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  1. IGB
  2. IGBF-3584

Fix UCSC data tracks disappearing

        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 testing IGBF-3528 we discovered that when the same UCSC REST or UCSC DAS track (for example, refGene) was loaded in two different genomes, the track would disappear.

          Task: Investigate this issue and propose a fix if possible.

          Note: This issue appears in 9.1.10 when loading UCSC DAS data as well as with the recent implementation of UCSC REST.

          To reproduce the issue:

          1. Select the mouse genome.
          2. Select Available Data > UCSC (DAS) > refGene
          3. Click Load Data
          4. Change to the human genome.
          5. Select Available Data > UCSC (DAS) > refGene
          6. Click Load Data
          7. Go back to the mouse genome
            1. The refGene added from UCSC should be missing from the Data Management Table. The data should still be present as a track, but grayed out as if it had not been loaded.

            Attachments

              Issue Links

              relates to

              Sub-task - The sub-task of the issue IGBF-3528 Implement logic to load data for genePred file type

              • 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-3528 [ IGBF-3528 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 3 [ 187 ] Spring 4 [ 188 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 4 [ 188 ] Spring 4, Spring 5 [ 188, 189 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Spring 4, Spring 5 [ 188, 189 ] Spring 4, Spring 6 [ 188, 190 ]
                nfreese Nowlan Freese made changes -
                Story Points 2 1
                nfreese Nowlan Freese made changes -
                Sprint Spring 4, Spring 6 [ 188, 190 ] Spring 4, Spring 7 [ 188, 191 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 4, Spring 7 [ 188, 191 ] Spring 4, Spring 8 [ 188, 192 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 4, Spring 8 [ 188, 192 ] Spring 4, Spring 9 [ 188, 193 ]
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Attachment Screenshot 2024-05-08 at 2.32.53 PM.png [ 18368 ]
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Attachment Screenshot 2024-05-08 at 2.33.14 PM.png [ 18369 ]
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Attachment Screenshot 2024-05-08 at 2.35.57 PM.png [ 18370 ]
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Attachment Screenshot 2024-05-08 at 2.36.28 PM.png [ 18371 ]
                Hide
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                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment -

                There are two issues mentioned in this ticket, I have investigated the first one. Steps to reproduce first issue are:

                1. Select any genome that has both UCSC DAS and UCSC REST Tracks available.
                2. Select the same track from both the data providers.
                3. Before implementing this ticket https://jira.bioviz.org/browse/IGBF-3703 while loading the empty tiers itself, only one track was visible, the other one would disappear as the tracks had the same names. However, after the implementation of that ticket, this issue was resolved as the track name was changed for the REST tracks.
                4. Clcik on the Load data button, now you will see one track has disappeared as the track name is being rewritten by some other method. This issue is fixed now. Updated code is available at branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3584. Tested and working as expected.
                  Screeshots before the fix:
                  Empty Tier Load

                  After load data

                  Screeshots after the fix:
                  Empty Tier Load

                  After load data
                Show
                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - There are two issues mentioned in this ticket, I have investigated the first one. Steps to reproduce first issue are: Select any genome that has both UCSC DAS and UCSC REST Tracks available. Select the same track from both the data providers. Before implementing this ticket https://jira.bioviz.org/browse/IGBF-3703 while loading the empty tiers itself, only one track was visible, the other one would disappear as the tracks had the same names. However, after the implementation of that ticket, this issue was resolved as the track name was changed for the REST tracks. Clcik on the Load data button, now you will see one track has disappeared as the track name is being rewritten by some other method. This issue is fixed now. Updated code is available at branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3584 . Tested and working as expected. Screeshots before the fix: Empty Tier Load After load data Screeshots after the fix: Empty Tier Load After load data
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 4, Spring 9 [ 188, 193 ] Spring 4, Spring 9, Spring 10 [ 188, 193, 194 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Tested on Mac with Sravani's branch.

                Both of the issues described in the description and Sravani's comment are fixed. Tracks are no longer greyed out when loading the same data set (UCSC REST) between two different genomes. If using DAS and UCSC REST the same datasets (for example, refGene) they no longer disappear.

                I'm unsure of why the getAnnotStyle in DataSet.java was originally being passed "method" twice. We had previously had some tickets looking into issues with how track names were being set (see IGBF-1933), but the code in Sravani's branch has not been modified since David worked on it. I tested BioViz Connect data, online Quickload data, local Quickload data, and local files and all of the track names appeared as I expected.

                Ready for pull request.

                Show
                nfreese Nowlan Freese added a comment - Tested on Mac with Sravani's branch. Both of the issues described in the description and Sravani's comment are fixed. Tracks are no longer greyed out when loading the same data set (UCSC REST) between two different genomes. If using DAS and UCSC REST the same datasets (for example, refGene) they no longer disappear. I'm unsure of why the getAnnotStyle in DataSet.java was originally being passed "method" twice. We had previously had some tickets looking into issues with how track names were being set (see IGBF-1933 ), but the code in Sravani's branch has not been modified since David worked on it. I tested BioViz Connect data, online Quickload data, local Quickload data, and local files and all of the track names appeared as I expected. 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
                Permalink
                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment -

                Pull request is raised: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1012. Please review and let me know if there are any issues.

                Show
                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - Pull request is raised: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1012 . Please review and let me know if there are any issues.
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                jsirigin Jaya Sravani Sirigineedi (Inactive) made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                nfreese Nowlan Freese made changes -
                Summary Investigate UCSC data tracks disappearing Fix UCSC data tracks disappearing
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Hide
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                ann.loraine Ann Loraine added a comment - - edited

                PR is merged. Installers are built and deployed to bioviz.org "early access" section.

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

                Tested using main branch installer on Mac.

                Loaded refGene track from UCSC REST and from DAS in the mouse genome. Neither track disappeared (correct behavior).
                Loaded refGene track from UCSC REST in mouse and then switched to human and loaded refGene from UCSC REST. When I returned to the mouse genome the track was not greyed out or removed (correct behavior).

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested using main branch installer on Mac. Loaded refGene track from UCSC REST and from DAS in the mouse genome. Neither track disappeared (correct behavior). Loaded refGene track from UCSC REST in mouse and then switched to human and loaded refGene from UCSC REST. When I returned to the mouse genome the track was not greyed out or removed (correct behavior). 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 (Inactive)
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: