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From chath...@apache.org
Subject airavata git commit: adding application argument of output when creating pbs script
Date Tue, 13 Jan 2015 19:29:27 GMT
Repository: airavata
Updated Branches:
  refs/heads/master dc22b7beb -> 7a3f11b15


adding application argument of output when creating pbs script


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/7a3f11b1
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/7a3f11b1
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/7a3f11b1

Branch: refs/heads/master
Commit: 7a3f11b15231d224edeb32c612d5a49bdb449693
Parents: dc22b7b
Author: Chathuri Wimalasena <kamalasini@gmail.com>
Authored: Tue Jan 13 14:29:14 2015 -0500
Committer: Chathuri Wimalasena <kamalasini@gmail.com>
Committed: Tue Jan 13 14:29:14 2015 -0500

----------------------------------------------------------------------
 .../java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java   | 2 +-
 .../org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java    | 4 ++++
 .../java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java     | 4 ++++
 3 files changed, 9 insertions(+), 1 deletion(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/7a3f11b1/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
index 7aea965..3b50228 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
@@ -382,7 +382,7 @@ public class BetterGfacImpl implements GFac,Watcher {
 
         for (OutputDataObjectType objectType : taskOutputs){
             if (objectType.isRequiredToAddedToCommandLine()){
-              objectType.setValue(jobExecutionContext.getOutputDir() + File.separator + objectType.getName());
+              objectType.setValue(jobExecutionContext.getOutputDir() + File.separator + objectType.getValue());
             }
             if (objectType.getType() == DataType.STDOUT){
                 objectType.setValue(jobExecutionContext.getOutputDir() + File.separator +
jobExecutionContext.getApplicationName() + ".stdout");

http://git-wip-us.apache.org/repos/asf/airavata/blob/7a3f11b1/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
index cdcc0ec..6a4d2ef 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
@@ -240,6 +240,10 @@ public class GFACGSISSHUtils {
         for (Object outputParam : outputParams.values()) {
             if (outputParam instanceof OutputDataObjectType) {
                 OutputDataObjectType output = (OutputDataObjectType) outputParam;
+                if (output.getApplicationArgument() != null
+                        && !output.getApplicationArgument().equals("")) {
+                    inputValues.add(output.getApplicationArgument());
+                }
                 if (output.getValue() != null && !output.getValue().equals("") &&
output.isRequiredToAddedToCommandLine()) {
                     inputValues.add(output.getValue());
                 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/7a3f11b1/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
index bf2576a..b313dc2 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
@@ -296,6 +296,10 @@ public class GFACSSHUtils {
         for (Object outputParam : outputParams.values()) {
             if (outputParam instanceof OutputDataObjectType) {
                 OutputDataObjectType output = (OutputDataObjectType) outputParam;
+                if (output.getApplicationArgument() != null
+                        && !output.getApplicationArgument().equals("")) {
+                    inputValues.add(output.getApplicationArgument());
+                }
                 if (output.getValue() != null && !output.getValue().equals("") &&
output.isRequiredToAddedToCommandLine()) {
                     inputValues.add(output.getValue());
                 }


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