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Posted to commits@airavata.apache.org by la...@apache.org on 2015/03/09 22:03:50 UTC
[1/2] airavata git commit: more fixed to support LSF
Repository: airavata
Updated Branches:
refs/heads/master fd557d829 -> 34b06cc99
more fixed to support LSF
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/fcbda21f
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/fcbda21f
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/fcbda21f
Branch: refs/heads/master
Commit: fcbda21f3fbbbc75afa01f4b590afe873c192de2
Parents: 04cecb4
Author: Lahiru Gunathilake <gl...@gmail.com>
Authored: Mon Mar 9 17:03:33 2015 -0400
Committer: Lahiru Gunathilake <gl...@gmail.com>
Committed: Mon Mar 9 17:03:33 2015 -0400
----------------------------------------------------------------------
.../airavata/api/server/AiravataAPIServer.java | 38 +++++++++---------
.../client/samples/CreateLaunchExperiment.java | 20 +++++++---
.../tools/RegisterSampleApplications.java | 10 +++--
.../store/store/impl/db/SSHCredentialTest.java | 2 +-
.../airavata/gfac/server/GfacServerHandler.java | 39 +++++++++---------
.../monitor/impl/pull/qstat/HPCPullMonitor.java | 42 +++++++++++++++++---
.../airavata/gfac/monitor/util/CommonUtils.java | 1 +
.../gfac/ssh/security/TokenizedSSHAuthInfo.java | 5 ++-
.../impl/DefaultSSHApiTestWithMyProxyAuth.java | 14 ++++---
.../gsi/ssh/impl/VanilaTestWithSSHAuth.java | 4 +-
10 files changed, 112 insertions(+), 63 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/AiravataAPIServer.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/AiravataAPIServer.java b/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/AiravataAPIServer.java
index 0e6da90..4d465f7 100644
--- a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/AiravataAPIServer.java
+++ b/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/AiravataAPIServer.java
@@ -302,26 +302,26 @@ public class AiravataAPIServer implements IServer, Watcher{
synchronized (mutex) {
Event.KeeperState state = watchedEvent.getState();
logger.info(state.name());
- if (state == Event.KeeperState.SyncConnected) {
- mutex.notify();
- } else if(state == Event.KeeperState.Expired ||
- state == Event.KeeperState.Disconnected){
- try {
- mutex = -1;
- zk = new ZooKeeper(AiravataZKUtils.getZKhostPort(), 6000, this);
- synchronized (mutex) {
- mutex.wait(); // waiting for the syncConnected event
+ switch(state){
+ case SyncConnected:
+ mutex.notify();
+ case Expired:case Disconnected:
+ try {
+ mutex = -1;
+ zk = new ZooKeeper(AiravataZKUtils.getZKhostPort(), 6000, this);
+ synchronized (mutex) {
+ mutex.wait(); // waiting for the syncConnected event
+ }
+ storeServerConfig();
+ } catch (IOException e) {
+ logger.error("Error while synchronizing with zookeeper", e);
+ } catch (ApplicationSettingsException e) {
+ logger.error("Error while synchronizing with zookeeper", e);
+ } catch (InterruptedException e) {
+ logger.error("Error while synchronizing with zookeeper", e);
+ } catch (AiravataSystemException e) {
+ logger.error("Error while synchronizing with zookeeper", e);
}
- storeServerConfig();
- } catch (IOException e) {
- logger.error("Error while synchronizing with zookeeper", e);
- } catch (ApplicationSettingsException e) {
- logger.error("Error while synchronizing with zookeeper", e);
- } catch (InterruptedException e) {
- logger.error("Error while synchronizing with zookeeper", e);
- } catch (AiravataSystemException e) {
- logger.error("Error while synchronizing with zookeeper", e);
- }
}
}
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/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 bb2ae6e..3d58197 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
@@ -58,7 +58,7 @@ public class CreateLaunchExperiment {
private static final String DEFAULT_GATEWAY = "php_reference_gateway";
private static Airavata.Client airavataClient;
- private static String echoAppId = "Echo_802454e5-6358-4371-9a04-3d5d59cecbc7";
+ private static String echoAppId = "Echo_8506337e-ab7a-46b6-9b71-4a461b6c5e35";
private static String mpiAppId = "HelloMPI_720e159f-198f-4daa-96ca-9f5eafee92c9";
private static String wrfAppId = "WRF_7ad5da38-c08b-417c-a9ea-da9298839762";
private static String amberAppId = "Amber_a56d457c-f239-4c0b-ba00-66bda936f7bc";
@@ -1348,27 +1348,37 @@ public class CreateLaunchExperiment {
public static String createExperimentForLSF(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(echoAppId);
+
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ inputDataObjectType.setValue("Hello World");
+ }
+ /*List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
InputDataObjectType input = new InputDataObjectType();
input.setName("Input_to_Echo");
input.setType(DataType.STRING);
input.setValue("Echoed_Output=Hello World");
input.setRequiredToAddedToCommandLine(true);
- exInputs.add(input);
+ exInputs.add(input);*/
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(echoAppId);
+ /*
List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
OutputDataObjectType output = new OutputDataObjectType();
output.setName("output_file");
output.setType(DataType.URI);
output.setValue("");
- exOut.add(output);
+
+ exOut.add(output);*/
Project project = ProjectModelUtil.createProject("default", "lg11w", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
+
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment(projectId, "lg11w", "sshEchoExperiment", "StressMem", echoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
+ simpleExperiment.setExperimentInputs(exInputs);
Map<String, String> computeResources = airavataClient.getAvailableAppInterfaceComputeResources(echoAppId);
if (computeResources != null && computeResources.size() != 0) {
@@ -1598,7 +1608,7 @@ public class CreateLaunchExperiment {
public static void launchExperiment(Airavata.Client client, String expId)
throws TException {
try {
- String tokenId ="aa-dcdb-48e3-9cd5-ac90b710d55e";
+ String tokenId ="-0bbb-403b-a88a-42b6dbe198e9";
client.launchExperiment(expId, tokenId);
} catch (ExperimentNotFoundException e) {
logger.error("Error occured while launching the experiment...", e.getMessage());
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/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 8ae2dd2..55dbcf8 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
@@ -497,11 +497,15 @@ public class RegisterSampleApplications {
// applicationInputs.add(input2); applicationInputs.add(input3);
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output",
- "", DataType.STRING, false, false);
-
+ "", DataType.STDOUT, false, false);
+
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Error",
+ "", DataType.STDERR, false, false);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
-
+ applicationOutputs.add(output2);
+
echoInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(echoName, echoDescription,
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java b/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java
index e78ab7a..e6969e6 100644
--- a/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java
+++ b/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java
@@ -67,7 +67,7 @@ public class SSHCredentialTest {
pubKeyStream.close();
sshCredential.setPrivateKey(bFilePub);
sshCredential.setPublicKey(bFilePub);
- sshCredential.setPassphrase("gjtlmiJdas7wph");
+ sshCredential.setPassphrase("ljclqowueqllad_lqlj");
writer.writeCredentials(sshCredential);
System.out.println(token);
} catch (ClassNotFoundException e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java b/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
index 1687462..4973a41 100644
--- a/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
+++ b/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
@@ -156,27 +156,26 @@ public class GfacServerHandler implements GfacService.Iface, Watcher{
synchronized (mutex) {
Event.KeeperState state = watchedEvent.getState();
logger.info(state.name());
- if (state == Event.KeeperState.SyncConnected) {
- mutex.notify();
- connected = true;
- } else if(state == Event.KeeperState.Expired ||
- state == Event.KeeperState.Disconnected){
- try {
- mutex = -1;
- zk = new ZooKeeper(AiravataZKUtils.getZKhostPort(), 6000, this);
- synchronized (mutex) {
- mutex.wait(); // waiting for the syncConnected event
+ switch (state){
+ case SyncConnected:
+ mutex.notify();
+ break;
+ case Expired:case Disconnected:
+ try {
+ zk = new ZooKeeper(AiravataZKUtils.getZKhostPort(), 6000, this);
+ synchronized (mutex) {
+ mutex.wait(); // waiting for the syncConnected event
+ }
+ storeServerConfig();
+ } catch (IOException e) {
+ logger.error(e.getMessage(), e);
+ } catch (ApplicationSettingsException e) {
+ logger.error(e.getMessage(), e);
+ } catch (InterruptedException e) {
+ logger.error(e.getMessage(), e);
+ } catch (KeeperException e) {
+ logger.error(e.getMessage(), e);
}
- storeServerConfig();
- } catch (IOException e) {
- logger.error(e.getMessage(), e);
- } catch (ApplicationSettingsException e) {
- logger.error(e.getMessage(), e);
- } catch (InterruptedException e) {
- logger.error(e.getMessage(), e);
- } catch (KeeperException e) {
- logger.error(e.getMessage(), e);
- }
}
}
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
index b7f08a6..f0b447e 100644
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
@@ -74,6 +74,8 @@ public class HPCPullMonitor extends PullMonitor {
private AuthenticationInfo authenticationInfo;
+ private ArrayList<MonitorID> removeList;
+
public HPCPullMonitor() {
connections = new HashMap<String, ResourceConnection>();
queue = new LinkedBlockingDeque<UserMonitorData>();
@@ -81,6 +83,7 @@ public class HPCPullMonitor extends PullMonitor {
cancelJobList = new LinkedBlockingQueue<String>();
completedJobsFromPush = new ArrayList<String>();
(new SimpleJobFinishConsumer(this.completedJobsFromPush)).listen();
+ removeList = new ArrayList<MonitorID>();
}
public HPCPullMonitor(MonitorPublisher monitorPublisher, AuthenticationInfo authInfo) {
@@ -91,6 +94,7 @@ public class HPCPullMonitor extends PullMonitor {
cancelJobList = new LinkedBlockingQueue<String>();
this.completedJobsFromPush = new ArrayList<String>();
(new SimpleJobFinishConsumer(this.completedJobsFromPush)).listen();
+ removeList = new ArrayList<MonitorID>();
}
public HPCPullMonitor(BlockingQueue<UserMonitorData> queue, MonitorPublisher publisher) {
@@ -100,6 +104,7 @@ public class HPCPullMonitor extends PullMonitor {
cancelJobList = new LinkedBlockingQueue<String>();
this.completedJobsFromPush = new ArrayList<String>();
(new SimpleJobFinishConsumer(this.completedJobsFromPush)).listen();
+ removeList = new ArrayList<MonitorID>();
}
@@ -182,20 +187,23 @@ public class HPCPullMonitor extends PullMonitor {
String cancelMId = iterator1.next();
if (cancelMId.equals(iMonitorID.getExperimentID() + "+" + iMonitorID.getTaskID())) {
iMonitorID.setStatus(JobState.CANCELED);
- CommonUtils.removeMonitorFromQueue(take, iMonitorID);
+// CommonUtils.removeMonitorFromQueue(take, iMonitorID);
+ removeList.add(iMonitorID);
logger.debugId(cancelMId, "Found a match in cancel monitor queue, hence moved to the " +
"completed job queue, experiment {}, task {} , job {}",
iMonitorID.getExperimentID(), iMonitorID.getTaskID(), iMonitorID.getJobID());
logger.info("Job cancelled: marking the Job as ************CANCELLED************ experiment {}, task {}, job name {} .",
iMonitorID.getExperimentID(), iMonitorID.getTaskID(), iMonitorID.getJobName());
sendNotification(iMonitorID);
- monitorIDListIterator.remove();
GFacThreadPoolExecutor.getFixedThreadPool().submit(new OutHandlerWorker(gfac, iMonitorID, publisher));
break;
}
}
iterator1 = cancelJobList.iterator();
}
+
+ cleanup(take);
+
synchronized (completedJobsFromPush) {
for (ListIterator<String> iterator = completedJobsFromPush.listIterator(); iterator.hasNext(); ) {
String completeId = iterator.next();
@@ -204,14 +212,14 @@ public class HPCPullMonitor extends PullMonitor {
if (completeId.equals(iMonitorID.getUserName() + "," + iMonitorID.getJobName())) {
logger.info("This job is finished because push notification came with <username,jobName> " + completeId);
iMonitorID.setStatus(JobState.COMPLETE);
- CommonUtils.removeMonitorFromQueue(take, iMonitorID);//we have to make this empty everytime we iterate, otherwise this list will accumulate and will lead to a memory leak
+// CommonUtils.removeMonitorFromQueue(take, iMonitorID);//we have to make this empty everytime we iterate, otherwise this list will accumulate and will lead to a memory leak
+ removeList.add(iMonitorID);
logger.debugId(completeId, "Push notification updated job {} status to {}. " +
"experiment {} , task {}.", iMonitorID.getJobID(), JobState.COMPLETE.toString(),
iMonitorID.getExperimentID(), iMonitorID.getTaskID());
logger.info("AMQP message recieved: marking the Job as ************COMPLETE************ experiment {}, task {}, job name {} .",
iMonitorID.getExperimentID(), iMonitorID.getTaskID(), iMonitorID.getJobName());
- iterator.remove();
sendNotification(iMonitorID);
GFacThreadPoolExecutor.getFixedThreadPool().submit(new OutHandlerWorker(gfac, iMonitorID, publisher));
break;
@@ -220,6 +228,8 @@ public class HPCPullMonitor extends PullMonitor {
}
}
+ cleanup(take);
+
// we have to get this again because we removed the already completed jobs with amqp messages
monitorID = iHostMonitorData.getMonitorIDs();
Map<String, JobState> jobStatuses = connection.getJobStatuses(monitorID);
@@ -232,7 +242,8 @@ public class HPCPullMonitor extends PullMonitor {
} else if (JobState.COMPLETE.equals(iMonitorID.getStatus())) {
logger.debugId(iMonitorID.getJobID(), "Moved job {} to completed jobs map, experiment {}, " +
"task {}", iMonitorID.getJobID(), iMonitorID.getExperimentID(), iMonitorID.getTaskID());
- CommonUtils.removeMonitorFromQueue(take, iMonitorID);
+// CommonUtils.removeMonitorFromQueue(take, iMonitorID);
+ removeList.add(iMonitorID);
logger.info("PULL Notification is complete: marking the Job as ************COMPLETE************ experiment {}, task {}, job name {} .",
iMonitorID.getExperimentID(), iMonitorID.getTaskID(), iMonitorID.getJobName());
GFacThreadPoolExecutor.getFixedThreadPool().submit(new OutHandlerWorker(gfac, iMonitorID, publisher));
@@ -244,6 +255,9 @@ public class HPCPullMonitor extends PullMonitor {
iMonitorID.setLastMonitored(new Timestamp((new Date()).getTime()));
}
+ cleanup(take);
+
+
for (Iterator<MonitorID> iterator = monitorID.listIterator(); iterator.hasNext(); ) {
MonitorID iMonitorID = iterator.next();
if (iMonitorID.getFailedCount() > FAILED_COUNT) {
@@ -268,7 +282,8 @@ public class HPCPullMonitor extends PullMonitor {
logger.info("Listing directory came as complete: marking the Job as ************COMPLETE************ experiment {}, task {}, job name {} .",
iMonitorID.getExperimentID(), iMonitorID.getTaskID(), iMonitorID.getJobName());
sendNotification(iMonitorID);
- CommonUtils.removeMonitorFromQueue(take, iMonitorID);
+// CommonUtils.removeMonitorFromQueue(take, iMonitorID);
+ removeList.add(iMonitorID);
GFacThreadPoolExecutor.getFixedThreadPool().submit(new OutHandlerWorker(gfac, iMonitorID, publisher));
} else {
iMonitorID.setFailedCount(0);
@@ -281,6 +296,8 @@ public class HPCPullMonitor extends PullMonitor {
}
}
+ cleanup(take);
+
} else {
logger.debug("Qstat Monitor doesn't handle non-gsissh hosts , host {}", iHostMonitorData.
@@ -434,4 +451,17 @@ public class HPCPullMonitor extends PullMonitor {
public void setCancelJobList(LinkedBlockingQueue<String> cancelJobList) {
this.cancelJobList = cancelJobList;
}
+
+
+ private void cleanup(UserMonitorData userMonitorData){
+ for(MonitorID iMonitorId:removeList){
+ try {
+ CommonUtils.removeMonitorFromQueue(userMonitorData, iMonitorId);
+ } catch (AiravataMonitorException e) {
+ logger.error(e.getMessage(), e);
+ logger.error("Error deleting the monitor data: " + iMonitorId.getJobID());
+ }
+ }
+ removeList.clear();
+ }
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
index 135349f..cbac726 100644
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
@@ -157,6 +157,7 @@ public class CommonUtils {
logger.info("This might not be an error because someone else removed this job from the queue");
}
+
public static void invokeOutFlowHandlers(JobExecutionContext jobExecutionContext) throws GFacException {
List<GFacHandlerConfig> handlers = jobExecutionContext.getGFacConfiguration().getOutHandlers();
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java
index 683985f..a416dbd 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java
@@ -21,6 +21,7 @@
package org.apache.airavata.gfac.ssh.security;
import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.common.utils.IOUtil;
import org.apache.airavata.common.utils.ServerSettings;
import org.apache.airavata.credential.store.credential.Credential;
import org.apache.airavata.credential.store.credential.impl.ssh.SSHCredential;
@@ -148,7 +149,7 @@ public class TokenizedSSHAuthInfo implements SSHPublicKeyFileAuthentication {
* @throws org.apache.airavata.gfac.GFacException If an error occurred while retrieving credentials.
* @throws org.apache.airavata.common.exception.ApplicationSettingsException
*/
- public SSHCredential getDefaultCredentials() throws GFacException, ApplicationSettingsException {
+ public SSHCredential getDefaultCredentials() throws GFacException, ApplicationSettingsException, IOException {
Properties configurationProperties = ServerSettings.getProperties();
String sshUserName = configurationProperties.getProperty(Constants.SSH_USER_NAME);
this.getRequestData().setRequestUser(sshUserName);
@@ -156,7 +157,7 @@ public class TokenizedSSHAuthInfo implements SSHPublicKeyFileAuthentication {
this.publicKeyFile = configurationProperties.getProperty(Constants.SSH_PUBLIC_KEY);
this.passPhrase = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY_PASS);
this.getRequestData().setRequestUser(sshUserName);
- return new SSHCredential(null, null, null, requestData.getGatewayId(), sshUserName);
+ return new SSHCredential(IOUtil.readToByteArray(new File(this.privateKeyFile)), IOUtil.readToByteArray(new File(this.publicKeyFile)), this.passPhrase, requestData.getGatewayId(), sshUserName);
}
public CredentialReader getCredentialReader() {
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
index 0ca7546..7a2fce3 100644
--- a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
+++ b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
@@ -27,16 +27,17 @@ import org.apache.airavata.gsi.ssh.api.authentication.GSIAuthenticationInfo;
import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
import org.apache.airavata.gsi.ssh.config.ConfigReader;
import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
+import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyAuthentication;
import org.apache.airavata.gsi.ssh.impl.authentication.MyProxyAuthenticationInfo;
import org.apache.airavata.gsi.ssh.util.CommonUtils;
+import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
-import java.io.File;
-import java.io.IOException;
+import java.io.*;
import java.util.ArrayList;
import java.util.List;
@@ -49,11 +50,14 @@ public class DefaultSSHApiTestWithMyProxyAuth {
}
- public static void main(String[]ars){
+ public static void main(String[]ars) throws IOException {
String myProxyUserName = "lg11w";
- DefaultPasswordAuthenticationInfo authenticationInfo
- = new DefaultPasswordAuthenticationInfo("");
+// DefaultPasswordAuthenticationInfo authenticationInfo
+// = new DefaultPasswordAuthenticationInfo("");
+ byte[] privateKey = IOUtils.toByteArray(new BufferedInputStream(new FileInputStream("/Users/lginnali/.ssh/id_dsa")));
+ byte[] publicKey = IOUtils.toByteArray(new BufferedInputStream(new FileInputStream("/Users/lginnali/.ssh/id_dsa.pub")));
+ DefaultPublicKeyAuthentication authenticationInfo = new DefaultPublicKeyAuthentication(privateKey,publicKey,"");
// Create command
CommandInfo commandInfo = new RawCommandInfo("source /etc/bashrc; bsub </home/lg11w/mywork/sshEchoExperiment_9d267072-ca65-4ca8-847a-cd3d130f6050/366787899.lsf");
http://git-wip-us.apache.org/repos/asf/airavata/blob/fcbda21f/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaTestWithSSHAuth.java
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diff --git a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaTestWithSSHAuth.java b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaTestWithSSHAuth.java
index 8d70a21..186aca6 100644
--- a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaTestWithSSHAuth.java
+++ b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaTestWithSSHAuth.java
@@ -75,8 +75,8 @@ public class VanilaTestWithSSHAuth {
System.setProperty("ssh.host",hostName);
System.setProperty("ssh.username", userName);
- System.setProperty("private.ssh.key", "/home/user/.ssh/id_dsa");
- System.setProperty("public.ssh.key", "/home/user/.ssh/id_dsa.pub");
+ System.setProperty("private.ssh.key", "/home/lginnali/.ssh/id_dsa");
+ System.setProperty("public.ssh.key", "/home/lginnali/.ssh/id_dsa.pub");
System.setProperty("ssh.working.directory", "/tmp");
this.hostName = System.getProperty("ssh.host");
[2/2] airavata git commit: Merge branch 'master' of
https://git-wip-us.apache.org/repos/asf/airavata
Posted by la...@apache.org.
Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/34b06cc9
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/34b06cc9
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/34b06cc9
Branch: refs/heads/master
Commit: 34b06cc9999d747cd21eee356049f5dbc47dc45e
Parents: fcbda21 fd557d8
Author: Lahiru Gunathilake <gl...@gmail.com>
Authored: Mon Mar 9 17:03:46 2015 -0400
Committer: Lahiru Gunathilake <gl...@gmail.com>
Committed: Mon Mar 9 17:03:46 2015 -0400
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.../server/handler/AiravataServerHandler.java | 43 ++++++++++++++++++++
.../data/impl/GwyResourceProfileImpl.java | 2 +-
.../integration/tools/DocumentCreatorNew.java | 7 +++-
3 files changed, 49 insertions(+), 3 deletions(-)
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