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From lah...@apache.org
Subject svn commit: r1441167 - in /airavata/trunk/modules/gfac-core: ./ src/main/java/org/apache/airavata/gfac/ src/main/java/org/apache/airavata/gfac/context/ src/main/java/org/apache/airavata/gfac/phoebus/ src/main/java/org/apache/airavata/gfac/provider/ src...
Date Thu, 31 Jan 2013 19:52:57 GMT
Author: lahiru
Date: Thu Jan 31 19:52:57 2013
New Revision: 1441167

URL: http://svn.apache.org/viewvc?rev=1441167&view=rev
Log:
adding GramProvider in to new gfac structure.

Added:
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/JobSubmissionFault.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GramProvider.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java
    airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java
Modified:
    airavata/trunk/modules/gfac-core/pom.xml
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/MessageContext.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/phoebus/PhoebusGridConfigurationHandler.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java

Modified: airavata/trunk/modules/gfac-core/pom.xml
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/pom.xml?rev=1441167&r1=1441166&r2=1441167&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/pom.xml (original)
+++ airavata/trunk/modules/gfac-core/pom.xml Thu Jan 31 19:52:57 2013
@@ -41,26 +41,26 @@
         </dependency>
         -->
         <dependency>
-            <groupId>cog-4_1_6_rc2</groupId>
+            <groupId>lead-security</groupId>
             <artifactId>puretls</artifactId>
             <type>jar</type>
-            <version>cog-4_1_6</version>
+            <version>0.9b4-1</version>
         </dependency>
-        <!--dependency>
-            <groupId>cog-4_1_6_rc2</groupId>
+        <dependency>
+            <groupId>lead-security</groupId>
             <artifactId>cryptix32</artifactId>
-            <version>cog-4_1_6</version>
+            <version>versionless</version>
         </dependency>
         <dependency>
-            <groupId>cog-4_1_6_rc2</groupId>
+            <groupId>lead-security</groupId>
             <artifactId>cryptix-asn1</artifactId>
-            <version>cog-4_1_6</version>
-        </dependency-->
-        <!--dependency>
-            <groupId>bouncycastle</groupId>
+            <version>versionless</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bouncycastle</groupId>
             <artifactId>bcprov-jdk15</artifactId>
-            <version>143</version>
-        </dependency-->
+            <version>1.45</version>
+        </dependency>
         <dependency>
             <groupId>commons-configuration</groupId>
             <artifactId>commons-configuration</artifactId>

Added: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/JobSubmissionFault.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/JobSubmissionFault.java?rev=1441167&view=auto
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/JobSubmissionFault.java
(added)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/JobSubmissionFault.java
Thu Jan 31 19:52:57 2013
@@ -0,0 +1,48 @@
+/*
+ *
+ * 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;
+
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.provider.GFacProvider;
+import org.apache.airavata.gfac.provider.GFacProviderException;
+
+public class JobSubmissionFault extends GFacProviderException{
+    
+    public static final String JOB_CANCEL = "JOB_CANCEL";
+
+    public static final String JOB_FAILED = "JOB_FAILED";
+
+    private String reason;
+
+    public JobSubmissionFault(GFacProvider provider, Throwable cause, String submitHost,
String contact, String rsl, JobExecutionContext jobExecutionContext) {
+        super(cause.getMessage(), cause,jobExecutionContext);
+    }
+
+    public void setReason(String reason) {
+        this.reason = reason;
+    }
+
+    public void sendFaultNotification(String message,
+			JobExecutionContext jobExecutionContext, Exception e,
+			String... additionalExceptiondata) {
+		
+	}
+}

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java?rev=1441167&r1=1441166&r2=1441167&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
Thu Jan 31 19:52:57 2013
@@ -24,7 +24,9 @@ package org.apache.airavata.gfac;
 import org.apache.airavata.commons.gfac.type.HostDescription;
 import org.apache.airavata.gfac.context.JobExecutionContext;
 import org.apache.airavata.gfac.provider.GFacProvider;
+import org.apache.airavata.gfac.provider.GramProvider;
 import org.apache.airavata.gfac.provider.impl.LocalProvider;
+import org.apache.airavata.schemas.gfac.GlobusHostType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -58,8 +60,11 @@ public class Scheduler {
      */
     private static GFacProvider getProvider(JobExecutionContext jobExecutionContext){
         HostDescription hostDescription = jobExecutionContext.getApplicationContext().getHostDescription();
-
-        return new LocalProvider();
+        if(hostDescription.getType() instanceof GlobusHostType){
+            return new GramProvider();
+        }else{
+            return new LocalProvider();
+        }
     }
 
 

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/MessageContext.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/MessageContext.java?rev=1441167&r1=1441166&r2=1441167&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/MessageContext.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/MessageContext.java
Thu Jan 31 19:52:57 2013
@@ -44,5 +44,8 @@ public class MessageContext extends Abst
         parameters.put(name, value);
     }
 
+    public Map<String,Object> getParameters(){
+        return parameters;
+    }
 
 }

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/phoebus/PhoebusGridConfigurationHandler.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/phoebus/PhoebusGridConfigurationHandler.java?rev=1441167&r1=1441166&r2=1441167&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/phoebus/PhoebusGridConfigurationHandler.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/phoebus/PhoebusGridConfigurationHandler.java
Thu Jan 31 19:52:57 2013
@@ -26,14 +26,14 @@ import org.globus.ftp.DataChannelAuthent
 import org.globus.ftp.GridFTPClient;
 
 public class PhoebusGridConfigurationHandler implements GridConfigurationHandler{
-    @Override
+
     public void handleSourceFTPClient(GridFTPClient client) throws Exception {
         if (PhoebusUtils.isPhoebusDriverConfigurationsDefined(client.getHost())) {
             client.setDataChannelAuthentication(DataChannelAuthentication.NONE);
             client.site("SITE SETNETSTACK phoebus:" + PhoebusUtils.getPhoebusDataChannelXIODriverParameters(client.getHost()));
         }
     }
-    @Override
+
     public void handleDestinationFTPClient(GridFTPClient client)
             throws Exception {
 

Added: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GramProvider.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GramProvider.java?rev=1441167&view=auto
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GramProvider.java
(added)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GramProvider.java
Thu Jan 31 19:52:57 2013
@@ -0,0 +1,131 @@
+/*
+ *
+ * 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;
+
+import org.apache.airavata.gfac.JobSubmissionFault;
+import org.apache.airavata.gfac.context.GSISecurityContext;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.notification.events.ExecutionFailEvent;
+import org.apache.airavata.gfac.utils.GramJobSubmissionListener;
+import org.apache.airavata.gfac.utils.GramProviderUtils;
+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.ietf.jgss.GSSCredential;
+import org.ietf.jgss.GSSException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class GramProvider implements GFacProvider {
+    private static final Logger log = LoggerFactory.getLogger(GramJobSubmissionListener.class);
+
+    private GramJob job;
+    private GramJobSubmissionListener listener;
+
+    // This method precpare the environment before the application invocation.
+    public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException
{
+        GramProviderUtils.makeDirectory(jobExecutionContext);
+        job = GramProviderUtils.setupEnvironment(jobExecutionContext);
+        listener = new GramJobSubmissionListener(job, jobExecutionContext);
+        job.addListener(listener);
+    }
+
+    public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException
{
+        System.out.println("Executing the job");
+        GlobusHostType host = (GlobusHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType();
+        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
+
+        StringBuffer buf = new StringBuffer();
+        try {
+
+            /*
+            * Set Security
+            */
+            GSISecurityContext gssContext = new GSISecurityContext(jobExecutionContext.getGFacConfiguration());
+            GSSCredential gssCred = gssContext.getGssCredentails();
+            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.debug("Request to contact:" + gateKeeper);
+
+            buf.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);
+
+            /*
+            * The first boolean is to specify the job is a batch job - use true for interactive
and false for batch.
+            * The second boolean is to specify to use the full proxy and not delegate a limited
proxy.
+            */
+            job.request(gateKeeper, false, false);
+            String gramJobid = job.getIDAsString();
+            log.info("JobID = " + gramJobid);
+
+            log.info(buf.toString());
+            /*
+            * Block untill job is done
+            */
+            listener.waitFor();
+
+            /*
+            * Remove listener
+            */
+            job.removeListener(listener);
+
+            /*
+            * Fail job
+            */
+            int jobStatus = listener.getStatus();
+
+            if (job.getExitCode() != 0 || jobStatus == GramJob.STATUS_FAILED) {
+                int errCode = listener.getError();
+                String errorMsg = "Job " + job.getID() + " on host " + host.getHostAddress()
+ " Job Exit Code = "
+                        + listener.getError();
+                JobSubmissionFault error = new JobSubmissionFault(this, new Exception(errorMsg),
"GFAC HOST",
+                        gateKeeper, job.getRSL(), jobExecutionContext);
+                jobExecutionContext.getNotifier().publish(new ExecutionFailEvent(error.getCause()));
+                throw error;
+            }
+        } catch (GramException e) {
+            JobSubmissionFault error = new JobSubmissionFault(this, e, host.getHostAddress(),
+                    host.getGlobusGateKeeperEndPointArray(0), job.getRSL(), jobExecutionContext);
+            jobExecutionContext.getNotifier().publish(new ExecutionFailEvent(error.getCause()));
+        } catch (GSSException e) {
+            throw new GFacProviderException(e.getMessage(), e, jobExecutionContext);
+        } catch (InterruptedException e) {
+            throw new GFacProviderException("Thread", e, jobExecutionContext);
+        } catch (SecurityException e) {
+            throw new GFacProviderException(e.getMessage(), e, jobExecutionContext);
+        } finally {
+            if (job != null) {
+                try {
+                    job.cancel();
+                } catch (Exception e) {
+                }
+            }
+        }
+
+    }
+
+    public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException
{
+    }
+}

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java?rev=1441167&r1=1441166&r2=1441167&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java
Thu Jan 31 19:52:57 2013
@@ -20,5 +20,86 @@
 */
 package org.apache.airavata.gfac.utils;
 
+import org.apache.airavata.gfac.ToolsException;
+import org.apache.airavata.gfac.context.GSISecurityContext;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.external.GridFtp;
+import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+import org.apache.airavata.schemas.gfac.GlobusHostType;
+import org.globus.gram.GramAttributes;
+import org.globus.gram.GramJob;
+import org.ietf.jgss.GSSCredential;
+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(GramJobSubmissionListener.class);
+
+    public static void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacProviderException
{
+        GlobusHostType host = (GlobusHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType();
+        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
+        GridFtp ftp = new GridFtp();
+
+        try {
+            GSISecurityContext gssContext = new GSISecurityContext(jobExecutionContext.getGFacConfiguration());
+            GSSCredential gssCred = gssContext.getGssCredentails();
+            String[] hostgridFTP = host.getGridFTPEndPointArray();
+            if (hostgridFTP == null || hostgridFTP.length == 0) {
+                hostgridFTP = new String[]{host.getHostAddress()};
+            }
+            boolean success = false;
+            GFacProviderException pe = null;// = new ProviderException("");
+            for (String endpoint : host.getGridFTPEndPointArray()) {
+                try {
+
+                    URI tmpdirURI = GFacUtils.createGsiftpURI(endpoint, app.getScratchWorkingDirectory());
+                    URI workingDirURI = GFacUtils.createGsiftpURI(endpoint, app.getStaticWorkingDirectory());
+                    URI inputURI = GFacUtils.createGsiftpURI(endpoint, app.getInputDataDirectory());
+                    URI outputURI = GFacUtils.createGsiftpURI(endpoint, app.getOutputDataDirectory());
+
+                    log.info("Host FTP = " + hostgridFTP[0]);
+                    log.info("temp directory = " + tmpdirURI);
+                    log.info("Working directory = " + workingDirURI);
+                    log.info("Input directory = " + inputURI);
+                    log.info("Output directory = " + outputURI);
+
+                    ftp.makeDir(tmpdirURI, gssCred);
+                    ftp.makeDir(workingDirURI, gssCred);
+                    ftp.makeDir(inputURI, gssCred);
+                    ftp.makeDir(outputURI, gssCred);
+
+                    success = true;
+                    break;
+                } catch (URISyntaxException e) {
+                    pe = new GFacProviderException("URI is malformatted:" + e.getMessage(),
e, jobExecutionContext);
+
+                } catch (ToolsException e) {
+                    pe = new GFacProviderException(e.getMessage(), e, jobExecutionContext);
+                }
+            }
+            if (success == false) {
+                throw pe;
+            }
+        } catch (SecurityException e) {
+            throw new GFacProviderException(e.getMessage(), e, jobExecutionContext);
+        }
+    }
+
+    public static GramJob setupEnvironment(JobExecutionContext jobExecutionContext) throws
GFacProviderException {
+        log.debug("Searching for Gate Keeper");
+        try {
+            GramAttributes jobAttr = GramRSLGenerator.configureRemoteJob(jobExecutionContext);
+            String rsl = jobAttr.toRSL();
+
+            log.debug("RSL = " + rsl);
+            GramJob job = new GramJob(rsl);
+            return job;
+        } catch (ToolsException te) {
+            throw new GFacProviderException(te.getMessage(), te, jobExecutionContext);
+        }
+    }
 }

Added: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java?rev=1441167&view=auto
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java
(added)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java
Thu Jan 31 19:52:57 2013
@@ -0,0 +1,204 @@
+/*
+ *
+ * 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.utils;
+
+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.schemas.gfac.HpcApplicationDeploymentType;
+import org.apache.airavata.schemas.gfac.NameValuePairType;
+import org.apache.airavata.schemas.gfac.URIArrayType;
+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.getMaxWallTime() > 0) {
+            log.debug("Setting max wall clock time to " + app.getMaxWallTime());
+
+            if (app.getMaxWallTime() > 30 && app.getQueue() != null &&
app.getQueue().getQueueName().equals("debug")) {
+                throw new ToolsException("NCSA debug Queue only support jobs < 30 minutes");
+            }
+
+            jobAttr.setMaxWallTime(app.getMaxWallTime());
+            jobAttr.set("proxy_timeout", "1");
+        } else {
+            jobAttr.setMaxWallTime(30);
+        }
+
+        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())) {
+                    String[] values = ((URIArrayType) actualParameter.getType()).getValueArray();
+                    for (String value : 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
+//        ContextHeaderDocument.ContextHeader currentContextHeader = WorkflowContextHeaderBuilder.getCurrentContextHeader();
+//        if (currentContextHeader.getWorkflowSchedulingContext() != null) {
+//            if (currentContextHeader != null &&
+//                    currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()
!= null &&
+//                    currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray().length
> 0) {
+//                try {
+//                    int cpuCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getCpuCount();
+//                    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");
+//                    context.getNotifier().publish(new ExecutionFailEvent(context, e, "No
Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will
be used");
+//                }
+//                try {
+//                    int nodeCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].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");
+//                    context.getExecutionContext().getNotifier().executionFail(context,
e, "No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor
will be used");
+//                }
+//                try {
+//                    String queueName = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].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");
+//                    context.getExecutionContext().getNotifier().executionFail(context,
e, "No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor
will be used");
+//                }
+//            }
+//        }
+//        if(currentContextHeader.getWorkflowOutputDataHandling() != null){
+//            if(currentContextHeader.getWorkflowOutputDataHandling().getApplicationOutputDataHandlingArray().length
!= 0)
+//            app.setOutputDataDirectory(currentContextHeader.getWorkflowOutputDataHandling().getApplicationOutputDataHandlingArray()[0].getOutputDataDirectory());
+//        }
+        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());
+            }
+        }
+        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;
+    }
+}

Added: airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java?rev=1441167&view=auto
==============================================================================
--- airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java
(added)
+++ airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java
Thu Jan 31 19:52:57 2013
@@ -0,0 +1,166 @@
+/*
+ *
+ * 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 com.amazonaws.services.importexport.model.JobType;
+import org.apache.airavata.client.AiravataAPIFactory;
+import org.apache.airavata.client.api.AiravataAPI;
+import org.apache.airavata.commons.gfac.type.*;
+import org.apache.airavata.gfac.Constants;
+import org.apache.airavata.gfac.GFacAPI;
+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.schemas.gfac.*;
+import org.apache.commons.lang.SystemUtils;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
+public class GramProviderTest {
+    private JobExecutionContext jobExecutionContext;
+    @Before
+    public void setUp() throws Exception {
+
+        GFacConfiguration gFacConfiguration = new GFacConfiguration(null);
+        gFacConfiguration.setMyProxyLifeCycle(3600);
+        gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
+        gFacConfiguration.setMyProxyUser("ogce");
+        gFacConfiguration.setMyProxyPassphrase("Jdas7wph");
+        gFacConfiguration.setTrustedCertLocation("/Users/lahirugunathilake/Downloads/certificates");
+        //have to set InFlwo Handlers and outFlowHandlers
+        jobExecutionContext = new JobExecutionContext(gFacConfiguration);
+        ApplicationContext applicationContext = new ApplicationContext();
+        jobExecutionContext.setApplicationContext(applicationContext);
+        /*
+           * Host
+           */
+        HostDescription host = new HostDescription(GlobusHostType.type);
+        host.getType().setHostAddress("ranger.tacc.teragrid.org");
+        host.getType().setHostName("ranger");
+        ((GlobusHostType)host.getType()).setGlobusGateKeeperEndPointArray(new String[]{"gatekeeper.ranger.tacc.teragrid.org:2119/jobmanager-sge"});
+        ((GlobusHostType)host.getType()).setGridFTPEndPointArray(new String[]{"gsiftp://gridftp.ranger.tacc.teragrid.org:2811/"});
+        applicationContext.setHostDescription(host);
+        /*
+           * 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("TG-STA110014S");
+
+        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 + "input");
+        app.setOutputDataDirectory(tempDir + File.separator + "output");
+        app.setStandardOutput(tempDir + File.separator + "echo.stdout");
+        app.setStandardError(tempDir + File.separator + "echo.stderr");
+
+        applicationContext.setApplicationDeploymentDescription(appDesc);
+
+        /*
+           * 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[] 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);
+
+        applicationContext.setServiceDescription(serv);
+
+        MessageContext inMessage = new MessageContext();
+        ActualParameter echo_input = new ActualParameter();
+		((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+        inMessage.addParameter("echo_input", echo_input);
+
+        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 {
+        GFacAPI gFacAPI = new GFacAPI();
+        gFacAPI.submitJob(jobExecutionContext);
+        MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
+        Assert.assertEquals(MappingFactory.toString((ActualParameter)outMessageContext.getParameter("echo_output")),
"hello");
+    }
+}



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