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  1. IGB
  2. IGBF-4108

Implement logic to load the genomes for GenArk

    Details

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

      Description

      Implement logic to load the GenArk genomes to IGB when the user clicks the Load button.

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          Activity

          Hide
          jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - - edited

          Completed the implementation and made a few changes that we discussed after the initial review. Here is the updated code:
          https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-4108
          https://bitbucket.org/jaya-sravani/ucsc-genark-data-provider/branch/IGBF-4108
          To test:

          • Pull both the branches into your local.
          • Build and run IGB from the given branch.
          • Build the ucsc-genark-data-provider service as well using "mvn clean install"
          • Now add the data provder as a plugin in IGB, while choosing the folder choose the generated target folder of the ucsc-genark-data-provider service.
          • Load any of the genomes from the table.
          • Review the pop-up window and the message it shows.
          • Check whether the genome is added as a Quickload with a prefix "GenArk_" in its name.
          • Check whether the genome is loaded into IGB. (there won't be any default dataset that will load but all the datasets should be shown under Available data and chromosomes should be loaded.)

          Please review the changes and let me know if there's any issue.

          Note: This ticket can be tested along with https://jira.bioviz.org/browse/IGBF-4167. PR for this is raised along with that ticket: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1069

          Show
          jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - - edited Completed the implementation and made a few changes that we discussed after the initial review. Here is the updated code: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-4108 https://bitbucket.org/jaya-sravani/ucsc-genark-data-provider/branch/IGBF-4108 To test: Pull both the branches into your local. Build and run IGB from the given branch. Build the ucsc-genark-data-provider service as well using "mvn clean install" Now add the data provder as a plugin in IGB, while choosing the folder choose the generated target folder of the ucsc-genark-data-provider service. Load any of the genomes from the table. Review the pop-up window and the message it shows. Check whether the genome is added as a Quickload with a prefix "GenArk_" in its name. Check whether the genome is loaded into IGB. (there won't be any default dataset that will load but all the datasets should be shown under Available data and chromosomes should be loaded.) Please review the changes and let me know if there's any issue. Note: This ticket can be tested along with https://jira.bioviz.org/browse/IGBF-4167 . PR for this is raised along with that ticket: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1069
          Hide
          nfreese Nowlan Freese added a comment - - edited

          Tested on Sravani's branch 4123 on Mac.

          • Popup appears when the "Load" button is clicked
          • The genome is added to the data provider with GenArk
          • IGB switches to the new genome
          • I can load data and sequence for the genome

          Ready for PR

          Show
          nfreese Nowlan Freese added a comment - - edited Tested on Sravani's branch 4123 on Mac. Popup appears when the "Load" button is clicked The genome is added to the data provider with GenArk IGB switches to the new genome I can load data and sequence for the genome Ready for PR
          Hide
          jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment -

          Raised a new PR for this as part of https://jira.bioviz.org/browse/IGBF-4123.

          Show
          jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - Raised a new PR for this as part of https://jira.bioviz.org/browse/IGBF-4123 .
          Hide
          ann.loraine Ann Loraine added a comment -

          Merged PR, built installers and deployed to Early Access section of BioViz.org.

          Show
          ann.loraine Ann Loraine added a comment - Merged PR, built installers and deployed to Early Access section of BioViz.org.
          Hide
          nfreese Nowlan Freese added a comment -

          Tested main branch on Mac:

          • Popup appears when the "Load" button is clicked
          • The genome is added to the data provider with GenArk
          • IGB switches to the new genome
          • I can load data and sequence for the genome

          Closing ticket.

          Show
          nfreese Nowlan Freese added a comment - Tested main branch on Mac: Popup appears when the "Load" button is clicked The genome is added to the data provider with GenArk IGB switches to the new genome I can load data and sequence for the genome Closing ticket.

            People

            • Assignee:
              jsirigin Jaya Sravani Sirigineedi (Inactive)
              Reporter:
              jsirigin Jaya Sravani Sirigineedi (Inactive)
            • Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: