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  1. IGB
  2. IGBF-2474

Remove DAS v1 support (UCSC DAS v1 service not responding)

        Details

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

          Description

          The DAS (version 1) test that relies on this URL - http://genome.cse.ucsc.edu/cgi-bin/das/dsn - is now failing.

          We should remove this test or create a mock object that will allow the test of our code to proceed even if the data source is not available.

          However, since the UCSC DAS service is no longer actively supported at UCSC, we should eliminate it from the code base. The UCSC DAS1 server was the only DAS service available, so we should probably remove it from the code base.

          Note: Removing DAS1 support will affect many places in the code, notably:

          • Places where default data sources are configured - see IGB Preferences JSON file
          • DAS module itself: "Core - DAS (data source) module"
          • POM files that declare dependencies on the DAS module within IGB

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. HELP-370 UCSC

              • Blocker - Blocks development and/or testing work, production could not run.
              • Closed

              Task - A task that needs to be done. IGBF-2793 Restore DASv1 support

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2473 Remove DAS v2 code

              • Major - Major loss of function.
              • Closed

                Activity

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                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                To start, turned off tests in DasDataProviderTest. Committed to master branch.

                Show
                ann.loraine Ann Loraine added a comment - - edited To start, turned off tests in DasDataProviderTest. Committed to master branch.
                Hide
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                prutha Prutha Kulkarni (Inactive) added a comment -

                Update:
                When I removed the DAS plugin and related dependencies from the codebase, the IGB is throwing and exception whenever I am clicking on any Genome to load it.
                The exception screenshot is attached to the ticket.
                I am investigating the same right now. Looks like the data is not getting loaded after the removal of that dependency.
                I am checking the "GeneralLoadUtils" class for the same as it is responsible for loading the data into IGB.
                I would mostly continue to work on it tomorrow as I was not able to figure out the cause today.

                Show
                prutha Prutha Kulkarni (Inactive) added a comment - Update: When I removed the DAS plugin and related dependencies from the codebase, the IGB is throwing and exception whenever I am clicking on any Genome to load it. The exception screenshot is attached to the ticket. I am investigating the same right now. Looks like the data is not getting loaded after the removal of that dependency. I am checking the "GeneralLoadUtils" class for the same as it is responsible for loading the data into IGB. I would mostly continue to work on it tomorrow as I was not able to figure out the cause today.
                Hide
                Permalink
                prutha Prutha Kulkarni (Inactive) added a comment -

                The code changes are present at :
                https://bitbucket.org/pkulka10/igb_prutha/commits/704ebb7507a36fb3595f7d5b802c264e6d5b7fa0

                For testing:
                Go to the "Downloads" section of my fork and download IGBF-2474 branch installer.
                Check if the IGB is functioning properly after removing the DAS v1 support from the codebase.

                Show
                prutha Prutha Kulkarni (Inactive) added a comment - The code changes are present at : https://bitbucket.org/pkulka10/igb_prutha/commits/704ebb7507a36fb3595f7d5b802c264e6d5b7fa0 For testing: Go to the "Downloads" section of my fork and download IGBF-2474 branch installer. Check if the IGB is functioning properly after removing the DAS v1 support from the codebase.
                Hide
                Permalink
                shamika Shamika Gajanan Kulkarni (Inactive) added a comment -

                I have reviewed this ticket. Everything looks fine. Kindly submit a PR for the same Prutha Kulkarni

                Show
                shamika Shamika Gajanan Kulkarni (Inactive) added a comment - I have reviewed this ticket. Everything looks fine. Kindly submit a PR for the same Prutha Kulkarni
                Hide
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                prutha Prutha Kulkarni (Inactive) added a comment -

                Dr. [~aloraine]
                Pull request has been submitted:
                https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/813/igbf-2474-remove-das-v1-support/diff

                Show
                prutha Prutha Kulkarni (Inactive) added a comment - Dr. [~aloraine] Pull request has been submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/813/igbf-2474-remove-das-v1-support/diff
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                PR is merged.
                To test, please download master branch installer from the team bitbucket repository.

                Show
                ann.loraine Ann Loraine added a comment - - edited PR is merged. To test, please download master branch installer from the team bitbucket repository.
                Hide
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                ann.loraine Ann Loraine added a comment -

                Request for Prutha Kulkarni:

                Could you provide a little more detail on specifics of testing?

                Show
                ann.loraine Ann Loraine added a comment - Request for Prutha Kulkarni : Could you provide a little more detail on specifics of testing?
                Hide
                Permalink
                prutha Prutha Kulkarni (Inactive) added a comment - - edited

                Testing steps:

                • Go to the "Downloads" section of my fork and download IGBF-2474 branch installer or Master installer(since the code is merged).
                • Check if the IGB is functioning properly after removing the DAS v1 support from the codebase. Genomes should load properly.
                • Check if the name and url for DAS v1 has been removed from 'Data Sources' in IGB Preferences.
                • To check if the codebase doesn't have any DAS V1 related functionality, clone my IGB on your system. With the help of CTRL+SHIFT+F search "das" globally in the IGB project. The code should either be commented or removed. Check each and every file that shows up in the search results.
                Show
                prutha Prutha Kulkarni (Inactive) added a comment - - edited Testing steps: Go to the "Downloads" section of my fork and download IGBF-2474 branch installer or Master installer(since the code is merged). Check if the IGB is functioning properly after removing the DAS v1 support from the codebase. Genomes should load properly. Check if the name and url for DAS v1 has been removed from 'Data Sources' in IGB Preferences. To check if the codebase doesn't have any DAS V1 related functionality, clone my IGB on your system. With the help of CTRL+SHIFT+F search "das" globally in the IGB project. The code should either be commented or removed. Check each and every file that shows up in the search results.
                Hide
                Permalink
                shamika Shamika Gajanan Kulkarni (Inactive) added a comment -

                Tested this ticket as per the steps mentioned above. Everything is working as expected. Moving to closed.

                Show
                shamika Shamika Gajanan Kulkarni (Inactive) added a comment - Tested this ticket as per the steps mentioned above. Everything is working as expected. Moving to closed.

                  People

                  • Assignee:
                    prutha Prutha Kulkarni (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: