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Posted to commits@airavata.apache.org by la...@apache.org on 2014/04/24 22:51:58 UTC
[02/11] creating gfac-bes and gfac-gram out from gfac-core
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/provider/impl/GramProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/provider/impl/GramProvider.java b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/provider/impl/GramProvider.java
new file mode 100644
index 0000000..0cf413c
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/provider/impl/GramProvider.java
@@ -0,0 +1,526 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.provider.impl;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.util.Map;
+import java.util.MissingResourceException;
+import java.util.Properties;
+import java.util.concurrent.ConcurrentHashMap;
+
+import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.common.utils.ServerSettings;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.JobSubmissionFault;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.airavata.gfac.notification.events.JobIDEvent;
+import org.apache.airavata.gfac.notification.events.StartExecutionEvent;
+import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.gfac.util.GramProviderUtils;
+import org.apache.airavata.gfac.utils.GFacUtils;
+import org.apache.airavata.gfac.util.GramJobSubmissionListener;
+import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
+import org.apache.airavata.model.workspace.experiment.ErrorCategory;
+import org.apache.airavata.model.workspace.experiment.JobState;
+import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+import org.apache.airavata.schemas.gfac.GlobusHostType;
+import org.globus.gram.GramException;
+import org.globus.gram.GramJob;
+import org.globus.gram.WaitingForCommitException;
+import org.globus.gram.internal.GRAMConstants;
+import org.globus.gram.internal.GRAMProtocolErrorConstants;
+import org.ietf.jgss.GSSCredential;
+import org.ietf.jgss.GSSException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class GramProvider extends AbstractProvider{
+ private static final Logger log = LoggerFactory.getLogger(GramJobSubmissionListener.class);
+
+ private GramJob job;
+ private GramJobSubmissionListener listener;
+ private boolean twoPhase = true;
+
+ /**
+ * If normal job submission fail due to an authorisation failure or script failure we
+ * will re-attempt to submit the job. In-order to avoid any recursive loop during a continuous
+ * failure we track whether failure paths are tried or not. Following booleans keeps track whether
+ * we already tried a failure path or not.
+ */
+ /**
+ * To track job submissions during a authorisation failure while requesting job.
+ */
+ private boolean renewCredentialsAttempt = false;
+ /**
+ * To track job submission during a script error situation.
+ */
+ private boolean reSubmissionInProgress = false;
+ /**
+ * To track authorisation failures during status monitoring.
+ */
+ private boolean authorisationFailedAttempt = false;
+
+ private static final Map<String, GramJob> currentlyExecutingJobCache
+ = new ConcurrentHashMap<String, GramJob>();
+
+ private static Properties resources;
+
+ static {
+ try {
+
+ String propFileName = "errors.properties";
+ resources = new Properties();
+ InputStream inputStream = GramProvider.class.getClassLoader()
+ .getResourceAsStream(propFileName);
+
+ if (inputStream == null) {
+ throw new FileNotFoundException("property file '" + propFileName
+ + "' not found in the classpath");
+ }
+
+ resources.load(inputStream);
+
+ } catch (FileNotFoundException mre) {
+ log.error("errors.properties not found", mre);
+ } catch (IOException e) {
+ log.error("Error reading errors.properties file", e);
+ }
+ }
+
+
+ // This method prepare the environment before the application invocation.
+ public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
+
+ try {
+ super.initialize(jobExecutionContext);
+ String strTwoPhase = ServerSettings.getSetting("TwoPhase");
+ if (strTwoPhase != null) {
+ twoPhase = Boolean.parseBoolean(strTwoPhase);
+ log.info("Two phase commit is set to " + twoPhase);
+ }
+ } catch (ApplicationSettingsException e) {
+ log.warn("Error reading TwoPhase property from configurations.", e);
+ }
+
+ job = GramProviderUtils.setupEnvironment(jobExecutionContext, twoPhase);
+ listener = new GramJobSubmissionListener(job, jobExecutionContext);
+ job.addListener(listener);
+ }
+
+ public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException{
+ jobExecutionContext.getNotifier().publish(new StartExecutionEvent());
+ GlobusHostType host = (GlobusHostType) jobExecutionContext.getApplicationContext().
+ getHostDescription().getType();
+ ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().
+ getApplicationDeploymentDescription().getType();
+
+ StringBuilder stringBuilder = new StringBuilder();
+ try {
+
+ GSSCredential gssCred = ((GSISecurityContext)jobExecutionContext.
+ getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getGssCredentials();
+ job.setCredentials(gssCred);
+ // We do not support multiple gatekeepers in XBaya GUI, so we simply pick the 0th element in the array
+ String gateKeeper = host.getGlobusGateKeeperEndPointArray(0);
+ log.info("Request to contact:" + gateKeeper);
+
+ stringBuilder.append("Finished launching job, Host = ").append(host.getHostAddress()).append(" RSL = ")
+ .append(job.getRSL()).append(" working directory = ").append(app.getStaticWorkingDirectory())
+ .append(" temp directory = ").append(app.getScratchWorkingDirectory())
+ .append(" Globus GateKeeper Endpoint = ").append(gateKeeper);
+
+ log.info(stringBuilder.toString());
+
+ submitJobs(gateKeeper, jobExecutionContext, host);
+
+ } catch (ApplicationSettingsException e) {
+ throw new GFacException(e.getMessage(), e);
+ } finally {
+ if (job != null) {
+ try {
+ /*
+ * Remove listener
+ */
+ job.removeListener(listener);
+ } catch (Exception e) {
+ log.error(e.getMessage());
+ }
+ }
+ }
+ }
+
+ private void submitJobs(String gateKeeper,
+ JobExecutionContext jobExecutionContext,
+ GlobusHostType globusHostType) throws GFacException, GFacProviderException {
+ boolean applicationSaved=false;
+ String taskID = jobExecutionContext.getTaskData().getTaskID();
+
+ if (twoPhase) {
+ try {
+ /*
+ * The first boolean is to force communication through SSLv3
+ * The second boolean is to specify the job is a batch job - use true for interactive and false for
+ * batch.
+ * The third boolean is to specify to use the full proxy and not delegate a limited proxy.
+ */
+ job.request(true, gateKeeper, false, false);
+
+ // Single boolean to track all authentication failures, therefore we need to re-initialize
+ // this here
+ renewCredentialsAttempt = false;
+
+ } catch (WaitingForCommitException e) {
+ String jobID = job.getIDAsString();
+
+ details.setJobID(jobID);
+ details.setJobDescription(job.getRSL());
+ jobExecutionContext.setJobDetails(details);
+ GFacUtils.saveJobStatus(details, JobState.UN_SUBMITTED, taskID);
+
+ applicationSaved=true;
+ String jobStatusMessage = "Un-submitted JobID= " + jobID;
+ log.info(jobStatusMessage);
+ jobExecutionContext.getNotifier().publish(new JobIDEvent(jobStatusMessage));
+
+ log.info("Two phase commit: sending COMMIT_REQUEST signal; Job id - " + jobID);
+
+ try {
+ job.signal(GramJob.SIGNAL_COMMIT_REQUEST);
+
+ } catch (GramException gramException) {
+ throw new GFacException("Error while sending commit request. Job Id - "
+ + job.getIDAsString(), gramException);
+ } catch (GSSException gssException) {
+
+ // User credentials are invalid
+ log.error("Error while submitting commit request - Credentials provided are invalid. Job Id - "
+ + job.getIDAsString(), e);
+ log.info("Attempting to renew credentials and re-submit commit signal...");
+ GFacUtils.saveErrorDetails(gssException.getLocalizedMessage(), CorrectiveAction.RETRY_SUBMISSION, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
+ renewCredentials(jobExecutionContext);
+
+ try {
+ job.signal(GramJob.SIGNAL_COMMIT_REQUEST);
+ } catch (GramException e1) {
+ GFacUtils.saveErrorDetails(gssException.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
+ throw new GFacException("Error while sending commit request. Job Id - "
+ + job.getIDAsString(), e1);
+ } catch (GSSException e1) {
+ GFacUtils.saveErrorDetails(gssException.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
+ throw new GFacException("Error while sending commit request. Job Id - "
+ + job.getIDAsString() + ". Credentials provided invalid", e1);
+ }
+ }
+ GFacUtils.updateJobStatus(details, JobState.SUBMITTED);
+ jobStatusMessage = "Submitted JobID= " + job.getIDAsString();
+ log.info(jobStatusMessage);
+ jobExecutionContext.getNotifier().publish(new JobIDEvent(jobStatusMessage));
+
+ } catch (GSSException e) {
+ // Renew credentials and re-submit
+ GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.RETRY_SUBMISSION, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
+
+ reSubmitJob(gateKeeper, jobExecutionContext, globusHostType, e);
+
+ } catch (GramException e) {
+ GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
+
+ throw new GFacException("An error occurred while submitting a job, job id = " + job.getIDAsString(), e);
+ }
+ } else {
+
+ /*
+ * The first boolean is to force communication through SSLv3
+ * The second boolean is to specify the job is a batch job - use true for interactive and false for
+ * batch.
+ * The third boolean is to specify to use the full proxy and not delegate a limited proxy.
+ */
+ try {
+
+ job.request(true, gateKeeper, false, false);
+ renewCredentialsAttempt = false;
+
+ } catch (GramException e) {
+ GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
+ throw new GFacException("An error occurred while submitting a job, job id = " + job.getIDAsString(), e);
+ } catch (GSSException e) {
+ GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.RETRY_SUBMISSION, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
+ // Renew credentials and re-submit
+ reSubmitJob(gateKeeper, jobExecutionContext, globusHostType, e);
+ }
+
+ String jobStatusMessage = "Un-submitted JobID= " + job.getIDAsString();
+ log.info(jobStatusMessage);
+ jobExecutionContext.getNotifier().publish(new JobIDEvent(jobStatusMessage));
+
+ }
+
+ currentlyExecutingJobCache.put(job.getIDAsString(), job);
+ /*
+ * Wait until job is done
+ */
+ listener.waitFor();
+
+ checkJobStatus(jobExecutionContext, globusHostType, gateKeeper);
+
+ }
+
+ private void renewCredentials(JobExecutionContext jobExecutionContext) throws GFacException {
+
+ renewCredentials(this.job, jobExecutionContext);
+ }
+
+ private void renewCredentials(GramJob gramJob, JobExecutionContext jobExecutionContext) throws GFacException {
+
+ try {
+ GSSCredential gssCred = ((GSISecurityContext)jobExecutionContext.
+ getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).renewCredentials();
+ gramJob.renew(gssCred);
+ } catch (GramException e1) {
+ throw new GFacException("Unable to renew credentials. Job Id - "
+ + gramJob.getIDAsString(), e1);
+ } catch (GSSException e1) {
+ throw new GFacException("Unable to renew credentials. Job Id - "
+ + gramJob.getIDAsString(), e1);
+ } catch (ApplicationSettingsException e) {
+ throw new GFacException(e.getLocalizedMessage(), e);
+ }
+ }
+
+ private void reSubmitJob(String gateKeeper,
+ JobExecutionContext jobExecutionContext,
+ GlobusHostType globusHostType, Exception e) throws GFacException, GFacProviderException {
+
+ if (!renewCredentialsAttempt) {
+
+ renewCredentialsAttempt = true;
+
+ // User credentials are invalid
+ log.error("Error while submitting job - Credentials provided are invalid. Job Id - "
+ + job.getIDAsString(), e);
+ log.info("Attempting to renew credentials and re-submit jobs...");
+
+ // Remove existing listener and register a new listener
+ job.removeListener(listener);
+ listener = new GramJobSubmissionListener(job, jobExecutionContext);
+
+ job.addListener(listener);
+
+ renewCredentials(jobExecutionContext);
+
+ submitJobs(gateKeeper, jobExecutionContext, globusHostType);
+
+ } else {
+ throw new GFacException("Error while submitting job - Credentials provided are invalid. Job Id - "
+ + job.getIDAsString(), e);
+ }
+
+ }
+
+ private void reSubmitJob(String gateKeeper,
+ JobExecutionContext jobExecutionContext,
+ GlobusHostType globusHostType) throws GFacException, GFacProviderException {
+
+ // User credentials are invalid
+ log.info("Attempting to renew credentials and re-submit jobs...");
+
+ // Remove existing listener and register a new listener
+ job.removeListener(listener);
+ listener = new GramJobSubmissionListener(job, jobExecutionContext);
+
+ job.addListener(listener);
+
+ renewCredentials(jobExecutionContext);
+
+ submitJobs(gateKeeper, jobExecutionContext, globusHostType);
+
+ }
+
+
+
+ public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException {
+ }
+
+ public void cancelJob(String jobId, JobExecutionContext jobExecutionContext) throws GFacException {
+ cancelSingleJob(jobId, jobExecutionContext);
+ }
+
+
+ private void cancelSingleJob(String jobId, JobExecutionContext context) throws GFacException {
+ // First check whether job id is in the cache
+ if (currentlyExecutingJobCache.containsKey(jobId)) {
+
+ synchronized (this) {
+ GramJob gramJob = currentlyExecutingJobCache.get(jobId);
+
+ // Even though we check using containsKey, at this point job could be null
+ if (gramJob != null && (gramJob.getStatus() != GRAMConstants.STATUS_DONE ||
+ gramJob.getStatus() != GRAMConstants.STATUS_FAILED)) {
+ cancelJob(gramJob, context);
+ }
+ }
+
+ } else {
+
+ try {
+ GSSCredential gssCred = ((GSISecurityContext)context.
+ getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getGssCredentials();
+
+ GramJob gramJob = new GramJob(null);
+ try {
+ gramJob.setID(jobId);
+ } catch (MalformedURLException e) {
+ throw new GFacException("Invalid job id - " + jobId, e);
+ }
+ gramJob.setCredentials(gssCred);
+
+ synchronized (this) {
+ if (gramJob.getStatus() != GRAMConstants.STATUS_DONE ||
+ gramJob.getStatus() != GRAMConstants.STATUS_FAILED) {
+ cancelJob(gramJob, context);
+ }
+ }
+ } catch (ApplicationSettingsException e) {
+ throw new GFacException(e);
+ }
+ }
+ }
+
+ private void cancelJob(GramJob gramJob, JobExecutionContext context) throws GFacException{
+
+ try {
+ gramJob.cancel();
+ } catch (GramException e) {
+ throw new GFacException("Error cancelling job, id - " + gramJob.getIDAsString(), e);
+ } catch (GSSException e) {
+
+ log.warn("Credentials invalid to cancel job. Attempting to renew credentials and re-try. " +
+ "Job id - " + gramJob.getIDAsString());
+ renewCredentials(gramJob, context);
+
+ try {
+ gramJob.cancel();
+ gramJob.signal(GramJob.SIGNAL_COMMIT_END);
+ } catch (GramException e1) {
+ throw new GFacException("Error cancelling job, id - " + gramJob.getIDAsString(), e1);
+ } catch (GSSException e1) {
+ throw new GFacException("Error cancelling job, invalid credentials. Job id - "
+ + gramJob.getIDAsString(), e);
+ }
+ }
+
+ }
+
+ public void initProperties(Map<String, String> properties) throws GFacException {
+
+ }
+
+ private void checkJobStatus(JobExecutionContext jobExecutionContext, GlobusHostType host, String gateKeeper)
+ throws GFacProviderException {
+ int jobStatus = listener.getCurrentStatus();
+
+ if (jobStatus == GramJob.STATUS_FAILED) {
+
+ String errorMsg = "Job " + job.getIDAsString() + " on host " + host.getHostAddress() + " Job Exit Code = "
+ + listener.getError() + " Error Description = " + getGramErrorString(listener.getError());
+
+ if (listener.getError() == GRAMProtocolErrorConstants.INVALID_SCRIPT_REPLY) {
+
+ // re-submitting without renewing
+ // TODO verify why we re-submit jobs when we get a invalid script reply
+ if (!reSubmissionInProgress) {
+ reSubmissionInProgress = true;
+
+ log.info("Invalid script reply received. Re-submitting job, id - " + job.getIDAsString());
+ try {
+ reSubmitJob(gateKeeper, jobExecutionContext, host);
+ } catch (GFacException e) {
+ throw new GFacProviderException
+ ("Error during re-submission. Original job submission data - " + errorMsg, e);
+ }
+ return;
+ }
+
+ } else if (listener.getError() == GRAMProtocolErrorConstants.ERROR_AUTHORIZATION) {
+
+ // re-submit with renewed credentials
+ if (!authorisationFailedAttempt) {
+ authorisationFailedAttempt = true;
+ log.info("Authorisation error contacting provider. Re-submitting job with renewed credentials.");
+
+ try {
+ renewCredentials(jobExecutionContext);
+ reSubmitJob(gateKeeper, jobExecutionContext, host);
+ } catch (GFacException e) {
+ throw new GFacProviderException
+ ("Error during re-submission. Original job submission data - " + errorMsg, e);
+ }
+
+ return;
+ }
+
+ } else if (listener.getError() == GRAMProtocolErrorConstants.USER_CANCELLED) {
+
+ log.info("User successfully cancelled job id " + job.getIDAsString());
+ return;
+ }
+
+
+
+ log.error(errorMsg);
+
+ synchronized (this) {
+ currentlyExecutingJobCache.remove(job.getIDAsString());
+ }
+
+ throw new JobSubmissionFault(new Exception(errorMsg), host.getHostAddress(), gateKeeper,
+ job.getRSL(), jobExecutionContext, getGramErrorString(listener.getError()),
+ listener.getError());
+
+ } else if (jobStatus == GramJob.STATUS_DONE) {
+ log.info("Job " + job.getIDAsString() + " on host " + host.getHostAddress() + " is successfully executed.");
+
+ synchronized (this) {
+ currentlyExecutingJobCache.remove(job.getIDAsString());
+ }
+ }
+ }
+
+ public String getGramErrorString(int errorCode) {
+
+ if (resources != null) {
+ try {
+ return resources.getProperty(String.valueOf(errorCode));
+ } catch (MissingResourceException mre) {
+ log.warn("Error reading globus error descriptions.", mre);
+ return "Error code: " + errorCode;
+ }
+ } else {
+ return "Error code: " + errorCode;
+ }
+
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramJobSubmissionListener.java
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diff --git a/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramJobSubmissionListener.java b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramJobSubmissionListener.java
new file mode 100644
index 0000000..5500853
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramJobSubmissionListener.java
@@ -0,0 +1,141 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.util;
+
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.airavata.gfac.notification.events.StatusChangeEvent;
+import org.apache.airavata.gfac.utils.GFacUtils;
+import org.globus.gram.GramJob;
+import org.globus.gram.GramJobListener;
+import org.ietf.jgss.GSSCredential;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class GramJobSubmissionListener implements GramJobListener{
+ private final Logger log = LoggerFactory.getLogger(GramJobSubmissionListener.class);
+
+ public static final int NO_ERROR = -42;
+ public static final int INITIAL_STATUS = -43;
+
+ private volatile boolean jobDone = false;
+ private volatile int error = NO_ERROR;
+ private int currentStatus = INITIAL_STATUS;
+
+ private JobExecutionContext context;
+ private GramJob job;
+
+ public GramJobSubmissionListener(GramJob job, JobExecutionContext context) {
+ this.job = job;
+ this.context = context;
+ }
+
+ /**
+ * This method is used to block the process until the currentStatus of the job is DONE or FAILED
+ */
+ public void waitFor() {
+ while (!isJobDone()) {
+ synchronized (this) {
+ try {
+ wait();
+ } catch (InterruptedException e) {}
+ }
+ }
+ }
+
+
+
+ private synchronized boolean isJobDone() {
+ return this.jobDone;
+ }
+
+ private void setStatus(int status, int error) {
+ try {
+ GFacUtils.updateJobStatus(context.getJobDetails(), GramProviderUtils.getApplicationJobStatus(status));
+ } catch (GFacException e) {
+ log.error("Error persisting status" + e.getLocalizedMessage(), e);
+ }
+ this.currentStatus = status;
+ this.error = error;
+
+ switch (this.currentStatus) {
+ case GramJob.STATUS_FAILED:
+ log.info("Job Error Code: " + error);
+ this.jobDone = true;
+ notifyAll();
+ case GramJob.STATUS_DONE:
+ this.jobDone = true;
+ notifyAll();
+ }
+
+ }
+
+ public synchronized void statusChanged(GramJob job) {
+
+ int jobStatus = job.getStatus();
+ String jobStatusMessage = "Status of job " + job.getIDAsString() + "is " + job.getStatusAsString();
+ /*
+ * Notify currentStatus change
+ */
+ this.context.getNotifier().publish(new StatusChangeEvent(jobStatusMessage));
+
+ /*
+ * Set new currentStatus if it is jobDone, notify all wait object
+ */
+ if (currentStatus != jobStatus) {
+ currentStatus = jobStatus;
+
+ setStatus(job.getStatus(), job.getError());
+
+ // Test to see whether we need to renew credentials
+ renewCredentials(job);
+ }
+ }
+
+ private void renewCredentials(GramJob job) {
+
+ try {
+
+ int proxyExpTime = job.getCredentials().getRemainingLifetime();
+ if (proxyExpTime < GSISecurityContext.CREDENTIAL_RENEWING_THRESH_HOLD) {
+ log.info("Job proxy expired. Trying to renew proxy");
+ GSSCredential gssCred = ((GSISecurityContext)context.
+ getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).renewCredentials();
+ job.renew(gssCred);
+ log.info("MyProxy credentials are renewed .");
+ }
+
+ } catch (Exception e) {
+ log.error("An error occurred while trying to renew credentials. Job id " + job.getIDAsString());
+ }
+
+
+ }
+
+ public synchronized int getError() {
+ return error;
+ }
+
+ public synchronized int getCurrentStatus() {
+ return currentStatus;
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramProviderUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramProviderUtils.java b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramProviderUtils.java
new file mode 100644
index 0000000..d76b067
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramProviderUtils.java
@@ -0,0 +1,114 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.util;
+
+import org.apache.airavata.gfac.ToolsException;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.gfac.utils.*;
+import org.apache.airavata.model.workspace.experiment.JobState;
+import org.globus.gram.GramAttributes;
+import org.globus.gram.GramJob;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+
+public class GramProviderUtils {
+ private static final Logger log = LoggerFactory.getLogger(GramProviderUtils.class);
+
+ public static GramJob setupEnvironment(JobExecutionContext jobExecutionContext, boolean enableTwoPhase) throws GFacProviderException {
+ log.debug("Searching for Gate Keeper");
+ try {
+ GramAttributes jobAttr = GramRSLGenerator.configureRemoteJob(jobExecutionContext);
+ String rsl = jobAttr.toRSL();
+
+ if (enableTwoPhase) {
+ rsl = rsl + "(twoPhase=yes)";
+ }
+
+ log.debug("RSL = " + rsl);
+ GramJob job = new GramJob(rsl);
+ return job;
+ } catch (ToolsException te) {
+ throw new GFacProviderException(te.getMessage(), te);
+ }
+ }
+
+ public static JobState getApplicationJobStatus(int gramStatus) {
+ switch (gramStatus) {
+ case GramJob.STATUS_UNSUBMITTED:
+ return JobState.HELD;
+ case GramJob.STATUS_ACTIVE:
+ return JobState.ACTIVE;
+ case GramJob.STATUS_DONE:
+ return JobState.COMPLETE;
+ case GramJob.STATUS_FAILED:
+ return JobState.FAILED;
+ case GramJob.STATUS_PENDING:
+ return JobState.QUEUED;
+ case GramJob.STATUS_STAGE_IN:
+ return JobState.QUEUED;
+ case GramJob.STATUS_STAGE_OUT:
+ return JobState.COMPLETE;
+ case GramJob.STATUS_SUSPENDED:
+ return JobState.SUSPENDED;
+ default:
+ return JobState.UNKNOWN;
+ }
+ }
+
+ public static URI createGsiftpURI(String host, String localPath) throws URISyntaxException {
+ StringBuffer buf = new StringBuffer();
+ if (!host.startsWith("gsiftp://"))
+ buf.append("gsiftp://");
+ buf.append(host);
+ if (!host.endsWith("/"))
+ buf.append("/");
+ buf.append(localPath);
+ return new URI(buf.toString());
+ }
+
+ public static URI createGsiftpURI(GridFTPContactInfo host, String localPath) throws URISyntaxException {
+ StringBuffer buf = new StringBuffer();
+
+ if (!host.hostName.startsWith("gsiftp://"))
+ buf.append("gsiftp://");
+ buf.append(host).append(":").append(host.port);
+ if (!host.hostName.endsWith("/"))
+ buf.append("/");
+ buf.append(localPath);
+ return new URI(buf.toString());
+ }
+
+ public static String createGsiftpURIAsString(String host, String localPath) throws URISyntaxException {
+ StringBuffer buf = new StringBuffer();
+ if (!host.startsWith("gsiftp://"))
+ buf.append("gsiftp://");
+ buf.append(host);
+ if (!host.endsWith("/"))
+ buf.append("/");
+ buf.append(localPath);
+ return buf.toString();
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramRSLGenerator.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramRSLGenerator.java b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramRSLGenerator.java
new file mode 100644
index 0000000..81782ff
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GramRSLGenerator.java
@@ -0,0 +1,211 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.util;
+
+import org.apache.airavata.common.utils.StringUtil;
+import org.apache.airavata.commons.gfac.type.ActualParameter;
+import org.apache.airavata.commons.gfac.type.MappingFactory;
+import org.apache.airavata.gfac.Constants;
+import org.apache.airavata.gfac.ToolsException;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.MessageContext;
+import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.model.workspace.experiment.ComputationalResourceScheduling;
+import org.apache.airavata.model.workspace.experiment.TaskDetails;
+import org.apache.airavata.schemas.gfac.*;
+import org.globus.gram.GramAttributes;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+public class GramRSLGenerator {
+ protected static final Logger log = LoggerFactory.getLogger(GramRSLGenerator.class);
+
+ private enum JobType {
+ SERIAL, SINGLE, MPI, MULTIPLE, CONDOR
+ }
+
+ ;
+
+ public static GramAttributes configureRemoteJob(JobExecutionContext context) throws ToolsException {
+ HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) context.getApplicationContext().getApplicationDeploymentDescription().getType();
+ GramAttributes jobAttr = new GramAttributes();
+ jobAttr.setExecutable(app.getExecutableLocation());
+ jobAttr.setDirectory(app.getStaticWorkingDirectory());
+ jobAttr.setStdout(app.getStandardOutput());
+ jobAttr.setStderr(app.getStandardError());
+ /*
+ * The env here contains the env of the host and the application. i.e the env specified in the host description
+ * and application description documents
+ */
+ NameValuePairType[] env = app.getApplicationEnvironmentArray();
+ if (env.length != 0) {
+ Map<String, String> nv = new HashMap<String, String>();
+ for (int i = 0; i < env.length; i++) {
+ String key = env[i].getName();
+ String value = env[i].getValue();
+ nv.put(key, value);
+ }
+
+ for (Map.Entry<String, String> entry : nv.entrySet()) {
+ jobAttr.addEnvVariable(entry.getKey(), entry.getValue());
+ }
+ }
+ jobAttr.addEnvVariable(Constants.INPUT_DATA_DIR_VAR_NAME, app.getInputDataDirectory());
+ jobAttr.addEnvVariable(Constants.OUTPUT_DATA_DIR_VAR_NAME, app.getOutputDataDirectory());
+
+
+
+ if (app.getStandardInput() != null && !"".equals(app.getStandardInput())) {
+ jobAttr.setStdin(app.getStandardInput());
+ } else {
+ MessageContext input = context.getInMessageContext();;
+ Map<String,Object> inputs = input.getParameters();
+ Set<String> keys = inputs.keySet();
+ for (String paramName : keys ) {
+ ActualParameter actualParameter = (ActualParameter) inputs.get(paramName);
+ if ("URIArray".equals(actualParameter.getType().getType().toString()) || "StringArray".equals(actualParameter.getType().getType().toString())
+ || "FileArray".equals(actualParameter.getType().getType().toString())) {
+ String[] values = null;
+ if (actualParameter.getType() instanceof URIArrayType) {
+ values = ((URIArrayType) actualParameter.getType()).getValueArray();
+ } else if (actualParameter.getType() instanceof StringArrayType) {
+ values = ((StringArrayType) actualParameter.getType()).getValueArray();
+ } else if (actualParameter.getType() instanceof FileArrayType) {
+ values = ((FileArrayType) actualParameter.getType()).getValueArray();
+ }
+ String value = StringUtil.createDelimiteredString(values, " ");
+ jobAttr.addArgument(value);
+ } else {
+ String paramValue = MappingFactory.toString(actualParameter);
+ jobAttr.addArgument(paramValue);
+ }
+ }
+ }
+ // Using the workflowContext Header values if user provided them in the request and overwrite the default values in DD
+ //todo finish the scheduling based on workflow execution context
+ TaskDetails taskData = context.getTaskData();
+ if(taskData != null && taskData.isSetTaskScheduling()){
+ ComputationalResourceScheduling computionnalResource = taskData.getTaskScheduling();
+ try {
+ int cpuCount = computionnalResource.getTotalCPUCount();
+ if(cpuCount>0){
+ app.setCpuCount(cpuCount);
+ }
+ } catch (NullPointerException e) {
+ log.debug("No Value sent in WorkflowContextHeader for CPU Count, value in the Deployment Descriptor will be used");
+ new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
+ }
+ try {
+ int nodeCount = computionnalResource.getNodeCount();
+ if(nodeCount>0){
+ app.setNodeCount(nodeCount);
+ }
+ } catch (NullPointerException e) {
+ log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
+ new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
+ }
+ try {
+ String queueName = computionnalResource.getQueueName();
+ if (queueName != null) {
+ if(app.getQueue() == null){
+ QueueType queueType = app.addNewQueue();
+ queueType.setQueueName(queueName);
+ }else{
+ app.getQueue().setQueueName(queueName);
+ }
+ }
+ } catch (NullPointerException e) {
+ log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
+ new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
+ }
+ try {
+ int maxwallTime = computionnalResource.getWallTimeLimit();
+ if(maxwallTime>0){
+ app.setMaxWallTime(maxwallTime);
+ }
+ } catch (NullPointerException e) {
+ log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
+ new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
+ }
+ }
+ if (app.getNodeCount() > 0) {
+ jobAttr.set("hostCount", String.valueOf(app.getNodeCount()));
+ log.debug("Setting number of Nodes to " + app.getCpuCount());
+ }
+ if (app.getCpuCount() > 0) {
+ log.debug("Setting number of procs to " + app.getCpuCount());
+ jobAttr.setNumProcs(app.getCpuCount());
+ }
+ if (app.getMinMemory() > 0) {
+ log.debug("Setting minimum memory to " + app.getMinMemory());
+ jobAttr.setMinMemory(app.getMinMemory());
+ }
+ if (app.getMaxMemory() > 0) {
+ log.debug("Setting maximum memory to " + app.getMaxMemory());
+ jobAttr.setMaxMemory(app.getMaxMemory());
+ }
+ if (app.getProjectAccount() != null) {
+ if (app.getProjectAccount().getProjectAccountNumber() != null) {
+ log.debug("Setting project to " + app.getProjectAccount().getProjectAccountNumber());
+ jobAttr.setProject(app.getProjectAccount().getProjectAccountNumber());
+ }
+ }
+ if (app.getQueue() != null) {
+ if (app.getQueue().getQueueName() != null) {
+ log.debug("Setting job queue to " + app.getQueue().getQueueName());
+ jobAttr.setQueue(app.getQueue().getQueueName());
+ }
+ }
+ if (app.getMaxWallTime() > 0) {
+ log.debug("Setting max wall clock time to " + app.getMaxWallTime());
+
+ jobAttr.setMaxWallTime(app.getMaxWallTime());
+ jobAttr.set("proxy_timeout", "1");
+ } else {
+ jobAttr.setMaxWallTime(30);
+ }
+ String jobType = JobType.SINGLE.toString();
+ if (app.getJobType() != null) {
+ jobType = app.getJobType().toString();
+ }
+ if (jobType.equalsIgnoreCase(JobType.SINGLE.toString())) {
+ log.debug("Setting job type to single");
+ jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
+ } if (jobType.equalsIgnoreCase(JobType.SERIAL.toString())) {
+ log.debug("Setting job type to single");
+ jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
+ } else if (jobType.equalsIgnoreCase(JobType.MPI.toString())) {
+ log.debug("Setting job type to mpi");
+ jobAttr.setJobType(GramAttributes.JOBTYPE_MPI);
+ } else if (jobType.equalsIgnoreCase(JobType.MULTIPLE.toString())) {
+ log.debug("Setting job type to multiple");
+ jobAttr.setJobType(GramAttributes.JOBTYPE_MULTIPLE);
+ } else if (jobType.equalsIgnoreCase(JobType.CONDOR.toString())) {
+ jobAttr.setJobType(GramAttributes.JOBTYPE_CONDOR);
+ }
+
+ return jobAttr;
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GridFTPContactInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GridFTPContactInfo.java b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GridFTPContactInfo.java
new file mode 100644
index 0000000..d37beba
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/util/GridFTPContactInfo.java
@@ -0,0 +1,61 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gfac.util;
+
+import org.apache.airavata.gfac.Constants;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class GridFTPContactInfo {
+ protected final static Logger log = LoggerFactory.getLogger(GridFTPContactInfo.class);
+ public String hostName;
+ public int port;
+
+ public GridFTPContactInfo(String hostName, int port) {
+ if (port <= 0 || port == 80) {
+ log.debug(hostName + "port recived " + port + " setting it to " + Constants.DEFAULT_GSI_FTP_PORT);
+ port = Constants.DEFAULT_GSI_FTP_PORT;
+ }
+ this.hostName = hostName;
+ this.port = port;
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (obj instanceof GridFTPContactInfo) {
+ return hostName.equals(((GridFTPContactInfo) obj).hostName) && port == ((GridFTPContactInfo) obj).port;
+ } else {
+ return false;
+ }
+ }
+
+ @Override
+ public int hashCode() {
+ return hostName.hashCode();
+ }
+
+ @Override
+ public String toString() {
+ StringBuffer buf = new StringBuffer();
+ buf.append(hostName).append(":").append(port);
+ return buf.toString();
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/main/resources/errors.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/main/resources/errors.properties b/modules/gfac/gfac-gram/src/main/resources/errors.properties
new file mode 100644
index 0000000..88c41b8
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/main/resources/errors.properties
@@ -0,0 +1,197 @@
+#
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
+# Directly copied from jglobus. Not a good way to manager error properties.
+1 = Parameter not supported
+2 = The RSL length is greater than the maximum allowed
+3 = No resources available
+4 = Bad directory specified
+5 = The executable does not exist
+6 = Insufficient funds
+7 = Authentication with the remote server failed
+8 = Job cancelled by user
+9 = Job cancelled by system
+
+10 = Data transfer to the server failed
+11 = The stdin file does not exist
+12 = The connection to the server failed (check host and port)
+13 = The provided RSL 'maxtime' value is invalid (not an integer or must be greater than 0)
+14 = The provided RSL 'count' value is invalid (not an integer or must be greater than 0)
+15 = The job manager received an invalid RSL
+16 = Could not connect to job manager
+17 = The job failed when the job manager attempted to run it
+18 = Paradyn error
+19 = The provided RSL 'jobtype' value is invalid
+
+20 = The provided RSL 'myjob' value is invalid
+21 = The job manager failed to locate an internal script argument file
+22 = The job manager failed to create an internal script argument file
+23 = The job manager detected an invalid job state
+24 = The job manager detected an invalid script response
+25 = The job manager detected an invalid job state
+26 = The provided RSL 'jobtype' value is not supported by this job manager
+27 = Unimplemented
+28 = The job manager failed to create an internal script submission file
+29 = The job manager cannot find the user proxy
+
+30 = The job manager failed to open the user proxy
+31 = The job manager failed to cancel the job as requested
+32 = System memory allocation failed
+33 = The interprocess job communication initialization failed
+34 = The interprocess job communication setup failed
+35 = The provided RSL 'host count' value is invalid
+36 = One of the provided RSL parameters is unsupported
+37 = The provided RSL 'queue' parameter is invalid
+38 = The provided RSL 'project' parameter is invalid
+39 = The provided RSL string includes variables that could not be identified
+
+40 = The provided RSL 'environment' parameter is invalid
+41 = The provided RSL 'dryrun' parameter is invalid
+42 = The provided RSL is invalid (an empty string)
+43 = The job manager failed to stage the executable
+44 = The job manager failed to stage the stdin file
+45 = The requested job manager type is invalid
+46 = The provided RSL 'arguments' parameter is invalid
+47 = The gatekeeper failed to run the job manager
+48 = The provided RSL could not be properly parsed
+49 = There is a version mismatch between GRAM components
+
+50 = The provided RSL 'arguments' parameter is invalid
+51 = The provided RSL 'count' parameter is invalid
+52 = The provided RSL 'directory' parameter is invalid
+53 = The provided RSL 'dryrun' parameter is invalid
+54 = The provided RSL 'environment' parameter is invalid
+55 = The provided RSL 'executable' parameter is invalid
+56 = The provided RSL 'host_count' parameter is invalid
+57 = The provided RSL 'jobtype' parameter is invalid
+58 = The provided RSL 'maxtime' parameter is invalid
+59 = The provided RSL 'myjob' parameter is invalid
+
+60 = The provided RSL 'paradyn' parameter is invalid
+61 = The provided RSL 'project' parameter is invalid
+62 = The provided RSL 'queue' parameter is invalid
+63 = The provided RSL 'stderr' parameter is invalid
+64 = The provided RSL 'stdin' parameter is invalid
+65 = The provided RSL 'stdout' parameter is invalid
+66 = The job manager failed to locate an internal script
+67 = The job manager failed on the system call pipe()
+68 = The job manager failed on the system call fcntl()
+69 = The job manager failed to create the temporary stdout filename
+
+70 = The job manager failed to create the temporary stderr filename
+71 = The job manager failed on the system call fork()
+72 = The executable file permissions do not allow execution
+73 = The job manager failed to open stdout
+74 = The job manager failed to open stderr
+75 = The cache file could not be opened in order to relocate the user proxy
+76 = Cannot access cache files in ~/.globus/.gass_cache, check permissions, quota, and disk space
+77 = The job manager failed to insert the contact in the client contact list
+78 = The contact was not found in the job manager's client contact list
+79 = Connecting to the job manager failed. Possible reasons: job terminated, invalid job contact, network problems, ...
+
+80 = The syntax of the job contact is invalid
+81 = The executable parameter in the RSL is undefined
+82 = The job manager service is misconfigured. condor arch undefined
+83 = The job manager service is misconfigured. condor os undefined
+84 = The provided RSL 'min_memory' parameter is invalid
+85 = The provided RSL 'max_memory' parameter is invalid
+86 = The RSL 'min_memory' value is not zero or greater
+87 = The RSL 'max_memory' value is not zero or greater
+88 = The creation of a HTTP message failed
+89 = Parsing incoming HTTP message failed
+
+90 = The packing of information into a HTTP message failed
+91 = An incoming HTTP message did not contain the expected information
+92 = The job manager does not support the service that the client requested
+93 = The gatekeeper failed to find the requested service
+94 = The jobmanager does not accept any new requests (shutting down)
+95 = The client failed to close the listener associated with the callback URL
+96 = The gatekeeper contact cannot be parsed
+97 = The job manager could not find the 'poe' command
+98 = The job manager could not find the 'mpirun' command
+99 = The provided RSL 'start_time' parameter is invalid"
+100 = The provided RSL 'reservation_handle' parameter is invalid
+
+101 = The provided RSL 'max_wall_time' parameter is invalid
+102 = The RSL 'max_wall_time' value is not zero or greater
+103 = The provided RSL 'max_cpu_time' parameter is invalid
+104 = The RSL 'max_cpu_time' value is not zero or greater
+105 = The job manager is misconfigured, a scheduler script is missing
+106 = The job manager is misconfigured, a scheduler script has invalid permissions
+107 = The job manager failed to signal the job
+108 = The job manager did not recognize/support the signal type
+109 = The job manager failed to get the job id from the local scheduler
+
+110 = The job manager is waiting for a commit signal
+111 = The job manager timed out while waiting for a commit signal
+112 = The provided RSL 'save_state' parameter is invalid
+113 = The provided RSL 'restart' parameter is invalid
+114 = The provided RSL 'two_phase' parameter is invalid
+115 = The RSL 'two_phase' value is not zero or greater
+116 = The provided RSL 'stdout_position' parameter is invalid
+117 = The RSL 'stdout_position' value is not zero or greater
+118 = The provided RSL 'stderr_position' parameter is invalid
+119 = The RSL 'stderr_position' value is not zero or greater
+
+120 = The job manager restart attempt failed
+121 = The job state file doesn't exist
+122 = Could not read the job state file
+123 = Could not write the job state file
+124 = The old job manager is still alive
+125 = The job manager state file TTL expired
+126 = It is unknown if the job was submitted
+127 = The provided RSL 'remote_io_url' parameter is invalid
+128 = Could not write the remote io url file
+129 = The standard output/error size is different
+
+130 = The job manager was sent a stop signal (job is still running)
+131 = The user proxy expired (job is still running)
+132 = The job was not submitted by original jobmanager
+133 = The job manager is not waiting for that commit signal
+134 = The provided RSL scheduler specific parameter is invalid
+135 = The job manager could not stage in a file
+136 = The scratch directory could not be created
+137 = The provided 'gass_cache' parameter is invalid
+138 = The RSL contains attributes which are not valid for job submission
+139 = The RSL contains attributes which are not valid for stdio update
+
+140 = The RSL contains attributes which are not valid for job restart
+141 = The provided RSL 'file_stage_in' parameter is invalid
+142 = The provided RSL 'file_stage_in_shared' parameter is invalid
+143 = The provided RSL 'file_stage_out' parameter is invalid
+144 = The provided RSL 'gass_cache' parameter is invalid
+145 = The provided RSL 'file_cleanup' parameter is invalid
+146 = The provided RSL 'scratch_dir' parameter is invalid
+147 = The provided scheduler-specific RSL parameter is invalid
+148 = A required RSL attribute was not defined in the RSL spec
+149 = The gass_cache attribute points to an invalid cache directory
+
+150 = The provided RSL 'save_state' parameter has an invalid value
+151 = The job manager could not open the RSL attribute validation file
+152 = The job manager could not read the RSL attribute validation file
+153 = The provided RSL 'proxy_timeout' is invalid
+154 = The RSL 'proxy_timeout' value is not greater than zero
+155 = The job manager could not stage out a file
+156 = The job contact string does not match any which the job manager is handling
+157 = Proxy delegation failed
+158 = The job manager could not lock the state lock file
+
+1000 = Failed to start up callback handler
+1003 = Job contact not set
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/main/resources/service.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/main/resources/service.properties b/modules/gfac/gfac-gram/src/main/resources/service.properties
new file mode 100644
index 0000000..391bfea
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/main/resources/service.properties
@@ -0,0 +1,58 @@
+#
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#
+
+
+#
+# Class which implemented Scheduler interface. It will be used to determine a Provider
+#
+scheduler.class= org.apache.airavata.core.gfac.scheduler.impl.SchedulerImpl
+
+#
+# Data Service Plugins classes
+#
+datachain.classes= org.apache.airavata.core.gfac.extension.data.RegistryDataService
+
+#
+# Pre execution Plugins classes. For example, GridFTP Input Staging
+#
+prechain.classes= org.apache.airavata.core.gfac.extension.pre.GridFtpInputStaging
+prechain.classes= org.apache.airavata.core.gfac.extension.pre.HttpInputStaging
+
+#
+# Post execution Plugins classes. For example, GridFTP Output Staging
+#
+postchain.classes= org.apache.airavata.core.gfac.extension.post.GridFtpOutputStaging
+postchain.classes= org.apache.airavata.core.gfac.extension.post.OutputRegister
+
+#
+# SSH private key location. It will be used by SSHProvider
+#
+# ssh.key=/home/user/.ssh/id_rsa
+# ssh.keypass=
+# ssh.username=usernameAtHost
+
+#
+# MyProxy credential. It will be used by GridFTP Plugins and GramProvider.
+#
+# myproxy.server=myproxy.teragrid.org
+# myproxy.user=username
+# myproxy.pass=password
+# myproxy.life=3600
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/test/java/org/apache/airavata/core/gfac/services/impl/GFacBaseTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/test/java/org/apache/airavata/core/gfac/services/impl/GFacBaseTestWithMyProxyAuth.java b/modules/gfac/gfac-gram/src/test/java/org/apache/airavata/core/gfac/services/impl/GFacBaseTestWithMyProxyAuth.java
new file mode 100644
index 0000000..24c364c
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/test/java/org/apache/airavata/core/gfac/services/impl/GFacBaseTestWithMyProxyAuth.java
@@ -0,0 +1,115 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.core.gfac.services.impl;
+
+import junit.framework.Assert;
+import org.apache.airavata.common.utils.AiravataUtils;
+import org.apache.airavata.common.utils.DatabaseTestCases;
+import org.apache.airavata.common.utils.DerbyUtil;
+import org.apache.airavata.credential.store.store.CredentialReader;
+import org.apache.airavata.credential.store.store.impl.CredentialReaderImpl;
+import org.apache.airavata.gfac.RequestData;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.log4j.Logger;
+import org.junit.BeforeClass;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 7/11/13
+ * Time: 1:31 AM
+ */
+
+public class GFacBaseTestWithMyProxyAuth extends DatabaseTestCases {
+
+ private static String myProxyUserName;
+ private static String myProxyPassword;
+
+ private static final Logger log = Logger.getLogger(GFacBaseTestWithMyProxyAuth.class);
+
+
+ @BeforeClass
+ public static void setUpClass() throws Exception {
+ AiravataUtils.setExecutionAsServer();
+
+ myProxyUserName = System.getProperty("myproxy.user");
+ myProxyPassword = System.getProperty("myproxy.password");
+
+ if (userName == null || password == null || userName.trim().equals("") || password.trim().equals("")) {
+ log.error("===== Please set myproxy.user and myproxy.password system properties. =======");
+ Assert.fail("Please set myproxy.user and myproxy.password system properties.");
+ }
+
+ log.info("Using my proxy user name - " + userName);
+
+ setUpDatabase();
+
+ }
+
+
+
+
+ public static void setUpDatabase() throws Exception {
+ DerbyUtil.startDerbyInServerMode(getHostAddress(), getPort(), getUserName(), getPassword());
+
+ waitTillServerStarts();
+
+ /*
+ * String createTable = "CREATE TABLE CREDENTIALS\n" + "(\n" + " GATEWAY_NAME VARCHAR(256) NOT NULL,\n" +
+ * " COMMUNITY_USER_NAME VARCHAR(256) NOT NULL,\n" + " CREDENTIAL BLOB NOT NULL,\n" +
+ * " PRIVATE_KEY BLOB NOT NULL,\n" + " NOT_BEFORE VARCHAR(256) NOT NULL,\n" +
+ * " NOT_AFTER VARCHAR(256) NOT NULL,\n" + " LIFETIME INTEGER NOT NULL,\n" +
+ * " REQUESTING_PORTAL_USER_NAME VARCHAR(256) NOT NULL,\n" +
+ * " REQUESTED_TIME TIMESTAMP DEFAULT '0000-00-00 00:00:00',\n" +
+ * " PRIMARY KEY (GATEWAY_NAME, COMMUNITY_USER_NAME)\n" + ")";
+ */
+
+ String createTable = "CREATE TABLE CREDENTIALS\n" + "(\n"
+ + " GATEWAY_ID VARCHAR(256) NOT NULL,\n"
+ + " TOKEN_ID VARCHAR(256) NOT NULL,\n"
+ + // Actual token used to identify the credential
+ " CREDENTIAL BLOB NOT NULL,\n" + " PORTAL_USER_ID VARCHAR(256) NOT NULL,\n"
+ + " TIME_PERSISTED TIMESTAMP DEFAULT CURRENT_TIMESTAMP,\n"
+ + " PRIMARY KEY (GATEWAY_ID, TOKEN_ID)\n" + ")";
+
+ String dropTable = "drop table CREDENTIALS";
+
+ try {
+ executeSQL(dropTable);
+ } catch (Exception e) {
+ }
+
+ executeSQL(createTable);
+
+ }
+
+ public GSISecurityContext getSecurityContext() throws Exception {
+ GSISecurityContext.setUpTrustedCertificatePath(System.getProperty("gsi.certificate.path"));
+ RequestData requestData = new RequestData();
+ requestData.setMyProxyServerUrl("myproxy.teragrid.org");
+ requestData.setMyProxyUserName(System.getProperty("myproxy.user"));
+ requestData.setMyProxyPassword(System.getProperty("myproxy.password"));
+ requestData.setMyProxyLifeTime(3600);
+ CredentialReader credentialReader = new CredentialReaderImpl(getDbUtil());
+ return new GSISecurityContext(credentialReader, requestData);
+ }
+
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTestWithMyProxyAuth.java b/modules/gfac/gfac-gram/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTestWithMyProxyAuth.java
new file mode 100644
index 0000000..ffaaaae
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTestWithMyProxyAuth.java
@@ -0,0 +1,225 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.core.gfac.services.impl;
+
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
+import org.apache.airavata.commons.gfac.type.ActualParameter;
+import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+import org.apache.airavata.commons.gfac.type.HostDescription;
+import org.apache.airavata.commons.gfac.type.MappingFactory;
+import org.apache.airavata.commons.gfac.type.ServiceDescription;
+import org.apache.airavata.gfac.GFacConfiguration;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.context.ApplicationContext;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.MessageContext;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.airavata.gfac.cpi.GFacImpl;
+import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+import org.apache.airavata.schemas.gfac.GlobusHostType;
+import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
+import org.apache.airavata.schemas.gfac.InputParameterType;
+import org.apache.airavata.schemas.gfac.JobTypeType;
+import org.apache.airavata.schemas.gfac.OutputParameterType;
+import org.apache.airavata.schemas.gfac.ProjectAccountType;
+import org.apache.airavata.schemas.gfac.QueueType;
+import org.apache.airavata.schemas.gfac.StringParameterType;
+import org.apache.airavata.schemas.gfac.URIParameterType;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+public class GramProviderTestWithMyProxyAuth extends GFacBaseTestWithMyProxyAuth {
+ private JobExecutionContext jobExecutionContext;
+
+
+// private static final String hostAddress = "blacklight.psc.teragrid.org";
+// private static final String hostName = "Blacklight";
+// private static final String gridftpAddress = "gsiftp://gridftp.blacklight.psc.teragrid.org:2812";
+// private static final String gramAddress = "";
+
+ //FIXME: move job properties to configuration file
+ private static final String hostAddress = "trestles.sdsc.edu";
+ private static final String hostName = "trestles";
+ private static final String gridftpAddress = "gsiftp://trestles.sdsc.edu:2811/";
+ private static final String gramAddress = "trestles-login2.sdsc.edu:2119/jobmanager-pbstest2";
+
+ @Before
+ public void setUp() throws Exception {
+ URL resource = GramProviderTestWithMyProxyAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+ assert resource != null;
+ System.out.println(resource.getFile());
+ GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()),null,null);
+// gFacConfiguration.setMyProxyLifeCycle(3600);
+// gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
+// gFacConfiguration.setMyProxyUser("*****");
+// gFacConfiguration.setMyProxyPassphrase("*****");
+// gFacConfiguration.setTrustedCertLocation("./certificates");
+// //have to set InFlwo Handlers and outFlowHandlers
+// gFacConfiguration.setInHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GramDirectorySetupHandler","org.apache.airavata.gfac.handler.GridFTPInputHandler"}));
+// gFacConfiguration.setOutHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GridFTPOutputHandler"}));
+
+ /*
+ * Host
+ */
+ HostDescription host = new HostDescription(GlobusHostType.type);
+ host.getType().setHostAddress(hostAddress);
+ host.getType().setHostName(hostName);
+ ((GlobusHostType)host.getType()).setGlobusGateKeeperEndPointArray(new String[]{gramAddress});
+ ((GlobusHostType)host.getType()).setGridFTPEndPointArray(new String[]{gridftpAddress});
+ /*
+ * App
+ */
+ ApplicationDescription appDesc = new ApplicationDescription(HpcApplicationDeploymentType.type);
+ HpcApplicationDeploymentType app = (HpcApplicationDeploymentType)appDesc.getType();
+ ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
+ name.setStringValue("EchoLocal");
+ app.setApplicationName(name);
+ ProjectAccountType projectAccountType = app.addNewProjectAccount();
+ projectAccountType.setProjectAccountNumber("sds128");
+
+ QueueType queueType = app.addNewQueue();
+ queueType.setQueueName("development");
+
+ app.setCpuCount(1);
+ app.setJobType(JobTypeType.SERIAL);
+ app.setNodeCount(1);
+ app.setProcessorsPerNode(1);
+
+ /*
+ * Use bat file if it is compiled on Windows
+ */
+ app.setExecutableLocation("/bin/echo");
+
+ /*
+ * Default tmp location
+ */
+ String tempDir = "/scratch/01437/ogce/test/";
+ String date = (new Date()).toString();
+ date = date.replaceAll(" ", "_");
+ date = date.replaceAll(":", "_");
+
+ tempDir = tempDir + File.separator
+ + "SimpleEcho" + "_" + date + "_" + UUID.randomUUID();
+
+ System.out.println(tempDir);
+ app.setScratchWorkingDirectory(tempDir);
+ app.setStaticWorkingDirectory(tempDir);
+ app.setInputDataDirectory(tempDir + File.separator + "inputData");
+ app.setOutputDataDirectory(tempDir + File.separator + "outputData");
+ app.setStandardOutput(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stdout");
+ app.setStandardError(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stderr");
+
+
+ /*
+ * Service
+ */
+ ServiceDescription serv = new ServiceDescription();
+ serv.getType().setName("SimpleEcho");
+
+ List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+
+ InputParameterType input = InputParameterType.Factory.newInstance();
+ input.setParameterName("echo_input");
+ input.setParameterType(StringParameterType.Factory.newInstance());
+ inputList.add(input);
+
+ InputParameterType input1 = InputParameterType.Factory.newInstance();
+ input.setParameterName("myinput");
+ URIParameterType uriType = URIParameterType.Factory.newInstance();
+ uriType.setValue("gsiftp://gridftp1.ls4.tacc.utexas.edu:2811//home1/01437/ogce/gram_20130215.log");
+ input.setParameterType(uriType);
+ inputList.add(input1);
+
+
+ InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
+
+ .size()]);
+ List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+ OutputParameterType output = OutputParameterType.Factory.newInstance();
+ output.setParameterName("echo_output");
+ output.setParameterType(StringParameterType.Factory.newInstance());
+ outputList.add(output);
+
+ OutputParameterType[] outputParamList = outputList
+ .toArray(new OutputParameterType[outputList.size()]);
+
+ serv.getType().setInputParametersArray(inputParamList);
+ serv.getType().setOutputParametersArray(outputParamList);
+
+ jobExecutionContext = new JobExecutionContext(gFacConfiguration,serv.getType().getName());
+ // Adding security context
+ jobExecutionContext.addSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT, getSecurityContext());
+ ApplicationContext applicationContext = new ApplicationContext();
+ jobExecutionContext.setApplicationContext(applicationContext);
+ applicationContext.setServiceDescription(serv);
+ applicationContext.setApplicationDeploymentDescription(appDesc);
+ applicationContext.setHostDescription(host);
+
+ MessageContext inMessage = new MessageContext();
+ ActualParameter echo_input = new ActualParameter();
+ ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+ inMessage.addParameter("echo_input", echo_input);
+
+ // added extra
+ ActualParameter copy_input = new ActualParameter();
+ copy_input.getType().changeType(URIParameterType.type);
+ ((URIParameterType)copy_input.getType()).setValue("file:///tmp/tmpstrace");
+
+ ActualParameter outlocation = new ActualParameter();
+ ((StringParameterType)outlocation.getType()).setValue("./outputData/.");
+ inMessage.addParameter("copy_input", copy_input);
+ inMessage.addParameter("outputlocation", outlocation);
+
+ // added extra
+
+
+
+ jobExecutionContext.setInMessageContext(inMessage);
+
+ MessageContext outMessage = new MessageContext();
+ ActualParameter echo_out = new ActualParameter();
+// ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+ outMessage.addParameter("echo_output", echo_out);
+
+ jobExecutionContext.setOutMessageContext(outMessage);
+
+ }
+
+ @Test
+ public void testGramProvider() throws GFacException {
+ GFacImpl gFacAPI = new GFacImpl();
+ gFacAPI.submitJob(jobExecutionContext);
+ MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
+ Assert.assertEquals(MappingFactory.toString((ActualParameter)outMessageContext.getParameter("echo_output")), "hello");
+ }
+
+ @Test
+ public void testGetJdbcUrl() {
+ System.out.println(getJDBCUrl());
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/test/resources/PBSTemplate.xslt
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/test/resources/PBSTemplate.xslt b/modules/gfac/gfac-gram/src/test/resources/PBSTemplate.xslt
new file mode 100644
index 0000000..e749e9c
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/test/resources/PBSTemplate.xslt
@@ -0,0 +1,73 @@
+<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under
+ the Apache License, Version 2.0 (theÏ "License"); you may not use this file except in compliance with the License. You may
+ obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to
+ in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF
+ ANY ~ KIND, either express or implied. See the License for the specific language governing permissions and limitations under
+ the License. -->
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
+<xsl:output method="text" />
+<xsl:template match="/ns:JobDescriptor">
+#! /bin/sh
+# PBS batch job script built by Globus job manager
+# <xsl:choose>
+ <xsl:when test="ns:shellName">
+##PBS -S <xsl:value-of select="ns:shellName"/>
+ </xsl:when></xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:queueName">
+#PBS -q <xsl:value-of select="ns:queueName"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:mailOptions">
+#PBS -m <xsl:value-of select="ns:mailOptions"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+<xsl:when test="ns:acountString">
+#PBS -A <xsl:value-of select="ns:acountString"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:maxWallTime">
+#PBS -l walltime=<xsl:value-of select="ns:maxWallTime"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#PBS -o <xsl:value-of select="ns:standardOutFile"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#PBS -e <xsl:value-of select="ns:standardErrorFile"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
+#PBS -l nodes=<xsl:value-of select="ns:nodes"/>:ppn=<xsl:value-of select="ns:processesPerNode"/>
+<xsl:text>
</xsl:text>
+ </xsl:when>
+ </xsl:choose>
+<xsl:for-each select="ns:exports/ns:name">
+<xsl:value-of select="."/>=<xsl:value-of select="./@value"/><xsl:text>
</xsl:text>
+export<xsl:text> </xsl:text><xsl:value-of select="."/>
+<xsl:text>
</xsl:text>
+</xsl:for-each>
+<xsl:for-each select="ns:preJobCommands/ns:command">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+ </xsl:for-each>
+cd <xsl:text> </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>
</xsl:text>
+ <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
+<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text> </xsl:text></xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text> </xsl:text>
+<xsl:for-each select="ns:inputs/ns:input">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+ </xsl:for-each>
+<xsl:for-each select="ns:postJobCommands/ns:command">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+</xsl:for-each>
+
+</xsl:template>
+
+</xsl:stylesheet>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/test/resources/gfac-config.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/test/resources/gfac-config.xml b/modules/gfac/gfac-gram/src/test/resources/gfac-config.xml
new file mode 100644
index 0000000..85d148d
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/test/resources/gfac-config.xml
@@ -0,0 +1,33 @@
+<!-- ~ Licensed to the Apache Software Foundation (ASF) under one ~ or more
+ contributor license agreements. See the NOTICE file ~ distributed with this
+ work for additional information ~ regarding copyright ownership. The ASF
+ licenses this file ~ to you under the Apache License, Version 2.0 (the ~
+ "License"); you may not use this file except in compliance ~ with the License.
+ You may obtain a copy of the License at ~ ~ http://www.apache.org/licenses/LICENSE-2.0
+ ~ ~ Unless required by applicable law or agreed to in writing, ~ software
+ distributed under the License is distributed on an ~ "AS IS" BASIS, WITHOUT
+ WARRANTIES OR CONDITIONS OF ANY ~ KIND, either express or implied. See the
+ License for the ~ specific language governing permissions and limitations
+ ~ under the License. -->
+
+<GFac>
+ <GlobalHandlers>
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.AppDescriptorCheckHandler">
+ <property name="name" value="value"/>
+ </Handler>
+ </InHandlers>
+ <OutHandlers></OutHandlers>
+ </GlobalHandlers>
+
+
+ <Provider class="org.apache.airavata.gfac.provider.impl.SSHProvider" host="org.apache.airavata.schemas.gfac.impl.SSHHostTypeImpl">
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.SSHDirectorySetupHandler"/>
+ <Handler class="org.apache.airavata.gfac.handler.SSHInputHandler"/>
+ </InHandlers>
+ <OutHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.SSHOutputHandler"/>
+ </OutHandlers>
+ </Provider>
+</GFac>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gram/src/test/resources/logging.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gram/src/test/resources/logging.properties b/modules/gfac/gfac-gram/src/test/resources/logging.properties
new file mode 100644
index 0000000..0584d38
--- /dev/null
+++ b/modules/gfac/gfac-gram/src/test/resources/logging.properties
@@ -0,0 +1,42 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#
+#default/fallback log4j configuration
+#
+
+# Set root logger level to WARN and its only appender to A1.
+log4j.rootLogger=INFO, A1, A2
+
+# A1 is set to be a rolling file appender with default params
+log4j.appender.A1=org.apache.log4j.RollingFileAppender
+log4j.appender.A1.File=target/seclogs.txt
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%d [%t] %-5p %c %x - %m%n
+
+# A2 is a console appender
+log4j.appender.A2=org.apache.log4j.ConsoleAppender
+
+# A2 uses PatternLayout.
+log4j.appender.A2.layout=org.apache.log4j.PatternLayout
+log4j.appender.A2.layout.ConversionPattern=%d [%t] %-5p %c{1} %x - %m%n
+
+log4j.logger.unicore.security=INFO
+
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-gsissh/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/pom.xml b/modules/gfac/gfac-gsissh/pom.xml
index 2f67b76..7360743 100644
--- a/modules/gfac/gfac-gsissh/pom.xml
+++ b/modules/gfac/gfac-gsissh/pom.xml
@@ -105,28 +105,4 @@
</dependency>
</dependencies>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-dependency-plugin</artifactId>
- <executions>
- <execution>
- <id>copy-dependencies</id>
- <phase>package</phase>
- <goals>
- <goal>copy-dependencies</goal>
- </goals>
- <configuration>
- <outputDirectory>target/lib</outputDirectory>
- <overWriteReleases>false</overWriteReleases>
- <overWriteSnapshots>true</overWriteSnapshots>
- </configuration>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
-
</project>
http://git-wip-us.apache.org/repos/asf/airavata/blob/13b505ae/modules/gfac/gfac-ssh/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/pom.xml b/modules/gfac/gfac-ssh/pom.xml
index d3df765..c463661 100644
--- a/modules/gfac/gfac-ssh/pom.xml
+++ b/modules/gfac/gfac-ssh/pom.xml
@@ -106,27 +106,4 @@
</dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-dependency-plugin</artifactId>
- <executions>
- <execution>
- <id>copy-dependencies</id>
- <phase>package</phase>
- <goals>
- <goal>copy-dependencies</goal>
- </goals>
- <configuration>
- <outputDirectory>target/lib</outputDirectory>
- <overWriteReleases>false</overWriteReleases>
- <overWriteSnapshots>true</overWriteSnapshots>
- </configuration>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
-
</project>