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  1. IGB
  2. IGBF-3503 Implement UCSC REST API logic in IGB
  3. IGBF-3542

Implement an API to get the chromosomes for a selected genome

        Details

        • Type: Sub-task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: 10.1.0
        • Labels:
          None
        • Story Points:
          2
        • Sprint:
          Fall 7, Fall 8, Spring 1, Spring 2, Spring 3

          Description

          Develop code to connect to the https://api.genome.ucsc.edu/list/chromosomes?genome=hg38 API and get the chromosomes for a selected genome

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              jsirigin Jaya Sravani Sirigineedi added a comment -

              Developed the code to integrate the API and get the chromosomes for the selected genome. Testing is in progress.

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              jsirigin Jaya Sravani Sirigineedi added a comment - Developed the code to integrate the API and get the chromosomes for the selected genome. Testing is in progress.
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              jsirigin Jaya Sravani Sirigineedi added a comment - - edited

              Tested the code, working as expected. Able to see the chromosomes list for the selected genome. Code is available at branch https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501
              To test:

              1. Download https://bitbucket.org/jaya-sravani/integrated-genome-browser/downloads/ installer or clone this branch to local https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501 and start the application.
              2. Select a particular genome, preferably one that doesn't have data in IGB quick load.
              3. See whether Chromosomes are visible in the Current Genome side panel.
              Show
              jsirigin Jaya Sravani Sirigineedi added a comment - - edited Tested the code, working as expected. Able to see the chromosomes list for the selected genome. Code is available at branch https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501 To test: Download https://bitbucket.org/jaya-sravani/integrated-genome-browser/downloads/ installer or clone this branch to local https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501 and start the application. Select a particular genome, preferably one that doesn't have data in IGB quick load. See whether Chromosomes are visible in the Current Genome side panel.
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              nfreese Nowlan Freese added a comment -

              Testing on Mac:

              1. Cloned Sravani's IGBF-3501 branch and started IGB.
              2. Disabled all data providers except for UCSC REST in the Data Sources tab.
              3. Selected the galGal6 genome (the galGal6 genome is available from UCSC but we do not have it in IGB Quickload).
              4. The chromosomes and their lengths are visible.
              5. There are no errors in the IGB logs.
              Show
              nfreese Nowlan Freese added a comment - Testing on Mac: Cloned Sravani's IGBF-3501 branch and started IGB. Disabled all data providers except for UCSC REST in the Data Sources tab. Selected the galGal6 genome (the galGal6 genome is available from UCSC but we do not have it in IGB Quickload). The chromosomes and their lengths are visible. There are no errors in the IGB logs.
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              jsirigin Jaya Sravani Sirigineedi added a comment -

              As discussed, closing this ticket because the data loading part is not implemented yet, will be done as part of this https://jira.bioviz.org/browse/IGBF-3528 subtask.

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              jsirigin Jaya Sravani Sirigineedi added a comment - As discussed, closing this ticket because the data loading part is not implemented yet, will be done as part of this https://jira.bioviz.org/browse/IGBF-3528 subtask.

                People

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

                  • Created:
                    Updated:
                    Resolved: