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Posted to commits@airavata.apache.org by ch...@apache.org on 2014/11/11 20:10:57 UTC
[10/16] airavata git commit: fixed simple experiment run
[AIRAVATA-1473]
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/gfac_appcatalog_int
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);
}