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  1. IGB
  2. IGBF-2878

Implement TrackHub Application 2 which is an endpoint for all the IGB requests.

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          3
        • Epic Link:
        • Sprint:
          Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9

          Description

          We need to implement a Django app that will extract the track hub link from the request and also the requested resource. The Django app will then use scripts written in ticket IGBF-2859 to return a correct response to IGB.

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              is blocked by

              Task - A task that needs to be done. IGBF-2875 Create contents.txt and genome.txt file using UCSC APIs

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2877 Create annot.xml file from track hub's trackDb.txt file

              • Major - Major loss of function.
              • Closed

                Activity

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                inaylor Irvin Naylor (Inactive) added a comment - - edited

                Review from both yesterday after Scrum and further local testing shows that everything looks good to merge and that everything is functioning as it should be. Chirag's pull request has been approved and merged to the main repository.

                https://bitbucket.org/Inaylor01/track-hub-converter-webapp/src/main/

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                inaylor Irvin Naylor (Inactive) added a comment - - edited Review from both yesterday after Scrum and further local testing shows that everything looks good to merge and that everything is functioning as it should be. Chirag's pull request has been approved and merged to the main repository. https://bitbucket.org/Inaylor01/track-hub-converter-webapp/src/main/
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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - - edited

                diff: https://bitbucket.org/chirag06/track-hub-converter-webapp/branch/IGBF-2878

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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - - edited diff: https://bitbucket.org/chirag06/track-hub-converter-webapp/branch/IGBF-2878
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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment -

                We can use swagger to create docs for the api:
                https://swagger.io/

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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - We can use swagger to create docs for the api: https://swagger.io/
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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment -

                Create a link manually for testing:
                http://127.0.0.1:8000/rest_api/?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt&fileName=/

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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - Create a link manually for testing: http://127.0.0.1:8000/rest_api/?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt&fileName=/
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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment -

                Currently we are parsing the trackdb file. We can also hit the following API to get the same data. The parsing script should become simple and clean.
                Link: https://api.genome.ucsc.edu/list/tracks?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ

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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - Currently we are parsing the trackdb file. We can also hit the following API to get the same data. The parsing script should become simple and clean. Link: https://api.genome.ucsc.edu/list/tracks?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ
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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment -

                The API does not parse fames and summary tags from trackdb file. Please go through the following link to understand about frames and summary.
                Link: https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html.

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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - The API does not parse fames and summary tags from trackdb file. Please go through the following link to understand about frames and summary. Link: https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html .

                  People

                  • Assignee:
                    chirag24 Chirag Chandrahas Shetty (Inactive)
                    Reporter:
                    chirag24 Chirag Chandrahas Shetty (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: