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Posted to commits@airavata.apache.org by ra...@apache.org on 2014/08/28 17:45:17 UTC
[1/4] git commit: Updated the client with new parameters.
Repository: airavata
Updated Branches:
refs/heads/master 6821ce1ac -> 4adcce986
Updated the client with new parameters.
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/b3775eca
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/b3775eca
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/b3775eca
Branch: refs/heads/master
Commit: b3775eca9affdbb9cc5306697913790f763ce443
Parents: 21cae7e
Author: raminder <ra...@apache.org>
Authored: Mon Aug 25 12:00:09 2014 -0400
Committer: raminder <ra...@apache.org>
Committed: Mon Aug 25 12:00:09 2014 -0400
----------------------------------------------------------------------
.../samples/CreateLaunchExperimentUS3.java | 54 ++++++++++++++++++--
.../client/tools/RegisterUS3Application.java | 12 ++---
2 files changed, 57 insertions(+), 9 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/b3775eca/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java
index b8aebc8..8fa3b70 100644
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java
@@ -61,8 +61,8 @@ public class CreateLaunchExperimentUS3 {
// addDescriptors();
// final String expId = createUS3ExperimentForTrestles(airavata);
// final String expId = createUS3ExperimentForStampede(airavata);
-// final String expId = createUS3ExperimentForLonestar(airavata);
- final String expId = createUS3ExperimentForAlamo(airavata);
+ final String expId = createUS3ExperimentForLonestar(airavata);
+// final String expId = createUS3ExperimentForAlamo(airavata);
System.out.println("Experiment ID : " + expId);
launchExperiment(airavata, expId);
System.out.println("Launched successfully");
@@ -104,7 +104,9 @@ public class CreateLaunchExperimentUS3 {
} catch (InterruptedException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
-
+
+// airavata.terminateExperiment(expId);
+
// Experiment experiment = airavata.getExperiment(expId);
// System.out.println("retrieved exp id : " + experiment.getExperimentID());
} catch (Exception e) {
@@ -197,7 +199,18 @@ public class CreateLaunchExperimentUS3 {
input.setKey("input");
input.setType(DataType.URI);
input.setValue("file:///home/airavata/input/hpcinput.tar");
+ DataObjectType input1 = new DataObjectType();
+ input1.setKey("walltime");
+ input1.setType(DataType.STRING);
+ input1.setValue("-walltime=60");
+ DataObjectType input2 = new DataObjectType();
+ input2.setKey("mgroupcount");
+ input2.setType(DataType.STRING);
+ input2.setValue("-mgroupcount=1");
+
exInputs.add(input);
+ exInputs.add(input1);
+ exInputs.add(input2);
List<DataObjectType> exOut = new ArrayList<DataObjectType>();
DataObjectType output = new DataObjectType();
@@ -257,7 +270,19 @@ public class CreateLaunchExperimentUS3 {
input.setKey("input");
input.setType(DataType.URI);
input.setValue("file:///home/airavata/input/hpcinput.tar");
+ DataObjectType input1 = new DataObjectType();
+ input1.setKey("walltime");
+ input1.setType(DataType.STRING);
+ input1.setValue("-walltime=60");
+ DataObjectType input2 = new DataObjectType();
+ input2.setKey("mgroupcount");
+ input2.setType(DataType.STRING);
+ input2.setValue("-mgroupcount=1");
+
exInputs.add(input);
+ exInputs.add(input1);
+ exInputs.add(input2);
+
List<DataObjectType> exOut = new ArrayList<DataObjectType>();
DataObjectType output = new DataObjectType();
@@ -318,7 +343,18 @@ public class CreateLaunchExperimentUS3 {
input.setKey("input");
input.setType(DataType.URI);
input.setValue("file:///home/airavata/input/hpcinput.tar");
+ DataObjectType input1 = new DataObjectType();
+ input1.setKey("walltime");
+ input1.setType(DataType.STRING);
+ input1.setValue("-walltime=60");
+ DataObjectType input2 = new DataObjectType();
+ input2.setKey("mgroupcount");
+ input2.setType(DataType.STRING);
+ input2.setValue("-mgroupcount=1");
+
exInputs.add(input);
+ exInputs.add(input1);
+ exInputs.add(input2);
List<DataObjectType> exOut = new ArrayList<DataObjectType>();
DataObjectType output = new DataObjectType();
@@ -379,7 +415,19 @@ public class CreateLaunchExperimentUS3 {
input.setKey("input");
input.setType(DataType.URI);
input.setValue("file:///home/airavata/input/hpcinput.tar");
+ DataObjectType input1 = new DataObjectType();
+ input1.setKey("walltime");
+ input1.setType(DataType.STRING);
+ input1.setValue("-walltime=60");
+ DataObjectType input2 = new DataObjectType();
+ input2.setKey("mgroupcount");
+ input2.setType(DataType.STRING);
+ input2.setValue("-mgroupcount=1");
+
exInputs.add(input);
+ exInputs.add(input1);
+ exInputs.add(input2);
+
List<DataObjectType> exOut = new ArrayList<DataObjectType>();
DataObjectType output = new DataObjectType();
http://git-wip-us.apache.org/repos/asf/airavata/blob/b3775eca/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java
index e98aa07..9f59a4f 100644
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java
@@ -1,7 +1,5 @@
package org.apache.airavata.client.tools;
-import java.math.BigInteger;
-import java.security.SecureRandom;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
@@ -31,9 +29,12 @@ public class RegisterUS3Application {
private final static Logger logger = LoggerFactory.getLogger(RegisterSampleApplications.class);
- public static final String THRIFT_SERVER_HOST = "gridfarm005.ucs.indiana.edu";
- public static final int THRIFT_SERVER_PORT = 8930;
- private static final String DEFAULT_GATEWAY = "default";
+// public static final String THRIFT_SERVER_HOST = "gridfarm005.ucs.indiana.edu";
+// public static final int THRIFT_SERVER_PORT = 8930;
+ private static final String DEFAULT_GATEWAY= "default";
+ public static final String THRIFT_SERVER_HOST = "gw111.iu.xsede.org";
+ public static final int THRIFT_SERVER_PORT = 9930;
+// private static final String DEFAULT_GATEWAY = "ultrascan";
private static Airavata.Client airavataClient;
//Host Id's
@@ -224,7 +225,6 @@ public class RegisterUS3Application {
"/mnt/glusterfs/work/");
GatewayResourceProfile gatewayResourceProfile = new GatewayResourceProfile();
- gatewayResourceProfile.setGatewayID(DEFAULT_GATEWAY);
gatewayResourceProfile.setGatewayName(DEFAULT_GATEWAY);
gatewayResourceProfile.addToComputeResourcePreferences(stampedeResourcePreferences);
gatewayResourceProfile.addToComputeResourcePreferences(trestlesResourcePreferences);
[3/4] git commit: Allow usee to send the file URL to move the files.
AIRAVATA-1419
Posted by ra...@apache.org.
Allow usee to send the file URL to move the files. AIRAVATA-1419
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/6c500f2c
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/6c500f2c
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/6c500f2c
Branch: refs/heads/master
Commit: 6c500f2cc923c58600a4d1094e119094c618cf2c
Parents: 6c4471a
Author: raminder <ra...@apache.org>
Authored: Thu Aug 28 11:17:06 2014 -0400
Committer: raminder <ra...@apache.org>
Committed: Thu Aug 28 11:17:06 2014 -0400
----------------------------------------------------------------------
.../ssh/handler/AdvancedSCPInputHandler.java | 123 ++++++++++++-------
.../ssh/handler/AdvancedSCPOutputHandler.java | 14 +++
2 files changed, 90 insertions(+), 47 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/6c500f2c/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
index 86dcb22..7e3ecbb 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
@@ -52,6 +52,8 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.util.*;
/**
@@ -133,11 +135,6 @@ public class AdvancedSCPInputHandler extends AbstractRecoverableHandler {
this.passPhrase);
}
// Server info
- ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
- Cluster pbsCluster = null;
- // here doesn't matter what the job manager is because we are only doing some file handling
- // not really dealing with monitoring or job submission, so we pa
- pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
String parentPath = inputPath + File.separator + jobExecutionContext.getExperimentID() + File.separator + jobExecutionContext.getTaskData().getTaskID();
if (index < oldIndex) {
parentPath = oldFiles.get(index);
@@ -149,48 +146,80 @@ public class AdvancedSCPInputHandler extends AbstractRecoverableHandler {
}
DataTransferDetails detail = new DataTransferDetails();
TransferStatus status = new TransferStatus();
-
- MessageContext input = jobExecutionContext.getInMessageContext();
- Set<String> parameters = input.getParameters().keySet();
- for (String paramName : parameters) {
- ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
- String paramValue = MappingFactory.toString(actualParameter);
- //TODO: Review this with type
- if ("URI".equals(actualParameter.getType().getType().toString())) {
- if (index < oldIndex) {
- log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
- ((URIParameterType) actualParameter.getType()).setValue(oldFiles.get(index));
- data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
- } else {
- String stageInputFile = stageInputFiles(pbsCluster, paramValue, parentPath);
- ((URIParameterType) actualParameter.getType()).setValue(stageInputFile);
- StringBuffer temp = new StringBuffer(data.append(stageInputFile).append(",").toString());
- status.setTransferState(TransferState.UPLOAD);
- detail.setTransferStatus(status);
- detail.setTransferDescription("Input Data Staged: " + stageInputFile);
- registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-
- GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
- }
- } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
- List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
- List<String> newFiles = new ArrayList<String>();
- for (String paramValueEach : split) {
- if (index < oldIndex) {
- log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
- newFiles.add(oldFiles.get(index));
- data.append(oldFiles.get(index++)).append(",");
- } else {
- String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
- StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
- GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
- newFiles.add(stageInputFiles);
- }
- }
- ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
- }
- inputNew.getParameters().put(paramName, actualParameter);
- }
+ Cluster pbsCluster = null;
+ // here doesn't matter what the job manager is because we are only doing some file handling
+ // not really dealing with monitoring or job submission, so we pa
+ String lastHost = null;
+
+ MessageContext input = jobExecutionContext.getInMessageContext();
+ Set<String> parameters = input.getParameters().keySet();
+ for (String paramName : parameters) {
+ ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
+ String paramValue = MappingFactory.toString(actualParameter);
+ // TODO: Review this with type
+ if ("URI".equals(actualParameter.getType().getType().toString())) {
+ try {
+ URL file = new URL(paramValue);
+ this.userName = file.getUserInfo();
+ this.hostName = file.getHost();
+ paramValue = file.getPath();
+ } catch (MalformedURLException e) {
+ log.error(e.getLocalizedMessage(),e);
+ }
+ ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
+ if (pbsCluster == null && (lastHost == null || !lastHost.equals(hostName))) {
+ pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
+ }
+ lastHost = hostName;
+
+ if (index < oldIndex) {
+ log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
+ ((URIParameterType) actualParameter.getType()).setValue(oldFiles.get(index));
+ data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
+ } else {
+ String stageInputFile = stageInputFiles(pbsCluster, paramValue, parentPath);
+ ((URIParameterType) actualParameter.getType()).setValue(stageInputFile);
+ StringBuffer temp = new StringBuffer(data.append(stageInputFile).append(",").toString());
+ status.setTransferState(TransferState.UPLOAD);
+ detail.setTransferStatus(status);
+ detail.setTransferDescription("Input Data Staged: " + stageInputFile);
+ registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
+
+ GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
+ }
+ } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
+ List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
+ List<String> newFiles = new ArrayList<String>();
+ for (String paramValueEach : split) {
+ try {
+ URL file = new URL(paramValue);
+ this.userName = file.getUserInfo();
+ this.hostName = file.getHost();
+ paramValueEach = file.getPath();
+ } catch (MalformedURLException e) {
+ log.error(e.getLocalizedMessage(),e);
+ }
+ ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
+ if (pbsCluster == null && (lastHost == null || !lastHost.equals(hostName))) {
+ pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
+ }
+ lastHost = hostName;
+
+ if (index < oldIndex) {
+ log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
+ newFiles.add(oldFiles.get(index));
+ data.append(oldFiles.get(index++)).append(",");
+ } else {
+ String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
+ StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
+ GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
+ newFiles.add(stageInputFiles);
+ }
+ }
+ ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
+ }
+ inputNew.getParameters().put(paramName, actualParameter);
+ }
} catch (Exception e) {
log.error(e.getMessage());
throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
http://git-wip-us.apache.org/repos/asf/airavata/blob/6c500f2c/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
index 9b9f7b2..116d769 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
@@ -45,6 +45,8 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@@ -117,12 +119,24 @@ public class AdvancedSCPOutputHandler extends AbstractHandler {
this.passPhrase);
}
// Server info
+ if(jobExecutionContext.getTaskData().getAdvancedOutputDataHandling().getOutputDataDir() != null){
+ try{
+ URL outputPathURL = new URL(jobExecutionContext.getTaskData().getAdvancedOutputDataHandling().getOutputDataDir());
+ this.userName = outputPathURL.getUserInfo();
+ this.hostName = outputPathURL.getHost();
+ outputPath = outputPathURL.getPath();
+ } catch (MalformedURLException e) {
+ log.error(e.getLocalizedMessage(),e);
+ }
+ }
ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
+ if(!jobExecutionContext.getTaskData().getAdvancedOutputDataHandling().isPersistOutputData()){
outputPath = outputPath + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID()
+ File.separator;
pbsCluster.makeDirectory(outputPath);
+ }
pbsCluster.scpTo(outputPath, standardError);
pbsCluster.scpTo(outputPath, standardOutput);
List<DataObjectType> outputArray = new ArrayList<DataObjectType>();
[2/4] git commit: Merge branch 'master' of
https://git-wip-us.apache.org/repos/asf/airavata
Posted by ra...@apache.org.
Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/6c4471ad
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/6c4471ad
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/6c4471ad
Branch: refs/heads/master
Commit: 6c4471ada3585716426ff3ed1d8712b53e9b7126
Parents: b3775ec 36d0b76
Author: raminder <ra...@apache.org>
Authored: Mon Aug 25 12:00:17 2014 -0400
Committer: raminder <ra...@apache.org>
Committed: Mon Aug 25 12:00:17 2014 -0400
----------------------------------------------------------------------
.../java-client-samples/pom.xml | 29 +-
.../client/samples/CancelExperiments.java | 2 -
.../client/samples/CreateLaunchExperiment.java | 145 +-
.../samples/CreateLaunchExperimentUS3.java | 80 +-
.../samples/TestCreateLaunchExperiment.java | 56 +-
.../tools/RegisterSampleApplications.java | 70 +-
modules/airavata-client/pom.xml | 5 -
.../airavata/client/AiravataAPIFactory.java | 24 +-
.../apache/airavata/client/AiravataClient.java | 256 +-
.../apache/airavata/client/api/AiravataAPI.java | 5 +-
.../airavata/client/api/AiravataManager.java | 6 +-
.../org/apache/airavata/client/api/BaseAPI.java | 3 +-
.../client/api/CredentialStoreManager.java | 22 +-
.../airavata/client/api/ExecutionManager.java | 172 +-
.../airavata/client/api/ProvenanceManager.java | 938 +++---
.../client/impl/AiravataManagerImpl.java | 264 +-
.../client/impl/ApplicationManagerImpl.java | 525 ++--
.../client/impl/CredentialStoreManagerImpl.java | 50 +-
.../client/impl/ExecutionManagerImpl.java | 366 ++-
.../client/impl/PasswordCallBackImpl.java | 78 +-
.../client/impl/ProvenanceManagerImpl.java | 1273 ++++----
.../client/impl/WorkflowManagerImpl.java | 365 +--
.../client/tools/DocumentCreatorNew.java | 34 +-
.../client/tools/PeriodicExecutorThread.java | 1 -
.../client/airavata/AiravataClientTest.java | 16 +-
.../catalog/data/util/AppCatalogJPAUtils.java | 1 +
.../main/resources/airavata-client.properties | 2 +-
.../main/resources/airavata-server.properties | 2 +-
modules/distribution/client/java/pom.xml | 10 -
.../java/src/main/assembly/bin-assembly.xml | 2 -
modules/distribution/server/pom.xml | 10 -
.../server/src/main/assembly/bin-assembly.xml | 2 -
modules/gfac/airavata-gfac-service/pom.xml | 25 +
.../airavata/gfac/server/GfacServerHandler.java | 27 +-
.../airavata/gfac/client/util/Initialize.java | 9 +-
.../gfac/bes/provider/impl/BESProvider.java | 88 +-
modules/gfac/gfac-core/pom.xml | 10 -
.../apache/airavata/gfac/GFacConfiguration.java | 16 +-
.../org/apache/airavata/gfac/Scheduler.java | 10 -
.../airavata/gfac/core/cpi/BetterGfacImpl.java | 34 +-
.../apache/airavata/gfac/core/cpi/GFacImpl.java | 1356 +++++----
.../gfac/core/handler/AbstractHandler.java | 4 +-
.../handler/AbstractRecoverableHandler.java | 4 +-
.../core/handler/AppDescriptorCheckHandler.java | 5 -
.../gfac/core/provider/AbstractProvider.java | 3 +-
.../provider/AbstractRecoverableProvider.java | 3 +-
.../airavata/gfac/core/utils/GFacUtils.java | 303 +-
.../apache/airavata/job/GFacConfigXmlTest.java | 10 +-
modules/gfac/gfac-ec2/pom.xml | 5 -
.../apache/airavata/gfac/ec2/EC2Provider.java | 18 +-
.../airavata/gfac/ec2/EC2ProviderTest.java | 6 +-
.../impl/GramProviderTestWithMyProxyAuth.java | 6 +-
.../gsissh/provider/impl/GSISSHProvider.java | 5 +-
.../impl/GSISSHProviderTestWithMyProxyAuth.java | 6 +-
.../gfac/services/impl/LocalProviderTest.java | 2 +-
modules/gfac/gfac-monitor/pom.xml | 10 -
.../handlers/GridPullMonitorHandler.java | 5 +-
.../handlers/GridPushMonitorHandler.java | 4 +-
.../monitor/impl/pull/qstat/HPCPullMonitor.java | 75 +-
.../gfac/ssh/provider/impl/SSHProvider.java | 3 +-
.../services/impl/BigRed2TestWithSSHAuth.java | 6 +-
.../impl/SSHProviderTestWithSSHAuth.java | 6 +-
.../integration/AbstractIntegrationTest.java | 22 +-
.../apache/airavata/integration/BaseCaseIT.java | 96 +-
.../airavata/integration/DataRetrievalIT.java | 24 +-
.../airavata/integration/ForEachCaseIT.java | 134 +-
.../integration/PasswordCallbackImpl.java | 78 +-
.../SingleAppIntegrationTestBase.java | 2 +-
.../WorkflowIntegrationTestBase.java | 341 +--
.../integration/WorkflowSamplesCaseIT.java | 162 +-
.../server/OrchestratorServerHandler.java | 38 +-
.../client/OrchestratorClientFactoryTest.java | 26 +-
.../orchestrator/client/util/Initialize.java | 7 +-
modules/orchestrator/orchestrator-core/pom.xml | 10 +-
.../core/OrchestratorConfiguration.java | 12 -
.../core/context/OrchestratorContext.java | 11 -
.../core/impl/GFACEmbeddedJobSubmitter.java | 6 +-
.../core/impl/GFACServiceJobSubmitter.java | 2 -
.../core/utils/OrchestratorUtils.java | 25 +-
.../cpi/impl/AbstractOrchestrator.java | 98 +-
.../cpi/impl/SimpleOrchestratorImpl.java | 10 +-
.../orchestrator/core/BaseOrchestratorTest.java | 38 +-
.../orchestrator/core/NewOrchestratorTest.java | 21 -
.../orchestrator/core/util/Initialize.java | 9 +-
modules/registry/airavata-jpa-registry/pom.xml | 5 -
.../registry/jpa/JPAResourceAccessor.java | 49 -
.../persistance/registry/jpa/ResourceUtils.java | 2 +-
.../registry/jpa/impl/AiravataJPARegistry.java | 2838 ------------------
...avataRegistryConnectionDataProviderImpl.java | 42 -
.../jpa/resources/ExperimentDataRetriever.java | 543 ----
.../registry/jpa/resources/UserResource.java | 7 +-
.../registry/jpa/AbstractResourceTest.java | 2 +-
.../registry/jpa/util/Initialize.java | 9 +-
modules/registry/pom.xml | 1 -
modules/registry/registry-api/pom.xml | 80 -
.../registry/api/AiravataExperiment.java | 73 -
.../registry/api/AiravataRegistry2.java | 65 -
.../AiravataRegistryConnectionDataProvider.java | 29 -
.../registry/api/AiravataRegistryFactory.java | 140 -
.../registry/api/AiravataSubRegistry.java | 97 -
.../airavata/registry/api/AiravataUser.java | 48 -
.../registry/api/ConfigurationRegistry.java | 59 -
.../registry/api/CredentialRegistry.java | 69 -
.../airavata/registry/api/DataRegistry.java | 50 -
.../registry/api/DescriptorRegistry.java | 74 -
.../airavata/registry/api/ExecutionErrors.java | 33 -
.../apache/airavata/registry/api/Gateway.java | 47 -
.../registry/api/OrchestratorRegistry.java | 120 -
.../airavata/registry/api/PasswordCallback.java | 25 -
.../airavata/registry/api/ProjectsRegistry.java | 50 -
.../registry/api/ProvenanceRegistry.java | 528 ----
.../registry/api/PublishedWorkflowRegistry.java | 45 -
.../airavata/registry/api/ResourceMetadata.java | 70 -
.../airavata/registry/api/UserRegistry.java | 39 -
.../registry/api/UserWorkflowRegistry.java | 43 -
.../airavata/registry/api/WorkspaceProject.java | 95 -
.../AiravataRegUninitializedException.java | 32 -
.../DeploymentDescriptionRetrieveException.java | 35 -
.../GatewayNotRegisteredException.java | 32 -
.../HostDescriptionRetrieveException.java | 33 -
.../RegAPIVersionIncompatibleException.java | 39 -
.../RegAccessorInstantiateException.java | 32 -
.../exception/RegAccessorInvalidException.java | 32 -
.../exception/RegAccessorNotFoundException.java | 32 -
.../RegAccessorUndefinedException.java | 40 -
.../registry/api/exception/RegException.java | 39 -
.../exception/RegistrySettingsException.java | 37 -
.../RegistrySettingsLoadException.java | 38 -
.../ServiceDescriptionRetrieveException.java | 35 -
.../UnimplementedRegOperationException.java | 32 -
.../UnknownRegConnectionDataException.java | 36 -
.../UnspecifiedRegistrySettingsException.java | 30 -
.../DescriptorAlreadyExistsException.java | 34 -
.../DescriptorDoesNotExistsException.java | 34 -
.../gateway/InsufficientDataException.java | 34 -
.../gateway/MalformedDescriptorException.java | 34 -
...PublishedWorkflowAlreadyExistsException.java | 34 -
...PublishedWorkflowDoesNotExistsException.java | 34 -
.../ApplicationJobAlreadyExistsException.java | 34 -
.../ApplicationJobDoesNotExistsException.java | 34 -
.../ExperimentAlreadyExistsException.java | 34 -
.../ExperimentDoesNotExistsException.java | 34 -
.../worker/ExperimentLazyLoadedException.java | 34 -
.../InvalidApplicationJobIDException.java | 34 -
.../UserWorkflowAlreadyExistsException.java | 34 -
.../UserWorkflowDoesNotExistsException.java | 34 -
.../WorkflowInstanceAlreadyExistsException.java | 34 -
.../WorkflowInstanceDoesNotExistsException.java | 34 -
...kflowInstanceNodeAlreadyExistsException.java | 34 -
...kflowInstanceNodeDoesNotExistsException.java | 34 -
.../WorkspaceProjectAlreadyExistsException.java | 34 -
.../WorkspaceProjectDoesNotExistsException.java | 34 -
.../registry/api/impl/ExperimentDataImpl.java | 221 --
.../api/impl/WorkflowExecutionDataImpl.java | 182 --
.../api/orchestrator/OrchestratorData.java | 113 -
.../orchestrator/impl/OrchestratorDataImpl.java | 112 -
.../registry/api/util/RegistryConstants.java | 36 -
.../registry/api/util/RegistrySettings.java | 127 -
.../registry/api/util/RegistryUtils.java | 124 -
.../registry/api/util/WebServiceUtil.java | 202 --
.../registry/api/workflow/ApplicationJob.java | 295 --
.../workflow/ApplicationJobExecutionError.java | 67 -
.../api/workflow/ApplicationJobStatusData.java | 63 -
.../registry/api/workflow/ExecutionError.java | 103 -
.../registry/api/workflow/ExperimentData.java | 123 -
.../api/workflow/ExperimentExecutionError.java | 40 -
.../api/workflow/ExperimentMetadata.java | 49 -
.../registry/api/workflow/ExperimentName.java | 49 -
.../registry/api/workflow/ExperimentUser.java | 48 -
.../registry/api/workflow/InputData.java | 34 -
.../api/workflow/NodeExecutionData.java | 236 --
.../api/workflow/NodeExecutionError.java | 58 -
.../api/workflow/NodeExecutionStatus.java | 78 -
.../registry/api/workflow/OutputData.java | 34 -
.../api/workflow/WorkflowExecution.java | 69 -
.../api/workflow/WorkflowExecutionData.java | 118 -
.../api/workflow/WorkflowExecutionError.java | 49 -
.../api/workflow/WorkflowExecutionStatus.java | 128 -
.../registry/api/workflow/WorkflowIOData.java | 58 -
.../api/workflow/WorkflowInstanceNode.java | 67 -
.../workflow/WorkflowInstanceNodePortData.java | 89 -
.../api/workflow/WorkflowNodeGramData.java | 83 -
.../api/workflow/WorkflowNodeIOData.java | 114 -
.../registry/api/workflow/WorkflowNodeType.java | 84 -
.../api/workflow/WorkflowRunTimeData.java | 90 -
modules/registry/registry-cpi/pom.xml | 5 +
.../registry/cpi/utils/RegistrySettings.java | 127 +
modules/test-suite/pom.xml | 6 -
modules/workflow-model/workflow-engine/pom.xml | 12 -
.../WorkflowInterpreterConfiguration.java | 2 -
modules/ws-messenger/messagebox/pom.xml | 5 -
modules/ws-messenger/messagebroker/pom.xml | 5 -
modules/xbaya-gui/pom.xml | 5 -
.../xbaya/registry/PasswordCallbackImpl.java | 78 +-
.../ui/experiment/LaunchApplicationWindow.java | 400 +++
.../airavata/xbaya/ui/menues/RunMenuItem.java | 9 +-
pom.xml | 2 +-
samples/java-client/experiment/pom.xml | 22 -
tools/registry-tool/pom.xml | 5 -
199 files changed, 4487 insertions(+), 14200 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/6c4471ad/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java
----------------------------------------------------------------------
[4/4] git commit: Merge branch 'master' of
https://git-wip-us.apache.org/repos/asf/airavata
Posted by ra...@apache.org.
Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/4adcce98
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/4adcce98
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/4adcce98
Branch: refs/heads/master
Commit: 4adcce9866c8e32f13e782d1ef3a62c2d4a7bd2c
Parents: 6c500f2 6821ce1
Author: raminder <ra...@apache.org>
Authored: Thu Aug 28 11:21:31 2014 -0400
Committer: raminder <ra...@apache.org>
Committed: Thu Aug 28 11:21:31 2014 -0400
----------------------------------------------------------------------
.../catalog/data/model/Configuration.java | 57 +++++++++++++++++
.../catalog/data/model/Configuration_PK.java | 65 ++++++++++++++++++++
.../catalog/data/util/AppCatalogJPAUtils.java | 7 ++-
.../src/main/resources/META-INF/persistence.xml | 1 +
.../src/main/resources/appcatalog-derby.sql | 11 ++++
.../src/main/resources/appcatalog-mysql.sql | 9 +++
.../src/test/resources/appcatalog-derby.sql | 11 ++++
.../main/resources/airavata-server.properties | 2 +-
.../main/resources/airavata-server.properties | 2 +-
.../monitor/impl/pull/qstat/HPCPullMonitor.java | 9 ++-
.../impl/pull/qstat/ResourceConnection.java | 5 ++
.../persistance/registry/jpa/ResourceUtils.java | 4 +-
12 files changed, 174 insertions(+), 9 deletions(-)
----------------------------------------------------------------------