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  1. IGB
  2. IGBF-1308

Fix contig name error in ProtAnnot window title

    Details

    • Story Points:
      0.5
    • Sprint:
      Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2

      Description

      The ProtAnnot header bar gives chrChr1 as the contig. It should be either chr1 or Chr1.

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            ieclabau Ivory Blakley (Inactive) created issue -
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            ann.loraine Ann Loraine added a comment -

            Good catch.

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            ann.loraine Ann Loraine added a comment - Good catch.
            ann.loraine Ann Loraine made changes -
            Field Original Value New Value
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Priority Trivial [ 5 ] Minor [ 4 ]
            ann.loraine Ann Loraine made changes -
            Fix Version/s 9.0.2 [ 10600 ]
            Labels Beginner
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            ann.loraine Ann Loraine made changes -
            Story Points 0.5
            ann.loraine Ann Loraine made changes -
            Sprint Summer 2018 Part 2 [ 49 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Summary contig name in ProtAnnot header bar has error Fix contig name error in ProtAnnot window title
            ann.loraine Ann Loraine made changes -
            Assignee Anh Moss [ aduong ]
            aduong Anh Moss (Inactive) made changes -
            Status Open [ 1 ] In Progress [ 3 ]
            Hide
            aduong Anh Moss (Inactive) added a comment -

            Please review the adjusted code:
            https://bitbucket.org/anhmoss/integrated-genome-browser/branch/IGBF-1308-ProtAnnotWindowTitle

            I found the code that was affecting the title of the ProtAnnot window, which was adding 'chr' as a prefix to any title that did not already start with 'chr'. This was an issue because not all titles started with the lowercase prefix 'chr', so it was appearing twice 'chrChr1' in chromosome titles. Other genomes, such as the blueberry genome, have scaffolds titled as 'scaffold00001'. Others are contigs, and etc. I fixed this error by deleting the code that was adding this prefix.

            To test:
            • I cleaned and rebuilt the ProtAnnot project.
            • Since the ProtAnnot app was still showing version 9.0.0, we removed the default remote repository, and then created, added and installed a local repository, which then reflected app version 9.0.1. This indicated that the ProtAnnot repo had a separate update cycle from IGB.
            • We talked to Kiran, and he said he had submitted a recent fix that might've interfered our code change, so we reverted my repo copy to an earlier commit (commit id: 5748edd7f) before his changes, rebuilt the ProtAnnot project, and was able to see our code changes reflected in ProtAnnot window.

            Thank you.

            Show
            aduong Anh Moss (Inactive) added a comment - Please review the adjusted code: https://bitbucket.org/anhmoss/integrated-genome-browser/branch/IGBF-1308-ProtAnnotWindowTitle I found the code that was affecting the title of the ProtAnnot window, which was adding 'chr' as a prefix to any title that did not already start with 'chr'. This was an issue because not all titles started with the lowercase prefix 'chr', so it was appearing twice 'chrChr1' in chromosome titles. Other genomes, such as the blueberry genome, have scaffolds titled as 'scaffold00001'. Others are contigs, and etc. I fixed this error by deleting the code that was adding this prefix. To test: • I cleaned and rebuilt the ProtAnnot project. • Since the ProtAnnot app was still showing version 9.0.0, we removed the default remote repository, and then created, added and installed a local repository, which then reflected app version 9.0.1. This indicated that the ProtAnnot repo had a separate update cycle from IGB. • We talked to Kiran, and he said he had submitted a recent fix that might've interfered our code change, so we reverted my repo copy to an earlier commit (commit id: 5748edd7f) before his changes, rebuilt the ProtAnnot project, and was able to see our code changes reflected in ProtAnnot window. Thank you.
            aduong Anh Moss (Inactive) made changes -
            Assignee Anh Moss [ aduong ]
            aduong Anh Moss (Inactive) made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Recent fix by Kiran blocks user from installing plug-ins (Apps) from local repository. Commit link:
            https://bitbucket.org/lorainelab/integrated-genome-browser/commits/bec9bf3567dd6370239ea136e6455491d6ff1275
            IGBF-1108:Added condition to check network connection before installing plugin

            Show
            ann.loraine Ann Loraine added a comment - - edited Recent fix by Kiran blocks user from installing plug-ins (Apps) from local repository. Commit link: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/bec9bf3567dd6370239ea136e6455491d6ff1275 IGBF-1108 :Added condition to check network connection before installing plugin
            ann.loraine Ann Loraine made changes -
            Link This issue relates to IGBF-1108 [ IGBF-1108 ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Status Needs 1st Level Review [ 10005 ] Reviewing [ 10301 ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Assignee Ivory Blakley [ ieclabau ]
            Show
            ieclabau Ivory Blakley (Inactive) added a comment - Found Anh's branch: https://bitbucket.org/anhmoss/integrated-genome-browser/branch/IGBF-1308-ProtAnnotWindowTitle
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            Since there is a recent commit that would make it hard to test this, I am using the released version installed on my machine.
            This shortly after the 9.0.1 release that is really close to the current master.

            functional test
            I checked out Anh's branch. I removed the target directory in the ProtAnnot module and then built the ProtAnnot module. I opened IGB (the released version). I added my local copy of the ProtAnnot target directory as an app repository, and disabled the bioviz one. installed protannot, selected a gene model, started protannot. The sequence name looks correct (no added "chr"). Then I uninstalled protannot, disabled the local app repo, re-enabled the bioviz app rep, and installed protannot (from bioviz). I selected the same gene model and started protannot. Now the sequence is incorrect, it displays as "chrChr1". This confirms that the Anh's changes removed the 'chr' that appears when you install protannot from bioviz.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - Since there is a recent commit that would make it hard to test this, I am using the released version installed on my machine. This shortly after the 9.0.1 release that is really close to the current master. functional test I checked out Anh's branch. I removed the target directory in the ProtAnnot module and then built the ProtAnnot module. I opened IGB (the released version). I added my local copy of the ProtAnnot target directory as an app repository, and disabled the bioviz one. installed protannot, selected a gene model, started protannot. The sequence name looks correct (no added "chr"). Then I uninstalled protannot, disabled the local app repo, re-enabled the bioviz app rep, and installed protannot (from bioviz). I selected the same gene model and started protannot. Now the sequence is incorrect, it displays as "chrChr1". This confirms that the Anh's changes removed the 'chr' that appears when you install protannot from bioviz.
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            code review,
            Looking at the changes in bitbucket, the change is very minor, and I do not see any potential for side effects.

            git review
            All changes are in a single commit with an appropriate message.
            The branch is currently two commits behind Anh's master, so it needs to be rebased.

            I am reassigning this to Anh to do the rebase and then submit a pull request.
            Anh, be sure to update your local master from upstream master, then rebase this branch onto your master, and push both master and this branch to your remote. Check that the branch says 'ahead by 1 commit' relative to your master.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - code review, Looking at the changes in bitbucket, the change is very minor, and I do not see any potential for side effects. git review All changes are in a single commit with an appropriate message. The branch is currently two commits behind Anh's master, so it needs to be rebased. I am reassigning this to Anh to do the rebase and then submit a pull request. Anh, be sure to update your local master from upstream master, then rebase this branch onto your master, and push both master and this branch to your remote. Check that the branch says 'ahead by 1 commit' relative to your master.
            ieclabau Ivory Blakley (Inactive) made changes -
            Assignee Ivory Blakley [ ieclabau ] Anh Moss [ aduong ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Status Reviewing [ 10301 ] Ready for Pull Request [ 10304 ]
            aduong Anh Moss (Inactive) made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            ann.loraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Needs Testing [ 10002 ]
            mason Mason Meyer (Inactive) made changes -
            Assignee Anh Moss [ aduong ] Mason Meyer [ mason ]
            mason Mason Meyer (Inactive) made changes -
            Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
            Hide
            ann.loraine Ann Loraine added a comment -

            Pull request merged.

            Show
            ann.loraine Ann Loraine added a comment - Pull request merged.
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Sprint Summer 2018 Part 2 [ 49 ] Summer 2018 Part 2, Summer 2018 Part 3 [ 49, 50 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            Hide
            mason Mason Meyer (Inactive) added a comment -

            I am not currently seeing this issue as resolved. When I open ProtAnnot using the IGB App Manager, I am seeing content in the title bar such as "chrChr1". Should I be testing this story a different way besides using the App Manager? For now, I am re-assigning this story to Ann and moving to To-Do.

            Show
            mason Mason Meyer (Inactive) added a comment - I am not currently seeing this issue as resolved. When I open ProtAnnot using the IGB App Manager, I am seeing content in the title bar such as "chrChr1". Should I be testing this story a different way besides using the App Manager? For now, I am re-assigning this story to Ann and moving to To-Do.
            mason Mason Meyer (Inactive) made changes -
            Assignee Mason Meyer [ mason ] Ann Loraine [ aloraine ]
            mason Mason Meyer (Inactive) made changes -
            Status Testing In Progress [ 10003 ] Open [ 1 ]
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            After clarifying the testing protocol, I am moving this back to Needs Testing and assigning it to Mason.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - After clarifying the testing protocol, I am moving this back to Needs Testing and assigning it to Mason.
            ieclabau Ivory Blakley (Inactive) made changes -
            Assignee Ann Loraine [ aloraine ] Mason Meyer [ mason ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Status Open [ 1 ] Needs Testing [ 10002 ]
            mason Mason Meyer (Inactive) made changes -
            Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Sprint Summer 2018 Part 2, Summer 2018 Part 3 [ 49, 50 ] Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 49, 50, 51 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Sprint Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 49, 50, 51 ] Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2 [ 49, 50, 51, 52 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            Hide
            mason Mason Meyer (Inactive) added a comment -

            My testing confirms that the contig name error is fixed in ProtAnnot. I am no longer seeing the additional "chr" text in the window title. I am also not experiencing any side effects related to this change, so the story will now be closed.

            Show
            mason Mason Meyer (Inactive) added a comment - My testing confirms that the contig name error is fixed in ProtAnnot. I am no longer seeing the additional "chr" text in the window title. I am also not experiencing any side effects related to this change, so the story will now be closed.
            mason Mason Meyer (Inactive) made changes -
            Resolution Done [ 10000 ]
            Status Testing In Progress [ 10003 ] Closed [ 6 ]
            ann.loraine Ann Loraine made changes -
            Assignee Mason Meyer [ mason ] Anh Moss [ aduong ]
            ann.loraine Ann Loraine made changes -
            Workflow Loraine Lab Workflow [ 17999 ] Fall 2019 Workflow Update [ 19896 ]
            ann.loraine Ann Loraine made changes -
            Workflow Fall 2019 Workflow Update [ 19896 ] Revised Fall 2019 Workflow Update [ 22015 ]

              People

              • Assignee:
                aduong Anh Moss (Inactive)
                Reporter:
                ieclabau Ivory Blakley (Inactive)
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                Dates

                • Created:
                  Updated:
                  Resolved: