Author: chathuri
Date: Thu Aug 22 21:36:21 2013
New Revision: 1516619
URL: http://svn.apache.org/r1516619
Log:
porting issues fixed while migration to branch
Modified:
airavata/branches/airavata-0.8-maintenance-branch/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/NodeSettingsImpl.java
airavata/branches/airavata-0.8-maintenance-branch/modules/commons/workflow-execution-context/src/main/java/org/apache/airavata/common/workflow/execution/context/WorkflowContextHeaderBuilder.java
airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/OutputUtils.java
airavata/branches/airavata-0.8-maintenance-branch/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/resources/ExperimentDataRetriever.java
airavata/branches/airavata-0.8-maintenance-branch/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
Modified:
airavata/branches/airavata-0.8-maintenance-branch/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/NodeSettingsImpl.java
URL:
http://svn.apache.org/viewvc/airavata/branches/airavata-0.8-maintenance-branch/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/NodeSettingsImpl.java?rev=1516619&r1=1516618&r2=1516619&view=diff
==============================================================================
---
airavata/branches/airavata-0.8-maintenance-branch/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/NodeSettingsImpl.java
(original)
+++
airavata/branches/airavata-0.8-maintenance-branch/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/NodeSettingsImpl.java
Thu Aug 22 21:36:21 2013
@@ -21,6 +21,7 @@
package org.apache.airavata.client.impl;
+import java.util.ArrayList;
import java.util.List;
import org.apache.airavata.client.api.HPCSettings;
@@ -92,6 +93,9 @@ public class NodeSettingsImpl implements
@Override
public List<NameValuePairType> getNameValuePair() {
+ if (nameValuePair==null){
+ nameValuePair=new ArrayList<NameValuePairType>();
+ }
return nameValuePair;
}
Modified:
airavata/branches/airavata-0.8-maintenance-branch/modules/commons/workflow-execution-context/src/main/java/org/apache/airavata/common/workflow/execution/context/WorkflowContextHeaderBuilder.java
URL:
http://svn.apache.org/viewvc/airavata/branches/airavata-0.8-maintenance-branch/modules/commons/workflow-execution-context/src/main/java/org/apache/airavata/common/workflow/execution/context/WorkflowContextHeaderBuilder.java?rev=1516619&r1=1516618&r2=1516619&view=diff
==============================================================================
---
airavata/branches/airavata-0.8-maintenance-branch/modules/commons/workflow-execution-context/src/main/java/org/apache/airavata/common/workflow/execution/context/WorkflowContextHeaderBuilder.java
(original)
+++
airavata/branches/airavata-0.8-maintenance-branch/modules/commons/workflow-execution-context/src/main/java/org/apache/airavata/common/workflow/execution/context/WorkflowContextHeaderBuilder.java
Thu Aug 22 21:36:21 2013
@@ -53,9 +53,22 @@ public class WorkflowContextHeaderBuilde
public WorkflowContextHeaderBuilder(ContextHeaderDocument.ContextHeader
document){
- this.contextHeader = document;
+ ContextHeaderDocument parse = null;
+ try {
+ ContextHeaderDocument doc =
ContextHeaderDocument.Factory.newInstance();
+ doc.setContextHeader(document);
+ parse =
ContextHeaderDocument.Factory.parse(doc.xmlText());
+ } catch (XmlException e) {
+ e.printStackTrace();
+ }
+ this.contextHeader = parse.getContextHeader();
if (contextHeader!=null) {
this.securityContext =
contextHeader.getSecurityContext();
+
this.workflowSchedulingContext=contextHeader.getWorkflowSchedulingContext();
+ this.soaServiceEprs=contextHeader.getSoaServiceEprs();
+
this.workflowMonitoringContext=contextHeader.getWorkflowMonitoringContext();
+
this.workflowOutputDataHandling=contextHeader.getWorkflowOutputDataHandling();
+ this.userIdentifier=contextHeader.getUserIdentifier();
}
}
@@ -164,7 +177,12 @@ public class WorkflowContextHeaderBuilde
}
public XmlElement getXml() {
- ContextHeaderDocument document =
ContextHeaderDocument.Factory.newInstance();
+ ContextHeaderDocument document = getDocument();
+ return XMLUtil.stringToXmlElement3(document.xmlText());
+ }
+
+ private ContextHeaderDocument getDocument() {
+ ContextHeaderDocument document =
ContextHeaderDocument.Factory.newInstance();
if (this.workflowMonitoringContext != null) {
this.contextHeader.setWorkflowMonitoringContext(this.workflowMonitoringContext);
}
@@ -184,8 +202,8 @@ public class WorkflowContextHeaderBuilde
this.contextHeader.setWorkflowOutputDataHandling(this.workflowOutputDataHandling);
}
document.setContextHeader(this.contextHeader);
- return XMLUtil.stringToXmlElement3(document.xmlText());
- }
+ return document;
+ }
public WorkflowContextHeaderBuilder setResourceSchedularUrl(String
resourceSchedular) {
this.soaServiceEprs.setResourceSchedulerUrl(resourceSchedular);
@@ -402,15 +420,16 @@ public class WorkflowContextHeaderBuilde
}
public static ContextHeaderDocument.ContextHeader
removeOtherSchedulingConfig(String nodeID, ContextHeaderDocument.ContextHeader
header) {
- String s = XMLUtil.xmlElementToString(new
WorkflowContextHeaderBuilder(header).getXml());
+ WorkflowContextHeaderBuilder.setCurrentContextHeader(header);
+ header=new WorkflowContextHeaderBuilder(header).getContextHeader();
try {
ApplicationSchedulingContextDocument.ApplicationSchedulingContext[]
applicationSchedulingContextArray =
header.getWorkflowSchedulingContext().getApplicationSchedulingContextArray();
-
+
int index = 0;
if (applicationSchedulingContextArray != null) {
for
(ApplicationSchedulingContextDocument.ApplicationSchedulingContext context :
applicationSchedulingContextArray) {
- if (context.getServiceId().equals(nodeID)) {
+ if (context.getWorkflowNodeId().equals(nodeID)) {
index++;
header.getWorkflowSchedulingContext().setApplicationSchedulingContextArray(new
ApplicationSchedulingContextDocument.ApplicationSchedulingContext[]{context});
break;
@@ -437,14 +456,6 @@ public class WorkflowContextHeaderBuilde
} catch (NullPointerException e) {
return header;
}
- ContextHeaderDocument parse = null;
- try {
- parse = ContextHeaderDocument.Factory.parse(s);
- } catch (XmlException e) {
- e.printStackTrace(); //To change body of catch statement use File
| Settings | File Templates.
- }
- //Set Old Context Header in to currentContextHeader
-
WorkflowContextHeaderBuilder.setCurrentContextHeader(parse.getContextHeader());
return header;
}
}
Modified:
airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
URL:
http://svn.apache.org/viewvc/airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java?rev=1516619&r1=1516618&r2=1516619&view=diff
==============================================================================
---
airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
(original)
+++
airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
Thu Aug 22 21:36:21 2013
@@ -200,9 +200,6 @@ public class GridFTPOutputHandler implem
} catch (URISyntaxException e) {
log.error(e.getMessage());
throw new GFacHandlerException("URI is malformatted:" +
e.getMessage(), jobExecutionContext, e,
readLastLinesofStdOut(localStdErrFile.getPath(), 20));
- } catch (NullPointerException e) {
- log.error(e.getMessage());
- throw new GFacHandlerException("Output is not produced in
stdout:" + e.getMessage(), jobExecutionContext, e,
readLastLinesofStdOut(localStdErrFile.getPath(), 20));
}
}
} catch (Exception e) {
Modified:
airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/OutputUtils.java
URL:
http://svn.apache.org/viewvc/airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/OutputUtils.java?rev=1516619&r1=1516618&r2=1516619&view=diff
==============================================================================
---
airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/OutputUtils.java
(original)
+++
airavata/branches/airavata-0.8-maintenance-branch/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/OutputUtils.java
Thu Aug 22 21:36:21 2013
@@ -28,6 +28,7 @@ import java.util.regex.Pattern;
import org.apache.airavata.commons.gfac.type.ActualParameter;
import org.apache.airavata.commons.gfac.type.MappingFactory;
+import org.apache.airavata.gfac.handler.GFacHandlerException;
import org.apache.airavata.schemas.gfac.StdErrParameterType;
import org.apache.airavata.schemas.gfac.StdOutParameterType;
import org.apache.airavata.schemas.gfac.URIParameterType;
@@ -37,6 +38,10 @@ public class OutputUtils {
public static Map<String, ActualParameter>
fillOutputFromStdout(Map<String, Object> output, String stdout, String stderr)
throws Exception {
+ if (stdout == null || stdout.equals("")){
+ throw new GFacHandlerException("Standard output is empty.");
+ }
+
Map<String, ActualParameter> result = new HashMap<String,
ActualParameter>();
Set<String> keys = output.keySet();
for (String paramName : keys) {
@@ -53,9 +58,6 @@ public class OutputUtils {
((StdErrParameterType) actual.getType()).setValue(stderr);
result.put(paramName, actual);
} else {
- if ("URI".equals(actual.getType().getType().toString()) &&
!((URIParameterType) actual.getType()).getValue().isEmpty()){
- continue;
- }
String parseStdout = parseStdout(stdout, paramName);
if (parseStdout != null) {
MappingFactory.fromString(actual, parseStdout);
Modified:
airavata/branches/airavata-0.8-maintenance-branch/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/resources/ExperimentDataRetriever.java
URL:
http://svn.apache.org/viewvc/airavata/branches/airavata-0.8-maintenance-branch/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/resources/ExperimentDataRetriever.java?rev=1516619&r1=1516618&r2=1516619&view=diff
==============================================================================
---
airavata/branches/airavata-0.8-maintenance-branch/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/resources/ExperimentDataRetriever.java
(original)
+++
airavata/branches/airavata-0.8-maintenance-branch/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/resources/ExperimentDataRetriever.java
Thu Aug 22 21:36:21 2013
@@ -414,7 +414,8 @@ public class ExperimentDataRetriever {
"ON e.experiment_ID = ed.experiment_ID " +
"LEFT JOIN Experiment_Metadata em " +
"ON ed.experiment_ID = em.experiment_ID " +
- "WHERE ed.username ='" + user + "'";
+ "WHERE ed.username ='" + user + "'" +
+ " ORDER BY e.submitted_date ASC";
rs = statement.executeQuery(queryString);
if (rs != null){
Modified:
airavata/branches/airavata-0.8-maintenance-branch/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
URL:
http://svn.apache.org/viewvc/airavata/branches/airavata-0.8-maintenance-branch/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java?rev=1516619&r1=1516618&r2=1516619&view=diff
==============================================================================
---
airavata/branches/airavata-0.8-maintenance-branch/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
(original)
+++
airavata/branches/airavata-0.8-maintenance-branch/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
Thu Aug 22 21:36:21 2013
@@ -23,12 +23,7 @@ package org.apache.airavata.xbaya.invoke
import java.io.File;
import java.io.StringReader;
import java.net.URL;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-import java.util.Set;
+import java.util.*;
import javax.xml.namespace.QName;
import javax.xml.stream.XMLInputFactory;
@@ -283,7 +278,7 @@ public class EmbeddedGFacInvoker impleme
*/
public synchronized boolean invoke() throws WorkflowException {
try {
- ContextHeaderDocument.ContextHeader contextHeader =
+ ContextHeaderDocument.ContextHeader contextHeader =
WorkflowContextHeaderBuilder.removeOtherSchedulingConfig(nodeID,this.configuration.getContextHeader());
String hostName = null;
HostDescription registeredHost;
@@ -507,6 +502,13 @@ public class EmbeddedGFacInvoker impleme
try {
waitToFinish();
if (outPut instanceof XmlElement) {
+ Iterator children = ((XmlElement) outPut).children();
+ while (children.hasNext()) {
+ Object next = children.next();
+ if (((XmlElement) next).getName().equals(name)) {
+ return ((XmlElement)((XmlElement)
next).children().next()).children().next();
+ }
+ }
return ((XmlElement) ((XmlElement) ((XmlElement)
outPut).children().next()).children().next()).children().next();
} else {
return outPut;
