Improved SRA tests, corrected error message #638

a-nikitiuk · Jun 7, 2016

Description

These changes are intended to resolve most of previously reported SRA-related issues:

#442 - updated tests to use much smaller files, so that footprint by SRA cache on Mac OS X is about 30 Mb (on other OS issue does not exist, since we use sparse files there and footprint is even smaller)
#459, #461 - now each network-related test checks if it can resolve an accession, and skips the test in case of failure
#460, #545 - updated error message in SRAFileReader, so that it tells about a possibility of a connection problem

Checklist

Code compiles correctly
New tests covering changes and new functionality
All tests passing
Extended the README / documentation, if necessary
Is not backward compatible (breaks binary or source compatibility)

coveralls · Jun 8, 2016

Coverage decreased (-0.006%) to 68.053% when pulling 5d75514 on a-nikitiuk:sra-fixes into e38b849 on samtools:master.

isn't it clear at some point in the code that a connection has been established but that the accession is bad? why not inform the user?

why were these changed? what's wrong with the old ones?

sorry, I see the comment now: I supposed these are the smaller files.

yes, that is the reason

yfarjoun · Jun 10, 2016

@a-nikitiuk back to you. only one comment really: can you not distinguish between a bad connection and a bad accesssion string? It seems that some part of the code must know, so perhaps you can give an return code to isValid() that will be more than a boolean and work with that. The problem is that if the accession becomes "bad" because of code change we will never find out because we will skip the test.

a-nikitiuk · Jun 10, 2016

Unfortunately, it is not possible in current version of NGS API. We are working on improvement, but that is not an easy and quick fix.

yfarjoun · Jun 10, 2016

In that case @a-nikitiuk I think it would be better to test connectivity with a single @BeforeGroup using an accession that is bound to exist (perhaps you have some sort of testing object that can be used for that?) and then remove the @BeforeTest so that each of the individual tests will fail if their accession is not valid. while this is fragile wrt losing connectivity in the middle of running the tests, it doesn't require a separate check that all the accessions are valid.

yfarjoun · Jun 28, 2016

@a-nikitiuk This needs to be rebased, and also did you have time to think about my suggestion of using @BeforeGroup rather than @BeforeTest ?

yfarjoun · Jul 12, 2016

@a-nikitiuk will you have time to rebase and replace @BeforeMethod with @BeforeTest ?

We would love to have these changes....

a-nikitiuk · Jul 13, 2016

Yeah, will do that. Sorry, did not have much time lately

a-nikitiuk · Jul 13, 2016

Rebased and added @BeforeGroups method

coveralls · Jul 13, 2016

Coverage increased (+0.006%) to 68.416% when pulling 2fcb11c on a-nikitiuk:sra-fixes into e7c7bf6 on samtools:master.

Since you are no longer asking to connect for every accession, wouldn't it be better to remove the first condition, so that if someone puts in a non-matching accession to a new test, it will fail?

If someone puts a non-matching accession, then this code will do nothing. However, it detects remote accessions from its first argument, and if remote accession is detected and canResolveNetworkAccession is false then it skips the test.

Oh, OK. can you then simply change the text in the Exception to:

note the accession that cannot be resolved, and
change "SRA accession" with "remote SRA accession"?

yfarjoun · Jul 26, 2016

@a-nikitiuk are you planing to make these changes, or should I do them?

a-nikitiuk · Jul 26, 2016

You can do them if you would like to. Or I will try to find time for that today-tomorrow

yfarjoun · Jul 26, 2016

OK. I'll leave it to you then! thanks!

On Tue, Jul 26, 2016 at 2:20 PM, a-nikitiuk notifications@github.com
wrote:

You can do them if you would like to. Or I will try to find time for that
today-tomorrow

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a-nikitiuk · Jul 28, 2016

Done

coveralls · Jul 28, 2016

Coverage decreased (-0.006%) to 68.45% when pulling b780a55 on a-nikitiuk:sra-fixes into 87b1e87 on samtools:master.

yfarjoun · Jul 29, 2016

thanks! 👍

yfarjoun was assigned by droazen Jun 10, 2016

droazen referenced this pull request Jun 28, 2016
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Review "Party" #548

yfarjoun added the Review-party candidate label Jul 8, 2016

a-nikitiuk Fixed SRA tests issues, corrected error message a060fd0

yfarjoun merged commit 0875b62 into samtools:master Jul 29, 2016
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@@ -61,7 +61,8 @@ public SRAFileReader(final SRAAccession acc) {
              this.acc = acc;
              if (!acc.isValid()) {
-    -            throw new IllegalArgumentException("Invalid SRA accession was passed to SRA reader: " + acc);
+    +            throw new IllegalArgumentException("SRAFileReader: cannot resolve SRA accession '" + acc + "'\n" +

@@ -46,7 +46,7 @@
       * Created by andrii.nikitiuk on 10/28/15.
       */
      public class SRAIndexTest extends AbstractSRATest {
-    -    private static final SRAAccession DEFAULT_ACCESSION = new SRAAccession("SRR1298981");
+    +    private static final SRAAccession DEFAULT_ACCESSION = new SRAAccession("SRR2096940");

              if(!SRAAccession.isSupported()){
                  throw new SkipException("Skipping SRA Test because SRA native code is unavailable.");
              }
          }
+    +    @BeforeMethod
+    +    public final void skipIfCantResolve(Method method, Object[] params) {
+    +        String accession = null;
+    +
+    +        if (params.length > 0) {
+    +            Object firstParam = params[0];
+    +            if (firstParam instanceof String) {
+    +                accession = (String)firstParam;
+    +            } else if (firstParam instanceof SRAAccession) {
+    +                accession = firstParam.toString();
+    +            }
+    +        }
+    +
+    +        if (accession != null &&
+    +                accession.matches(SRAAccession.REMOTE_ACCESSION_PATTERN) && !canResolveNetworkAccession) {

samtools/htsjdk

Improved SRA tests, corrected error message #638

a-nikitiuk commented Jun 7, 2016 • edited

coveralls commented Jun 8, 2016

yfarjoun commented on the diff Jun 10, 2016

yfarjoun commented on the diff Jun 10, 2016

yfarjoun commented Jun 10, 2016

a-nikitiuk commented Jun 10, 2016

yfarjoun was assigned by droazen Jun 10, 2016

yfarjoun commented Jun 10, 2016

yfarjoun commented Jun 28, 2016

droazen referenced this pull request Jun 28, 2016

Review "Party" #548

yfarjoun added the Review-party candidate label Jul 8, 2016

yfarjoun commented Jul 12, 2016

a-nikitiuk commented Jul 13, 2016

a-nikitiuk commented Jul 13, 2016

coveralls commented Jul 13, 2016

yfarjoun commented on the diff Jul 14, 2016

yfarjoun commented Jul 26, 2016

a-nikitiuk commented Jul 26, 2016

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yfarjoun commented Jul 29, 2016

yfarjoun merged commit `0875b62` into samtools:master Jul 29, 2016
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This was referenced Aug 23, 2016

SRA test creating a huge local file/cache #442

SRA tests fail with missing accession #545

Improve error messages when instantiating an SRAFileReader #460

Fix inexplicable SRA test failures #461

Disable failing SRA tests until they can be made more robust #459

jamesemery added a commit to jamesemery/htsjdk that referenced this pull request Sep 1, 2016

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Improved SRA tests, corrected error message #638

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a-nikitiuk commented Jun 7, 2016 • edited

Description

Checklist

coveralls commented Jun 8, 2016

yfarjoun commented on the diff Jun 10, 2016

yfarjoun commented on the diff Jun 10, 2016

yfarjoun commented Jun 10, 2016

a-nikitiuk commented Jun 10, 2016

yfarjoun was assigned by droazen Jun 10, 2016

yfarjoun commented Jun 10, 2016

yfarjoun commented Jun 28, 2016

droazen referenced this pull request Jun 28, 2016

yfarjoun added the Review-party candidate label Jul 8, 2016

yfarjoun commented Jul 12, 2016

a-nikitiuk commented Jul 13, 2016

a-nikitiuk commented Jul 13, 2016

coveralls commented Jul 13, 2016

yfarjoun commented on the diff Jul 14, 2016

yfarjoun commented Jul 26, 2016

a-nikitiuk commented Jul 26, 2016

yfarjoun commented Jul 26, 2016

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a-nikitiuk commented Jul 28, 2016

coveralls commented Jul 28, 2016

yfarjoun commented Jul 29, 2016

Hide details View details yfarjoun merged commit 0875b62 into samtools:master Jul 29, 2016 1 of 2 checks passed

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This was referenced Aug 23, 2016

jamesemery added a commit to jamesemery/htsjdk that referenced this pull request Sep 1, 2016

yfarjoun merged commit `0875b62` into samtools:master Jul 29, 2016
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