Sonar issues: Issues reported for GFac-core
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                 Key: AIRAVATA-98
                 URL: https://issues.apache.org/jira/browse/AIRAVATA-98
             Project: Airavata
          Issue Type: Bug
            Reporter: Saminda Wijeratne
            Priority: Critical


org.apache.airavata.core.gfac.notification.impl.WorkflowTrackingNotification
1. Unread field: 
org.apache.airavata.core.gfac.notification.impl.WorkflowTrackingNotification.receiver
77      this.receiver = this.notifier.createEntity(receiverWorkflowID, 
receiverServiceID, receiverWorkflowNodeID,

org.apache.airavata.core.gfac.context.security.impl.utils.MyProxyManager
1. Redundant nullcheck of proxyloc which is known to be null in 
org.apache.airavata.core.gfac.context.security.impl.utils.MyProxyManager.renewProxy()
84      if (proxyloc == null) {

2. 
org.apache.airavata.core.gfac.context.security.impl.utils.MyProxyManager.renewProxy()
 may fail to close stream on exception
101     FileOutputStream fout = new FileOutputStream(proxyfile);

3. A method/constructor shouldn't explicitly throw java.lang.Exception
73      public GSSCredential renewProxy() throws Exception {

4. Expression can be simplified.
91      if (proxyfile.exists() == false) {
94      if (dir.exists() == false) {

5. 
org.apache.airavata.core.gfac.context.security.impl.utils.MyProxyManager.renewProxy()
 ignores exceptional return value of java.io.File.mkdirs()
98      proxyfile.createNewFile();

org.apache.airavata.core.gfac.provider.utils.JobSubmissionListener
1. Variable 'log' must be private and have accessor methods.
48      protected final Logger log = 
LoggerFactory.getLogger(JobSubmissionListener.class);

2. Avoid using if statements without curly braces
83      if (setStatus(job.getStatus(), job.getError()))
84           break;

3. Magic Number 
67      if (proxyExpTime < 900) {
93      wait(60 * 1000l);

org.apache.airavata.core.gfac.provider.SSHProvider
1. Dead store to host in 
org.apache.airavata.core.gfac.provider.SSHProvider.setupEnvironment(InvocationContext)
150     HostDescription host = context.getExecutionDescription().getHost();

2. 'command' hides a field.
114     StringBuilder command = new StringBuilder();

3. 
org.apache.airavata.core.gfac.provider.SSHProvider.retrieveOutput(InvocationContext)
 ignores exceptional return value of java.io.File.mkdir()
272  logDir.mkdir();

4. Redundant throws: 'SecurityException' is unchecked exception.
71      private void initSSHSecurity(InvocationContext context, SSHClient ssh) 
throws SecurityException, IOException {

5. Magic Number
128     cmd.join(5, TimeUnit.SECONDS);
220     cmd.join(5, TimeUnit.SECONDS);

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