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From shame...@apache.org
Subject airavata git commit: Fixed issues with SSH Fork
Date Fri, 06 Nov 2015 22:50:57 GMT
Repository: airavata
Updated Branches:
  refs/heads/master 85fb6b694 -> 140d9bd50


Fixed issues with SSH Fork


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/140d9bd5
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/140d9bd5
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/140d9bd5

Branch: refs/heads/master
Commit: 140d9bd503c713833ec18d248c02a3faf74b5102
Parents: 85fb6b6
Author: Shameera Rathnayaka <shameerainfo@gmail.com>
Authored: Fri Nov 6 17:50:51 2015 -0500
Committer: Shameera Rathnayaka <shameerainfo@gmail.com>
Committed: Fri Nov 6 17:50:51 2015 -0500

----------------------------------------------------------------------
 .../apache/airavata/gfac/core/GFacUtils.java    | 82 ++++++++++----------
 .../impl/task/SSHForkJobSubmissionTask.java     |  3 +-
 2 files changed, 45 insertions(+), 40 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/140d9bd5/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
index 6652504..c3de6a2 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
@@ -463,52 +463,56 @@ public class GFacUtils {
 
         List<String> inputValues = new ArrayList<String>();
         List<InputDataObjectType> processInputs = processModel.getProcessInputs();
+        if (processInputs != null) {
 
-        // sort the inputs first and then build the command ListR
-        Comparator<InputDataObjectType> inputOrderComparator = new Comparator<InputDataObjectType>()
{
-            @Override
-            public int compare(InputDataObjectType inputDataObjectType, InputDataObjectType
t1) {
-                return inputDataObjectType.getInputOrder() - t1.getInputOrder();
-            }
-        };
-        Set<InputDataObjectType> sortedInputSet = new TreeSet<InputDataObjectType>(inputOrderComparator);
-        for (InputDataObjectType input : processInputs) {
-            sortedInputSet.add(input);
-        }
-        for (InputDataObjectType inputDataObjectType : sortedInputSet) {
-            if (!inputDataObjectType.isRequiredToAddedToCommandLine()) {
-                continue;
-            }
-            if (inputDataObjectType.getApplicationArgument() != null
-                    && !inputDataObjectType.getApplicationArgument().equals(""))
{
-                inputValues.add(inputDataObjectType.getApplicationArgument());
-            }
-
-            if (inputDataObjectType.getValue() != null
-                    && !inputDataObjectType.getValue().equals("")) {
-                if (inputDataObjectType.getType() == DataType.URI) {
-                    // set only the relative path
-                    String filePath = inputDataObjectType.getValue();
-                    filePath = filePath.substring(filePath.lastIndexOf(File.separatorChar)
+ 1, filePath.length());
-                    inputValues.add(filePath);
-                } else {
-                    inputValues.add(inputDataObjectType.getValue());
+            // sort the inputs first and then build the command ListR
+            Comparator<InputDataObjectType> inputOrderComparator = new Comparator<InputDataObjectType>()
{
+                @Override
+                public int compare(InputDataObjectType inputDataObjectType, InputDataObjectType
t1) {
+                    return inputDataObjectType.getInputOrder() - t1.getInputOrder();
+                }
+            };
+            Set<InputDataObjectType> sortedInputSet = new TreeSet<InputDataObjectType>(inputOrderComparator);
+            for (InputDataObjectType input : processInputs) {
+                sortedInputSet.add(input);
+            }
+            for (InputDataObjectType inputDataObjectType : sortedInputSet) {
+                if (!inputDataObjectType.isRequiredToAddedToCommandLine()) {
+                    continue;
+                }
+                if (inputDataObjectType.getApplicationArgument() != null
+                        && !inputDataObjectType.getApplicationArgument().equals(""))
{
+                    inputValues.add(inputDataObjectType.getApplicationArgument());
                 }
 
+                if (inputDataObjectType.getValue() != null
+                        && !inputDataObjectType.getValue().equals("")) {
+                    if (inputDataObjectType.getType() == DataType.URI) {
+                        // set only the relative path
+                        String filePath = inputDataObjectType.getValue();
+                        filePath = filePath.substring(filePath.lastIndexOf(File.separatorChar)
+ 1, filePath.length());
+                        inputValues.add(filePath);
+                    } else {
+                        inputValues.add(inputDataObjectType.getValue());
+                    }
+
+                }
             }
         }
 
         List<OutputDataObjectType> processOutputs = processModel.getProcessOutputs();
-        for (OutputDataObjectType output : processOutputs) {
-            if (output.getApplicationArgument() != null
-                    && !output.getApplicationArgument().equals("")) {
-                inputValues.add(output.getApplicationArgument());
-            }
-            if (output.getValue() != null && !output.getValue().equals("") &&
output.isRequiredToAddedToCommandLine()) {
-                if (output.getType() == DataType.URI) {
-                    String filePath = output.getValue();
-                    filePath = filePath.substring(filePath.lastIndexOf(File.separatorChar)
+ 1, filePath.length());
-                    inputValues.add(filePath);
+        if (processOutputs != null) {
+            for (OutputDataObjectType output : processOutputs) {
+                if (output.getApplicationArgument() != null
+                        && !output.getApplicationArgument().equals("")) {
+                    inputValues.add(output.getApplicationArgument());
+                }
+                if (output.getValue() != null && !output.getValue().equals("") &&
output.isRequiredToAddedToCommandLine()) {
+                    if (output.getType() == DataType.URI) {
+                        String filePath = output.getValue();
+                        filePath = filePath.substring(filePath.lastIndexOf(File.separatorChar)
+ 1, filePath.length());
+                        inputValues.add(filePath);
+                    }
                 }
             }
         }

http://git-wip-us.apache.org/repos/asf/airavata/blob/140d9bd5/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SSHForkJobSubmissionTask.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SSHForkJobSubmissionTask.java
b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SSHForkJobSubmissionTask.java
index 3a14b2e..45b8a3a 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SSHForkJobSubmissionTask.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SSHForkJobSubmissionTask.java
@@ -167,7 +167,8 @@ public class SSHForkJobSubmissionTask implements JobSubmissionTask {
 
     @Override
     public TaskStatus recover(TaskContext taskContext) {
-        return null;
+        //TODO implement recovery scenario instead of calling execute.
+        return execute(taskContext);
     }
 
 	@Override


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