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 <[email protected]> Authored: Tue Jan 13 14:29:14 2015 -0500 Committer: Chathuri Wimalasena <[email protected]> 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()); }
