Author: lahiru
Date: Mon Aug 19 17:48:16 2013
New Revision: 1515530
URL: http://svn.apache.org/r1515530
Log:
adding new methods to execute a pbs job.
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SCPTo.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SCPTo.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SCPTo.java?rev=1515530&r1=1515529&r2=1515530&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SCPTo.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SCPTo.java
Mon Aug 19 17:48:16 2013
@@ -38,13 +38,20 @@ public class SCPTo {
JSch.setConfig("userauth.gssapi-with-mic",
"com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials");
}
+
private ServerInfo serverInfo;
private AuthenticationInfo authenticationInfo;
private ConfigReader configReader;
-
+ /**
+ * We need to pass certificateLocation when we use SCPTo method standalone
+ * @param serverInfo
+ * @param authenticationInfo
+ * @param certificateLocation
+ * @param configReader
+ */
public SCPTo(ServerInfo serverInfo, AuthenticationInfo authenticationInfo,
String certificateLocation, ConfigReader configReader) {
System.setProperty("X509_CERT_DIR", certificateLocation);
this.serverInfo = serverInfo;
@@ -53,14 +60,27 @@ public class SCPTo {
}
/**
+ * This can be used when use SCPTo method within SSHAPi because
SSHApiFactory already set the system property certificateLocation
+ * @param serverInfo
+ * @param authenticationInfo
+ * @param configReader
+ */
+ public SCPTo(ServerInfo serverInfo, AuthenticationInfo authenticationInfo
+ , ConfigReader configReader) {
+ this.serverInfo = serverInfo;
+ this.authenticationInfo = authenticationInfo;
+ this.configReader = configReader;
+ }
+ /**
* This method will scp the lFile to the rFile location
- * @param rFile remote file Path to use in scp
- * @param lFile local file path to use in scp
+ *
+ * @param rFile remote file Path to use in scp
+ * @param lFile local file path to use in scp
* @throws IOException
* @throws JSchException
* @throws SSHApiException
*/
- public void scpTo(String rFile, String lFile) throws IOException,
JSchException, SSHApiException {
+ public Session scpTo(String rFile, String lFile) throws IOException,
JSchException, SSHApiException {
FileInputStream fis = null;
String prefix = null;
if (new File(lFile).isDirectory()) {
@@ -102,7 +122,7 @@ public class SCPTo {
boolean ptimestamp = true;
// exec 'scp -t rfile' remotely
- String command="scp " + (ptimestamp ? "-p" :"") +" -t "+rFile;
+ String command = "scp " + (ptimestamp ? "-p" : "") + " -t " + rFile;
Channel channel = session.openChannel("exec");
((ChannelExec) channel).setCommand(command);
@@ -112,83 +132,87 @@ public class SCPTo {
channel.connect();
- if(checkAck(in)!=0){
+ if (checkAck(in) != 0) {
System.exit(0);
- }
+ }
- File _lfile = new File(lFile);
+ File _lfile = new File(lFile);
- if(ptimestamp){
- command="T "+(_lfile.lastModified()/1000)+" 0";
- // The access time should be sent here,
- // but it is not accessible with JavaAPI ;-<
- command+=(" "+(_lfile.lastModified()/1000)+" 0\n");
- out.write(command.getBytes()); out.flush();
- if(checkAck(in)!=0){
+ if (ptimestamp) {
+ command = "T " + (_lfile.lastModified() / 1000) + " 0";
+ // The access time should be sent here,
+ // but it is not accessible with JavaAPI ;-<
+ command += (" " + (_lfile.lastModified() / 1000) + " 0\n");
+ out.write(command.getBytes());
+ out.flush();
+ if (checkAck(in) != 0) {
System.exit(0);
- }
- }
+ }
+ }
- // send "C0644 filesize filename", where filename should not
include '/'
- long filesize=_lfile.length();
- command="C0644 "+filesize+" ";
- if(lFile.lastIndexOf('/')>0){
- command+=lFile.substring(lFile.lastIndexOf('/')+1);
- }
- else{
- command+=lFile;
- }
- command+="\n";
- out.write(command.getBytes()); out.flush();
- if(checkAck(in)!=0){
+ // send "C0644 filesize filename", where filename should not include
'/'
+ long filesize = _lfile.length();
+ command = "C0644 " + filesize + " ";
+ if (lFile.lastIndexOf('/') > 0) {
+ command += lFile.substring(lFile.lastIndexOf('/') + 1);
+ } else {
+ command += lFile;
+ }
+ command += "\n";
+ out.write(command.getBytes());
+ out.flush();
+ if (checkAck(in) != 0) {
System.exit(0);
- }
+ }
- // send a content of lFile
- fis=new FileInputStream(lFile);
- byte[] buf=new byte[1024];
- while(true){
- int len=fis.read(buf, 0, buf.length);
- if(len<=0) break;
- out.write(buf, 0, len); //out.flush();
- }
- fis.close();
- fis=null;
- // send '\0'
- buf[0]=0; out.write(buf, 0, 1); out.flush();
- if(checkAck(in)!=0){
+ // send a content of lFile
+ fis = new FileInputStream(lFile);
+ byte[] buf = new byte[1024];
+ while (true) {
+ int len = fis.read(buf, 0, buf.length);
+ if (len <= 0) break;
+ out.write(buf, 0, len); //out.flush();
+ }
+ fis.close();
+ fis = null;
+ // send '\0'
+ buf[0] = 0;
+ out.write(buf, 0, 1);
+ out.flush();
+ if (checkAck(in) != 0) {
System.exit(0);
- }
- out.close();
+ }
+ out.close();
- channel.disconnect();
- session.disconnect();
+ channel.disconnect();
+ session.disconnect();
+ return session;
}
- static int checkAck(InputStream in) throws IOException{
- int b=in.read();
- // b may be 0 for success,
- // 1 for error,
- // 2 for fatal error,
- // -1
- if(b==0) return b;
- if(b==-1) return b;
-
- if(b==1 || b==2){
- StringBuffer sb=new StringBuffer();
- int c;
- do {
- c=in.read();
- sb.append((char)c);
- }
- while(c!='\n');
- if(b==1){ // error
- System.out.print(sb.toString());
- }
- if(b==2){ // fatal error
- System.out.print(sb.toString());
- }
- }
- return b;
- }
+ static int checkAck(InputStream in) throws IOException {
+ int b = in.read();
+ // b may be 0 for success,
+ // 1 for error,
+ // 2 for fatal error,
+ // -1
+ if (b == 0) return b;
+ if (b == -1) return b;
+
+ if (b == 1 || b == 2) {
+ StringBuffer sb = new StringBuffer();
+ int c;
+ do {
+ c = in.read();
+ sb.append((char) c);
+ }
+ while (c != '\n');
+ if (b == 1) { // error
+ System.out.print(sb.toString());
+ }
+ if (b == 2) { // fatal error
+ System.out.print(sb.toString());
+ }
+ }
+ return b;
+ }
}
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java?rev=1515530&r1=1515529&r2=1515530&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java
Mon Aug 19 17:48:16 2013
@@ -44,4 +44,7 @@ public interface SSHApi {
AuthenticationInfo authenticationInfo,
CommandOutput commandOutput) throws
SSHApiException;
+ void submitJob(CommandInfo commandInfo, ServerInfo serverInfo,
+ AuthenticationInfo authenticationInfo, CommandOutput
commandOutput,
+ String pbsFilePath,String workingDirectory)throws
SSHApiException;
}
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java?rev=1515530&r1=1515529&r2=1515530&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java
Mon Aug 19 17:48:16 2013
@@ -51,6 +51,7 @@ public class DefaultSSHApi implements SS
/**
* Initializes default SSH API. During initialization basic configurations
* are read.
+ *
* @throws SSHApiException If an error occurred while reading basic
configurations.
*/
public DefaultSSHApi() throws SSHApiException {
@@ -62,8 +63,8 @@ public class DefaultSSHApi implements SS
}
public void executeCommand(CommandInfo commandInfo, ServerInfo serverInfo,
- AuthenticationInfo authenticationInfo,
- CommandOutput commandOutput) throws
SSHApiException {
+ AuthenticationInfo authenticationInfo,
+ CommandOutput commandOutput) throws
SSHApiException {
JSch jsch = new ExtendedJSch();
@@ -86,7 +87,7 @@ public class DefaultSSHApi implements SS
// Not a good way, but we dont have any choice
if (session instanceof ExtendedSession) {
-
((ExtendedSession)session).setAuthenticationInfo(authenticationInfo);
+ ((ExtendedSession)
session).setAuthenticationInfo(authenticationInfo);
}
try {
@@ -114,7 +115,6 @@ public class DefaultSSHApi implements SS
}
-
channel.setInputStream(null);
((ChannelExec) channel).setErrStream(commandOutput.getStandardError());
@@ -138,4 +138,26 @@ public class DefaultSSHApi implements SS
}
+
+ public void submitJob(CommandInfo commandInfo, ServerInfo serverInfo,
+ AuthenticationInfo authenticationInfo,
+ CommandOutput commandOutput, String pbsFilePath,
String workingDirectory) throws SSHApiException {
+ try {
+ SCPTo scpTo = new SCPTo(serverInfo, authenticationInfo, new
ConfigReader());
+ scpTo.scpTo(workingDirectory, pbsFilePath);
+ } catch (JSchException e) {
+ throw new SSHApiException("An exception occurred while connecting
to server." +
+ "Connecting server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ } catch (IOException e){
+ throw new SSHApiException("An exception occurred while connecting
to server." +
+ "Connecting server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+
this.executeCommand(commandInfo,serverInfo,authenticationInfo,commandOutput);
+ }
+
}
Modified:
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java?rev=1515530&r1=1515529&r2=1515530&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java
(original)
+++
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java
Mon Aug 19 17:48:16 2013
@@ -38,9 +38,6 @@ public class SCPToTest {
@BeforeTest
public void setUp() throws Exception {
- System.setProperty("myproxy.user", "ogce");
- System.setProperty("myproxy.password", "Jdas7wph");
- System.setProperty("basedir",
"/Users/lahirugunathilake/work/airavata/sandbox/gsissh");
myProxyUserName = System.getProperty("myproxy.user");
myProxyPassword = System.getProperty("myproxy.password");
Modified:
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java?rev=1515530&r1=1515529&r2=1515530&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
(original)
+++
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
Mon Aug 19 17:48:16 2013
@@ -39,6 +39,8 @@ public class DefaultSSHApiTest {
private String myProxyUserName;
private String myProxyPassword;
private String certificateLocation;
+ private String pbsFilePath;
+ private String workingDirectory;
@BeforeTest
public void setUp() throws Exception {
@@ -53,6 +55,9 @@ public class DefaultSSHApiTest {
certificateLocation = pomFileDirectory.getAbsolutePath() +
"/certificates";
+ pbsFilePath = pomFileDirectory.getAbsolutePath() + File.separator +
"src" + File.separator + "test" + File.separator + "resources" + File.separator
+ "sleep.pbs";
+
+ workingDirectory = File.separator + "home" + File.separator + "ogce" ;
if (myProxyUserName == null || myProxyPassword == null) {
System.out.println(">>>>>> Please run tests with my proxy user
name and password. " +
"E.g :- mvn clean install -Dmyproxy.user=xxx
-Dmyproxy.password=xxx <<<<<<<");
@@ -87,7 +92,7 @@ public class DefaultSSHApiTest {
}
@Test
- public void testSubmitJob() throws Exception {
+ public void testSubmitSimpleCommand() throws Exception {
// Create authentication
AuthenticationInfo authenticationInfo
= new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
@@ -108,4 +113,27 @@ public class DefaultSSHApiTest {
// Execute command
sshApi.executeCommand(commandInfo, serverInfo, authenticationInfo,
commandOutput);
}
+
+ @Test
+ public void testSubmitJob() throws Exception {
+ // Create authentication
+ AuthenticationInfo authenticationInfo
+ = new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
+ 7512, 17280000);
+
+ // Create command
+ CommandInfo commandInfo = new RawCommandInfo("/opt/torque/bin/qsub
/home/ogce/sleep.pbs");
+
+ // Server info
+ ServerInfo serverInfo = new ServerInfo("ogce" ,"trestles.sdsc.edu");
+
+ // Output
+ CommandOutput commandOutput = new SystemCommandOutput();
+
+ // Get the API
+ SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
+
+ // Execute command
+ sshApi.submitJob(commandInfo, serverInfo, authenticationInfo,
commandOutput, pbsFilePath, workingDirectory);
+ }
}
