zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

GATKRunReport now tracks the errorMessage and errorThrown during post for later analysis 

-- This is primarily useful in the unit tests, as I now print out additional information on why a test might have failed, if it in fact did.
This commit is contained in:
Mark DePristo 2013-02-02 19:24:31 -05:00
parent 6382d5bdc9
commit 8d08780582
1 changed files with 65 additions and 26 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

91
public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
View File

@ -165,6 +165,11 @@ public class GATKRunReport {
@Element(required = true, name = "percent-time-waiting-for-io")
private String percentTimeWaitingForIO;
/** The error message, if one occurred, or null if none did */
public String errorMessage = null;
/** The error that occurred, if one did, or null if none did */
public Throwable errorThrown = null;
/**
* How should the GATK report its usage?
*/
@ -542,11 +547,7 @@ public class GATKRunReport {
private final byte[] contents;
/** The s3Object that we created to upload, or null if it failed */
public S3Object s3Object;
/** The error message, if one occurred, or null if none did */
public String errorMsg = null;
/** The error that occurred, if one did, or null if none did */
public Throwable errorThrow;
public S3Object s3Object = null;
@Requires({"filename != null", "contents != null"})
public S3PutRunnable(final String filename, final byte[] contents){
@ -583,24 +584,15 @@ public class GATKRunReport {
throw new IllegalStateException("Unexpected AWS exception");
}
} catch ( S3ServiceException e ) {
setException("S3 exception occurred", e);
exceptDuringRunReport("S3 exception occurred", e);
} catch ( NoSuchAlgorithmException e ) {
setException("Couldn't calculate MD5", e);
exceptDuringRunReport("Couldn't calculate MD5", e);
} catch ( IOException e ) {
setException("Couldn't read report file", e);
exceptDuringRunReport("Couldn't read report file", e);
} catch ( Exception e ) {
exceptDuringRunReport("An unexpected exception occurred during posting", e);
}
}
/**
* Set the error message and thrown exception, if one did occurred
*
* @param msg the error message
* @param e the exception that occurred
*/
private void setException(final String msg, final Throwable e){
errorMsg=msg;
errorThrow=e;
}
}
/**
@ -643,11 +635,7 @@ public class GATKRunReport {
logger.debug("Uploaded to AWS: " + s3run.s3Object);
return 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");
}
// an exception occurred, the thread should have already invoked the exceptDuringRunReport function
}
} catch ( IOException e ) {
exceptDuringRunReport("Couldn't read report file", e);
@ -658,12 +646,21 @@ public class GATKRunReport {
return null;
}
// ---------------------------------------------------------------------------
//
// Error handling code
//
// ---------------------------------------------------------------------------
/**
* Note that an exception occurred during creating or writing this report
* @param msg the message to print
* @param e the exception that occurred
*/
private void exceptDuringRunReport(String msg, Throwable e) {
@Ensures("exceptionOccurredDuringPost()")
private void exceptDuringRunReport(final String msg, final Throwable e) {
this.errorMessage = msg;
this.errorThrown = e;
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());
}
@ -671,10 +668,52 @@ public class GATKRunReport {
* Note that an exception occurred during creating or writing this report
* @param msg the message to print
*/
private void exceptDuringRunReport(String msg) {
@Ensures("exceptionOccurredDuringPost()")
private void exceptDuringRunReport(final String msg) {
this.errorMessage = 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);
}
/**
* Did an error occur during the posting of this run report?
* @return true if so, false if not
*/
public boolean exceptionOccurredDuringPost() {
return getErrorMessage() != null;
}
/**
* If an error occurred during posting of this report, retrieve the message of the error that occurred, or null if
* no error occurred
* @return a string describing the error that occurred, or null if none did
*/
public String getErrorMessage() {
return errorMessage;
}
/**
* Get the throwable that caused the exception during posting of this message, or null if none was available
*
* Note that getting a null valuable from this function doesn't not imply that no error occurred. Some
* errors that occurred many not have generated a throwable.
*
* @return the Throwable that caused the error, or null if no error occurred or was not caused by a throwable
*/
public Throwable getErrorThrown() {
return errorThrown;
}
/**
* Helper method to format the exception that occurred during posting, or a string saying none occurred
* @return a non-null string
*/
@Ensures("result != null")
protected String formatError() {
return exceptionOccurredDuringPost()
? String.format("Exception message=%s with cause=%s", getErrorMessage(), getErrorThrown())
: "No exception occurred";
}
// ---------------------------------------------------------------------------
//
// Equals and hashcode -- purely for comparing reports for testing