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

Example 11 with URI

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

the class FileExample method main.

/**
 * This example shows the use of Files in JavaGAT.
 *
 * This example requires three valid URIs as arguments. At the first URI
 * there should exist a file. This file will be copied to the second URI,
 * then deleted at it's origin, and afterwards moved from the second to the
 * third URI. It's just an example of the File object, there are much more
 * possibilities using the File object.
 *
 * @param args
 *                a String array of size 3 with each element containing a
 *                String representation of a valid URI.
 */
public static void main(String[] args) {
    if (args.length != 3) {
        System.out.println("\tUsage: bin/run_gat_app examples20.FileExample <location1> <location2> <location3> (where location is a valid JavaGAT URI)\n\n" + "\tprogram does:\n" + "\t\tcp <location1> <location2>\n" + "\t\trm <location1>\n" + "\t\tmv <location2> <location3>\n");
        System.exit(1);
    }
    try {
        new FileExample().start(new URI(args[0]), new URI(args[1]), new URI(args[2]));
    } catch (URISyntaxException e) {
        System.out.println(e);
        System.out.println("\tUsage: bin/run_gat_app examples20.FileExample <location1> <location2> <location3> (where location is a valid JavaGAT URI)\n\n" + "\tprogram does:\n" + "\t\tcp <location1> <location2>\n" + "\t\trm <location1>\n" + "\t\tmv <location2> <location3>\n");
        System.exit(1);
    }
    GAT.end();
}

Example 12 with URI

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

the class SshLsfResourceBrokerAdaptor method sshLsfSubmission.

/*private java.io.File createJobScript(JobDescription description)
			throws GATInvocationException {

		java.io.File temp;

		SoftwareDescription sd = description.getSoftwareDescription();

		try {
			temp = java.io.File.createTempFile("lsf-sub", null);
		} catch (IOException e) {
			throw new GATInvocationException("Cannot create file", e);
		}
		PrintWriter job = null;
		try {
			job = new PrintWriter(new BufferedWriter(new FileWriter(temp)));

			job.print("#!/bin/sh\n");
			job.print("# job script\n");

			// Support DIRECTORY
			String dir = sd.getStringAttribute(SoftwareDescription.DIRECTORY, null);
			if (dir != null) {
				job.print("cd " + dir + "\n");
			}

			// Support environment.
			Map<String, Object> env = sd.getEnvironment();
			if (env != null) {
				Set<String> s = env.keySet();
				Object[] keys = s.toArray();

				for (int i = 0; i < keys.length; i++) {
					String val = (String) env.get(keys[i]);
					job.print(keys[i] + "=" + val + " && export " + keys[i] + "\n");
				}
			}

			// Construct command.
			StringBuffer cmd = new StringBuffer();

			cmd.append(sd.getExecutable().toString());
			if (sd.getArguments() != null) {
				String[] args = sd.getArguments();
				for (int i = 0; i < args.length; ++i) {
					cmd.append(" ");
					cmd.append(args[i]);
				}
			}
			job.print(cmd.toString() + "\n");
			//job.print("exit $?\n");
		} catch (Throwable e) {
			throw new GATInvocationException(
					"Cannot create temporary job script file "
							+ temp.getAbsolutePath(), e);
		} finally {
			if (job != null)
				job.close();
		}
		return temp;
	}*/
private String sshLsfSubmission(SshLSFJob lsfJob, JobDescription description, java.io.File bsubFile, ResourceBroker subBroker, Sandbox sandbox) throws GATInvocationException {
    java.io.File slurmResultFile = null;
    try {
        if (logger.isDebugEnabled()) {
            logger.debug("***** Doing sandbox prestage " + sandbox.getSandboxPath());
        }
        sandbox.prestage();
        if (logger.isDebugEnabled()) {
            logger.debug("***** Sandbox prestage done " + sandbox.getSandboxPath());
        }
        // Create sbatch job
        SoftwareDescription sd = new SoftwareDescription();
        sd.setExecutable("sh");
        sd.setArguments("-c", "bsub < " + bsubFile.getName() + " 2>submit.err");
        // + " && rm -rf " + bsubFile.getName() + " submit.err");
        sd.setAttributes(description.getSoftwareDescription().getAttributes());
        sd.addAttribute(SoftwareDescription.SANDBOX_USEROOT, "true");
        slurmResultFile = java.io.File.createTempFile("GAT", "tmp");
        try {
            sd.setStdout(GAT.createFile(gatContext, new URI(slurmResultFile.toURI())));
            sd.addPreStagedFile(GAT.createFile(gatContext, new URI(bsubFile.toURI())));
        } catch (Throwable e1) {
            try {
                sandbox.removeSandboxDir();
            } catch (Throwable e) {
            // ignore
            }
            throw new GATInvocationException("Could not create GAT object for temporary " + slurmResultFile.getAbsolutePath(), e1);
        }
        // sd.addAttribute(SoftwareDescription.DIRECTORY, sd.getStringAttribute(SoftwareDescription, defaultVal)));
        JobDescription jd = new JobDescription(sd);
        if (logger.isDebugEnabled()) {
            logger.debug("Submitting lsf job: " + sd);
        }
        Job job = subBroker.submitJob(jd, this, "job.status");
        if (logger.isDebugEnabled()) {
            logger.debug("Job submitted.");
        }
        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) {
            try {
                sandbox.removeSandboxDir();
            } catch (Throwable e) {
            // ignore
            }
            logger.debug("jobState = " + job.getState() + ", exit status = " + job.getExitStatus());
            throw new GATInvocationException("Could not submit LSF job");
        }
        // submit success.
        BufferedReader in = new BufferedReader(new FileReader(slurmResultFile.getAbsolutePath()));
        String result = in.readLine();
        if (logger.isDebugEnabled()) {
            logger.debug("bsub result line = " + result);
        }
        // Check for LSF bsub result ...
        // TODO Check if LSF return the same
        String job_prefix = "Job <";
        if (result.contains(job_prefix)) {
            int i = result.indexOf(job_prefix);
            result = result.substring(i + job_prefix.length(), result.indexOf(">", i));
        }
        return result;
    } catch (IOException e) {
        try {
            sandbox.removeSandboxDir();
        } catch (Throwable e1) {
        // ignore
        }
        throw new GATInvocationException("Got IOException", e);
    } finally {
        slurmResultFile.delete();
        bsubFile.delete();
    }
}

Example 13 with URI

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

the class FileAdaptorTest method copyFileTest.

private AdaptorTestResultEntry copyFileTest(GATContext gatContext, Preferences preferences, String host, String filename, int tabs, boolean correctValue) {
    FileInterface file = null;
    try {
        file = GAT.createFile(gatContext, preferences, "any://" + host + "/" + filename).getFileInterface();
    } catch (GATObjectCreationException e) {
        return new AdaptorTestResultEntry(false, 0, e);
    }
    long start = System.currentTimeMillis();
    try {
        file.copy(new URI("any:///" + filename + ".copy"));
    } catch (GATInvocationException e) {
        return new AdaptorTestResultEntry(false, 0, e);
    } catch (URISyntaxException e) {
        return new AdaptorTestResultEntry(false, 0, e);
    }
    long stop = System.currentTimeMillis();
    boolean exists = new java.io.File(filename + ".copy").exists();
    if (exists) {
        new java.io.File(filename + ".copy").delete();
    }
    return new AdaptorTestResultEntry(exists == correctValue, (stop - start), null);
}

Example 14 with URI

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

the class AdvertServiceAdaptorTest method importTest.

private AdaptorTestResultEntry importTest(AdvertService advert, String importLocation) {
    long start = System.currentTimeMillis();
    try {
        advert.importDataBase(new URI(importLocation));
    } 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 15 with URI

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

the class LogicalFileAdaptorTest method test.

public AdaptorTestResult test(String adaptor, String[] hosts) throws URISyntaxException {
    if (hosts.length != 4) {
        System.out.println("please provide 4 hosts (comma separated, no spaces)");
        System.exit(1);
    }
    AdaptorTestResult adaptorTestResult = new AdaptorTestResult(adaptor, hosts[0]);
    GATContext gatContext = new GATContext();
    Preferences preferences = new Preferences();
    preferences.put("logicalfile.adaptor.name", adaptor);
    LogicalFile logicalFile = null;
    try {
        logicalFile = GAT.createLogicalFile(gatContext, preferences, "test-logical-file", LogicalFile.CREATE);
    } catch (GATObjectCreationException e) {
        e.printStackTrace();
        GAT.end();
        System.exit(1);
    }
    adaptorTestResult.put("replicate [0]", replicateTest(gatContext, preferences, logicalFile, new URI("any://" + hosts[0] + "/JavaGAT-test-logical-file"), false));
    adaptorTestResult.put("add       [0]", addTest(gatContext, preferences, logicalFile, new URI("any://" + hosts[0] + "/JavaGAT-test-logical-file"), true));
    adaptorTestResult.put("add false [1]", addTest(gatContext, preferences, logicalFile, new URI("any://" + hosts[1] + "/JavaGAT-test-logical-file"), false));
    adaptorTestResult.put("replicate [1]", replicateTest(gatContext, preferences, logicalFile, new URI("any://" + hosts[1] + "/JavaGAT-test-logical-file"), true));
    adaptorTestResult.put("remove    [1]", removeTest(gatContext, preferences, logicalFile, new URI("any://" + hosts[1] + "/JavaGAT-test-logical-file"), true));
    adaptorTestResult.put("add true  [1]", addTest(gatContext, preferences, logicalFile, new URI("any://" + hosts[1] + "/JavaGAT-test-logical-file"), true));
    adaptorTestResult.put("replicate2[1]", replicateTest(gatContext, preferences, logicalFile, new URI("any://" + hosts[1] + "/JavaGAT-test-logical-file"), false));
    adaptorTestResult.put("replicate [2]", replicateTest(gatContext, preferences, logicalFile, new URI("any://" + hosts[2] + "/JavaGAT-test-logical-file"), true));
    adaptorTestResult.put("closest   [3]", closestTest(gatContext, preferences, logicalFile, new URI("any://" + hosts[3] + "/JavaGAT-test-logical-file"), true));
    return adaptorTestResult;
}