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Posted to commits@airavata.apache.org by ms...@apache.org on 2014/11/11 16:18:05 UTC
[1/2] airavata git commit: fixed simple experiment run [AIRAVATA-1473]
Repository: airavata
Updated Branches:
refs/heads/master 97b384b06 -> 5413e6718
fixed simple experiment run [AIRAVATA-1473]
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/febd0c40
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/febd0c40
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/febd0c40
Branch: refs/heads/master
Commit: febd0c40d6445d364d42fb13884075906e44507a
Parents: 47e8214
Author: msmemon <sh...@gmail.com>
Authored: Tue Nov 11 16:12:48 2014 +0100
Committer: msmemon <sh...@gmail.com>
Committed: Tue Nov 11 16:12:48 2014 +0100
----------------------------------------------------------------------
.../client/samples/CreateLaunchExperiment.java | 22 ++++--
.../tools/RegisterSampleApplications.java | 9 ++-
.../server/src/main/assembly/bin-assembly.xml | 25 ++++---
.../gfac/bes/provider/impl/BESProvider.java | 16 ++---
.../bes/security/UNICORESecurityContext.java | 6 +-
.../gfac/bes/utils/DataTransferrer.java | 53 +++++++++++++-
.../airavata/gfac/bes/utils/JSDLUtils.java | 6 +-
.../gfac/bes/utils/UASDataStagingProcessor.java | 73 +++++++++++---------
.../registry/jpa/impl/ExperimentRegistry.java | 7 +-
9 files changed, 148 insertions(+), 69 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
index 2845bc6..e0b47bb 100644
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
@@ -42,6 +42,8 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
+import java.util.Random;
+import java.util.UUID;
public class CreateLaunchExperiment {
@@ -53,7 +55,7 @@ public class CreateLaunchExperiment {
private static final String DEFAULT_GATEWAY = "default.registry.gateway";
private static Airavata.Client airavataClient;
- private static String echoAppId = "Echo_6281480a-9887-4a0f-8311-59bbaf738e54";
+ private static String echoAppId = "Echo_70892623-ef16-4efb-a9f0-b12a2861e27a";
private static String wrfAppId = "WRF_5f097c9c-7066-49ec-aed7-4e39607b3adc";
private static String amberAppId = "Amber_89906be6-5678-49a6-9d04-a0604fbdef2e";
@@ -179,7 +181,7 @@ public class CreateLaunchExperiment {
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
- simpleExperiment.setUserConfigurationData(userConfigurationData);
+
return client.createExperiment(simpleExperiment);
}
}
@@ -203,18 +205,24 @@ public class CreateLaunchExperiment {
public static String createEchoExperimentForFSD(Airavata.Client client) throws TException {
try {
+ // these are template variables and do not need to have values, as it is a data model.
List<DataObjectType> exInputs = new ArrayList<DataObjectType>();
DataObjectType input = new DataObjectType();
input.setKey("Input_to_Echo");
input.setType(DataType.STRING);
input.setValue("Echoed_Output=Hello World");
exInputs.add(input);
+ DataObjectType i2 = new DataObjectType();
+ i2.setKey("Input_to_Echo1");
+ i2.setType(DataType.URI);
+ i2.setValue("http://shrib.com/22QmrrX4");
+ exInputs.add(i2);
List<DataObjectType> exOut = new ArrayList<DataObjectType>();
DataObjectType output = new DataObjectType();
- output.setKey("echo_output");
+ output.setKey("Echoed_Output");
output.setType(DataType.STRING);
- output.setValue("");
+ output.setValue("22QmrrX4");
exOut.add(output);
@@ -235,7 +243,13 @@ public class CreateLaunchExperiment {
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
+
+ // set output directory
+ AdvancedOutputDataHandling dataHandling = new AdvancedOutputDataHandling();
+ dataHandling.setOutputDataDir("/tmp/airavata/output/"+UUID.randomUUID().toString()+"/");
+ userConfigurationData.setAdvanceOutputDataHandling(dataHandling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
+
return client.createExperiment(simpleExperiment);
}
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
index bd4023b..1e4b591 100644
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
@@ -531,12 +531,17 @@ public class RegisterSampleApplications {
InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Input_to_Echo", "Hello World",
DataType.STRING, null, false, "A test string to Echo", null);
+
+ InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("Input_to_Echo1", "http://shrib.com/22QmrrX4",
+ DataType.URI, null, false, "A test uri to Echo", null);
+
List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
applicationInputs.add(input1);
+ applicationInputs.add(input2);
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output",
- "", DataType.STRING);
+ "22QmrrX4", DataType.STRING);
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
@@ -1036,7 +1041,7 @@ public class RegisterSampleApplications {
//Register Echo
String echoAppDeployId = airavataClient.registerApplicationDeployment(
RegisterSampleApplicationsUtils.createApplicationDeployment(echoModuleId, fsdResourceId,
- "/bin/date", ApplicationParallelismType.SERIAL, echoDescription));
+ "/bin/echo", ApplicationParallelismType.SERIAL, echoDescription));
System.out.println("Echo on FSD deployment Id " + echoAppDeployId);
} catch (TException e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/distribution/server/src/main/assembly/bin-assembly.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/server/src/main/assembly/bin-assembly.xml b/modules/distribution/server/src/main/assembly/bin-assembly.xml
index 32cb5e7..6ab1d13 100644
--- a/modules/distribution/server/src/main/assembly/bin-assembly.xml
+++ b/modules/distribution/server/src/main/assembly/bin-assembly.xml
@@ -17,13 +17,13 @@
<!ELEMENT formats (format)*>
<!ELEMENT format (#PCDATA)>
<!ELEMENT fileSets (fileSet)*>
- <!ELEMENT fileSet (directory|outputDirectory|includes)*>
+ <!ELEMENT fileSet (directory|outputDirectory|fileMode|includes)*>
<!ELEMENT directory (#PCDATA)>
<!ELEMENT outputDirectory (#PCDATA)>
<!ELEMENT includes (include)*>
<!ELEMENT include (#PCDATA)>
<!ELEMENT dependencySets (dependencySet)*>
- <!ELEMENT dependencySet (outputDirectory|includes)*>
+ <!ELEMENT dependencySet (outputDirectory|outputFileNameMapping|includes)*>
]>
<assembly>
<id>bin</id>
@@ -159,8 +159,7 @@
<dependencySets>
<dependencySet>
<outputDirectory>lib</outputDirectory>
- <outputFileNameMapping>${artifact.artifactId}.${artifact.extension}
- </outputFileNameMapping>
+ <outputFileNameMapping>${artifact.artifactId}.${artifact.extension}</outputFileNameMapping>
<includes>
<include>org.apache.derby:derby:jar</include>
<include>org.apache.derby:derbytools:jar</include>
@@ -280,16 +279,17 @@
<include>pl.edu.icm.saml:samly2</include>
<include>org.apache.ws.security:wss4j</include>
<include>org.json:json</include>
- <include>org.apache.cxf:cxf-rt-databinding-xmlbeans</include>
- <include>org.apache.cxf:cxf-api</include>
+ <!-- CXF deps start -->
<include>org.codehaus.woodstox:woodstox-core-asl</include>
<include>org.codehaus.woodstox:stax2-api</include>
+ <include>org.apache.cxf:cxf-rt-databinding-xmlbeans</include>
+ <include>org.apache.cxf:cxf-api</include>
<include>org.apache.ws.xmlschema:xmlschema-core</include>
+ <include>org.apache.cxf:cxf-api</include>
+ <include>org.apache.cxf:cxf-rt-databinding-xmlbeans</include>
<include>org.apache.cxf:cxf-rt-core</include>
- <include>com.sun.xml.bind:jaxb-impl</include>
<include>org.apache.cxf:cxf-rt-frontend-jaxws</include>
- <include>xml-resolver:xml-resolver</include>
- <include>asm:asm</include>
+ <include>org.apache.cxf:cxf-rt-frontend-simple</include>
<include>org.apache.cxf:cxf-rt-bindings-soap</include>
<include>org.apache.cxf:cxf-rt-databinding-jaxb</include>
<include>org.apache.cxf:cxf-rt-bindings-xml</include>
@@ -298,8 +298,13 @@
<include>org.apache.cxf:cxf-rt-ws-policy</include>
<include>org.apache.cxf:cxf-rt-transports-http</include>
<include>org.apache.cxf:cxf-rt-features-clustering</include>
- <include>org.apache.neethi:neethi</include>
<include>org.apache.cxf:cxf-rt-frontend-jaxws</include>
+ <include>org.apache.cxf:cxf-bundle</include>
+ <!-- // CXF deps end -->
+ <include>com.sun.xml.bind:jaxb-impl</include>
+ <include>org.apache.neethi:neethi:3.0.2</include>
+ <include>xml-resolver:xml-resolver</include>
+ <include>asm:asm</include>
<include>xml-resolver:xml-resolver</include>
<include>org.eclipse.jetty:jetty-servlet</include>
<include>org.eclipse.jetty:jetty-security</include>
http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java
index 7ed038a..044ffa2 100644
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java
+++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java
@@ -187,17 +187,17 @@ public class BESProvider extends AbstractProvider implements GFacProvider,
.toString();
}
log.info("JobID: " + jobId);
- jobDetails.setJobID(activityEpr.toString());
- jobDetails.setJobDescription(activityEpr.toString());
+ jobDetails.setJobID(jobId);
+ jobDetails.setJobDescription(jobId);
jobExecutionContext.setJobDetails(jobDetails);
try {
log.info(formatStatusMessage(activityEpr.getAddress()
.getStringValue(), factory.getActivityStatus(activityEpr)
.toString()));
-
+
jobExecutionContext.getNotifier().publish(new UnicoreJobIDEvent(jobId));
- GFacUtils.saveJobStatus(jobExecutionContext, details,JobState.SUBMITTED);
+// GFacUtils.saveJobStatus(jobExecutionContext, details,JobState.SUBMITTED);
factory.getActivityStatus(activityEpr);
log.info(formatStatusMessage(activityEpr.getAddress()
@@ -215,8 +215,8 @@ public class BESProvider extends AbstractProvider implements GFacProvider,
JobState applicationJobStatus = getApplicationJobStatus(activityStatus);
String jobStatusMessage = "Status of job " + jobId + "is "
+ applicationJobStatus;
- GFacUtils.updateJobStatus(jobExecutionContext, jobDetails,
- applicationJobStatus);
+ //TODO: properly use GFacUtils..
+// GFacUtils.updateJobStatus(jobExecutionContext, jobDetails, applicationJobStatus);
jobExecutionContext.getNotifier().publish(
new StatusChangeEvent(jobStatusMessage));
@@ -272,8 +272,8 @@ public class BESProvider extends AbstractProvider implements GFacProvider,
+ applicationJobStatus;
jobExecutionContext.getNotifier().publish(
new StatusChangeEvent(jobStatusMessage));
- GFacUtils.updateJobStatus(jobExecutionContext, jobDetails,
- applicationJobStatus);
+ //TODO: properly use GFacUtils..
+// GFacUtils.updateJobStatus(jobExecutionContext, jobDetails, applicationJobStatus);
throw new GFacProviderException(
jobExecutionContext.getExperimentID() + "Job Canceled");
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java
index 7285c2c..d5e2b9f 100644
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java
+++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java
@@ -44,7 +44,7 @@ public class UNICORESecurityContext extends X509SecurityContext {
try{
X509Credential cred = getX509Credentials();
secProperties = new DefaultClientConfiguration(dcValidator, cred);
-// setExtraSettings();
+ setExtraSettings();
}
catch (Exception e) {
throw new GFacException(e.getMessage(), e);
@@ -103,8 +103,8 @@ public class UNICORESecurityContext extends X509SecurityContext {
p = new Properties();
}
- p.setProperty("http.connection.timeout", "300000");
- p.setProperty("http.socket.timeout", "300000");
+ p.setProperty("http.connection.timeout", "5000");
+ p.setProperty("http.socket.timeout", "5000");
secProperties.setExtraSettings(p);
http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java
index f811f97..79fbae4 100644
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java
+++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java
@@ -26,7 +26,9 @@ import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import org.apache.airavata.commons.gfac.type.ActualParameter;
@@ -39,6 +41,7 @@ import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
import org.apache.airavata.schemas.gfac.StringArrayType;
import org.apache.airavata.schemas.gfac.StringParameterType;
+import org.apache.airavata.schemas.gfac.URIArrayType;
import org.apache.airavata.schemas.gfac.URIParameterType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -119,7 +122,8 @@ public class DataTransferrer {
String localFileName = null;
//TODO: why analysis.tar? it wont scale to other gateways..
if(stringPrm == null || stringPrm.isEmpty()){
- localFileName = "analysis-results.tar";
+ continue;
+// localFileName = "analysis-results.tar";
}else{
localFileName = stringPrm.substring(stringPrm.lastIndexOf("/")+1);
}
@@ -199,16 +203,59 @@ public class DataTransferrer {
throw new GFacProviderException(e.getLocalizedMessage(),e);
}
String stderrLocation = downloadLocation+File.separator+stderrFileName;
- FileDownloader f2 = new FileDownloader(stderrFileName,stderrLocation, Mode.overwrite);
+// FileDownloader f2 = new FileDownloader(stderrFileName,stderrLocation, Mode.overwrite);
try {
- f2.perform(storageClient);
+ f1.setFrom(stderrFileName);
+ f1.setTo(stderrLocation);
+ f1.perform(storageClient);
String stderror = readFile(stderrLocation);
appDesc.setStandardError(stderror);
} catch (Exception e) {
throw new GFacProviderException(e.getLocalizedMessage(),e);
}
+
+ if(UASDataStagingProcessor.isUnicoreEndpoint(jobContext)) {
+ String scriptExitCodeFName = "UNICORE_SCRIPT_EXIT_CODE";
+ f1.setFrom(scriptExitCodeFName);
+ f1.setTo(downloadLocation+File.separator+scriptExitCodeFName);
+
+ }
+ }
+
+ public List<String> extractOutStringParams(JobExecutionContext context) {
+
+ Map<String, Object> outputParams = context.getOutMessageContext()
+ .getParameters();
+
+ List<String> outPrmsList = new ArrayList<String>();
+
+ for (String paramKey : outputParams.keySet()) {
+
+ ActualParameter outParam = (ActualParameter) outputParams
+ .get(paramKey);
+
+ String paramDataType = outParam.getType().getType().toString();
+
+ if ("String".equals(paramDataType)) {
+ String strPrm = ((StringParameterType) outParam.getType())
+ .getValue();
+ outPrmsList.add(strPrm);
+ }
+
+ else if (("StringArray").equals(paramDataType)) {
+ String[] uriArray = ((URIArrayType) outParam.getType())
+ .getValueArray();
+ for (String u : uriArray) {
+ outPrmsList.add(u);
+ }
+
+ }
+ }
+
+ return outPrmsList;
}
+
private String readFile(String localFile) throws IOException {
BufferedReader instream = new BufferedReader(new FileReader(localFile));
StringBuffer buff = new StringBuffer();
http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java
index d2474f0..e7dc672 100644
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java
+++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java
@@ -122,10 +122,12 @@ public class JSDLUtils
SourceTargetType target = newDS.addNewTarget();
try {
- uri = (uri == null) ? null : URIUtils.encodeAll(uri);
+ if (uri != null) {
+ URIUtils.encodeAll(uri);
+ target.setURI(uri);
+ }
} catch (URIException e) {
}
- target.setURI(uri);
newDS.setFileName(file);
if (fileSystem != null && !fileSystem.equals("Work")) { //$NON-NLS-1$
newDS.setFilesystemName(fileSystem);
http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java
index 6ab7ed0..76624cc 100644
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java
+++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java
@@ -22,6 +22,8 @@
package org.apache.airavata.gfac.bes.utils;
import java.io.File;
+import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import org.apache.airavata.commons.gfac.type.ActualParameter;
@@ -48,17 +50,19 @@ public class UASDataStagingProcessor {
if (context.getInMessageContext().getParameters().size() > 0) {
buildDataStagingFromInputContext(context, value, smsUrl, appDepType);
}
- MessageContext outMessage = new MessageContext();
- ActualParameter a1 = new ActualParameter();
- a1.getType().changeType(StringParameterType.type);
- ((StringParameterType)a1.getType()).setValue("analysis-results.tar");
- outMessage.addParameter("o1", a1);
- context.setOutMessageContext(outMessage);
-
+// MessageContext outMessage = new MessageContext();
+// ActualParameter a1 = new ActualParameter();
+// a1.getType().changeType(StringParameterType.type);
+// ((StringParameterType)a1.getType()).setValue("analysis-results.tar");
+// outMessage.addParameter("o1", a1);
+// context.setOutMessageContext(outMessage);
+
+ // now download for string typed outputs are to be done
if (context.getOutMessageContext().getParameters().size() > 0) {
buildFromOutputContext(context, value, smsUrl, appDepType);
}
- createStdOutURIs(value, appDepType, smsUrl, isUnicoreEndpoint(context));
+ //TODO need a review for us3 gateway..
+// createStdOutURIs(value, appDepType, smsUrl, isUnicoreEndpoint(context));
}
private static void createInURISMSElement(JobDefinitionType value,
@@ -85,7 +89,16 @@ public class UASDataStagingProcessor {
HpcApplicationDeploymentType appDepType, String smsUrl,
boolean isUnicore) throws Exception {
+ // no need to use smsUrl for output location, because output location is activity's working directory
+ if(isUnicore) {
+ String scriptExitCodeFName = "UNICORE_SCRIPT_EXIT_CODE";
+ String scriptExitCode = smsUrl+"#/output/"+scriptExitCodeFName;
+ JSDLUtils.addDataStagingTargetElement(value, null,
+ scriptExitCodeFName, null);
+ }
+
+ if(!isUnicore) {
String stdout = ApplicationProcessor.getApplicationStdOut(value, appDepType);
String stderr = ApplicationProcessor.getApplicationStdErr(value, appDepType);
@@ -93,20 +106,16 @@ public class UASDataStagingProcessor {
String stdoutFileName = (stdout == null || stdout.equals("")) ? "stdout"
: stdout;
String stdoutURI = smsUrl+"#/output/"+stdoutFileName;
+
JSDLUtils.addDataStagingTargetElement(value, null, stdoutFileName,
- stdoutURI);
+ null);
String stderrFileName = (stdout == null || stderr.equals("")) ? "stderr"
: stderr;
String stderrURI = smsUrl+"#/output/"+stderrFileName;
- JSDLUtils.addDataStagingTargetElement(value, null, stderrFileName,
- stderrURI);
- if(isUnicore) {
- String scriptExitCodeFName = "UNICORE_SCRIPT_EXIT_CODE";
- String scriptExitCode = smsUrl+"#/output/"+scriptExitCodeFName;
- JSDLUtils.addDataStagingTargetElement(value, null,
- scriptExitCodeFName, scriptExitCode.toString());
+ JSDLUtils.addDataStagingTargetElement(value, null, stderrFileName,
+ null);
}
}
@@ -119,7 +128,7 @@ public class UASDataStagingProcessor {
String finalSMSPath = smsUrl + "#/output/"+prmValue;
- JSDLUtils.addDataStagingTargetElement(value, null, prmValue, finalSMSPath);
+ JSDLUtils.addDataStagingTargetElement(value, null, prmValue, null);
}
@@ -159,22 +168,19 @@ public class UASDataStagingProcessor {
}
}
- else if ("String".equals(paramDataType) || "StringArray".equals(paramDataType)) {
- return value;
- }
- else if ("String".equals(paramDataType)) {
- String stringPrm = ((StringParameterType) outParam
- .getType()).getValue();
- createOutStringElements(value, appDepType, smsUrl, stringPrm);
- }
-
- else if ("StringArray".equals(paramDataType)) {
- String[] valueArray = ((StringArrayType) outParam.getType())
- .getValueArray();
- for (String v : valueArray) {
- createOutStringElements(value, appDepType, smsUrl, v);
- }
- }
+// else if ("String".equals(paramDataType)) {
+// String stringPrm = ((StringParameterType) outParam
+// .getType()).getValue();
+// createOutStringElements(value, appDepType, smsUrl, stringPrm);
+// }
+//
+// else if ("StringArray".equals(paramDataType)) {
+// String[] valueArray = ((StringArrayType) outParam.getType())
+// .getValueArray();
+// for (String v : valueArray) {
+// createOutStringElements(value, appDepType, smsUrl, v);
+// }
+// }
}
return value;
@@ -212,7 +218,6 @@ public class UASDataStagingProcessor {
ApplicationProcessor.addApplicationArgument(value, appDepType, stringPrm);
}
}
-
}
public static boolean isUnicoreEndpoint(JobExecutionContext context) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java
----------------------------------------------------------------------
diff --git a/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java b/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java
index 03ca6fc..8e9ae58 100644
--- a/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java
+++ b/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java
@@ -93,9 +93,10 @@ public class ExperimentRegistry {
List<DataObjectType> experimentOutputs = experiment.getExperimentOutputs();
if (experimentOutputs != null && !experimentOutputs.isEmpty()){
- for (DataObjectType output : experimentOutputs){
- output.setValue("");
- }
+ //TODO: short change.
+// for (DataObjectType output : experimentOutputs){
+// output.setValue("");
+// }
addExpOutputs(experimentOutputs, experimentID);
}
[2/2] airavata git commit: Merge branch 'master' of
https://git-wip-us.apache.org/repos/asf/airavata
Posted by ms...@apache.org.
Merge branch 'master' of
https://git-wip-us.apache.org/repos/asf/airavata
Conflicts:
airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/5413e671
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/5413e671
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/5413e671
Branch: refs/heads/master
Commit: 5413e6718fd1e3fefc42858ccde98c1558414a87
Parents: febd0c4 97b384b
Author: msmemon <sh...@gmail.com>
Authored: Tue Nov 11 16:19:47 2014 +0100
Committer: msmemon <sh...@gmail.com>
Committed: Tue Nov 11 16:19:47 2014 +0100
----------------------------------------------------------------------
airavata-api/airavata-api-server/pom.xml | 2 +-
.../airavata/api/server/WorkflowServer.java | 164 -
.../server/handler/AiravataServerHandler.java | 436 +-
.../server/handler/WorkflowServerHandler.java | 158 -
.../AiravataExperimentStatusUpdator.java | 9 +-
.../java/org/apache/airavata/api/Airavata.java | 42649 +++++++++++------
.../api/client/AiravataClientFactory.java | 30 +-
.../apache/airavata/api/workflow/Workflow.java | 8191 ----
.../api/workflow/workflowAPIConstants.java | 56 -
.../main/resources/lib/airavata/Airavata.cpp | 10791 +++--
.../src/main/resources/lib/airavata/Airavata.h | 2733 +-
.../lib/airavata/Airavata_server.skeleton.cpp | 75 +-
.../main/resources/lib/airavata/Workflow.cpp | 36 +-
.../src/main/resources/lib/airavata/Workflow.h | 4 +-
.../lib/airavata/Workflow_server.skeleton.cpp | 2 +-
.../resources/lib/airavata/airavataAPI_types.h | 1 +
.../resources/lib/Airavata/API/Airavata.php | 11298 +++--
.../resources/lib/Airavata/API/Workflow.php | 1927 +
.../client/samples/CreateLaunchExperiment.java | 13 +-
airavata-api/generate-thrift-files.sh | 6 +-
.../airavataAPI.thrift | 3158 +-
.../appcatalog/cpi/ApplicationInterface.java | 2 +
.../appcatalog/cpi/ComputeResource.java | 13 +-
.../data/impl/ApplicationInterfaceImpl.java | 16 +
.../catalog/data/impl/ComputeResourceImpl.java | 91 +-
.../data/resources/AppModuleResource.java | 28 +-
.../data/resources/BatchQueueResource.java | 18 +-
.../data/resources/HostAliasResource.java | 12 +-
.../data/resources/HostIPAddressResource.java | 11 +-
.../data/util/AppCatalogThriftConversion.java | 2 +-
.../app/catalog/test/ComputeResourceTest.java | 19 +-
.../resources/schemas/GFacParameterTypes.xsd | 2 +-
modules/commons/utils/pom.xml | 6 +
.../apache/airavata/common/utils/JSONUtil.java | 157 +
.../airavata/common/utils/WSConstants.java | 3 +-
.../main/resources/airavata-server.properties | 4 +-
.../impl/password/PasswordCredential.java | 3 +-
modules/distribution/api-server/pom.xml | 203 +
.../src/main/assembly/bin-assembly.xml | 137 +
.../src/main/assembly/src-assembly.xml | 74 +
.../api-server/src/main/resources/INSTALL | 55 +
.../api-server/src/main/resources/LICENSE | 2387 +
.../api-server/src/main/resources/NOTICE | 163 +
.../api-server/src/main/resources/README | 121 +
.../src/main/resources/bin/api-server.sh | 118 +
.../api-server/src/main/resources/bin/logo.txt | 34 +
.../java/src/main/assembly/bin-assembly.xml | 280 +-
modules/distribution/gfac-server/pom.xml | 486 +
.../src/main/assembly/bin-assembly.xml | 305 +
.../src/main/assembly/src-assembly.xml | 75 +
.../gfac-server/src/main/resources/INSTALL | 55 +
.../gfac-server/src/main/resources/LICENSE | 2387 +
.../gfac-server/src/main/resources/NOTICE | 163 +
.../gfac-server/src/main/resources/README | 121 +
.../src/main/resources/bin/gfac-server.sh | 118 +
.../gfac-server/src/main/resources/bin/logo.txt | 34 +
.../distribution/orchestrator-server/pom.xml | 325 +
.../src/main/assembly/bin-assembly.xml | 230 +
.../src/main/assembly/src-assembly.xml | 75 +
.../src/main/resources/INSTALL | 55 +
.../src/main/resources/LICENSE | 2387 +
.../src/main/resources/NOTICE | 163 +
.../src/main/resources/README | 121 +
.../src/main/resources/bin/logo.txt | 34 +
.../main/resources/bin/orchestrator-server.sh | 118 +
modules/distribution/pom.xml | 5 +-
modules/distribution/server/pom.xml | 22 +-
.../server/src/main/assembly/bin-assembly.xml | 4 +
.../src/main/resources/bin/airavata-server.sh | 2 +-
modules/gfac/airavata-gfac-service/pom.xml | 5 +
modules/gfac/airavata-gfac-stubs/pom.xml | 60 +
.../airavata/gfac/client/GFACInstance.java | 62 +
.../airavata/gfac/client/GFacClientFactory.java | 42 +
.../apache/airavata/gfac/cpi/GfacService.java | 2867 ++
.../gfac/cpi/gfac_cpi_serviceConstants.java | 55 +
.../org/apache/airavata/gfac/Constants.java | 2 -
.../airavata/gfac/core/utils/GFacUtils.java | 3 +-
.../handler/GSISSHDirectorySetupHandler.java | 30 +-
.../gfac/gsissh/handler/GSISSHInputHandler.java | 11 +-
.../gsissh/handler/GSISSHOutputHandler.java | 10 +-
.../gsissh/provider/impl/GSISSHProvider.java | 13 +-
.../gsissh/security/GSISecurityContext.java | 2 -
.../security/TokenizedMyProxyAuthInfo.java | 2 +-
.../gfac/gsissh/util/GFACGSISSHUtils.java | 2 +-
.../impl/GSISSHProviderTestWithMyProxyAuth.java | 2 +-
.../airavata/gfac/monitor/HPCMonitorID.java | 15 +-
.../monitor/impl/pull/qstat/HPCPullMonitor.java | 123 +-
.../impl/pull/qstat/ResourceConnection.java | 9 +-
.../airavata/gfac/monitor/util/CommonUtils.java | 15 +-
.../ssh/handler/AdvancedSCPInputHandler.java | 27 +-
.../ssh/handler/AdvancedSCPOutputHandler.java | 42 +-
.../ssh/handler/SSHDirectorySetupHandler.java | 6 +-
.../gfac/ssh/handler/SSHInputHandler.java | 9 +-
.../gfac/ssh/handler/SSHOutputHandler.java | 7 +-
.../gfac/ssh/provider/impl/SSHProvider.java | 12 +-
.../gfac/ssh/security/SSHSecurityContext.java | 2 -
.../airavata/gfac/ssh/util/GFACSSHUtils.java | 120 +-
.../services/impl/BigRed2TestWithSSHAuth.java | 2 +-
.../impl/SSHProviderTestWithSSHAuth.java | 2 +-
modules/gfac/pom.xml | 1 +
.../airavata-orchestrator-service/pom.xml | 10 +
.../client/OrchestratorClientFactory.java | 45 -
.../orchestrator/cpi/OrchestratorService.java | 4467 --
.../cpi/orchestrator_cpi_serviceConstants.java | 55 -
.../server/OrchestratorServerHandler.java | 180 +-
.../orchestrator/util/DataModelUtils.java | 53 +
.../util/OrchestratorRecoveryHandler.java | 2 +-
.../OrchestratorServerThreadPoolExecutor.java | 35 +
.../airavata-orchestrator-stubs/pom.xml | 60 +
.../client/OrchestratorClientFactory.java | 44 +
.../orchestrator/cpi/OrchestratorService.java | 4568 ++
.../cpi/orchestrator_cpi_serviceConstants.java | 55 +
.../sample/OrchestratorClientSample.java | 134 +
.../orchestrator-client-sdks/pom.xml | 70 -
.../client/sample/OrchestratorClientSample.java | 138 -
modules/orchestrator/orchestrator-core/pom.xml | 7 +-
.../core/context/OrchestratorContext.java | 3 +-
.../orchestrator/core/gfac/GFACInstance.java | 62 -
.../core/gfac/GFacClientFactory.java | 42 -
.../core/impl/GFACEmbeddedJobSubmitter.java | 6 +-
.../core/impl/GFACServiceJobSubmitter.java | 6 +-
.../orchestrator/core/job/JobSubmitter.java | 3 +-
.../orchestrator/core/BaseOrchestratorTest.java | 9 -
.../orchestrator.cpi.service.thrift | 2 +-
modules/orchestrator/pom.xml | 2 +-
modules/workflow-model/workflow-engine/pom.xml | 7 +-
.../workflow/engine/WorkflowEngineImpl.java | 5 +-
.../engine/interpretor/WorkflowInterpreter.java | 2 +-
.../workflow-model/workflow-model-core/pom.xml | 6 +
.../model/component/ws/WSComponent.java | 6 +
.../component/ws/WSComponentApplication.java | 86 +-
.../model/gpel/script/WorkflowWSDL.java | 10 +-
.../workflow/model/graph/ControlEdge.java | 10 +
.../workflow/model/graph/ControlPort.java | 10 +-
.../airavata/workflow/model/graph/DataEdge.java | 10 +
.../airavata/workflow/model/graph/DataPort.java | 5 +
.../airavata/workflow/model/graph/Graph.java | 4 +
.../workflow/model/graph/GraphFactory.java | 7 +
.../model/graph/amazon/InstanceDataPort.java | 7 +
.../workflow/model/graph/impl/EdgeImpl.java | 16 +
.../workflow/model/graph/impl/GraphImpl.java | 66 +
.../workflow/model/graph/impl/NodeImpl.java | 108 +-
.../workflow/model/graph/impl/PortImpl.java | 28 +
.../workflow/model/graph/system/InputNode.java | 38 +
.../workflow/model/graph/system/OutputNode.java | 10 +
.../model/graph/system/ParameterNode.java | 56 +
.../model/graph/system/SystemDataPort.java | 12 +
.../workflow/model/graph/system/SystemNode.java | 5 +
.../workflow/model/graph/ws/WSGraph.java | 133 +-
.../workflow/model/graph/ws/WSGraphFactory.java | 149 +-
.../workflow/model/graph/ws/WSNode.java | 24 +
.../workflow/model/graph/ws/WSPort.java | 11 +
.../workflow/model/graph/ws/WorkflowNode.java | 10 +
.../airavata/workflow/model/wf/Workflow.java | 89 +-
modules/xbaya-gui/pom.xml | 7 +-
.../airavata/xbaya/ThriftServiceType.java | 3 +-
.../apache/airavata/xbaya/XBayaConstants.java | 2 +-
.../xbaya/core/generators/WorkflowFiler.java | 17 +-
.../airavata/xbaya/messaging/Monitor.java | 2 +-
.../ui/dialogs/registry/RegistryWindow.java | 13 +-
.../workflow/ParameterPropertyWindow.java | 8 +-
.../dialogs/workflow/WorkflowImportWindow.java | 8 +-
.../workflow/WorkflowPropertyWindow.java | 67 +-
.../RegistryWorkflowPublisherWindow.java | 8 +-
.../WorkflowInterpreterLaunchWindow.java | 18 +-
.../airavata/xbaya/ui/graph/GraphCanvas.java | 14 +-
.../apache/airavata/xbaya/util/XBayaUtil.java | 4 +-
pom.xml | 6 +
168 files changed, 70801 insertions(+), 36907 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/5413e671/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
----------------------------------------------------------------------
diff --cc airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
index e0b47bb,f039988..05395e6
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
@@@ -55,10 -53,10 +55,11 @@@ public class CreateLaunchExperiment
private static final String DEFAULT_GATEWAY = "default.registry.gateway";
private static Airavata.Client airavataClient;
- private static String echoAppId = "Echo_70892623-ef16-4efb-a9f0-b12a2861e27a";
- private static String wrfAppId = "WRF_5f097c9c-7066-49ec-aed7-4e39607b3adc";
- private static String amberAppId = "Amber_89906be6-5678-49a6-9d04-a0604fbdef2e";
+ private static String echoAppId = "Echo_636b4530-6fb2-4c9e-998a-b41e648aa70f";
+ private static String wrfAppId = "WRF_d41bdc86-e280-4eb6-a045-708f69a8c116";
+ private static String amberAppId = "Amber_b23ee051-90d6-4892-827e-622a2f6c95ee";
+
+
private static String localHost = "localhost";
private static String trestlesHostName = "trestles.sdsc.xsede.org";
private static String unicoreHostName = "fsd-cloud15.zam.kfa-juelich.de";
http://git-wip-us.apache.org/repos/asf/airavata/blob/5413e671/modules/commons/gfac-schema/src/main/resources/schemas/GFacParameterTypes.xsd
----------------------------------------------------------------------
diff --cc modules/commons/gfac-schema/src/main/resources/schemas/GFacParameterTypes.xsd
index d1663d4,d1663d4..235b09c
--- a/modules/commons/gfac-schema/src/main/resources/schemas/GFacParameterTypes.xsd
+++ b/modules/commons/gfac-schema/src/main/resources/schemas/GFacParameterTypes.xsd
@@@ -63,7 -63,7 +63,7 @@@
<sequence>
<element name="value" nillable="true" type="xsd:string" />
</sequence>
-- <attribute name="type" fixed="StdErr" />
++ <attribute name="type" fixed="StdErr" />
</extension>
</complexContent>
</complexType>
http://git-wip-us.apache.org/repos/asf/airavata/blob/5413e671/modules/distribution/client/java/src/main/assembly/bin-assembly.xml
----------------------------------------------------------------------
diff --cc modules/distribution/client/java/src/main/assembly/bin-assembly.xml
index f89438d,f89438d..a5d9d01
--- a/modules/distribution/client/java/src/main/assembly/bin-assembly.xml
+++ b/modules/distribution/client/java/src/main/assembly/bin-assembly.xml
@@@ -1,10 -1,10 +1,13 @@@
--<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file
-- distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under
-- the Apache License, Version 2.0 (theÏ "License"); you may not use this file except in compliance with the License. You may
-- obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to
-- in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF
-- ANY ~ KIND, either express or implied. See the License for the specific language governing permissions and limitations under
-- the License. -->
++<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor
++ license agreements. See the NOTICE file distributed with this work for additional
++ information regarding copyright ownership. The ASF licenses this file to
++ you under the Apache License, Version 2.0 (theÏ "License"); you may not use
++ this file except in compliance with the License. You may obtain a copy of
++ the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required
++ by applicable law or agreed to in writing, software distributed under the
++ License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
++ OF ANY ~ KIND, either express or implied. See the License for the specific
++ language governing permissions and limitations under the License. -->
<!DOCTYPE assembly [
<!ELEMENT assembly (id|includeBaseDirectory|baseDirectory|formats|fileSets|dependencySets)*>
@@@ -23,136 -23,136 +26,141 @@@
<!ELEMENT dependencySet (outputDirectory|includes)*>
]>
<assembly>
-- <id>bin</id>
-- <includeBaseDirectory>true</includeBaseDirectory>
-- <baseDirectory>${archieve.name}-${version}</baseDirectory>
-- <formats>
-- <format>tar.gz</format>
-- <format>zip</format>
-- </formats>
-- <fileSets>
-- <!-- ********************** copy release notes files ********************** -->
-- <fileSet>
-- <directory>../../../</directory>
-- <outputDirectory>.</outputDirectory>
-- <includes>
-- <include>RELEASE_NOTES</include>
-- </includes>
-- </fileSet>
-- <!-- ********************** copy licenses, readme etc. ********************** -->
-- <fileSet>
-- <directory>src/main/resources/</directory>
-- <outputDirectory>.</outputDirectory>
-- <includes>
-- <include>conf/*</include>
-- <include>LICENSE</include>
-- <include>NOTICE</include>
-- <include>README</include>
-- <include>INSTALL</include>
-- </includes>
-- </fileSet>
-- <fileSet>
-- <directory>${project.build.directory}/conf</directory>
-- <outputDirectory>conf</outputDirectory>
-- <includes>
-- <include>*.properties</include>
-- </includes>
-- </fileSet>
-- <fileSet>
-- <directory>../../../../samples/java-client</directory>
-- <outputDirectory>samples</outputDirectory>
-- <excludes>
-- <exclude>**/*.iml</exclude>
-- <exclude>**/pom.xml</exclude>
-- <exclude>**/target/**</exclude>
-- </excludes>
++ <id>bin</id>
++ <includeBaseDirectory>true</includeBaseDirectory>
++ <baseDirectory>${archieve.name}-${version}</baseDirectory>
++ <formats>
++ <format>tar.gz</format>
++ <format>zip</format>
++ </formats>
++ <fileSets>
++ <!-- ********************** copy release notes files ********************** -->
++ <fileSet>
++ <directory>../../../</directory>
++ <outputDirectory>.</outputDirectory>
++ <includes>
++ <include>RELEASE_NOTES</include>
++ </includes>
++ </fileSet>
++ <!-- ********************** copy licenses, readme etc. ********************** -->
++ <fileSet>
++ <directory>src/main/resources/</directory>
++ <outputDirectory>.</outputDirectory>
++ <includes>
++ <include>conf/*</include>
++ <include>LICENSE</include>
++ <include>NOTICE</include>
++ <include>README</include>
++ <include>INSTALL</include>
++ </includes>
++ </fileSet>
++ <fileSet>
++ <directory>${project.build.directory}/conf</directory>
++ <outputDirectory>conf</outputDirectory>
++ <includes>
++ <include>*.properties</include>
++ </includes>
++ </fileSet>
++ <fileSet>
++ <directory>../../../../samples/java-client</directory>
++ <outputDirectory>samples</outputDirectory>
++ <excludes>
++ <exclude>**/*.iml</exclude>
++ <exclude>**/pom.xml</exclude>
++ <exclude>**/target/**</exclude>
++ </excludes>
-- </fileSet>
-- </fileSets>
++ </fileSet>
++ </fileSets>
-- <dependencySets>
-- <dependencySet>
-- <outputDirectory>lib</outputDirectory>
-- <outputFileNameMapping>${artifact.artifactId}.${artifact.extension}</outputFileNameMapping>
-- <includes>
-- <include>org.apache.derby:derby:jar</include>
-- <include>org.apache.derby:derbytools:jar</include>
-- <include>org.apache.derby:derbynet:jar</include>
-- <include>org.apache.derby:derbyclient:jar</include>
-- </includes>
-- </dependencySet>
-- <dependencySet>
-- <outputDirectory>lib</outputDirectory>
-- <includes>
-- <include>org.slf4j:slf4j-api:jar</include>
-- <include>org.slf4j:slf4j-jcl:jar</include>
-- <include>org.slf4j:slf4j-log4j12:jar</include>
-- <include>javax.jcr:jcr:jar</include>
-- <include>commons-collections:commons-collections</include>
-- <include>commons-configuration:commons-configuration</include>
-- <include>commons-lang:commons-lang</include>
-- <include>org.ogce:xpp3:jar</include>
-- <include>org.ogce:xpp5:jar</include>
-- <include>org.ogce:xsul:jar</include>
-- <include>org.ogce:xsul5:jar</include>
-- <include>org.ogce:gpel-client:jar</include>
-- <include>org.ogce:atomixmiser:jar</include>
-- <include>org.python:jython:jar</include>
-- <include>org.apache.xmlbeans:xmlbeans</include>
-- <!--<include>com.amazonaws:aws-java-sdk</include> -->
-- <!--<include>amazon:MapReduce.Service.Client</include> -->
-- <include>net.java.dev.jets3t:jets3t</include>
-- <include>org.apache.airavata:airavata-orchestrator-core:jar</include>
-- <include>org.apache.airavata:airavata-gfac-schema-utils:jar</include>
-- <include>org.apache.airavata:airavata-common-utils:jar</include>
-- <include>org.apache.airavata:airavata-workflow-execution-context:jar</include>
-- <include>org.apache.airavata:airavata-registry-cpi:jar</include>
-- <include>org.apache.airavata:airavata-jpa-registry:jar</include>
-- <include>org.apache.airavata:airavata-data-models:jar</include>
-- <include>org.apache.airavata:airavata-api-stubs:jar</include>
-- <include>org.apache.airavata:airavata-credential-store:jar</include>
-- <include>org.apache.airavata:airavata-gfac-core:jar</include>
-- <include>commons-cli:commons-cli:jar</include>
-- <!--include>org.apache.airavata:airavata-message-monitor:jar</include>
-- <include>org.apache.airavata:airavata-workflow-model-core:jar</include>
-- <include>org.apache.airavata:airavata-messenger-commons:jar</include>
-- <include>org.apache.airavata:airavata-messenger-client:jar</include-->
-- <include>org.apache.airavata:airavata-workflow-tracking:jar</include>
-- <include>org.apache.airavata:gsissh:jar</include>
-- <include>org.apache.airavata:airavata-model-utils:jar</include>
-- <include>org.apache.airavata:airavata-orchestrator-service:jar</include>
-- <include>org.apache.openjpa:openjpa-all:jar</include>
-- <include>xerces:xercesImpl:jar:2.9.1</include>
-- <include>com.sun.jersey:jersey-json</include>
-- <include>com.sun.jersey.contribs:jersey-multipart</include>
-- <include>org.codehaus.jackson:jackson-jaxrs</include>
-- <include>org.codehaus.jackson:jackson-core-asl</include>
-- <include>org.codehaus.jackson:jackson-mapper-asl</include>
-- <include>org.codehaus.jackson:jackson-xc</include>
-- <include>com.sun.jersey:jersey-core:jar</include>
-- <include>com.sun.jersey:jersey-client:jar</include>
-- <include>org.apache.airavata:json</include>
-- <include>commons-codec:commons-codec:jar</include>
-- <include>wsdl4j:wsdl4j:jar</include>
-- <include>org.apache.axis2:axis2-kernel:jar</include>
-- <include>commons-httpclient:commons-httpclient:jar</include>
-- <include>org.apache.ws.commons.axiom:axiom-api:jar</include>
-- <include>org.apache.axis2:axis2:jar</include>
-- <include>org.apache.ws.commons.schema:XmlSchema:jar</include>
-- <include>org.apache.ws.commons.axiom:axiom-impl:jar</include>
-- <include>org.apache.neethi:neethi:jar</include>
-- <include>org.apache.axis2:axis2-transport-local:jar</include>
-- <include>org.apache.axis2:axis2-transport-http:jar</include>
-- <include>javax.mail:mail:jar</include>
-- <include>org.apache.woden:woden-api:jar</include>
-- <include>org.apache.httpcomponents:httpcore:jar</include>
-- <include>org.apache.axis2:axis2-adb:jar</include>
-- <include>log4j:log4j:jar</include>
-- <include>de.odysseus.staxon:staxon:jar:1.2</include>
-- <include>de.odysseus.staxon:staxon-jackson:jar:1.2</include>
-- <include>org.apache.thrift:libthrift:jar:0.9.1</include>
-- </includes>
-- </dependencySet>
-- </dependencySets>
++ <dependencySets>
++ <dependencySet>
++ <outputDirectory>lib</outputDirectory>
++ <outputFileNameMapping>${artifact.artifactId}.${artifact.extension}
++ </outputFileNameMapping>
++ <includes>
++ <include>org.apache.derby:derby:jar</include>
++ <include>org.apache.derby:derbytools:jar</include>
++ <include>org.apache.derby:derbynet:jar</include>
++ <include>org.apache.derby:derbyclient:jar</include>
++ </includes>
++ </dependencySet>
++ <dependencySet>
++ <outputDirectory>lib</outputDirectory>
++ <includes>
++ <include>org.slf4j:slf4j-api:jar</include>
++ <include>org.slf4j:slf4j-jcl:jar</include>
++ <include>org.slf4j:slf4j-log4j12:jar</include>
++ <include>javax.jcr:jcr:jar</include>
++ <include>commons-collections:commons-collections</include>
++ <include>commons-configuration:commons-configuration</include>
++ <include>commons-lang:commons-lang</include>
++ <include>org.ogce:xpp3:jar</include>
++ <include>org.ogce:xpp5:jar</include>
++ <include>org.ogce:xsul:jar</include>
++ <include>org.ogce:xsul5:jar</include>
++ <include>org.ogce:gpel-client:jar</include>
++ <include>org.ogce:atomixmiser:jar</include>
++ <include>org.python:jython:jar</include>
++ <include>org.apache.xmlbeans:xmlbeans</include>
++ <!--<include>com.amazonaws:aws-java-sdk</include> -->
++ <!--<include>amazon:MapReduce.Service.Client</include> -->
++ <include>net.java.dev.jets3t:jets3t</include>
++ <include>org.apache.airavata:airavata-orchestrator-core:jar
++ </include>
++ <include>org.apache.airavata:airavata-gfac-schema-utils:jar
++ </include>
++ <include>org.apache.airavata:airavata-common-utils:jar</include>
++ <include>org.apache.airavata:airavata-workflow-execution-context:jar
++ </include>
++ <include>org.apache.airavata:airavata-registry-cpi:jar</include>
++ <include>org.apache.airavata:airavata-jpa-registry:jar</include>
++ <include>org.apache.airavata:airavata-data-models:jar</include>
++ <include>org.apache.airavata:airavata-api-stubs:jar</include>
++ <include>org.apache.airavata:airavata-credential-store:jar</include>
++ <include>org.apache.airavata:airavata-gfac-core:jar</include>
++ <include>commons-cli:commons-cli:jar</include>
++ <!--include>org.apache.airavata:airavata-message-monitor:jar</include>
++ <include>org.apache.airavata:airavata-workflow-model-core:jar</include> <include>org.apache.airavata:airavata-messenger-commons:jar</include>
++ <include>org.apache.airavata:airavata-messenger-client:jar</include -->
++ <include>org.apache.airavata:airavata-workflow-tracking:jar
++ </include>
++ <include>org.apache.airavata:gsissh:jar</include>
++ <include>org.apache.airavata:airavata-model-utils:jar</include>
++ <include>org.apache.airavata:airavata-orchestrator-service:jar
++ </include>
++ <include>org.apache.openjpa:openjpa-all:jar</include>
++ <include>xerces:xercesImpl:jar:2.9.1</include>
++ <include>com.sun.jersey:jersey-json</include>
++ <include>com.sun.jersey.contribs:jersey-multipart</include>
++ <include>org.codehaus.jackson:jackson-jaxrs</include>
++ <include>org.codehaus.jackson:jackson-core-asl</include>
++ <include>org.codehaus.jackson:jackson-mapper-asl</include>
++ <include>org.codehaus.jackson:jackson-xc</include>
++ <include>com.sun.jersey:jersey-core:jar</include>
++ <include>com.sun.jersey:jersey-client:jar</include>
++ <include>org.apache.airavata:json</include>
++ <include>commons-codec:commons-codec:jar</include>
++ <include>wsdl4j:wsdl4j:jar</include>
++ <include>org.apache.axis2:axis2-kernel:jar</include>
++ <include>commons-httpclient:commons-httpclient:jar</include>
++ <include>org.apache.ws.commons.axiom:axiom-api:jar</include>
++ <include>org.apache.axis2:axis2:jar</include>
++ <include>org.apache.ws.commons.schema:XmlSchema:jar</include>
++ <include>org.apache.ws.commons.axiom:axiom-impl:jar</include>
++ <include>org.apache.neethi:neethi:jar</include>
++ <include>org.apache.axis2:axis2-transport-local:jar</include>
++ <include>org.apache.axis2:axis2-transport-http:jar</include>
++ <include>javax.mail:mail:jar</include>
++ <include>org.apache.woden:woden-api:jar</include>
++ <include>org.apache.httpcomponents:httpcore:jar</include>
++ <include>org.apache.axis2:axis2-adb:jar</include>
++ <include>log4j:log4j:jar</include>
++ <include>de.odysseus.staxon:staxon:jar:1.2</include>
++ <include>de.odysseus.staxon:staxon-jackson:jar:1.2</include>
++ <include>org.apache.thrift:libthrift:jar:0.9.1</include>
++ </includes>
++ </dependencySet>
++ </dependencySets>
</assembly>
http://git-wip-us.apache.org/repos/asf/airavata/blob/5413e671/modules/distribution/server/src/main/assembly/bin-assembly.xml
----------------------------------------------------------------------