines) {
        if (line.startsWith("-jar")) {
            assertTrue(line, line.startsWith(
                    "-jar register.jar --updatepath 10 --path " + outputsDir.getAbsolutePath() + " --size "));
            assertTrue(line, line.endsWith(" --workspacefilefailed true"));
        }
    }
}

From source file:edu.ucsd.crbs.cws.cluster.submission.TestJobCmdScriptCreatorImpl.java

@Test
public void testCreateAndRunScriptWithKeplerThatHasSQLExceptionInStdOutFile() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//from w ww.  ja v  a2s. co  m
    File baseDirectory = Folder.newFolder();
    File tempDirectory = new File(baseDirectory + File.separator + "subdir");
    File outputsDir = new File(tempDirectory + File.separator + Constants.OUTPUTS_DIR_NAME);
    assertTrue(outputsDir.mkdirs());

    JobEmailNotificationData emailNotifyData = createJobEmailNotificationData();

    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript(getAndCheckForTrueBinaryFile().getAbsolutePath());
    jb.setRegisterUpdateJar("register.jar");
    jb.setJavaCommand("/bin/echo");
    jb.setRetryCount(1);

    JobCmdScriptCreatorImpl scriptCreator = new JobCmdScriptCreatorImpl("/workflowsdir", jb, emailNotifyData);

    Job j = new Job();
    Workflow w = new Workflow();
    w.setId(new Long(5));
    j.setWorkflow(w);

    FileWriter fw = new FileWriter(outputsDir.getAbsoluteFile() + File.separator + "stdout");
    fw.write("     [null]\n" + "     [null]     ... 4 more\n"
            + "     [null] Caused by: java.lang.Exception: Failed to call application initializer class \"org.kepler.gui.KeplerInitializer\".  Perhaps the configuration file \"file:/sharktopus/megashark/cws/bin/Kepler-20141020.103034/common/configs/ptolemy/configs/kepler/ConfigRedirectGUIWithCache.xml\" has a problem?\n"
            + "     [null] Caused by: java.sql.SQLException: Unable to start HSQL server for jdbc:hsqldb:hsql://localhost:26343/hsqldb;filepath=hsqldb:file:/home/churas/.kepler/cache-2.4/cachedata/hsqldb\n"
            + "     [null]     at ptolemy.actor.gui.ConfigurationApplication.readConfiguration(ConfigurationApplication.java:716)      at org.kepler.util.sql.HSQL._getConnection(HSQL.java:683)\n"
            + "     [null]\n");
    fw.flush();
    fw.close();

    String jobCmd = scriptCreator.create(tempDirectory.getAbsolutePath(), j, new Long(10));

    assertTrue(jobCmd != null);
    assertTrue(
            jobCmd.equals(outputsDir.getAbsolutePath() + File.separator + JobCmdScriptCreatorImpl.JOB_CMD_SH));
    File checkCmdFile = new File(jobCmd);
    assertTrue(checkCmdFile.canExecute());

    RunCommandLineProcessImpl rclpi = new RunCommandLineProcessImpl();
    rclpi.setWorkingDirectory(outputsDir.getAbsolutePath());
    String result;
    try {
        result = rclpi.runCommandLineProcess(jobCmd);
    } catch (Exception ex) {
        assertTrue(ex.getMessage(), ex.getMessage().startsWith("Non zero exit code (101)"));
    }

    String logFile = tempDirectory.getAbsoluteFile() + File.separator + "job...log";
    File checkLogFile = new File(logFile);
    assertTrue(logFile + " and we ran " + jobCmd, checkLogFile.exists());
    List<String> lines = IOUtils.readLines(new FileReader(logFile));
    boolean exitFound = false;
    for (String line : lines) {
        if (line.startsWith("exitcode: ")) {
            assertTrue(line, line.equals("exitcode: 101"));
            exitFound = true;
        }
    }
    assertTrue(exitFound);

    checkWorkflowFailed(outputsDir.getAbsolutePath(), "Error running Kepler due to internal database",
            "SQLException was found in stdout file");
}