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Posted to commits@airavata.apache.org by la...@apache.org on 2011/10/21 01:56:30 UTC
svn commit: r1187137 - in /incubator/airavata/trunk/modules:
commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/
commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/app/
gfac-core/src/main/java/org/apache/airava...
Author: lahiru
Date: Thu Oct 20 23:56:29 2011
New Revision: 1187137
URL: http://svn.apache.org/viewvc?rev=1187137&view=rev
Log:
Applying the patch (AIRAVATA-153-patch-ver1.diff) for the issue AIRAVATA-153
Thanks Heshan for the contribution
Modified:
incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/DataType.java
incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/ServiceDescription.java
incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/app/ShellApplicationDeployment.java
incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/LocalProvider.java
incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/SSHProvider.java
incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/GramRSLGenerator.java
incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionAdvancedOptionDialog.java
incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionRegistrationWindow.java
Modified: incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/DataType.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/DataType.java?rev=1187137&r1=1187136&r2=1187137&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/DataType.java (original)
+++ incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/DataType.java Thu Oct 20 23:56:29 2011
@@ -43,4 +43,29 @@ public class DataType implements Type {
public String toString() {
return this.type;
}
+
+ /* TODO:
+ private org.apache.airavata.schemas.gfac.DataType dataType;
+
+ public DataType() {
+ dataType = org.apache.airavata.schemas.gfac.DataType.Factory.newInstance();
+ }
+
+ public DataType(String type) {
+ this.dataType.set(type);
+ //this.dataType.set(org.apache.airavata.schemas.gfac.DataType.DOUBLE);
+ }
+
+ public void setType(String type) {
+ this.dataType.set(type);
+ }
+
+ public String getType() {
+ return this.dataType.getStringValue();
+ }
+
+ public String toString() {
+ return this.dataType.toString();
+ }
+ */
}
\ No newline at end of file
Modified: incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/ServiceDescription.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/ServiceDescription.java?rev=1187137&r1=1187136&r2=1187137&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/ServiceDescription.java (original)
+++ incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/ServiceDescription.java Thu Oct 20 23:56:29 2011
@@ -28,7 +28,7 @@ import java.util.List;
public class ServiceDescription implements Type {
private ServiceDescriptionType serviceDescriptionType;
- private List<Parameter> inputParameters;
+ private List<org.apache.airavata.commons.gfac.type.Parameter> inputParameters;
private List<Parameter> outputParameters;
public ServiceDescription() {
@@ -62,5 +62,6 @@ public class ServiceDescription implemen
public void setOutputParameters(List<Parameter> outputParameters) {
this.outputParameters = outputParameters;
+ //this.serviceDescriptionType.setOutputParametersArray(outputParameters);
}
}
Modified: incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/app/ShellApplicationDeployment.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/app/ShellApplicationDeployment.java?rev=1187137&r1=1187136&r2=1187137&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/app/ShellApplicationDeployment.java (original)
+++ incubator/airavata/trunk/modules/commons/gfac-schema/src/main/java/org/apache/airavata/commons/gfac/type/app/ShellApplicationDeployment.java Thu Oct 20 23:56:29 2011
@@ -24,16 +24,15 @@ package org.apache.airavata.commons.gfac
import org.apache.airavata.commons.gfac.type.ApplicationDeploymentDescription;
import org.apache.airavata.schemas.gfac.ShellApplicationDeploymentType;
-import java.util.Map;
-
public class ShellApplicationDeployment extends ApplicationDeploymentDescription {
private ShellApplicationDeploymentType shellApplicationDeploymentType;
- // TODO
- private Map<String, String> env;
public ShellApplicationDeployment() {
shellApplicationDeploymentType = ShellApplicationDeploymentType.Factory.newInstance();
+ ShellApplicationDeploymentType.Env env =
+ ShellApplicationDeploymentType.Factory.newInstance().getEnv();
+ shellApplicationDeploymentType.setEnv(env);
}
public ShellApplicationDeployment(ShellApplicationDeploymentType sadt) {
@@ -48,12 +47,12 @@ public class ShellApplicationDeployment
this.shellApplicationDeploymentType.setExecutable(executable);
}
- public Map<String, String> getEnv() {
- return env;
+ public ShellApplicationDeploymentType.Env getEnv() {
+ return this.shellApplicationDeploymentType.getEnv();
}
- public void setEnv(Map<String, String> env) {
- this.env = env;
+ public void setEnv(ShellApplicationDeploymentType.Env entries) {
+ this.shellApplicationDeploymentType.setEnv(entries);
}
public String getStdOut() {
Modified: incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/LocalProvider.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/LocalProvider.java?rev=1187137&r1=1187136&r2=1187137&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/LocalProvider.java (original)
+++ incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/LocalProvider.java Thu Oct 20 23:56:29 2011
@@ -21,18 +21,6 @@
package org.apache.airavata.core.gfac.provider.impl;
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import org.apache.airavata.commons.gfac.type.ApplicationDeploymentDescription;
import org.apache.airavata.commons.gfac.type.app.ShellApplicationDeployment;
import org.apache.airavata.commons.gfac.type.parameter.AbstractParameter;
@@ -43,6 +31,13 @@ import org.apache.airavata.core.gfac.uti
import org.apache.airavata.core.gfac.utils.GfacUtils;
import org.apache.airavata.core.gfac.utils.InputUtils;
import org.apache.airavata.core.gfac.utils.OutputUtils;
+import org.apache.airavata.schemas.gfac.ShellApplicationDeploymentType;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
/**
* {@link LocalProvider} will execute jobs (application) on local machine.
@@ -134,7 +129,15 @@ public class LocalProvider extends Abstr
this.builder = new ProcessBuilder(cmdList);
// get the env of the host and the application
- Map<String, String> nv = app.getEnv();
+ ShellApplicationDeploymentType.Env.Entry[] env = app.getEnv().getEntryArray();
+
+ Map<String, String> nv = null;
+ for (int i=0; i<env.length; i++) {
+ String key = app.getEnv().getEntryArray(i).getKey();
+ String value = app.getEnv().getEntryArray(i).getValue();
+ nv.put(key,value);
+ }
+
if(app.getEnv() != null){
builder.environment().putAll(nv);
}
Modified: incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/SSHProvider.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/SSHProvider.java?rev=1187137&r1=1187136&r2=1187137&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/SSHProvider.java (original)
+++ incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/SSHProvider.java Thu Oct 20 23:56:29 2011
@@ -21,15 +21,6 @@
package org.apache.airavata.core.gfac.provider.impl;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.concurrent.TimeUnit;
-
import net.schmizz.sshj.SSHClient;
import net.schmizz.sshj.connection.ConnectionException;
import net.schmizz.sshj.connection.channel.direct.Session;
@@ -37,7 +28,6 @@ import net.schmizz.sshj.connection.chann
import net.schmizz.sshj.transport.TransportException;
import net.schmizz.sshj.userauth.keyprovider.KeyProvider;
import net.schmizz.sshj.xfer.scp.SCPFileTransfer;
-
import org.apache.airavata.commons.gfac.type.app.ShellApplicationDeployment;
import org.apache.airavata.commons.gfac.type.parameter.AbstractParameter;
import org.apache.airavata.core.gfac.context.invocation.InvocationContext;
@@ -49,6 +39,16 @@ import org.apache.airavata.core.gfac.uti
import org.apache.airavata.core.gfac.utils.GfacUtils;
import org.apache.airavata.core.gfac.utils.InputUtils;
import org.apache.airavata.core.gfac.utils.OutputUtils;
+import org.apache.airavata.schemas.gfac.ShellApplicationDeploymentType;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.concurrent.TimeUnit;
/**
* Execute application using remote SSH
@@ -179,7 +179,14 @@ public class SSHProvider extends Abstrac
session.exec("cd " + app.getWorkingDir());
// get the env of the host and the application
- Map<String, String> nv = app.getEnv();
+ ShellApplicationDeploymentType.Env.Entry[] env = app.getEnv().getEntryArray();
+
+ Map<String, String> nv = null;
+ for (int i=0; i<env.length; i++) {
+ String key = app.getEnv().getEntryArray(i).getKey();
+ String value = app.getEnv().getEntryArray(i).getValue();
+ nv.put(key,value);
+ }
// extra env's
nv.put(GFacConstants.INPUT_DATA_DIR_VAR_NAME, app.getInputDir());
Modified: incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/GramRSLGenerator.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/GramRSLGenerator.java?rev=1187137&r1=1187136&r2=1187137&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/GramRSLGenerator.java (original)
+++ incubator/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/GramRSLGenerator.java Thu Oct 20 23:56:29 2011
@@ -21,18 +21,19 @@
package org.apache.airavata.core.gfac.provider.utils;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Map.Entry;
-
import org.apache.airavata.commons.gfac.type.app.GramApplicationDeployment;
import org.apache.airavata.core.gfac.context.invocation.InvocationContext;
import org.apache.airavata.core.gfac.exception.ToolsException;
import org.apache.airavata.core.gfac.utils.GFacConstants;
+import org.apache.airavata.schemas.gfac.ShellApplicationDeploymentType;
import org.globus.gram.GramAttributes;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Map.Entry;
+
/**
* Utilities for generating GRAM RSL
*/
@@ -57,7 +58,15 @@ public class GramRSLGenerator {
* the env specified in the host description and application description
* documents
*/
- Map<String, String> nv = app.getEnv();
+ ShellApplicationDeploymentType.Env.Entry[] env = app.getEnv().getEntryArray();
+
+ Map<String, String> nv = null;
+ for (int i=0; i<env.length; i++) {
+ String key = app.getEnv().getEntryArray(i).getKey();
+ String value = app.getEnv().getEntryArray(i).getValue();
+ nv.put(key,value);
+ }
+
for (Entry<String, String> entry : nv.entrySet()) {
jobAttr.addEnvVariable(entry.getKey(), entry.getValue());
}
Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionAdvancedOptionDialog.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionAdvancedOptionDialog.java?rev=1187137&r1=1187136&r2=1187137&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionAdvancedOptionDialog.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionAdvancedOptionDialog.java Thu Oct 20 23:56:29 2011
@@ -30,6 +30,7 @@ import javax.swing.event.TableModelListe
import javax.swing.table.DefaultTableModel;
import org.apache.airavata.commons.gfac.type.app.ShellApplicationDeployment;
+import org.apache.airavata.schemas.gfac.ShellApplicationDeploymentType;
import org.apache.airavata.xbaya.XBayaEngine;
public class ApplicationDescriptionAdvancedOptionDialog extends JDialog {
@@ -367,13 +368,13 @@ public class ApplicationDescriptionAdvan
getShellApplicationDescription().setStdOut(txtSTDOUT.getText());
getShellApplicationDescription().setStdErr(txtSTDERR.getText());
- getShellApplicationDescription().setEnv(new HashMap<String, String>());
+ getShellApplicationDescription().setEnv(ShellApplicationDeploymentType.Factory.newInstance().getEnv());
for(int i=0;i<defaultTableModel.getRowCount();i++){
String varName = (String)defaultTableModel.getValueAt(i, 0);
if (varName!=null && !varName.equals("")) {
String varValue = (String) defaultTableModel.getValueAt(i, 1);
- getShellApplicationDescription().getEnv()
- .put(varName, varValue);
+ getShellApplicationDescription().getEnv().addNewEntry().setKey(varName);
+ getShellApplicationDescription().getEnv().addNewEntry().setValue(varValue);
}
}
}
@@ -386,7 +387,16 @@ public class ApplicationDescriptionAdvan
txtSTDOUT.setText(getShellApplicationDescription().getStdOut());
txtSTDERR.setText(getShellApplicationDescription().getStdErr());
tableModelChanging=true;
- Map<String, String> env = getShellApplicationDescription().getEnv();
+
+ ShellApplicationDeploymentType.Env.Entry[] entry = getShellApplicationDescription().getEnv().getEntryArray();
+
+ Map<String, String> env = null;
+ for (int i=0; i<entry.length; i++) {
+ String key = getShellApplicationDescription().getEnv().getEntryArray(i).getKey();
+ String value = getShellApplicationDescription().getEnv().getEntryArray(i).getValue();
+ env.put(key,value);
+ }
+
while(defaultTableModel.getRowCount()>0){
defaultTableModel.removeRow(0);
}
Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionRegistrationWindow.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionRegistrationWindow.java?rev=1187137&r1=1187136&r2=1187137&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionRegistrationWindow.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/ApplicationDescriptionRegistrationWindow.java Thu Oct 20 23:56:29 2011
@@ -34,6 +34,7 @@ import javax.swing.JPanel;
import org.apache.airavata.common.utils.NameValidator;
import org.apache.airavata.common.utils.StringUtil;
import org.apache.airavata.commons.gfac.type.app.ShellApplicationDeployment;
+import org.apache.airavata.schemas.gfac.ShellApplicationDeploymentType;
import org.apache.airavata.xbaya.XBayaEngine;
import org.apache.airavata.xbaya.gui.GridPanel;
import org.apache.airavata.xbaya.gui.XBayaComboBox;
@@ -327,16 +328,24 @@ public class ApplicationDescriptionRegis
shellApplicationDeployment.setWorkingDir(StringUtil.trimSpaceInString(this.workDirectoryTextField.getText()));
shellApplicationDeployment.setTmpDir(StringUtil.trimSpaceInString(this.tempDirTextField.getText()));
- Map<String, String> env = shellApplicationDeployment.getEnv();
+ ShellApplicationDeploymentType.Env.Entry[] entries = shellApplicationDeployment.getEnv().getEntryArray();
+
+ Map<String, String> env = null;
+ for (int i=0; i<entries.length; i++) {
+ String key = shellApplicationDeployment.getEnv().getEntryArray(i).getKey();
+ String value = shellApplicationDeployment.getEnv().getEntryArray(i).getValue();
+ env.put(key, value);
+ }
+
env.put("ProjectName",projectName);
env.put("JobType",jobType);
- env.put("Queue",queue);
- env.put("HostName",hostName);
+ env.put("Queue", queue);
+ env.put("HostName", hostName);
if (maxWallTime!=null) {
- env.put("MaxWallTime",maxWallTime.toString());
+ env.put("MaxWallTime", maxWallTime.toString());
}
if (pCount!=null) {
- env.put("Pcount",pCount.toString());
+ env.put("Pcount", pCount.toString());
}
/*--- save to registry ---*/