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  1. IGB
  2. IGBF-4355

Investigate com.affymetrix.igb.external.LoaderTest failing

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Minor
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: When I build IGB with tests (mvn clean install) it is hanging on the com.affymetrix.igb.external.LoaderTest and several exceptions are thrown.

          Task: Investigate why the com.affymetrix.igb.external.LoaderTest is failing.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-4382 Investigate UCSC External View not working

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2860 Disable Ensembl external view

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese added a comment -

                I disabled the checkDownLoadEnsembl test that was causing the build to hang. It was checking if it could retrieve an image from Ensembl, which hasn't worked in several years and was removed as an option from the External View tab in IGBF-2860.

                Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/373d16b319109d4896164767b91e6b18c8cf4264
                Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-4355

                To review:
                Build IGB with tests (mvn clean install) and check that it does not pause during the LoaderTest.

                Show
                nfreese Nowlan Freese added a comment - I disabled the checkDownLoadEnsembl test that was causing the build to hang. It was checking if it could retrieve an image from Ensembl, which hasn't worked in several years and was removed as an option from the External View tab in IGBF-2860 . Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/373d16b319109d4896164767b91e6b18c8cf4264 Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-4355 To review: Build IGB with tests (mvn clean install) and check that it does not pause during the LoaderTest.
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                pkulzer Paige Kulzer added a comment -

                Fetched Nowlan's branch and ran mvn clean install to test this fix. The build is no longer hanging on the Ensembl test nor is an error being thrown at that step.

                Recommending PR!

                Show
                pkulzer Paige Kulzer added a comment - Fetched Nowlan's branch and ran mvn clean install to test this fix. The build is no longer hanging on the Ensembl test nor is an error being thrown at that step. Recommending PR!
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                nfreese Nowlan Freese added a comment -

                PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1097

                Show
                nfreese Nowlan Freese added a comment - PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1097
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                ann.loraine Ann Loraine added a comment - - edited

                PR is merged.
                Installers are built and deployed to early access section of bioviz.org.

                Note this change only affects developers as it disables a test that was hanging. (See above for details.)

                Show
                ann.loraine Ann Loraine added a comment - - edited PR is merged. Installers are built and deployed to early access section of bioviz.org. Note this change only affects developers as it disables a test that was hanging. (See above for details.)
                Hide
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                pkulzer Paige Kulzer added a comment -

                Pulled the latest IGB branch for testing. The build is now proceeding relatively uninhibited because the Ensembl test is not being run.

                Closing ticket!

                Show
                pkulzer Paige Kulzer added a comment - Pulled the latest IGB branch for testing. The build is now proceeding relatively uninhibited because the Ensembl test is not being run. Closing ticket!

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
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                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: