airavata-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From hes...@apache.org
Subject svn commit: r1461795 - in /airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider: impl/EC2Provider.java utils/ProviderUtils.java
Date Wed, 27 Mar 2013 18:55:11 GMT
Author: heshan
Date: Wed Mar 27 18:55:11 2013
New Revision: 1461795

URL: http://svn.apache.org/r1461795
Log:
AIRAVATA-803 Generating the command dynamically.

Modified:
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/EC2Provider.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ProviderUtils.java

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/EC2Provider.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/EC2Provider.java?rev=1461795&r1=1461794&r2=1461795&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/EC2Provider.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/EC2Provider.java
Wed Mar 27 18:55:11 2013
@@ -42,13 +42,13 @@ import com.sshtools.j2ssh.util.Base64;
 import org.apache.airavata.commons.gfac.type.ActualParameter;
 import org.apache.airavata.commons.gfac.type.ApplicationDescription;
 import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.context.security.AmazonSecurityContext;
 import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.security.AmazonSecurityContext;
 import org.apache.airavata.gfac.notification.events.EC2ProviderEvent;
 import org.apache.airavata.gfac.provider.GFacProvider;
 import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.gfac.provider.utils.ProviderUtils;
 import org.apache.airavata.schemas.gfac.Ec2ApplicationDeploymentType;
-import org.apache.airavata.schemas.gfac.InputParameterType;
 import org.apache.airavata.schemas.gfac.OutputParameterType;
 import org.apache.airavata.schemas.gfac.StringParameterType;
 import org.bouncycastle.openssl.PEMWriter;
@@ -124,7 +124,7 @@ public class EC2Provider implements GFac
     }
 
     public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException
{
-        final String command2 = "sh run.sh SRR042383.21414#CTGGCACGGAGTTAGCCGATCCTTATTCATAAAGTACATGCAAACGGGTATCCATACTCGACTTTATTCCTTTATAAAAGAAGTTTACAACCCATAGGGCAGTCATCCTTCACGCTACTTGGCTGGTTCAGGCCTGCGCCCATTGACCAATATTCCTCACTGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCGTGCCGCCGGTCGCCATCAGTCTTAGCAAGCTAAGACCATGCTGCCCCTGACTTGCATGTGTTAAGCCTGTAGCTTAGCGTTC
SRR042383.31933#CTGGCACGGAGTTAGCCGATCCTTATTCATAAAGTACATGCAAACGGGTATCCATACCCGACTTTATTCCTTTATAAAAGAAGTTTACAACCCATAGGGCAGTCATCCTTCACGCTACTTGGCTGGTTCAGGCTCTCGCCCATTGACCAATATTCCTCACTGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAAATCTTCCTTTCAGAAGGCTATCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCGTGCG"
+ '\n'
 ;
+//        final String command2 = "sh run.sh SRR042383.21414#CTGGCACGGAGTTAGCCGATCCTTATTCATAAAGTACATGCAAACGGGTATCCATACTCGACTTTATTCCTTTATAAAAGAAGTTTACAACCCATAGGGCAGTCATCCTTCACGCTACTTGGCTGGTTCAGGCCTGCGCCCATTGACCAATATTCCTCACTGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCGTGCCGCCGGTCGCCATCAGTCTTAGCAAGCTAAGACCATGCTGCCCCTGACTTGCATGTGTTAAGCCTGTAGCTTAGCGTTC
SRR042383.31933#CTGGCACGGAGTTAGCCGATCCTTATTCATAAAGTACATGCAAACGGGTATCCATACCCGACTTTATTCCTTTATAAAAGAAGTTTACAACCCATAGGGCAGTCATCCTTCACGCTACTTGGCTGGTTCAGGCTCTCGCCCATTGACCAATATTCCTCACTGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAAATCTTCCTTTCAGAAGGCTATCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCGTGCG"
+ '\
 n';
 
         String shellCmd = createShellCmd(jobExecutionContext);
 
@@ -176,7 +176,7 @@ public class EC2Provider implements GFac
             log.info("ssh session is open successfully...");
             session.requestPseudoTerminal("vt100", 80, 25, 0, 0, "");
             session.startShell();
-            session.getOutputStream().write(command2.getBytes());
+            session.getOutputStream().write(shellCmd.getBytes());
 
             InputStream in = session.getInputStream();
             byte buffer[] = new byte[255];
@@ -215,25 +215,31 @@ public class EC2Provider implements GFac
 
     }
 
-    private String createShellCmd(JobExecutionContext jobExecutionContext) {
+    private String createShellCmd(JobExecutionContext jobExecutionContext) throws GFacProviderException
{
         String command = "";
         ApplicationDescription appDesc = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
 
         if(appDesc.getType() instanceof Ec2ApplicationDeploymentType) {
             Ec2ApplicationDeploymentType type = (Ec2ApplicationDeploymentType) appDesc.getType();
-            command = type.getExecutableType() + " " + type.getExecutable() + " ";
 
-            InputParameterType[] inputParams = jobExecutionContext.getApplicationContext().
-                    getServiceDescription().getType().getInputParametersArray();
+            if(type.getExecutable() !=null) {
+                command = type.getExecutableType() + " " + type.getExecutable();
+            } else {
+                command = "sh" + " " + type.getExecutable();
+            }
+
+            List<String> inputParams = null;
+            try {
+                inputParams = ProviderUtils.getInputParameters(jobExecutionContext);
+            } catch (GFacProviderException e) {
+                throw new GFacProviderException("Error in extracting input values from JobExecutionContext");
+            }
 
-            for(InputParameterType inparamType : inputParams){
-                String paramName = inparamType.getParameterName();
-                Object parameter = jobExecutionContext.getInMessageContext().getParameter(paramName);
-                //TODO : check
-//                command = command + ((StringParameterType)parameter).getValue() + " ";
+            for(String param : inputParams){
+                command = " " + command + " " + param;
             }
 
-            System.out.println("Command to be executed on EC2 : " + command);
+            log.info("Command to be executed on EC2 : " + command);
         }
 
         return command;

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ProviderUtils.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ProviderUtils.java?rev=1461795&r1=1461794&r2=1461795&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ProviderUtils.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ProviderUtils.java
Wed Mar 27 18:55:11 2013
@@ -1,3 +1,24 @@
+/*
+ *
+ * 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.utils;
 
 import org.apache.airavata.commons.gfac.type.ActualParameter;



Mime
View raw message