Examples with GATInvocationException org.gridlab.gat.GATInvocationException used on opensource projects

Example 46 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class LsfFileAdaptor method listFiles.

/*
     * (non-Javadoc)
     * 
     * @see org.gridlab.gat.io.File#listFiles()
     */
public org.gridlab.gat.io.File[] listFiles() throws GATInvocationException {
    if (!isDirectory()) {
        throw new GATInvocationException("this is not a directory: " + location);
    }
    File[] r = f.listFiles();
    if (r == null) {
        throw new GATInvocationException("IO error in LSF file adaptor");
    }
    ArrayList<File> l = new ArrayList<File>();
    for (int i = 0; i < r.length; i++) {
        if (!(ignoreHiddenFiles && r[i].isHidden())) {
            l.add(r[i]);
        }
    }
    org.gridlab.gat.io.File[] res = new org.gridlab.gat.io.File[l.size()];
    for (int i = 0; i < res.length; i++) {
        try {
            res[i] = GAT.createFile(gatContext, localToURI(l.get(i).getPath()));
        } catch (Exception e) {
            throw new GATInvocationException("LsfFile", e);
        }
    }
    return res;
}

Example 47 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class LsfFileAdaptor method copy.

/**
 * This method copies the physical file represented by this File instance to
 * a physical file identified by the passed URI.
 *
 * @param destination
 *                The new location
 */
public void copy(URI destination) throws GATInvocationException {
    destination = newcorrectURI(destination);
    String path = getPath();
    String destPath = destination.getPath();
    if (logger.isInfoEnabled()) {
        logger.info("copy of " + path + " to " + destPath);
    }
    if (destPath.equals(path)) {
        if (logger.isInfoEnabled()) {
            logger.info("copy, source is the same file as dest.");
        }
        return;
    }
    File destFile = getFile(destination);
    if (!exists()) {
        throw new GATInvocationException("the source file does not exist, path = " + path);
    }
    if (isDirectory()) {
        if (logger.isDebugEnabled()) {
            logger.debug("copy, it is a dir");
        }
        copyDir(f, destFile);
        return;
    }
    if (logger.isDebugEnabled()) {
        logger.debug("copy, it is a file");
    }
    if (gatContext.getPreferences().containsKey("file.create")) {
        if (((String) gatContext.getPreferences().get("file.create")).equalsIgnoreCase("true")) {
            File destinationParentFile = destFile.getParentFile();
            if (destinationParentFile != null) {
                boolean result = destinationParentFile.mkdirs();
                if (logger.isDebugEnabled()) {
                    logger.debug("new dirs created: " + result);
                }
            }
        }
    }
    // if the destination URI is a dir, append the file name.
    if (destFile.isDirectory()) {
        destPath = destPath + File.separator + getName();
        destFile = new File(destPath);
    }
    try {
        destFile.createNewFile();
    } catch (IOException e) {
        throw new GATInvocationException("Creating file failed", e);
    }
    copy(f, destFile);
}

Example 48 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class SshLSFJob method kill.

protected void kill(String jobID) {
    try {
        // Create qdel job
        SoftwareDescription sd = new SoftwareDescription();
        sd.setExecutable("bkill");
        sd.setArguments(jobID);
        sd.addAttribute(SoftwareDescription.SANDBOX_USEROOT, "true");
        sd.addAttribute(SoftwareDescription.SANDBOX_ROOT, sandbox.getSandboxPath());
        sd.addAttribute(SoftwareDescription.STOP_ON_EXIT, "false");
        JobDescription jd = new JobDescription(sd);
        Job job = jobHelper.submitJob(jd, this, "job.status");
        synchronized (job) {
            while (job.getState() != Job.JobState.STOPPED && job.getState() != Job.JobState.SUBMISSION_ERROR) {
                try {
                    job.wait();
                } catch (InterruptedException e) {
                // ignore
                }
            }
        }
        if (job.getState() != Job.JobState.STOPPED || job.getExitStatus() != 0) {
            throw new GATInvocationException("Could not submit scancel job");
        }
    } catch (Throwable e) {
        logger.info("Failed to stop sshSlurm job: " + jobID, e);
    }
}

Example 49 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class AdvertServiceAdaptorTest method exportTest.

private AdaptorTestResultEntry exportTest(AdvertService advert, String exportLocation) {
    long start = System.currentTimeMillis();
    try {
        advert.exportDataBase(new URI(exportLocation));
    } catch (GATInvocationException e) {
        return new AdaptorTestResultEntry(false, 0, e);
    } catch (URISyntaxException e) {
        return new AdaptorTestResultEntry(false, 0, e);
    }
    long stop = System.currentTimeMillis();
    return new AdaptorTestResultEntry(true, (stop - start), null);
}

Example 50 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class AllFileInputStreamAdaptorsTest method printResults.

private static void printResults(AdaptorTestResult[] results, String host) throws IOException {
    File outFile = new File("FileInputStream-results-" + host + ".html");
    if (!outFile.exists()) {
        outFile.createNewFile();
    }
    FileOutputStream out = new FileOutputStream(outFile);
    out.write("<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.01//EN\">\n".getBytes());
    out.write("<html>\n".getBytes());
    out.write("<head>\n".getBytes());
    out.write("<title>JavaGAT test results: File</title>\n".getBytes());
    out.write(("<script>\n" + "function showhide(id){\n" + "\tif (document.getElementById){\n" + "\t\tobj = document.getElementById(id);\n" + "\t\tif (obj.style.display == \"none\"){\n" + "\t\t\tobj.style.display = \"\";\n" + "\t\t} else {\n" + "\t\t\tobj.style.display = \"none\";\n" + "\t\t}\n" + "\t}\n" + "}\n" + "</script>\n").getBytes());
    out.write("</head>\n".getBytes());
    out.write("<body>\n".getBytes());
    out.write("<table frame=box cellpadding=5 cellspacing=0>\n".getBytes());
    out.write("<tr>\n".getBytes());
    out.write("<td></td>\n".getBytes());
    for (AdaptorTestResult result : results) {
        out.write(("<td align=right>" + result.getAdaptor() + "</td>\n").getBytes());
    }
    out.write("</tr>\n".getBytes());
    boolean background = true;
    String[] keys = results[0].getTestResultEntries().keySet().toArray(new String[results[0].getTestResultEntries().size()]);
    Arrays.sort(keys);
    for (String key : keys) {
        if (background) {
            out.write("<tr bgcolor=#DDDDDD>\n".getBytes());
        } else {
            out.write("<tr bgcolor=#FFFFFF>\n".getBytes());
        }
        background = !background;
        out.write(("<td>" + key + "</td>\n").getBytes());
        for (AdaptorTestResult result : results) {
            AdaptorTestResultEntry entry = result.getTestResultEntries().get(key);
            if (entry == null) {
                out.write("<td align=right>not present</td>\n".getBytes());
                continue;
            }
            if (entry.getException() == null && !entry.getResult()) {
                out.write("<td align=right bgcolor=#FFDDDD>".getBytes());
            } else {
                out.write("<td align=right>".getBytes());
            }
            if (entry.getException() == null) {
                out.write((entry.getTime() + " ms").getBytes());
            } else {
                if (entry.getException() instanceof GATInvocationException && ((GATInvocationException) entry.getException()).getExceptions().length > 0 && ((GATInvocationException) entry.getException()).getExceptions()[0] instanceof UnsupportedOperationException) {
                    out.write("n.i.".getBytes());
                } else if (entry.getException() instanceof GATObjectCreationException && ((GATObjectCreationException) entry.getException()).getExceptions().length > 0 && ((GATObjectCreationException) entry.getException()).getExceptions()[0] instanceof GATObjectCreationException && ((GATObjectCreationException) ((GATObjectCreationException) entry.getException()).getExceptions()[0]).getExceptions().length > 0 && ((GATObjectCreationException) ((GATObjectCreationException) entry.getException()).getExceptions()[0]).getExceptions()[0] instanceof AdaptorNotApplicableException) {
                    out.write("n.a.".getBytes());
                } else {
                    out.write(("<div style=\"display: none;\" id=\"" + result.getAdaptor() + key + "\">\n").getBytes());
                    out.write((entry.getException().toString().replace("\n", "<br/>\n") + "\n").getBytes());
                    StringWriter s = new StringWriter();
                    PrintWriter p = new PrintWriter(s);
                    entry.getException().printStackTrace(p);
                    out.write((s.toString().replace("\n", "<br/>\n") + "\n").getBytes());
                    out.write("</div>\n".getBytes());
                    out.write(("<a href=\"#\" onclick=\"showhide('" + result.getAdaptor() + key + "'); return(false);\">show/hide</a>\n").getBytes());
                }
            }
            out.write("</td>\n".getBytes());
        }
        out.write("</tr>\n".getBytes());
    }
    out.write("<tr>\n".getBytes());
    out.write("<td>total</td>\n".getBytes());
    for (AdaptorTestResult result : results) {
        out.write(("<td align=right>" + result.getTotalRunTime() + " ms</td>\n").getBytes());
    }
    out.write("</tr>\n".getBytes());
    out.write("<tr>\n".getBytes());
    out.write("<td>average</td>\n".getBytes());
    for (AdaptorTestResult result : results) {
        out.write(("<td align=right>" + result.getAverageRunTime() + " ms</td>\n").getBytes());
    }
    out.write("</tr>\n".getBytes());
    out.write("</table>\n".getBytes());
    out.write("</body>\n".getBytes());
    out.write("</html>\n".getBytes());
}