Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2011

Re-opened: Property Search in Advanced Search tab throws IllegalArgumentException

    Details

    • Story Points:
      1
    • Sprint:
      Spring 2019 Sprint 5, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct

      Description

      Investigate and determine why this happens.
      Find out if it affects released branch 9.0.2 (get from bioviz.org).
      Read user's guide Advanced Search documentation as background.

      To repeat:

      1) Click Advanced Search tab
      2) Select PropertySearch, don't enter query string (leave text blank)
      3) Click Search icon (magnifying glass button on right of text entry)

      Observe exception:

      14:51:37.494 ERROR c.a.genometry.thread.CThreadWorker - Comparison method violates its general contract!
      java.lang.IllegalArgumentException: Comparison method violates its general contract!
      at java.util.TimSort.mergeHi(TimSort.java:899) ~[na:1.8.0_192]
      at java.util.TimSort.mergeAt(TimSort.java:516) ~[na:1.8.0_192]
      at java.util.TimSort.mergeCollapse(TimSort.java:441) ~[na:1.8.0_192]
      at java.util.TimSort.sort(TimSort.java:245) ~[na:1.8.0_192]
      at java.util.Arrays.sort(Arrays.java:1512) ~[na:1.8.0_192]
      at java.util.ArrayList.sort(ArrayList.java:1462) ~[na:1.8.0_192]
      at java.util.Collections.sort(Collections.java:175) ~[na:1.8.0_192]
      at com.affymetrix.igb.searchmodeidorprops.SearchModeIDOrProps.findLocalSyms(SearchModeIDOrProps.java:180) ~[na:na]
      at com.affymetrix.igb.searchmodeidorprops.SearchModeIDOrProps.search(SearchModeIDOrProps.java:105) ~[na:na]
      at com.affymetrix.igb.searchmodeidorprops.SearchModeID.search(SearchModeID.java:86) ~[na:na]
      at com.affymetrix.igb.keywordsearch.KeyWordSearch.search(KeyWordSearch.java:65) ~[na:na]
      at com.affymetrix.igb.search.SearchView$SearchAction$1.runInBackground(SearchView.java:175) ~[na:na]
      at com.affymetrix.igb.search.SearchView$SearchAction$1.runInBackground(SearchView.java:155) ~[na:na]
      at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) ~[na:na]
      at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_192]
      at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_192]
      at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_192]
      at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_192]
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_192]
      at java.lang.Thread.run(Thread.java:748) [na:1.8.0_192]

        Attachments

          Issue Links

            Activity

            Hide
            aloraine Ann Loraine added a comment -

            Please build a branch-specific installer for functional testing and then move to Needs Review.

            Regarding building the installer:

            Unfortunately there's a bug with the pipeline file that blocks automatic building of the branch specific installer, so you have to run the pipeline manually.
            (Bug is being fixed with https://jira.transvar.org/browse/IGBF-2027)

            Show
            aloraine Ann Loraine added a comment - Please build a branch-specific installer for functional testing and then move to Needs Review. Regarding building the installer: Unfortunately there's a bug with the pipeline file that blocks automatic building of the branch specific installer, so you have to run the pipeline manually. (Bug is being fixed with https://jira.transvar.org/browse/IGBF-2027 )
            Hide
            noor91zahara Noor Zahara added a comment -

            I have manually ran the pipleline.

            Show
            noor91zahara Noor Zahara added a comment - I have manually ran the pipleline.
            Hide
            aloraine Ann Loraine added a comment -

            The IllegalArgumentException no longer occurs.
            However, another problem has come up.
            When the user fails to enter a search string in the Advanced Search tab and clicks the "run search" (magnifying glass) button, the search proceeds and all items currently in memory get returned.
            It looks like the residue search does not have this behavior. If the user tries to search without entering a search string, a dialog appears letting them know that they need to enter a query string to run the search.
            Also, if the user enters * (globbing character that ought to match anything), a regular expression error appears.
            This UI clearly needs some love to improve usability and predictability. Will create another ticket for that and link to this one.
            Recommending PR.

            Show
            aloraine Ann Loraine added a comment - The IllegalArgumentException no longer occurs. However, another problem has come up. When the user fails to enter a search string in the Advanced Search tab and clicks the "run search" (magnifying glass) button, the search proceeds and all items currently in memory get returned. It looks like the residue search does not have this behavior. If the user tries to search without entering a search string, a dialog appears letting them know that they need to enter a query string to run the search. Also, if the user enters * (globbing character that ought to match anything), a regular expression error appears. This UI clearly needs some love to improve usability and predictability. Will create another ticket for that and link to this one. Recommending PR.
            Hide
            prutha Prutha Kulkarni (Inactive) added a comment -

            Tested the ticket using branch the installer IGBF-2011. I was able to search without entering any keyword in the search box with no exceptions on run time. Noor Zahara could you please mention a detailed set of instructions for testing so that anyone who has not worked on IGB can easily navigate to advanced search tab just by following those instructions. Also doing it would expedite the process of 9.1.0 release. Moving it to DONE.
            Thanks.

            Show
            prutha Prutha Kulkarni (Inactive) added a comment - Tested the ticket using branch the installer IGBF-2011 . I was able to search without entering any keyword in the search box with no exceptions on run time. Noor Zahara could you please mention a detailed set of instructions for testing so that anyone who has not worked on IGB can easily navigate to advanced search tab just by following those instructions. Also doing it would expedite the process of 9.1.0 release. Moving it to DONE. Thanks.
            Show
            aloraine Ann Loraine added a comment - For reference, here is the commit: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/e3aec2f3b29eb070b0f7edb481552d12337e8bbf

              People

              • Assignee:
                noor91zahara Noor Zahara
                Reporter:
                aloraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                3 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: