Example usage for org.apache.commons.io IOUtils readLines

List of usage examples for org.apache.commons.io IOUtils readLines

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Introduction

In this page you can find the example usage for org.apache.commons.io IOUtils readLines.

Prototype

public static List readLines(Reader input) throws IOException

Source Link

Document

Get the contents of a Reader as a list of Strings, one entry per line.

Usage

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

@Test
public void testCreateAndRunScriptWithFakeFailingKeplerWithOnlyErrorEmailIsSet() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//  w ww. jav  a  2 s  .  c om
    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());

    FileWriter fw = new FileWriter(outputsDir.getAbsoluteFile() + File.separator + "WORKFLOW.FAILED.txt.tmp");
    fw.write("simple.error.message=simple\n");
    fw.write("detailed.error.message=detailed\n");
    fw.flush();
    fw.close();

    JobEmailNotificationData emailNotifyData = createJobEmailNotificationData();
    emailNotifyData.setErrorEmail("error@error.com");
    File stderrFile = new File(outputsDir.getAbsolutePath() + File.separator + "stderr");
    assertTrue(stderrFile.createNewFile());

    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript("/bin/mv WORKFLOW.FAILED.txt.tmp WORKFLOW.FAILED.txt;#");
    jb.setRegisterUpdateJar("register.jar");
    jb.setJavaCommand("/bin/echo");
    jb.setEchoCommand("/bin/echo");
    jb.setMailCommand("cat >> email.${finishedMessage};/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));
    w.setName("worky");

    j.setWorkflow(w);
    j.setId(2345L);
    j.setName("myjoby");
    j.setOwner("bob");

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

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

    String result;
    try {
        result = rclpi.runCommandLineProcess(jobCmd);
        fail("Expected exception");
    } catch (Exception ex) {
        assertTrue(ex.getMessage().startsWith("Non zero exit code (101)"));
    }

    File emailStartFile = new File(outputsDir.getAbsolutePath() + File.separator + "email.");
    assertTrue(!emailStartFile.exists());

    File emailFailedFile = new File(outputsDir.getAbsolutePath() + File.separator + "email.failed");
    List<String> lines = IOUtils.readLines(new FileReader(emailFailedFile));
    for (String line : lines) {
        if (line.startsWith("Dear")) {
            assertTrue(line.contains("Dear bob,"));
        }
    }
}

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

@Test
public void testCreateAndRunScriptWithFakeKeplerThatSucceedsWithPreExistingWorkflowFailedFile()
        throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//  www .  j a va2 s.  com
    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 + "WORKFLOW.FAILED.txt");
    fw.write("simple.error.message=simple\n");
    fw.write("detailed.error.message=detailed\n");
    fw.flush();
    fw.close();

    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);

    List<String> yos = IOUtils.readLines(new FileReader(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);//  ww 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(
            "/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 testCreateAndRunScriptWithFakeKeplerThatSimulatesUSR2Signal() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//from   w w w .j ava 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:com.jaspersoft.studio.statistics.UsageManager.java

/**
 * Check on the server if there is a newer version of Jaspersoft Studio
 * /*from w w w  . j  av  a  2s . com*/
 * @return a not null VersionCheckResult that contains information on the new version and if there is a new version
 */
public VersionCheckResult checkVersion() {
    String uuid = getAppDataFolder().getName();
    String versionKnownByTheStats = getInstallationInfoContainer().getProperty(VERSION_INFO);
    int newInstallation = 0;
    // Read if there is an UUID in the preferences used to track the older versions
    PropertiesHelper ph = PropertiesHelper.getInstance();
    String backward_uuid = ph.getString(BACKWARD_UUID_PROPERTY, null);
    if (backward_uuid == null) {
        // If the backward value is null then i'm already using the new system, check if it
        // is a new installation or an update
        if (versionKnownByTheStats == null) {
            // Since the last version was not yet initialized it is a new installation
            newInstallation = 1;
        } else if (!versionKnownByTheStats.equals(getVersion())) {
            // There is a version stored in the file, that is the last version known by the server, if it is
            // different from the real version then there were an update
            newInstallation = 2;
        }
    } else {
        // If the backward value is != null then it isn't for sure a new installation, maybe there were
        // but since i'm inside the new code then it should be an update.
        newInstallation = 2;
        setInstallationInfo(VERSION_INFO, getVersion());
    }

    StringBuilder urlBuilder = new StringBuilder();
    urlBuilder.append(HEARTBEAT_SERVER_URL);
    urlBuilder.append("?version=");//$NON-NLS-1$
    urlBuilder.append(getVersion());
    urlBuilder.append("&uuid=");//$NON-NLS-1$
    urlBuilder.append(uuid);
    urlBuilder.append("&new=");//$NON-NLS-1$
    urlBuilder.append(newInstallation);
    urlBuilder.append("&isRCP=");//$NON-NLS-1$
    urlBuilder.append(String.valueOf(isRCP()));

    String urlstr = urlBuilder.toString();
    System.out.println("Invoking URL: " + urlstr); //$NON-NLS-1$ 
    VersionCheckResult result = new VersionCheckResult();
    try {
        Executor exec = Executor.newInstance();
        URI fullURI = new URI(urlstr);
        HttpUtils.setupProxy(exec, fullURI);
        HttpHost proxy = HttpUtils.getUnauthProxy(exec, fullURI);
        Request req = Request.Get(urlstr);
        if (proxy != null)
            req.viaProxy(proxy);
        String response = exec.execute(req).returnContent().asString();

        String serverVersion = null;
        String optmsg = ""; //$NON-NLS-1$ 
        for (String inputLine : IOUtils.readLines(new StringReader(response))) {
            if (serverVersion == null) {
                serverVersion = inputLine.trim();
            } else {
                optmsg += inputLine;
            }
        }
        // Update the installation info only if the informations was given correctly to the server
        setInstallationInfo(VERSION_INFO, getVersion());
        // Remove the old backward compatibility value if present to switch to the new system
        if (backward_uuid != null) {
            ph.removeString(BACKWARD_UUID_PROPERTY, InstanceScope.SCOPE);
        }
        result = new VersionCheckResult(serverVersion, optmsg, getVersion());
    } catch (Exception ex) {
        ex.printStackTrace();
        JaspersoftStudioPlugin.getInstance().logError(Messages.UsageManager_errorUpdateCheck, ex);
    }
    return result;
}

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

@Test
public void testCreateAndRunScriptWithFakeKeplerThatSimulatesUSR2SignalButAlreadyHasWorkFlowFailedFile()
        throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//from w  ww  .j  a  va 2s  .  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("mv " + outputsDir.getAbsoluteFile() + File.separator + "WORKFLOW.FAILED.txt2 "
            + outputsDir.getAbsoluteFile() + File.separator + "WORKFLOW.FAILED.txt; 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);

    FileWriter fw = new FileWriter(outputsDir.getAbsoluteFile() + File.separator + "WORKFLOW.FAILED.txt2");
    fw.write("simple.error.message=simple\n");
    fw.write("detailed.error.message=detailed\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 (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"));
        }
    }

    File failedFile = checkWorkflowFailed(outputsDir.getAbsolutePath(), "simple", "detailed");

    lines = IOUtils.readLines(new FileReader(failedFile));
    boolean jobFound = false;
    for (String line : lines) {
        if (line.startsWith(" Job received")) {
            assertTrue(line,
                    line.equals(" Job received USR2 signal which in SGE meant it is about to be killed"));
            jobFound = true;
        }
    }
    assertTrue(jobFound);
}

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

@Test
public void testCreateAndRunScriptWithKeplerThatHasExceptionInStdErrFile() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//from  w  ww  .  ja  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(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 + "stderr");
    fw.write("Exception in thread \"main\" Java returned: 1\n"
            + "   at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:106)\n"
            + "   at org.kepler.build.runner.Kepler.main(Kepler.java:109)\n" + "Caused by: Java returned: 1\n"
            + "   at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:106)\n"
            + "   at org.kepler.build.runner.Kepler.run(Kepler.java:266)\n"
            + "   at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102)\n" + "   ... 1 more\n"
            + "Caused by: Java returned: 1\n"
            + "   at org.apache.tools.ant.taskdefs.Java.execute(Java.java:111)\n"
            + "   at org.kepler.build.Run.runSuite(Run.java:379)\n"
            + "   at org.kepler.build.Run.run(Run.java:240)\n"
            + "   at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102)\n" + "   ... 3 more");
    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));
    for (String line : lines) {
        if (line.startsWith("exitcode: ")) {
            assertTrue(line, line.equals("exitcode: 101"));
        }
    }

    checkWorkflowFailed(outputsDir.getAbsolutePath(), "Error running Kepler",
            "Found Exception in thread main Java returned: 1 in the stderr file for Kepler");
}

From source file:com.logiware.accounting.domain.EdiInvoice.java

private void createMaerskLineInvoice(File file) throws Exception {
    InputStream inputStream = null;
    try {/* www . j  a va 2 s.co  m*/
        TradingPartnerDAO tradingPartnerDAO = new TradingPartnerDAO();
        vendorNumber = "MAEINC0001";
        vendorName = tradingPartnerDAO.getAccountName(this.vendorNumber);
        status = ConstantsInterface.STATUS_EDI_OPEN;
        company = Company.MAERSK_LINE;
        CompanyModel companyModel = new SystemRulesDAO().getCompanyDetails();
        this.billToParty = companyModel.getName() + "\n" + companyModel.getAddress();
        inputStream = new FileInputStream(file);
        List<String> lines = IOUtils.readLines(inputStream);
        ediInvoiceContainers = new ArrayList<EdiInvoiceContainer>();
        ediInvoiceDetails = new ArrayList<EdiInvoiceDetail>();
        for (String line : lines) {
            if (CommonUtils.isStartsWith(line, "B3")) {
                String[] values = line.split("\\*");
                invoiceNumber = values[2]; //Invoice Number
                searchInvoiceNumber = invoiceNumber.replaceAll("[^\\p{Alpha}\\p{Digit}]+", "");
                etd = DateUtils.parseDate(values[6], "yyyyMMdd"); //ETD
                invoiceAmount = (Double.parseDouble(values[7].replaceAll("[^0-9.]", "")) / 100); //Invoice Amount
                eta = DateUtils.parseDate(values[9], "yyyyMMdd"); //ETA
                invoiceDate = DateUtils.parseDate(values[12], "yyyyMMdd"); //Invoice Date
                Vendor vendor = tradingPartnerDAO.getVendor(vendorNumber);
                Integer termValue = 0;
                String termDesc = "Due Upon Receipt";
                if (null != vendor && null != vendor.getCterms()) {
                    termValue = Integer.parseInt(vendor.getCterms().getCode());
                    termDesc = vendor.getCterms().getCodedesc();
                }
                dueDate = DateUtils.addDays(invoiceDate, termValue);
                paymentTerms = termDesc;
            } else if (CommonUtils.isStartsWith(line, "N9")) {
                String[] values = line.split("\\*");
                if (StringUtils.equalsIgnoreCase(values[1], "BN")) {
                    bookingNumber = values[2]; //Booking Number
                } else if (StringUtils.equalsIgnoreCase(values[1], "MB")) {
                    masterBl = values[2]; //Master BL
                } else if (StringUtils.equalsIgnoreCase(values[1], "SI")) {
                    yourReference1 = values[2]; // Your Reference
                }
            } else if (CommonUtils.isStartsWith(line, "V1")) {
                String[] values = line.split("\\*");
                vesselName = values[2]; //Vessel Name
                voyageNumber = values[4]; //Voyage Number
            } else if (CommonUtils.isStartsWith(line, "L11")) {
                String[] values = line.split("\\*");
                if (StringUtils.equalsIgnoreCase(values[2], "BM")) {
                    blNumber = values[1]; //Bl Number
                }
            } else if (CommonUtils.isStartsWith(line, "C3")) {
                String[] values = line.split("\\*");
                currency = values[1]; //Currency
            } else if (CommonUtils.isStartsWith(line, "R4")) {
                String[] values = line.split("\\*");
                if (StringUtils.equalsIgnoreCase(values[1], "D")) {
                    portOfDischarge = values[4]; //Port of Discharge
                } else if (StringUtils.equalsIgnoreCase(values[1], "E")) {
                    placeOfDelivery = values[4]; //Place of Delivery
                } else if (StringUtils.equalsIgnoreCase(values[1], "L")) {
                    portOfLoading = values[4]; //Port of Loading
                } else if (StringUtils.equalsIgnoreCase(values[1], "R")) {
                    placeOfReceipt = values[4]; //Place of Receipt
                }
            } else if (CommonUtils.isStartsWith(line, "L1")) {
                String[] values = line.split("\\*");
                EdiInvoiceDetail ediInvoiceDetail = new EdiInvoiceDetail();
                ediInvoiceDetail.setEdiInvoice(this);
                ediInvoiceDetail.setCurrency(currency);
                ediInvoiceDetail.setDescription(values[12]); //Description of Charges
                ediInvoiceDetail.setQuantity(values[17]); //Qty
                ediInvoiceDetail.setUom(values[8]); //UoM
                ediInvoiceDetail.setPrice(values[2]); //Unit Price
                ediInvoiceDetails.add(ediInvoiceDetail);
            } else if (CommonUtils.isStartsWith(line, "N7")) {
                String[] values = line.split("\\*");
                ediInvoiceContainers
                        .add(new EdiInvoiceContainer(values[1] + "-" + values[2] + "-" + values[3], this)); //Container No
            }
        }
    } catch (Exception e) {
        log.info("createMaerskLineInvoice failed on " + new Date(), e);
    } finally {
        if (null != inputStream) {
            inputStream.close();
        }
    }
}

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

@Test
public void testCreateAndRunScriptWithKeplerThatHasSQLExceptionInStdOutFile() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);// w  w w .  j  a v a2  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(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");
}

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

@Test
public void testCreateAndRunScriptWhereUpdateFailsWithThreeRetries() throws Exception {
    assumeTrue(SystemUtils.IS_OS_UNIX);//from  w w w  .  ja  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();
    emailNotifyData.setErrorEmail("error@error.com > emailargs");
    JobBinaries jb = new JobBinaries();
    jb.setKeplerScript(getAndCheckForTrueBinaryFile().getAbsolutePath());
    jb.setRegisterUpdateJar("register.jar");
    jb.setMailCommand("cat > email.${finishedMessage};/bin/echo");
    jb.setJavaCommand(getAndCheckForFalseBinaryFile().getAbsolutePath());
    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;
    try {
        result = rclpi.runCommandLineProcess(jobCmd);
    } catch (Exception ex) {
        assertTrue(ex.getMessage(), ex.getMessage().startsWith("Non zero exit code (102)"));
    }

    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: 102"));
        }
    }

    lines = IOUtils
            .readLines(new FileReader(outputsDir.getAbsoluteFile() + File.separator + "WORKFLOW.FAILED.txt"));
    for (String line : lines) {
        if (line.startsWith("simple.error.message")) {
            assertTrue(line, line.equals("simple.error.message=Unable to update WorkspaceFile"));
        }
        if (line.startsWith("detailed.error.message")) {
            assertTrue(line, line.equals(
                    "detailed.error.message=Received non zero exit code (1) when trying to update WorkspaceFile"));
        }
    }

    File emailFailedFile = new File(outputsDir.getAbsolutePath() + File.separator + "email.failed");

    assertTrue(emailFailedFile.exists());

    lines = IOUtils.readLines(new FileReader(emailFailedFile));
    boolean yourFound = false;
    boolean unableFound = false;
    for (String line : lines) {
        if (line.startsWith("Your Unknown job: ")) {
            assertTrue(line.contains(" has failed"));
            yourFound = true;
        }
        if (line.contains("WORKFLOW.FAILED.txt:")) {
            assertTrue(line.contains("Unable to update WorkspaceFile"));
            unableFound = true;
        }
    }
    assertTrue(yourFound);
    assertTrue(unableFound);

}