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  1. IGB
  2. IGBF-2357

Fix failed test case

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          0.5
        • Epic Link:
        • Sprint:
          Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun

          Description

          Suddenly one of the genometry test cases is failing:

          "java.lang.NullPointerException
          at com.affymetrix.genometry.parsers.TwoBitParserTest.testOriginal(TwoBitParserTest.java:67)
          at com.affymetrix.genometry.parsers.TwoBitParserTest.testCaseFiles(TwoBitParserTest.java:47)"

          We need to investigate why this is occurring and correct the problem.

          While fixing the test, improve test coverage to make the code more resilient to bugs and safer to modify.

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              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2291 Upgrade JDK version to 1.8.0.241 for loraine lab java repositories

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine added a comment -

                Unfortunately there is another failed test. Please take a look and fix the test, ideally also improving the testing coverage and robustness of the tests.

                Show
                ann.loraine Ann Loraine added a comment - Unfortunately there is another failed test. Please take a look and fix the test, ideally also improving the testing coverage and robustness of the tests.
                Hide
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Please review the fix:
                https://bitbucket.org/srishtitiwari/integrated-genome-browser/commits/b3976f26b910063373b6fc06158072f440a60313

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - Please review the fix: https://bitbucket.org/srishtitiwari/integrated-genome-browser/commits/b3976f26b910063373b6fc06158072f440a60313
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                ann.loraine Ann Loraine added a comment -

                Please submit PR.

                Show
                ann.loraine Ann Loraine added a comment - Please submit PR.
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                PR submitted:

                https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/790/igbf-2357-fix-failed-test-case/diff

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - PR submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/790/igbf-2357-fix-failed-test-case/diff
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                https://www.baeldung.com/junit-assert-exception

                From a quick investigation, I figured out that there are changes in implementation around unit assert exception. This could be a possible reason why this test was not previously failing.

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - https://www.baeldung.com/junit-assert-exception From a quick investigation, I figured out that there are changes in implementation around unit assert exception. This could be a possible reason why this test was not previously failing.
                Hide
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                pbadzuh Philip Badzuh (Inactive) added a comment -

                The latest version of IGB from the master branch builds successfully and the breaking test now passes. Moving to done.

                -------------------------------------------------------------------------------
                Test set: com.affymetrix.genometry.parsers.TwoBitParserTest
                -------------------------------------------------------------------------------
                Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.335 sec - in com.affymetrix.genometry.parsers.TwoBitParserTest

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - The latest version of IGB from the master branch builds successfully and the breaking test now passes. Moving to done. ------------------------------------------------------------------------------- Test set: com.affymetrix.genometry.parsers.TwoBitParserTest ------------------------------------------------------------------------------- Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.335 sec - in com.affymetrix.genometry.parsers.TwoBitParserTest

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
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                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: