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  1. IGB
  2. IGBF-1139

Disable "View Read Sequence" for all file formats except PSLX and BAM

    Details

    • Story Points:
      2
    • Sprint:
      Fall 2017

      Description

      It seems that the "View Read Sequence" option is enabled for BED files and other files but this option should only be enabled for BAM and PSLX files.

      To access this feature, right-click on a gene model and you can see the option in the context menu (see screenshot).

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          Activity

          Hide
          djoshi4 Deepti Joshi (Inactive) added a comment - - edited

          Issue is ready for first level review.

          Link to the issue branch on bitbucket:
          https://bitbucket.org/djoshi4/deepti-fork-igb/branch/IGBF-1139-Disable_View_Read_Sequence_for_BEDFiles

          Show
          djoshi4 Deepti Joshi (Inactive) added a comment - - edited Issue is ready for first level review. Link to the issue branch on bitbucket: https://bitbucket.org/djoshi4/deepti-fork-igb/branch/IGBF-1139-Disable_View_Read_Sequence_for_BEDFiles
          Hide
          sneha Sneha Ramesh Watharkar (Inactive) added a comment - - edited

          "View Read Sequence" is now greyed out for unsupported files on right-click menu. Uploaded screenshot "Screenshot from 2017-05-24.png".

          Done with #1 first level review.

          Show
          sneha Sneha Ramesh Watharkar (Inactive) added a comment - - edited "View Read Sequence" is now greyed out for unsupported files on right-click menu. Uploaded screenshot "Screenshot from 2017-05-24.png". Done with #1 first level review.
          Hide
          ieclabau Ivory Blakley (Inactive) added a comment -

          Code:
          Please see my comments on bitbucket,
          https://bitbucket.org/djoshi4/deepti-fork-igb/commits/850949f2886b5d434e590596814d870776315304?at=IGBF-1139-Disable_View_Read_Sequence_for_BEDFiles

          Functionality:
          GOOD: The feature is enabled for bam file selections and disabled (grayed out) for bed, gff, gtf file selections which don't have their own sequence info.
          POOR: If you select multiple things, "show read sequence" is enabled, but selecting it produces an error: "An unknown error occurred. Please use the Help menu to contact the IGB support team for assistance." This was not caused by any the code edited here. But it would have been ideal to have included this as part of the initial issue description. In addition to only being enabled if the selection has sequence, it should only be enabled if there is only one item selected.

          Sending back to To Do.
          Deepti, you may want to make modifications or add comments after you review my comments on bitbucket.
          In light of the single-selections-only aspect, decide if you think that should be its own issue (while this issue moves on) or if that is closely enough entwined that it should be part of this issue and merged as a single pull request. (I think I would keep it all in one issue).

          Show
          ieclabau Ivory Blakley (Inactive) added a comment - Code: Please see my comments on bitbucket, https://bitbucket.org/djoshi4/deepti-fork-igb/commits/850949f2886b5d434e590596814d870776315304?at=IGBF-1139-Disable_View_Read_Sequence_for_BEDFiles Functionality: GOOD: The feature is enabled for bam file selections and disabled (grayed out) for bed, gff, gtf file selections which don't have their own sequence info. POOR: If you select multiple things, "show read sequence" is enabled, but selecting it produces an error: "An unknown error occurred. Please use the Help menu to contact the IGB support team for assistance." This was not caused by any the code edited here. But it would have been ideal to have included this as part of the initial issue description. In addition to only being enabled if the selection has sequence, it should only be enabled if there is only one item selected. Sending back to To Do. Deepti, you may want to make modifications or add comments after you review my comments on bitbucket. In light of the single-selections-only aspect, decide if you think that should be its own issue (while this issue moves on) or if that is closely enough entwined that it should be part of this issue and merged as a single pull request. (I think I would keep it all in one issue).
          Hide
          djoshi4 Deepti Joshi (Inactive) added a comment -

          As discussed, I have made changes to the code to disable "View Read Sequence" (on the right click context menu as well as on the tool bar View menu) if user selects more than one sequences. Also added comments about the changes in the two classes.

          Moving to Needs 1st level review for Ivory to do the review.

          Show
          djoshi4 Deepti Joshi (Inactive) added a comment - As discussed, I have made changes to the code to disable "View Read Sequence" (on the right click context menu as well as on the tool bar View menu) if user selects more than one sequences. Also added comments about the changes in the two classes. Moving to Needs 1st level review for Ivory to do the review.
          Hide
          ieclabau Ivory Blakley (Inactive) added a comment -

          Looks good!

          Show
          ieclabau Ivory Blakley (Inactive) added a comment - Looks good!
          Hide
          ieclabau Ivory Blakley (Inactive) added a comment -

          I'm passing this back to Deepti to make a pull request.

          Show
          ieclabau Ivory Blakley (Inactive) added a comment - I'm passing this back to Deepti to make a pull request.
          Hide
          mason Mason Meyer (Inactive) added a comment -

          My testing confirms that this issue is resolved. The "View Read Sequence" option has been disabled for all file types other than BAM and PSLX and for those file types, the feature continues to function as expected. I found no other side effects from this change; the context menu entries appear as they should and all are functioning as expected. Additionally, the "View Read Sequence" option only appears when one read is selected and is disabled when multiple reads are selected, as expected. Since this issue is resolved, it will now be closed.

          Show
          mason Mason Meyer (Inactive) added a comment - My testing confirms that this issue is resolved. The "View Read Sequence" option has been disabled for all file types other than BAM and PSLX and for those file types, the feature continues to function as expected. I found no other side effects from this change; the context menu entries appear as they should and all are functioning as expected. Additionally, the "View Read Sequence" option only appears when one read is selected and is disabled when multiple reads are selected, as expected. Since this issue is resolved, it will now be closed.

            People

            • Assignee:
              mason Mason Meyer (Inactive)
              Reporter:
              mason Mason Meyer (Inactive)
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              Dates

              • Created:
                Updated:
                Resolved: