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  1. IGB
  2. IGBF-3146

Remove "useq" packages from genometry bundle in IGB

    Details

    • Story Points:
      1
    • Sprint:
      Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15

      Description

      The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.

      See:

      core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java

      Note that "Runtime" lines are incompatible with Java 18. See this commit for invocation of Runtime obsolete stack trace setting method.

        Attachments

          Activity

          Hide
          karthik Karthik Raveendran added a comment -

          The code parsing and supporting "useq" files in IGB has been removed from the codebase. Commit

          Show
          karthik Karthik Raveendran added a comment - The code parsing and supporting "useq" files in IGB has been removed from the codebase. Commit
          Hide
          nfreese Nowlan Freese added a comment - - edited
          • Remove the following comment in GeneralLoadUtils.java
            Get GenomeVersion for USEQ file format.
          • Check line 54 of TrackDefaultView.java for use of "useq".
          • Should we remove the following useq test files?
            core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_Graph.useq
            core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_Region.useq
            core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_StrandedReadCoverage_Graph.useq
          • I'm also seeing a lot of imports being replaced with "". This seems like the IDE automatically making the change and I think we should not change them to "".

          I removed the above useq references in addition to Karthik's changes and pushed my branch (https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3146).

          Show
          nfreese Nowlan Freese added a comment - - edited Remove the following comment in GeneralLoadUtils.java Get GenomeVersion for USEQ file format. Check line 54 of TrackDefaultView.java for use of "useq". Should we remove the following useq test files? core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_Graph.useq core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_Region.useq core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_StrandedReadCoverage_Graph.useq I'm also seeing a lot of imports being replaced with " ". This seems like the IDE automatically making the change and I think we should not change them to " ". I removed the above useq references in addition to Karthik's changes and pushed my branch ( https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3146 ).
          Hide
          karthik Karthik Raveendran added a comment - - edited

          Add the additional changes and removed import errors. Commit

          Show
          karthik Karthik Raveendran added a comment - - edited Add the additional changes and removed import errors. Commit
          Hide
          nfreese Nowlan Freese added a comment -

          We have fixed the issue with Karthik's branch, here is the new commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/70b1c45edfb1f1169ebdef6bcc85844a94d73f5a

          Show
          nfreese Nowlan Freese added a comment - We have fixed the issue with Karthik's branch, here is the new commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/70b1c45edfb1f1169ebdef6bcc85844a94d73f5a
          Hide
          nfreese Nowlan Freese added a comment -

          Testing on Mac OS 12.5
          Reset preferences to default and delete the .igb folder.

          Attempting to load the attached useq file into the H_sapiens_Mar_2006 genome resulted in a "Format not recognized" error. This is the appropriate behavior.
          In the A_thaliana_Jun_2009 genome, loaded the RNA-Seq > Auxin arf19 > Graph - Scaled > Col-0 control scaled coverage graph file successfully.
          In the Graph tab, used Single-Graph Operations to successfully copy and divide the graph.
          In the Graph tab, used Multi-Graph Operations to successfully Sum two graphs.

          Since I can find no files in IGB that include mention of useq and the other IGB graph functionality does not appear to be affected, ready for pull request.

          Show
          nfreese Nowlan Freese added a comment - Testing on Mac OS 12.5 Reset preferences to default and delete the .igb folder. Attempting to load the attached useq file into the H_sapiens_Mar_2006 genome resulted in a "Format not recognized" error. This is the appropriate behavior. In the A_thaliana_Jun_2009 genome, loaded the RNA-Seq > Auxin arf19 > Graph - Scaled > Col-0 control scaled coverage graph file successfully. In the Graph tab, used Single-Graph Operations to successfully copy and divide the graph. In the Graph tab, used Multi-Graph Operations to successfully Sum two graphs. Since I can find no files in IGB that include mention of useq and the other IGB graph functionality does not appear to be affected, ready for pull request.
          Show
          karthik Karthik Raveendran added a comment - - edited PR submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/905
          Hide
          ann.loraine Ann Loraine added a comment -

          Merged.

          Show
          ann.loraine Ann Loraine added a comment - Merged.
          Hide
          ann.loraine Ann Loraine added a comment -

          Master branch is built and ready for testing.

          Show
          ann.loraine Ann Loraine added a comment - Master branch is built and ready for testing.
          Hide
          nfreese Nowlan Freese added a comment -

          Testing master branch installer on Mac OS 12.5
          Reset preferences to default and delete the .igb folder.

          Attempting to load the attached useq file into the H_sapiens_Mar_2006 genome resulted in a "Format not recognized" error. This is the appropriate behavior.
          In the A_thaliana_Jun_2009 genome, loaded the RNA-Seq > Auxin arf19 > Graph - Scaled > Col-0 control scaled coverage graph file successfully.

          Closing ticket.

          Show
          nfreese Nowlan Freese added a comment - Testing master branch installer on Mac OS 12.5 Reset preferences to default and delete the .igb folder. Attempting to load the attached useq file into the H_sapiens_Mar_2006 genome resulted in a "Format not recognized" error. This is the appropriate behavior. In the A_thaliana_Jun_2009 genome, loaded the RNA-Seq > Auxin arf19 > Graph - Scaled > Col-0 control scaled coverage graph file successfully. Closing ticket.

            People

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

              Dates

              • Created:
                Updated:
                Resolved: