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  1. IGB
  2. IGBF-3936

Test Data Provider and UCSC related issues

        Details

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

          Description

          Test Data Provider and UCSC related issues where that were fixed after the ensembl code was added in the new released IGB that doesn't have the code anymore.
          https://jira.bioviz.org/browse/IGBF-3926
          https://jira.bioviz.org/browse/IGBF-3920
          https://jira.bioviz.org/browse/IGBF-3921
          https://jira.bioviz.org/browse/IGBF-3584
          https://jira.bioviz.org/browse/IGBF-3853

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              jsirigin Jaya Sravani Sirigineedi added a comment - - edited

              Tested all the mentioned tickets in the description and found one issue for DAS provider which is mentioned in this ticket: https://jira.bioviz.org/browse/IGBF-3584. There are two issues mentioned in that ticket and the issue I am seeing for DAS is:

              Reproduce the issue:

              1. Add UCSC DAS as a custom data provider using this URL (https://genome.ucsc.edu/cgi-bin/das)
              2. Select the mouse genome.
              3. Select Available Data > UCSC (DAS) > refGene
              4. Click Load Data
              5. Change to the human genome.
              6. Select Available Data > UCSC (DAS) > refGene
              7. Click Load Data
              8. Go back to the mouse genome
              9. 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.
              Show
              jsirigin Jaya Sravani Sirigineedi added a comment - - edited Tested all the mentioned tickets in the description and found one issue for DAS provider which is mentioned in this ticket: https://jira.bioviz.org/browse/IGBF-3584 . There are two issues mentioned in that ticket and the issue I am seeing for DAS is: Reproduce the issue: Add UCSC DAS as a custom data provider using this URL ( https://genome.ucsc.edu/cgi-bin/das ) Select the mouse genome. Select Available Data > UCSC (DAS) > refGene Click Load Data Change to the human genome. Select Available Data > UCSC (DAS) > refGene Click Load Data Go back to the mouse genome 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.
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              jsirigin Jaya Sravani Sirigineedi added a comment -

              Fixed the issue by making the type variable unique as it's being used to set the method of a dataset which is important for displaying tracks, that variable has to be unique for each dataset and across genomes too. As this variable was set the same for both the human and mouse genomes, it's loading the human genome dataset in the mouse genome. I have tested the old IGB versions and this issue has been there from the start of DAS, it hasn't been introduced by any UCSC REST changes or any other fixes. Here is the updated code, tested and working as expected: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3936. Please review and let me know if there are any issues.

              Show
              jsirigin Jaya Sravani Sirigineedi added a comment - Fixed the issue by making the type variable unique as it's being used to set the method of a dataset which is important for displaying tracks, that variable has to be unique for each dataset and across genomes too. As this variable was set the same for both the human and mouse genomes, it's loading the human genome dataset in the mouse genome. I have tested the old IGB versions and this issue has been there from the start of DAS, it hasn't been introduced by any UCSC REST changes or any other fixes. Here is the updated code, tested and working as expected: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3936 . Please review and let me know if there are any issues.
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              nfreese Nowlan Freese added a comment - - edited

              I'm seeing a test failure in DASFeatureParserTest.testLinks while building IGB:

              DASFeatureParserTest.testLinks -- Time elapsed: 0.053 s <<< FAILURE!
org.opentest4j.AssertionFailedError: expected: <affyU133Plus2> but was: <https://genome.ucsc.edu/cgi-bin/das/hg18affyU133Plus2>

              Following the testing instructions above, the DAS refGene tracks no longer disappear when loading from two different genomes.

              Show
              nfreese Nowlan Freese added a comment - - edited I'm seeing a test failure in DASFeatureParserTest.testLinks while building IGB: DASFeatureParserTest.testLinks -- Time elapsed: 0.053 s <<< FAILURE! org.opentest4j.AssertionFailedError: expected: <affyU133Plus2> but was: <https: //genome.ucsc.edu/cgi-bin/das/hg18affyU133Plus2> Following the testing instructions above, the DAS refGene tracks no longer disappear when loading from two different genomes.
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              jsirigin Jaya Sravani Sirigineedi added a comment -

              Fixed the test case failure, here is the updated code: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3936.

              Show
              jsirigin Jaya Sravani Sirigineedi added a comment - Fixed the test case failure, here is the updated code: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3936 .
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              nfreese Nowlan Freese added a comment - - edited

              Tested using Sravani's branch on Mac.

              • Able to build branch locally with tests.
              • Following the testing instructions above, the DAS refGene tracks no longer disappear when loading from two different genomes.

              Ready for pull request to main branch and release-10.1.0

              Show
              nfreese Nowlan Freese added a comment - - edited Tested using Sravani's branch on Mac. Able to build branch locally with tests. Following the testing instructions above, the DAS refGene tracks no longer disappear when loading from two different genomes. Ready for pull request to main branch and release-10.1.0
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              jsirigin Jaya Sravani Sirigineedi added a comment -

              Created two PRs one for the release branch and the other for the main, the source branch is based on the release branch. Here are the PRs:
              https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1049
              https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1050

              Show
              jsirigin Jaya Sravani Sirigineedi added a comment - Created two PRs one for the release branch and the other for the main, the source branch is based on the release branch. Here are the PRs: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1049 https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1050
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              ann.loraine Ann Loraine added a comment - - edited

              Both PRs are merged.

              notes to: Nowlan Freese and Jaya Sravani Sirigineedi

              Show
              ann.loraine Ann Loraine added a comment - - edited Both PRs are merged. notes to: Nowlan Freese and Jaya Sravani Sirigineedi Delaying building installers for the main branch because we ought to increment its version code to avoid conflicts with release-10.1.0. New release-10.1.0 installers are built and in the Download section of team repository: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads .
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              nfreese Nowlan Freese added a comment - - edited

              Tested using installer for release-10.1.0 as well as main branch installer - the DAS refGene tracks no longer disappear when loading from two different genomes.

              Closing ticket.

              Show
              nfreese Nowlan Freese added a comment - - edited Tested using installer for release-10.1.0 as well as main branch installer - the DAS refGene tracks no longer disappear when loading from two different genomes. Closing ticket.

                People

                • Assignee:
                  jsirigin Jaya Sravani Sirigineedi
                  Reporter:
                  jsirigin Jaya Sravani Sirigineedi
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                    Updated:
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