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Posted to commits@airavata.apache.org by ra...@apache.org on 2014/02/26 22:26:01 UTC
git commit: added ConfigurationData support. AIRAVATA-1032
Repository: airavata
Updated Branches:
refs/heads/master bc954ece5 -> 3a453bb14
added ConfigurationData support. AIRAVATA-1032
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/3a453bb1
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/3a453bb1
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/3a453bb1
Branch: refs/heads/master
Commit: 3a453bb14856f7cfe909cda650a1fe66f15f99a5
Parents: bc954ec
Author: raminder <ra...@apache.org>
Authored: Wed Feb 26 16:25:44 2014 -0500
Committer: raminder <ra...@apache.org>
Committed: Wed Feb 26 16:25:44 2014 -0500
----------------------------------------------------------------------
.../gfac/context/JobExecutionContext.java | 35 +++++++++++++----
.../java/org/apache/airavata/gfac/cpi/GFac.java | 2 -
.../gfac/handler/GridFTPOutputHandler.java | 10 ++---
.../gfac/provider/impl/BESProvider.java | 9 +++--
.../provider/utils/ApplicationProcessor.java | 5 ++-
.../gfac/provider/utils/DataTransferrer.java | 22 +++--------
.../gfac/provider/utils/ResourceProcessor.java | 21 +++++-----
.../airavata/gfac/utils/GramRSLGenerator.java | 41 +++++++++-----------
.../gfac/services/impl/AbstractBESTest.java | 10 ++---
.../orchestrator/core/BaseOrchestratorTest.java | 2 -
.../orchestrator/core/NewOrchestratorTest.java | 4 +-
.../core/OrchestratorTestWithGRAM.java | 4 +-
.../core/OrchestratorTestWithGSISSH.java | 5 ++-
.../xbaya/invoker/EmbeddedGFacInvoker.java | 10 ++---
14 files changed, 89 insertions(+), 91 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
index 5d03005..b8e6f87 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
@@ -26,6 +26,7 @@ import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.SecurityContext;
import org.apache.airavata.gfac.notification.GFacNotifier;
import org.apache.airavata.gfac.provider.GFacProvider;
+import org.apache.airavata.model.experiment.ConfigurationData;
import org.apache.airavata.schemas.wec.ContextHeaderDocument;
import java.util.ArrayList;
@@ -44,8 +45,10 @@ public class JobExecutionContext extends AbstractContext{
private MessageContext outMessageContext;
private GFacNotifier notifier;
+
+ private ConfigurationData configurationData;
- private ContextHeaderDocument.ContextHeader contextHeader;
+// private ContextHeaderDocument.ContextHeader contextHeader;
// Keep track of the current path of the message. Before hitting provider its in-path.
// After provider its out-path.
@@ -71,6 +74,8 @@ public class JobExecutionContext extends AbstractContext{
private String serviceName;
private String experimentID;
+
+ private String status;
/**
* Security context is used to handle authentication for input handlers and providers.
@@ -181,13 +186,21 @@ public class JobExecutionContext extends AbstractContext{
this.inPath = false;
}
- public ContextHeaderDocument.ContextHeader getContextHeader() {
- return contextHeader;
- }
+// public ContextHeaderDocument.ContextHeader getContextHeader() {
+// return contextHeader;
+// }
+//
+// public void setContextHeader(ContextHeaderDocument.ContextHeader contextHeader) {
+// this.contextHeader = contextHeader;
+// }
- public void setContextHeader(ContextHeaderDocument.ContextHeader contextHeader) {
- this.contextHeader = contextHeader;
- }
+ public ConfigurationData getConfigurationData() {
+ return configurationData;
+ }
+
+ public void setConfigurationData(ConfigurationData configurationData) {
+ this.configurationData = configurationData;
+ }
public SecurityContext getSecurityContext(String name) throws GFacException{
SecurityContext secContext = securityContext.get(name);
@@ -198,4 +211,12 @@ public class JobExecutionContext extends AbstractContext{
securityContext.put(name, value);
}
+ public String getStatus() {
+ return status;
+ }
+
+ public void setStatus(String status) {
+ this.status = status;
+ }
+
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFac.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFac.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFac.java
index b18cdd9..2358735 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFac.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFac.java
@@ -22,8 +22,6 @@ package org.apache.airavata.gfac.cpi;
import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.context.JobExecutionContext;
-import org.apache.airavata.model.experiment.ConfigurationData;
-import org.apache.airavata.registry.cpi.DataType;
/**
* This is the GFac CPI interface which needs to be implemented by an internal class, this simply have a single method to submit a job to
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
index be4d250..55cf2f7 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
@@ -48,6 +48,7 @@ import org.apache.airavata.gfac.external.GridFtp;
import org.apache.airavata.gfac.provider.GFacProviderException;
import org.apache.airavata.gfac.utils.GFacUtils;
import org.apache.airavata.gfac.utils.OutputUtils;
+import org.apache.airavata.model.experiment.ConfigurationData;
import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
import org.apache.airavata.schemas.gfac.GlobusHostType;
import org.apache.airavata.schemas.gfac.HostDescriptionType;
@@ -178,15 +179,12 @@ public class GridFTPOutputHandler implements GFacHandler {
"and ApplicationDescriptor output Parameter Names");
}
// If users has given an output Data path to download the output files this will download the file on machine where GFac is installed
- ContextHeaderDocument.ContextHeader currentContextHeader = jobExecutionContext.getContextHeader();
- if(currentContextHeader != null && currentContextHeader.getWorkflowOutputDataHandling() != null){
- ApplicationOutputDataHandling[] handlings = currentContextHeader.getWorkflowOutputDataHandling().getApplicationOutputDataHandlingArray();
- if(handlings != null && handlings.length != 0){
- String outputDataDirectory = handlings[0].getOutputDataDirectory();
+ ConfigurationData configurationData = jobExecutionContext.getConfigurationData();
+ if(configurationData != null && configurationData.getAdvanceOutputDataHandling() != null){
+ String outputDataDirectory = configurationData.getAdvanceOutputDataHandling().getOutputdataDir();
if(outputDataDirectory != null && !"".equals(outputDataDirectory)){
stageOutputFiles(jobExecutionContext,outputDataDirectory);
}
- }
}
} catch (ToolsException e) {
log.error(e.getMessage());
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/BESProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/BESProvider.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/BESProvider.java
index 76ed230..a341f32 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/BESProvider.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/BESProvider.java
@@ -434,11 +434,12 @@ public class BESProvider implements GFacProvider {
}
private String getUserName(JobExecutionContext context) {
- if (context.getContextHeader() != null) {
- return context.getContextHeader().getUserIdentifier();
- } else {
+ //FIXME: get experiment user
+// if (context.getContextHeader() != null) {
+// return context.getContextHeader().getUserIdentifier();
+// } else {
return "";
- }
+// }
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ApplicationProcessor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ApplicationProcessor.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ApplicationProcessor.java
index d4b26a6..b9d7422 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ApplicationProcessor.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ApplicationProcessor.java
@@ -112,9 +112,10 @@ public class ApplicationProcessor {
}
public static String getUserNameFromContext(JobExecutionContext jobContext) {
- if(jobContext.getContextHeader() == null)
+ if(jobContext.getConfigurationData() == null)
return null;
- return jobContext.getContextHeader().getUserIdentifier();
+ //FIXME: Discuss to get user and change this
+ return "admin";
}
public static boolean isParallelJob(HpcApplicationDeploymentType appDepType) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/DataTransferrer.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/DataTransferrer.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/DataTransferrer.java
index 52396f1..e008f37 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/DataTransferrer.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/DataTransferrer.java
@@ -34,13 +34,12 @@ import org.apache.airavata.commons.gfac.type.ApplicationDescription;
import org.apache.airavata.gfac.Constants;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.model.experiment.ConfigurationData;
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.URIParameterType;
-import org.apache.airavata.schemas.wec.ApplicationOutputDataHandlingDocument.ApplicationOutputDataHandling;
-import org.apache.airavata.schemas.wec.ContextHeaderDocument;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -232,20 +231,11 @@ public class DataTransferrer {
}
private String getDownloadLocation() {
- String outputDataDirectory = null;
- ContextHeaderDocument.ContextHeader currentContextHeader = jobContext
- .getContextHeader();
- if (currentContextHeader != null
- && currentContextHeader.getWorkflowOutputDataHandling() != null) {
- ApplicationOutputDataHandling[] handlings = currentContextHeader
- .getWorkflowOutputDataHandling()
- .getApplicationOutputDataHandlingArray();
- if (handlings != null && handlings.length != 0) {
- outputDataDirectory = handlings[0]
- .getOutputDataDirectory();
- return outputDataDirectory;
- }
+ ConfigurationData configurationData = jobContext.getConfigurationData();
+ if (configurationData != null && configurationData.getAdvanceOutputDataHandling() != null) {
+ String outputDataDirectory = configurationData.getAdvanceOutputDataHandling().getOutputdataDir();
+ return outputDataDirectory;
}
- return outputDataDirectory;
+ return null;
}
}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ResourceProcessor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ResourceProcessor.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ResourceProcessor.java
index 93c8c92..83f28f0 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ResourceProcessor.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/utils/ResourceProcessor.java
@@ -23,6 +23,8 @@ package org.apache.airavata.gfac.provider.utils;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.model.experiment.ComputationalResourceScheduling;
+import org.apache.airavata.model.experiment.ConfigurationData;
import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
import org.apache.airavata.schemas.gfac.QueueType;
import org.apache.airavata.schemas.wec.ContextHeaderDocument;
@@ -39,14 +41,11 @@ public class ResourceProcessor {
.getType();
createMemory(value, appDepType);
- ContextHeaderDocument.ContextHeader currentContextHeader = context.getContextHeader();
- if(currentContextHeader != null){
- if (currentContextHeader.getWorkflowSchedulingContext() != null) {
- if (currentContextHeader != null &&
- currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray() != null &&
- currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray().length > 0) {
+ ConfigurationData configurationData = context.getConfigurationData();
+ if(configurationData != null && configurationData.isSetComputationalResourceScheduling()){
+ ComputationalResourceScheduling computionResource= configurationData.getComputationalResourceScheduling();
try {
- int cpuCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getCpuCount();
+ int cpuCount = computionResource.getTotalCPUCount();
if(cpuCount>0){
// appDepType.setCpuCount(cpuCount);
NumberOfProcessesType num = NumberOfProcessesType.Factory.newInstance();
@@ -58,7 +57,7 @@ public class ResourceProcessor {
new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
}
try {
- int nodeCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getNodeCount();
+ int nodeCount = computionResource.getNodeCount();
if(nodeCount>0){
appDepType.setNodeCount(nodeCount);
}
@@ -66,7 +65,7 @@ public class ResourceProcessor {
new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
}
try {
- String queueName = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getQueueName();
+ String queueName = computionResource.getQueueName();
if (queueName != null) {
if(appDepType.getQueue() == null){
QueueType queueType = appDepType.addNewQueue();
@@ -79,16 +78,14 @@ public class ResourceProcessor {
new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
}
try {
- int maxwallTime = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getMaxWallTime();
+ int maxwallTime = computionResource.getWallTimeLimit();
if(maxwallTime>0){
appDepType.setMaxWallTime(maxwallTime);
}
} catch (NullPointerException e) {
new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
}
- }
}
- }
if (appDepType.getCpuCount() > 0) {
RangeValueType rangeType = new RangeValueType();
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java
index 3c05c89..16b1f3e 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramRSLGenerator.java
@@ -20,6 +20,10 @@
*/
package org.apache.airavata.gfac.utils;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
import org.apache.airavata.common.utils.StringUtil;
import org.apache.airavata.commons.gfac.type.ActualParameter;
import org.apache.airavata.commons.gfac.type.MappingFactory;
@@ -28,16 +32,18 @@ import org.apache.airavata.gfac.ToolsException;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.context.MessageContext;
import org.apache.airavata.gfac.provider.GFacProviderException;
-import org.apache.airavata.schemas.gfac.*;
-import org.apache.airavata.schemas.wec.ContextHeaderDocument;
+import org.apache.airavata.model.experiment.ComputationalResourceScheduling;
+import org.apache.airavata.model.experiment.ConfigurationData;
+import org.apache.airavata.schemas.gfac.FileArrayType;
+import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
+import org.apache.airavata.schemas.gfac.NameValuePairType;
+import org.apache.airavata.schemas.gfac.QueueType;
+import org.apache.airavata.schemas.gfac.StringArrayType;
+import org.apache.airavata.schemas.gfac.URIArrayType;
import org.globus.gram.GramAttributes;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-
public class GramRSLGenerator {
protected static final Logger log = LoggerFactory.getLogger(GramRSLGenerator.class);
@@ -104,14 +110,11 @@ public class GramRSLGenerator {
}
// Using the workflowContext Header values if user provided them in the request and overwrite the default values in DD
//todo finish the scheduling based on workflow execution context
- ContextHeaderDocument.ContextHeader currentContextHeader = context.getContextHeader();
- if(currentContextHeader != null){
- if (currentContextHeader.getWorkflowSchedulingContext() != null) {
- if (currentContextHeader != null &&
- currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray() != null &&
- currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray().length > 0) {
+ ConfigurationData configurationData = context.getConfigurationData();
+ if(configurationData != null && configurationData.getComputationalResourceScheduling() != null){
+ ComputationalResourceScheduling computionnalResource = configurationData.getComputationalResourceScheduling();
try {
- int cpuCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getCpuCount();
+ int cpuCount = computionnalResource.getTotalCPUCount();
if(cpuCount>0){
app.setCpuCount(cpuCount);
}
@@ -120,7 +123,7 @@ public class GramRSLGenerator {
new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
}
try {
- int nodeCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getNodeCount();
+ int nodeCount = computionnalResource.getNodeCount();
if(nodeCount>0){
app.setNodeCount(nodeCount);
}
@@ -129,7 +132,7 @@ public class GramRSLGenerator {
new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
}
try {
- String queueName = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getQueueName();
+ String queueName = computionnalResource.getQueueName();
if (queueName != null) {
if(app.getQueue() == null){
QueueType queueType = app.addNewQueue();
@@ -143,7 +146,7 @@ public class GramRSLGenerator {
new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
}
try {
- int maxwallTime = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getMaxWallTime();
+ int maxwallTime = computionnalResource.getWallTimeLimit();
if(maxwallTime>0){
app.setMaxWallTime(maxwallTime);
}
@@ -151,12 +154,6 @@ public class GramRSLGenerator {
log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
}
- }
- }
-// if(currentContextHeader.getWorkflowOutputDataHandling() != null){
-// if(currentContextHeader.getWorkflowOutputDataHandling().getApplicationOutputDataHandlingArray().length != 0)
-// app.setOutputDataDirectory(currentContextHeader.getWorkflowOutputDataHandling().getApplicationOutputDataHandlingArray()[0].getOutputDataDirectory());
-// }
}
if (app.getNodeCount() > 0) {
jobAttr.set("hostCount", String.valueOf(app.getNodeCount()));
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTest.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTest.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTest.java
index 2dc4131..efbd164 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTest.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTest.java
@@ -103,11 +103,11 @@ public abstract class AbstractBESTest extends GFacBaseTestCase {
}
protected void submitJob() throws Exception {
- ContextHeader contextHeader = ContextHeader.Factory.newInstance();
- buildOutputLocation(contextHeader);
-
- buildUserName(contextHeader, userName);
- jobExecutionContext.setContextHeader(contextHeader);
+// ContextHeader contextHeader = ContextHeader.Factory.newInstance();
+// buildOutputLocation(contextHeader);
+//
+// buildUserName(contextHeader, userName);
+// jobExecutionContext.setContextHeader(contextHeader);
}
protected GFacConfiguration getGFACConfig() throws Exception {
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java
----------------------------------------------------------------------
diff --git a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java
index b3ec514..a10ce12 100644
--- a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java
+++ b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java
@@ -36,7 +36,6 @@ public class BaseOrchestratorTest {
private GatewayResource gatewayResource;
private WorkerResource workerResource;
private UserResource userResource;
- private OrchestratorDataResource orchestratorDataResource;
private Initialize initialize;
private DocumentCreator documentCreator;
@@ -46,7 +45,6 @@ public class BaseOrchestratorTest {
gatewayResource = (GatewayResource) ResourceUtils.getGateway("default");
workerResource = (WorkerResource) ResourceUtils.getWorker(gatewayResource.getGatewayName(), "admin");
userResource = (UserResource) gatewayResource.create(ResourceType.USER);
- orchestratorDataResource = (OrchestratorDataResource) gatewayResource.create(ResourceType.ORCHESTRATOR);
userResource.setUserName("admin");
userResource.setPassword("admin");
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/NewOrchestratorTest.java
----------------------------------------------------------------------
diff --git a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/NewOrchestratorTest.java b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/NewOrchestratorTest.java
index e14d1e4..8bda644 100644
--- a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/NewOrchestratorTest.java
+++ b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/NewOrchestratorTest.java
@@ -55,7 +55,7 @@ public class NewOrchestratorTest extends BaseOrchestratorTest {
createJobRequestWithDocuments(getAiravataAPI());
}
- private void createJobRequestWithDocuments(AiravataAPI airavataAPI) {
+ private void createJobRequestWithDocuments(AiravataAPI airavataAPI) throws Exception{
// creating host description
//Using new airavata-api methods to store experiment metadata
@@ -83,7 +83,7 @@ public class NewOrchestratorTest extends BaseOrchestratorTest {
configurationData.setApplicationId("Echo");
Registry registry = new RegistryImpl();
- experimentID = (String) registry.add(ParentDataType.EXPERIMENT_BASIC_DATA, basicMetadata);
+ experimentID = (String) registry.add(ParentDataType.EXPERIMENT, basicMetadata);
registry.add(ChildDataType.EXPERIMENT_CONFIGURATION_DATA, configurationData, experimentID);
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGRAM.java
----------------------------------------------------------------------
diff --git a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGRAM.java b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGRAM.java
index 1c62a0d..b33ee65 100644
--- a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGRAM.java
+++ b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGRAM.java
@@ -51,7 +51,7 @@ public class OrchestratorTestWithGRAM extends BaseOrchestratorTest {
createJobRequestWithDocuments();
}
- private void createJobRequestWithDocuments() {
+ private void createJobRequestWithDocuments() throws Exception{
//Using new airavata-api methods to store experiment metadata
BasicMetadata basicMetadata = new BasicMetadata();
basicMetadata.setExperimentName("test-trestles");
@@ -76,7 +76,7 @@ public class OrchestratorTestWithGRAM extends BaseOrchestratorTest {
configurationData.setApplicationId("SimpleEcho1");
Registry registry = new RegistryImpl();
- experimentID = (String) registry.add(ParentDataType.EXPERIMENT_BASIC_DATA, basicMetadata);
+ experimentID = (String) registry.add(ParentDataType.EXPERIMENT, basicMetadata);
registry.add(ChildDataType.EXPERIMENT_CONFIGURATION_DATA, configurationData, experimentID);
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGSISSH.java
----------------------------------------------------------------------
diff --git a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGSISSH.java b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGSISSH.java
index 6393523..9d321f0 100644
--- a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGSISSH.java
+++ b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGSISSH.java
@@ -21,6 +21,7 @@
package org.apache.airavata.orchestrator.core;
import junit.framework.Assert;
+
import org.apache.airavata.client.api.AiravataAPI;
import org.apache.airavata.common.utils.AiravataUtils;
import org.apache.airavata.model.experiment.*;
@@ -52,7 +53,7 @@ public class OrchestratorTestWithGSISSH extends BaseOrchestratorTest {
createJobRequestWithDocuments();
}
- private void createJobRequestWithDocuments() {
+ private void createJobRequestWithDocuments() throws Exception{
//Using new airavata-api methods to store experiment metadata
BasicMetadata basicMetadata = new BasicMetadata();
basicMetadata.setExperimentName("test-trestles-gsissh");
@@ -77,7 +78,7 @@ public class OrchestratorTestWithGSISSH extends BaseOrchestratorTest {
configurationData.setApplicationId("SimpleEcho2");
Registry registry = new RegistryImpl();
- experimentID = (String) registry.add(ParentDataType.EXPERIMENT_BASIC_DATA, basicMetadata);
+ experimentID = (String) registry.add(ParentDataType.EXPERIMENT, basicMetadata);
registry.add(ChildDataType.EXPERIMENT_CONFIGURATION_DATA, configurationData, experimentID);
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3a453bb1/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
----------------------------------------------------------------------
diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
index c76ab14..ccee415 100644
--- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
+++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
@@ -404,9 +404,6 @@ public class EmbeddedGFacInvoker implements Invoker {
private void addSecurityContext(HostDescription registeredHost, Properties configurationProperties,
JobExecutionContext jobExecutionContext, ContextHeaderDocument.ContextHeader contextHeader) throws WorkflowException {
RequestData requestData;
- if (registeredHost.getType() instanceof GlobusHostType || registeredHost.getType() instanceof UnicoreHostType
- || registeredHost.getType() instanceof GsisshHostType) {
-
/* todo fix the credential store and uncomment following code block
SecurityContextDocument.SecurityContext.CredentialManagementService credentialManagementService
= getCredentialManagementService(contextHeader);
@@ -473,12 +470,12 @@ public class EmbeddedGFacInvoker implements Invoker {
}
jobExecutionContext.addSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT, context);
- } else if (registeredHost.getType() instanceof Ec2HostType) {
+ //Adding Amanzon Keys
if (this.configuration.getAmazonSecurityContext() != null) {
jobExecutionContext.addSecurityContext(AmazonSecurityContext.AMAZON_SECURITY_CONTEXT,
this.configuration.getAmazonSecurityContext());
- }
- } else if (registeredHost.getType() instanceof SSHHostType) {
+ }
+ //Adding SSH security
String sshUserName = configurationProperties.getProperty(Constants.SSH_USER_NAME);
String sshPrivateKey = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY);
String sshPrivateKeyPass = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY_PASS);
@@ -511,7 +508,6 @@ public class EmbeddedGFacInvoker implements Invoker {
sshSecurityContext.setKeyPass(sshPrivateKeyPass);
}
jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, sshSecurityContext);
- }
}
/**