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From lah...@apache.org
Subject svn commit: r1527759 - in /airavata/trunk/modules/gfac-core: ./ src/main/java/org/apache/airavata/gfac/ src/main/java/org/apache/airavata/gfac/provider/impl/ src/main/java/org/apache/airavata/gfac/utils/
Date Mon, 30 Sep 2013 20:17:04 GMT
Author: lahiru
Date: Mon Sep 30 20:17:04 2013
New Revision: 1527759

URL: http://svn.apache.org/r1527759
Log:
adding GSISSHProvider.

Added:
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
Modified:
    airavata/trunk/modules/gfac-core/pom.xml
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacAPI.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java

Modified: airavata/trunk/modules/gfac-core/pom.xml
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/pom.xml?rev=1527759&r1=1527758&r2=1527759&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/pom.xml (original)
+++ airavata/trunk/modules/gfac-core/pom.xml Mon Sep 30 20:17:04 2013
@@ -201,6 +201,29 @@
             <artifactId>guava</artifactId>
             <version>12.0</version>
         </dependency>
+
+	<!-- gsi-ssh api dependencies -->
+	<dependency>
+		<groupId>org.apache.airavata</groupId>
+    		<artifactId>gsissh</artifactId>
+    		<version>0.1-SNAPSHOT</version>
+	</dependency>
+ 	<dependency>
+            <groupId>com.jcraft</groupId>
+            <artifactId>jsch</artifactId>
+            <version>0.1.50</version>
+        </dependency>
+	<dependency>
+            <groupId>edu.illinois.ncsa</groupId>
+            <artifactId>bcgss</artifactId>
+            <version>146</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.xmlbeans</groupId>
+            <artifactId>xmlbeans</artifactId>
+            <version>${xmlbeans.version}</version>
+        </dependency>
+
     </dependencies>
 
     <build>
@@ -221,4 +244,4 @@
         </plugins>
     </build>
 
-</project>
\ No newline at end of file
+</project>

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacAPI.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacAPI.java?rev=1527759&r1=1527758&r2=1527759&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacAPI.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacAPI.java Mon
Sep 30 20:17:04 2013
@@ -73,14 +73,10 @@ public class GFacAPI {
                 disposeProvider(provider, jobExecutionContext);
             }
 
-        } catch (GFacException e) {
+        }catch (Exception e){
             jobExecutionContext.setProperty(ERROR_SENT,"true");
             jobExecutionContext.getNotifier().publish(new ExecutionFailEvent(e.getCause()));
-            throw e;
-        } catch (Exception e){
-            jobExecutionContext.setProperty(ERROR_SENT,"true");
-            jobExecutionContext.getNotifier().publish(new ExecutionFailEvent(e.getCause()));
-            throw new GFacException(e);
+            throw new GFacException(e.getMessage(),e);
         }
         finally {
             try{
@@ -98,7 +94,7 @@ public class GFacAPI {
     private void initProvider(GFacProvider provider, JobExecutionContext jobExecutionContext)
throws GFacException {
         try {
             provider.initialize(jobExecutionContext);
-        } catch (GFacProviderException e) {
+        } catch (Exception e) {
             throw new GFacException("Error while initializing provider " + provider.getClass().getName()
+ ".", e);
         }
     }
@@ -106,7 +102,7 @@ public class GFacAPI {
     private void executeProvider(GFacProvider provider, JobExecutionContext jobExecutionContext)
throws GFacException {
         try {
             provider.execute(jobExecutionContext);
-        } catch (GFacProviderException e) {
+        } catch (Exception e) {
             throw new GFacException("Error while executing provider " + provider.getClass().getName()
+ " functionality.", e);
         }
     }
@@ -114,7 +110,7 @@ public class GFacAPI {
     private void disposeProvider(GFacProvider provider, JobExecutionContext jobExecutionContext)
throws GFacException {
         try {
             provider.dispose(jobExecutionContext);
-        } catch (GFacProviderException e) {
+        } catch (Exception e) {
             throw new GFacException("Error while invoking provider " + provider.getClass().getName()
+ " dispose method.", e);
         }
     }

Added: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java?rev=1527759&view=auto
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
(added)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
Mon Sep 30 20:17:04 2013
@@ -0,0 +1,151 @@
+/*
+ *
+ * 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 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.GFacException;
+import org.apache.airavata.gfac.RequestData;
+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.notification.events.StartExecutionEvent;
+import org.apache.airavata.gfac.provider.GFacProvider;
+import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.gsi.ssh.api.AuthenticationInfo;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
+import org.apache.airavata.gsi.ssh.api.ServerInfo;
+import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gsi.ssh.impl.DefaultJobSubmissionListener;
+import org.apache.airavata.gsi.ssh.impl.MyProxyAuthenticationInfo;
+import org.apache.airavata.gsi.ssh.impl.PBSCluster;
+import org.apache.airavata.gsi.ssh.listener.JobSubmissionListener;
+import org.apache.airavata.schemas.gfac.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.*;
+
+public class GSISSHProvider implements GFacProvider {
+    private static final Logger log = LoggerFactory.getLogger(GSISSHProvider.class);
+
+    public void initProperties(Map<String, String> properties) throws GFacProviderException,
GFacException {
+
+    }
+
+    public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException,
GFacException {
+        //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException,
GFacException {
+        jobExecutionContext.getNotifier().publish(new StartExecutionEvent());
+        GsisshHostType host = (GsisshHostType) jobExecutionContext.getApplicationContext().
+                getHostDescription().getType();
+        HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) jobExecutionContext.getApplicationContext().
+                getApplicationDeploymentDescription().getType();
+        try {
+
+            GSISecurityContext gssCred = ((GSISecurityContext) jobExecutionContext.
+                    getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT));
+            RequestData requestData = gssCred.getRequestData();
+            ServerInfo serverInfo = new ServerInfo(requestData.getMyProxyUserName(), host.getHostAddress(),
22);
+            AuthenticationInfo authenticationInfo
+                    = new MyProxyAuthenticationInfo(requestData.getMyProxyUserName(), requestData.getMyProxyPassword(),
requestData.getMyProxyServerUrl(),
+                    7512, 17280000, System.getProperty(Constants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY));
+
+            // This installed path is a mandetory field, because this could change based
on the computing resource
+            Cluster cluster = new PBSCluster(serverInfo, authenticationInfo,host.getInstalledParentPath());
+            JobDescriptor jobDescriptor = new JobDescriptor();
+            jobDescriptor.setWorkingDirectory(app.getScratchWorkingDirectory());
+            jobDescriptor.setShellName("/bin/bash");
+            Random random = new Random();
+            int i = random.nextInt();
+            jobDescriptor.setJobName(app.getApplicationName() + String.valueOf(i));
+            jobDescriptor.setExecutablePath(app.getExecutableLocation());
+            jobDescriptor.setAllEnvExport(true);
+            jobDescriptor.setMailOptions("n");
+            jobDescriptor.setStandardOutFile(app.getStandardOutput());
+            jobDescriptor.setStandardErrorFile(app.getStandardError());
+            jobDescriptor.setNodes(app.getNodeCount());
+            jobDescriptor.setProcessesPerNode(app.getProcessorsPerNode());
+            jobDescriptor.setMaxWallTime(maxWallTimeCalculator(app.getMaxWallTime()));
+            jobDescriptor.setAcountString(app.getProjectAccount().getProjectAccountNumber());
+            jobDescriptor.setQueueName(app.getQueue().getQueueName());
+            jobDescriptor.setOwner(requestData.getMyProxyUserName());
+            List<String> inputValues = new ArrayList<String>();
+            MessageContext input = jobExecutionContext.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, " ");
+                    inputValues.add(value);
+                } else {
+                    String paramValue = MappingFactory.toString(actualParameter);
+                    inputValues.add(paramValue);
+                }
+            }
+            jobDescriptor.setInputValues(inputValues);
+
+            JobSubmissionListener listener = new DefaultJobSubmissionListener();
+            cluster.submitAsyncJob(jobDescriptor, listener);
+        } catch (SSHApiException e) {
+            String error = "Error submitting the job to host " + host.getHostAddress() +
e.getMessage();
+            log.error(error);
+            throw new GFacProviderException(error, e);
+        } catch (Exception e) {
+            String error = "Error submitting the job to host " + host.getHostAddress() +
e.getMessage();
+            log.error(error);
+            throw new GFacProviderException(error, e);
+        }
+    }
+
+    public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException,
GFacException {
+        //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    public void cancelJob(String jobId, JobExecutionContext jobExecutionContext) throws GFacException
{
+        //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    private String maxWallTimeCalculator(int maxWalltime) {
+        if (maxWalltime < 60) {
+            return "00:" + maxWalltime + ":00";
+        } else {
+            int minutes = maxWalltime % 60;
+            int hours = maxWalltime / 60;
+            return hours + ":" + minutes + ":00";
+        }
+    }
+}

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java?rev=1527759&r1=1527758&r2=1527759&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java
Mon Sep 30 20:17:04 2013
@@ -52,9 +52,7 @@ public class GramJobSubmissionListener i
      */
     public void waitFor()  {
         while (!isJobDone()) {
-
             synchronized (this) {
-
                 try {
                     wait();
                 } catch (InterruptedException e) {}



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