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  1. IGB
  2. IGBF-3722

Fix Color By Property matching any part of numeric value

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Minor
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: 10.1.0
        • Labels:
          None

          Description

          Situation: While adding additional properties to the Color By feature in IGB (IGBF-3640) we found that the Color By > Property behaved oddly. For example, if no value is entered for the property > id then everything is counted as being a match. Or, for example, if an id contains the string AT1G29990 and the value searched for is AT1G2, then all annotations with AT1G2 would be identified.

          Task: Determine if this is the intended behavior. While this may make sense for searching for strings, it may be confusing for users with the expanded properties now including numeric values.

          To reproduce the issue:

          1. Start IGB
          2. Open the A_thaliana_Jun_2009 genome
          3. Right-click on the Araport track name
          4. Select Color By...
          5. In the Color By dropdown, select Property
          6. In the property dropdown, select id
          7. Enter a value of AT1G2
          8. Click OK

            Attachments

              Issue Links

              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3640 Expand color by and Filter by to include the props

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-3129 [ 21675 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3640 [ IGBF-3640 ]
                nfreese Nowlan Freese made changes -
                Description Situation: While adding additional properties to the Color By feature in IGB (IGBF-3640) we found that the Color By > Property behaved oddly. For example, if no value is entered for the property > id then everything is counted as being a match. Or, for example, if an id contains the string AT1G29990 and the value searched for is AT1G, then all annotations with AT1G would be identified.

                Task: Determine if this is the intended behavior. While this may make sense for searching for strings, it may be confusing for users with the expanded properties now including numeric values.                 		Situation: While adding additional properties to the Color By feature in IGB (IGBF-3640) we found that the Color By > Property behaved oddly. For example, if no value is entered for the property > id then everything is counted as being a match. Or, for example, if an id contains the string AT1G29990 and the value searched for is AT1G2, then all annotations with AT1G2 would be identified.

                Task: Determine if this is the intended behavior. While this may make sense for searching for strings, it may be confusing for users with the expanded properties now including numeric values.

                To reproduce the issue:
                # Start IGB
                # Open the A_thaliana_Jun_2009 genome
                # Right-click on the Araport track name
                # Select Color By...
                # In the Color By dropdown, select Property
                # In the property dropdown, select id
                # Enter a value of AT1G2
                # Click OK
                jsirigin Jaya Sravani Sirigineedi made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Sprint Summer 1 [ 195 ] Spring 10 [ 194 ]
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                jsirigin Jaya Sravani Sirigineedi added a comment - - edited

                Investigated the issue and fixed it for numeric values. Updated code is available at branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3722. Please review and let me know if there any issues.



                To Test:

                1. Build the jar file for the branch in your local or download the installer.
                2. Start the application, select any species, and select any one of the ucsc rest tracks that has extra properties (bed, bigBed, bedDetail, and bigGenePRed track types have extra properties).
                3. Load data for the track and right-click on the track name to see the options menu
                4. Click on Color by option and select property from the dropdown items
                5. Now, in the property dropdown list, you should be able to see the extra properties that are present in that track
                6. Select any property whose value is numeric
                7. Test the value by giving the exact number that any of the displayed annotations have, and giving part of the number and giving a number that none of the annotations have.
                Show
                jsirigin Jaya Sravani Sirigineedi added a comment - - edited Investigated the issue and fixed it for numeric values. Updated code is available at branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3722 . Please review and let me know if there any issues. To Test: Build the jar file for the branch in your local or download the installer. Start the application, select any species, and select any one of the ucsc rest tracks that has extra properties (bed, bigBed, bedDetail, and bigGenePRed track types have extra properties). Load data for the track and right-click on the track name to see the options menu Click on Color by option and select property from the dropdown items Now, in the property dropdown list, you should be able to see the extra properties that are present in that track Select any property whose value is numeric Test the value by giving the exact number that any of the displayed annotations have, and giving part of the number and giving a number that none of the annotations have.
                jsirigin Jaya Sravani Sirigineedi made changes -
                Attachment Screenshot 2024-05-13 at 4.05.08 PM.png [ 18381 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Attachment Screenshot 2024-05-13 at 4.07.11 PM.png [ 18382 ]
                Attachment Screenshot 2024-05-13 at 4.07.07 PM.png [ 18383 ]
                Attachment Screenshot 2024-05-13 at 4.06.46 PM.png [ 18384 ]
                Attachment Screenshot 2024-05-13 at 4.05.38 PM.png [ 18385 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Summary Investigate Color By Property matching any part of the string Fix Color By Property matching any part of numeric value
                Hide
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                nfreese Nowlan Freese added a comment -

                Tested on Mac using Sravani's branch.

                Color by... Property for numeric values now matches only exact values. Strings still match when only a partial match is found (after discussing with Sravani, we decided that this behavior is convenient for users).

                Ready for pull request.

                Show
                nfreese Nowlan Freese added a comment - Tested on Mac using Sravani's branch. Color by... Property for numeric values now matches only exact values. Strings still match when only a partial match is found (after discussing with Sravani, we decided that this behavior is convenient for users). Ready for pull request.
                nfreese Nowlan Freese made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                Hide
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                jsirigin Jaya Sravani Sirigineedi added a comment - - edited

                Raised the pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1011. Please review and let me know if there are any issues.

                Show
                jsirigin Jaya Sravani Sirigineedi added a comment - - edited Raised the pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1011 . Please review and let me know if there are any issues.
                jsirigin Jaya Sravani Sirigineedi made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment - - edited

                PR is merged. Installers are build and deployed to bioviz.org "early access" section for testing.

                Show
                ann.loraine Ann Loraine added a comment - - edited PR is merged. Installers are build and deployed to bioviz.org "early access" section for testing.
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
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                nfreese Nowlan Freese added a comment -

                Tested main branch installer on Mac.

                Color by... Property for numeric values now matches only exact values. Strings still match when only a partial match is found.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested main branch installer on Mac. Color by... Property for numeric values now matches only exact values. Strings still match when only a partial match is found. Closing ticket.
                nfreese Nowlan Freese made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 10.1.0 [ 11000 ]

                  People

                  • Assignee:
                    jsirigin Jaya Sravani Sirigineedi
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: