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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

                Ascending order - Click to sort in descending order
                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1531 [ 17617 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 7 [ 230 ] Fall 7, Fall 8 [ 230, 231 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 7, Fall 8 [ 230, 231 ] Fall 7, Fall 8, Fall 9 [ 230, 231, 232 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2860 [ IGBF-2860 ]
                Hide
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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.
                nfreese Nowlan Freese made changes -
                Story Points 1 0.25
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-4382 [ IGBF-4382 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Hide
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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!
                pkulzer Paige Kulzer made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Nowlan Freese [ nfreese ]
                Hide
                Permalink
                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
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                Hide
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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.)
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Hide
                Permalink
                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!
                pkulzer Paige Kulzer made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Nowlan Freese [ nfreese ]

                  People

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

                    Dates

                    • Created:
                      Updated:
                      Resolved: