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 <[email protected]> Authored: Fri Nov 6 17:50:51 2015 -0500 Committer: Shameera Rathnayaka <[email protected]> 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
