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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

        Issue Links

          Activity

          Hide
          aloraine Ann Loraine added a comment - - edited

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

          Show
          aloraine Ann Loraine added a comment - - edited To start, turned off tests in DasDataProviderTest. Committed to master branch.
          Hide
          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
          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
          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
          Show
          prutha Prutha Kulkarni (Inactive) added a comment - Dr. Ann Loraine Pull request has been submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/813/igbf-2474-remove-das-v1-support/diff
          Hide
          aloraine Ann Loraine added a comment - - edited

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

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

          Request for Prutha Kulkarni:

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

          Show
          aloraine Ann Loraine added a comment - Request for Prutha Kulkarni : Could you provide a little more detail on specifics of testing?
          Hide
          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
          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:
              aloraine Ann Loraine
            • Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved:

                Development

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