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Posted to commits@airavata.apache.org by sc...@apache.org on 2017/06/30 17:22:20 UTC
[1/2] airavata git commit: fixing issue in widlcard output file
transfer
Repository: airavata
Updated Branches:
refs/heads/develop fa8924435 -> 867135d41
fixing issue in widlcard output file transfer
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/2e667f25
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/2e667f25
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/2e667f25
Branch: refs/heads/develop
Commit: 2e667f25bfc64b6b642e3217796747da7c02ea33
Parents: 51005a1
Author: scnakandala <su...@gmail.com>
Authored: Fri Jun 30 13:21:20 2017 -0400
Committer: scnakandala <su...@gmail.com>
Committed: Fri Jun 30 13:21:20 2017 -0400
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.../apache/airavata/gfac/core/GFacUtils.java | 6 -----
.../gfac/impl/task/SCPDataStageTask.java | 26 +++++++++++++++++++-
2 files changed, 25 insertions(+), 7 deletions(-)
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http://git-wip-us.apache.org/repos/asf/airavata/blob/2e667f25/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
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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 37cbea3..1bb9e6f 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
@@ -71,7 +71,6 @@ import java.net.URISyntaxException;
import java.net.URL;
import java.net.UnknownHostException;
import java.nio.ByteBuffer;
-import java.nio.file.Paths;
import java.security.SecureRandom;
import java.util.*;
import java.util.regex.Matcher;
@@ -967,11 +966,6 @@ public class GFacUtils {
ReplicaCatalog replicaCatalog = RegistryFactory.getReplicaCatalog();
String productUri = replicaCatalog.registerDataProduct(dataProductModel);
-
- if(expOutput.getName().contains("*")){
- String actualFileName = Paths.get(outputVal).getFileName().toString();
- expOutput.setName(actualFileName);
- }
expOutput.setValue(productUri);
}
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/2e667f25/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SCPDataStageTask.java
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diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SCPDataStageTask.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SCPDataStageTask.java
index dd7acaf..eb902a5 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SCPDataStageTask.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SCPDataStageTask.java
@@ -40,11 +40,16 @@ import org.apache.airavata.model.appcatalog.storageresource.StorageResourceDescr
import org.apache.airavata.model.application.io.InputDataObjectType;
import org.apache.airavata.model.application.io.OutputDataObjectType;
import org.apache.airavata.model.commons.ErrorModel;
+import org.apache.airavata.model.experiment.ExperimentModel;
+import org.apache.airavata.model.process.ProcessModel;
import org.apache.airavata.model.status.ProcessState;
import org.apache.airavata.model.status.TaskState;
import org.apache.airavata.model.status.TaskStatus;
import org.apache.airavata.model.task.DataStagingTaskModel;
import org.apache.airavata.model.task.TaskTypes;
+import org.apache.airavata.registry.cpi.ExperimentCatalog;
+import org.apache.airavata.registry.cpi.ExperimentCatalogModelType;
+import org.apache.airavata.registry.cpi.RegistryException;
import org.apache.thrift.TException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -163,6 +168,15 @@ public class SCPDataStageTask implements Task {
String sourceParentPath = (new File(sourceURI.getPath())).getParentFile().getPath();
List<String> fileNames = taskContext.getParentProcessContext().getDataMovementRemoteCluster()
.getFileNameFromExtension(fileName, sourceParentPath, sshSession);
+
+ ExperimentCatalog experimentCatalog = processContext.getExperimentCatalog();
+
+ String experimentId = processContext.getExperimentId();
+ ExperimentModel experiment = (ExperimentModel)experimentCatalog.get(ExperimentCatalogModelType.EXPERIMENT, experimentId);
+
+ String processId = processContext.getProcessId();
+ ProcessModel processModel = processContext.getProcessModel();
+
for(int i=0; i<fileNames.size(); i++){
String temp = fileNames.get(i);
if(temp != null && temp != ""){
@@ -176,6 +190,16 @@ public class SCPDataStageTask implements Task {
//Wildcard support is only enabled for output data staging
if (processState == ProcessState.OUTPUT_DATA_STAGING) {
+ OutputDataObjectType outputDataObjectType = new OutputDataObjectType();
+ outputDataObjectType.setName(fileName);
+ experiment.addToExperimentOutputs(outputDataObjectType);
+ processModel.addToProcessOutputs(outputDataObjectType);
+
+ experimentCatalog.update(ExperimentCatalogModelType.EXPERIMENT, experiment, experimentId);
+ experimentCatalog.update(ExperimentCatalogModelType.PROCESS, processModel, processId);
+
+ taskContext.setProcessOutput(outputDataObjectType);
+
makeDir(taskContext, destinationURI);
// TODO - save updated subtask model with new destination
outputDataStaging(taskContext, sshSession, sourceURI, destinationURI);
@@ -254,7 +278,7 @@ public class SCPDataStageTask implements Task {
errorModel.setActualErrorMessage(e.getMessage());
errorModel.setUserFriendlyMessage(msg);
taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
- } catch (GFacException e) {
+ } catch (RegistryException | GFacException e) {
String msg = "Data staging failed";
log.error(msg, e);
status.setState(TaskState.FAILED);
[2/2] airavata git commit: merge
Posted by sc...@apache.org.
merge
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/867135d4
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/867135d4
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/867135d4
Branch: refs/heads/develop
Commit: 867135d4137e61cd201bc02f91c5308a5aa66fa5
Parents: 2e667f2 fa89244
Author: scnakandala <su...@gmail.com>
Authored: Fri Jun 30 13:22:05 2017 -0400
Committer: scnakandala <su...@gmail.com>
Committed: Fri Jun 30 13:22:05 2017 -0400
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.../service/security/KeyCloakSecurityManager.java | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
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