Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java

@@ -52,6 +52,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
+import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.zip.GZIPOutputStream;
 
 
@@ -84,6 +85,10 @@ public class GATKRunReport {
      */
     private static File REPORT_SENTINEL = new File(REPORT_DIR.getAbsolutePath() + "/ENABLE");
 
+    // number of milliseconds before the S3 put operation is timed-out:
+    private static final long S3PutTimeOut = 30 * 1000;
+
+
     /**
      * our log
      */
@@ -263,23 +268,24 @@ public class GATKRunReport {
         }
     }
 
-    private void postReportToAWSS3() {
+    private class S3PutRunnable implements Runnable {
-        // modifying example code from http://jets3t.s3.amazonaws.com/toolkit/code-samples.html
+
-        this.hostName = Utils.resolveHostname(); // we want to fill in the host name
+        public AtomicBoolean isSuccess;
-        final String key = getKey();
+        private final String key;
-        logger.debug("Generating GATK report to AWS S3 with key " + key);
+        private final byte[] report;
+
+        public S3Object s3Object;
+        public String errorMsg;
+        public Throwable errorThrow;
+
+        public S3PutRunnable(String key, byte[] report){
+            isSuccess = new AtomicBoolean();
+            this.key = key;
+            this.report = report;
+        }
+
+        public void run() {
             try {
-            // create an byte output stream so we can capture the output as a byte[]
-            final ByteArrayOutputStream byteStream = new ByteArrayOutputStream(8096);
-            final OutputStream outputStream = new GZIPOutputStream(byteStream);
-            postReportToStream(outputStream);
-            outputStream.close();
-            final byte[] report = byteStream.toByteArray();
-
-            // stop us from printing the annoying, and meaningless, mime types warning
-            Logger mimeTypeLogger = Logger.getLogger(org.jets3t.service.utils.Mimetypes.class);
-            mimeTypeLogger.setLevel(Level.FATAL);
-
                 // Your Amazon Web Services (AWS) login credentials are required to manage S3 accounts. These credentials
                 // are stored in an AWSCredentials object:
 
@@ -297,15 +303,66 @@ public class GATKRunReport {
                 S3Object fileObject = new S3Object(key, report);
                 //logger.info("Created S3Object" + fileObject);
                 //logger.info("Uploading " + localFile + " to AWS bucket");
-            S3Object s3Object = s3Service.putObject(REPORT_BUCKET_NAME, fileObject);
+                s3Object = s3Service.putObject(REPORT_BUCKET_NAME, fileObject);
-            logger.debug("Uploaded to AWS: " + s3Object);
+                isSuccess.set(true);
-            logger.info("Uploaded run statistics report to AWS S3");
             } catch ( S3ServiceException e ) {
-            exceptDuringRunReport("S3 exception occurred", e);
+                setException("S3 exception occurred", e);
             } catch ( NoSuchAlgorithmException e ) {
-            exceptDuringRunReport("Couldn't calculate MD5", e);
+                setException("Couldn't calculate MD5", e);
+            } catch ( IOException e ) {
+                setException("Couldn't read report file", e);
+            }
+        }
+
+        private void setException(String msg, Throwable e){
+            errorMsg=msg;
+            errorThrow=e;
+        }
+    }
+
+    private void postReportToAWSS3() {
+        // modifying example code from http://jets3t.s3.amazonaws.com/toolkit/code-samples.html
+        this.hostName = Utils.resolveHostname(); // we want to fill in the host name
+        final String key = getKey();
+        logger.debug("Generating GATK report to AWS S3 with key " + key);
+        try {
+            // create an byte output stream so we can capture the output as a byte[]
+            final ByteArrayOutputStream byteStream = new ByteArrayOutputStream(8096);
+            final OutputStream outputStream = new GZIPOutputStream(byteStream);
+            postReportToStream(outputStream);
+            outputStream.close();
+            final byte[] report = byteStream.toByteArray();
+
+            // stop us from printing the annoying, and meaningless, mime types warning
+            Logger mimeTypeLogger = Logger.getLogger(org.jets3t.service.utils.Mimetypes.class);
+            mimeTypeLogger.setLevel(Level.FATAL);
+
+            // Set the S3 upload on its own thread with timeout:
+            S3PutRunnable s3run = new S3PutRunnable(key,report);
+            Thread s3thread = new Thread(s3run);
+            s3thread.setDaemon(true);
+            s3thread.setName("S3Put-Thread");
+            s3thread.start();
+
+            s3thread.join(S3PutTimeOut);
+
+            if(s3thread.isAlive()){
+                s3thread.interrupt();
+                exceptDuringRunReport("Run statistics report upload to AWS S3 timed-out");
+            } else if(s3run.isSuccess.get()) {
+                logger.info("Uploaded run statistics report to AWS S3");
+                logger.debug("Uploaded to AWS: " + s3run.s3Object);
+            } else {
+                if((s3run.errorMsg != null) && (s3run.errorThrow != null)){
+                    exceptDuringRunReport(s3run.errorMsg,s3run.errorThrow);
+                } else {
+                    exceptDuringRunReport("Run statistics report upload to AWS S3 failed");
+                }
+            }
         } catch ( IOException e ) {
             exceptDuringRunReport("Couldn't read report file", e);
+        } catch ( InterruptedException e) {
+            exceptDuringRunReport("Run statistics report upload interrupted", e);
         }
     }