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Now that logging is so standard, only prints messages about logging to DEBUG. Also, found a way to silence the mime.types warning, that doesn't matter at all to us. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5543 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-03-31 16:49:39 +00:00
parent 7b452ea2b9
commit c7445a6fbd
1 changed files with 12 additions and 9 deletions
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21
java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
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@ -24,6 +24,7 @@
package org.broadinstitute.sting.gatk.phonehome; package org.broadinstitute.sting.gatk.phonehome;
import org.apache.log4j.Level;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.CommandLineUtils; import org.broadinstitute.sting.commandline.CommandLineUtils;
import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.CommandLineGATK;
@ -175,7 +176,7 @@ public class GATKRunReport {
if ( type == PhoneHomeOption.NO_ET ) if ( type == PhoneHomeOption.NO_ET )
throw new ReviewedStingException("Trying to create a run report when type is NO_ET!"); throw new ReviewedStingException("Trying to create a run report when type is NO_ET!");
logger.info("Aggregating data for run report"); logger.debug("Aggregating data for run report");
mGATKHeader = CommandLineGATK.createApplicationHeader(); mGATKHeader = CommandLineGATK.createApplicationHeader();
currentPath = System.getProperty("user.dir"); currentPath = System.getProperty("user.dir");
@ -245,7 +246,7 @@ public class GATKRunReport {
} }
public void postReport(PhoneHomeOption type) { public void postReport(PhoneHomeOption type) {
logger.info("Posting report of type " + type); logger.debug("Posting report of type " + type);
switch (type) { switch (type) {
case NO_ET: // don't do anything case NO_ET: // don't do anything
break; break;
@ -312,7 +313,7 @@ public class GATKRunReport {
String filename = getID() + ".report.xml.gz"; String filename = getID() + ".report.xml.gz";
File file = new File(rootDir, filename); File file = new File(rootDir, filename);
postReportToFile(file); postReportToFile(file);
logger.info("Wrote report to " + file); logger.debug("Wrote report to " + file);
return file; return file;
} catch ( Exception e ) { } catch ( Exception e ) {
// we catch everything, and no matter what eat the error // we catch everything, and no matter what eat the error
@ -325,10 +326,12 @@ public class GATKRunReport {
// modifying example code from http://jets3t.s3.amazonaws.com/toolkit/code-samples.html // modifying example code from http://jets3t.s3.amazonaws.com/toolkit/code-samples.html
this.hostName = resolveHostname(); // we want to fill in the host name this.hostName = resolveHostname(); // we want to fill in the host name
File localFile = postReportToLocalDisk(new File("./")); File localFile = postReportToLocalDisk(new File("./"));
logger.info("Generating GATK report to AWS S3 based on local file " + localFile); logger.debug("Generating GATK report to AWS S3 based on local file " + localFile);
if ( localFile != null ) { if ( localFile != null ) { // we succeeded in creating the local file
try { try {
// we succeeded in creating the local file // 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 // Your Amazon Web Services (AWS) login credentials are required to manage S3 accounts. These credentials
// are stored in an AWSCredentials object: // are stored in an AWSCredentials object:
@ -348,7 +351,7 @@ public class GATKRunReport {
//logger.info("Created S3Object" + fileObject); //logger.info("Created S3Object" + fileObject);
//logger.info("Uploading " + localFile + " to AWS bucket"); //logger.info("Uploading " + localFile + " to AWS bucket");
S3Object s3Object = s3Service.putObject(REPORT_BUCKET_NAME, fileObject); S3Object s3Object = s3Service.putObject(REPORT_BUCKET_NAME, fileObject);
logger.info("Uploaded to AWS: " + s3Object); logger.debug("Uploaded to AWS: " + s3Object);
} catch ( S3ServiceException e ) { } catch ( S3ServiceException e ) {
exceptDuringRunReport("S3 exception occurred", e); exceptDuringRunReport("S3 exception occurred", e);
} catch ( NoSuchAlgorithmException e ) { } catch ( NoSuchAlgorithmException e ) {
@ -362,12 +365,12 @@ public class GATKRunReport {
} }
private void exceptDuringRunReport(String msg, Throwable e) { private void exceptDuringRunReport(String msg, Throwable e) {
logger.warn("A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***]. Message is: " + msg + ". Error message is: " + e.getMessage()); logger.debug("A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***]. Message is: " + msg + ". Error message is: " + e.getMessage());
//e.printStackTrace(); //e.printStackTrace();
} }
private void exceptDuringRunReport(String msg) { private void exceptDuringRunReport(String msg) {
logger.warn("A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***]. Message is " + msg); logger.debug("A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***]. Message is " + msg);
} }