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  1. IGB
  2. IGBF-3146

Remove "useq" packages from genometry bundle in IGB

        Details

        • Story Points:
          1
        • Epic Link:
        • 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.

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              relates to

              Task - A task that needs to be done. IGBF-3705 Add USEQ support back to IGB

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1531 [ 17617 ]
                ann.loraine Ann Loraine made changes -
                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 the need to update it for newer versions of Java. 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 the need to update it for newer versions of Java.

                See:

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

                Note that "Runtime" lines are incompatible with Java 18.
                ann.loraine Ann Loraine made changes -
                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 the need to update it for newer versions of Java.

                See:

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

                Note that "Runtime" lines are incompatible with Java 18.                 		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.
                ann.loraine Ann Loraine made changes -
                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.                 		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 details|https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f].
                ann.loraine Ann Loraine made changes -
                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 details|https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f].                 		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 |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for obsolete (as of Java 11?) Runtime method invocation.
                ann.loraine Ann Loraine made changes -
                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 |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for obsolete (as of Java 11?) Runtime method invocation.                 		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 |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for invocation of Runtime obsolete stack trace setting method invocation.
                ann.loraine Ann Loraine made changes -
                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 |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for invocation of Runtime obsolete stack trace setting method invocation.                 		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 |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for invocation of Runtime obsolete stack trace setting method.
                ann.loraine Ann Loraine made changes -
                Story Points 1 0.25
                ann.loraine Ann Loraine made changes -
                Sprint Summer 4 2022 July 4 [ 150 ] Summer 4 2022 July 4, Summer 5 2022 July 18 [ 150, 151 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 4 2022 July 4, Summer 5 2022 July 18 [ 150, 151 ] Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 150, 151, 152 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
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                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
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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                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 ).
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 9.1.10 Major Release [ 10700 ]
                Hide
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                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
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Hide
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                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
                nfreese Nowlan Freese made changes -
                Attachment chr17_H_sapiens_Mar_2006_Graph.useq [ 17257 ]
                Hide
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                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.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                karthik Karthik Raveendran made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
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                karthik Karthik Raveendran added a comment - - edited

                PR submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/905

                Show
                karthik Karthik Raveendran added a comment - - edited PR submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/905
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Assignee Karthik Raveendran [ karthik ]
                Hide
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                ann.loraine Ann Loraine added a comment -

                Merged.

                Show
                ann.loraine Ann Loraine added a comment - Merged.
                nfreese Nowlan Freese made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 150, 151, 152 ] Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15 [ 150, 151, 152, 153 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                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.
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Post-merge Testing In Progress [ 10003 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Summary Investigate: Remove "useq" packages from genometry bundle in IGB Remove "useq" packages from genometry bundle in IGB
                nfreese Nowlan Freese made changes -
                Story Points 0.25 1
                Hide
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                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.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3705 [ IGBF-3705 ]

                  People

                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: