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  1. IGB
  2. IGBF-1424

Investigate: Can we enable IGB to show a genome from Quickload even if annots.xml is not available?

        Details

        • Type: Improvement
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Winter 2018 Sprint 1, Winter 2018 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov

          Description

          Sometimes we have a genome sequence available but no annotation files.
          In such a case, it makes sense to provide the sequence (2bit) file, the genome.txt file, but not the annots.xml file, since the annots.xml file would contain no files.
          However, IGB gives an error if there is no annots.xml file to load.
          Change this so that if a Quickload genome directory lacks an annots.xml file, IGB can still show the genome sequence and load files from the users desktop.

          To do this task, you will need to dig into the DataProviders system. You will need to understand what happens when a Quickload site's genome directory is accessed.

          To get familiar with it,

          • review the Quickload documentation on wiki.transvar.org
          • search and review previous Quickload-related issues in Jira

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              5 older comments
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              ann.loraine Ann Loraine added a comment -

              Please see comment on your branch

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              ann.loraine Ann Loraine added a comment - Please see comment on your branch
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              prutha Prutha Kulkarni (Inactive) added a comment -

              Prof. [~aloraine], I have made the changes to the branch which can be found at.
              https://bitbucket.org/pkulka10/igb_prutha/branch/IGBF-1424#diff
              Space changes were not needed exactly.

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              prutha Prutha Kulkarni (Inactive) added a comment - Prof. [~aloraine] , I have made the changes to the branch which can be found at. https://bitbucket.org/pkulka10/igb_prutha/branch/IGBF-1424#diff Space changes were not needed exactly.
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              ann.loraine Ann Loraine added a comment -

              Please submit PR. Thank you!

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              ann.loraine Ann Loraine added a comment - Please submit PR. Thank you!
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              prutha Prutha Kulkarni (Inactive) added a comment -

              [~aloraine], a PR submitted for the same.
              Changes are present at:
              https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/752/igbf-1424-enable-igb-to-show-a-genome-from/diff
              Could you please merge it into the master?

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              prutha Prutha Kulkarni (Inactive) added a comment - [~aloraine] , a PR submitted for the same. Changes are present at: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/752/igbf-1424-enable-igb-to-show-a-genome-from/diff Could you please merge it into the master?
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              pbole Pawan Bole (Inactive) added a comment -

              Validated the following scenarios:
              1) Without annots.xml
              2) Empty annots.xml
              3) Malformed annots.xml

              For the above three scenarios, it is working as expected loading blank screen.

              Show
              pbole Pawan Bole (Inactive) added a comment - Validated the following scenarios: 1) Without annots.xml 2) Empty annots.xml 3) Malformed annots.xml For the above three scenarios, it is working as expected loading blank screen.

                People

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

                  Dates

                  • Created:
                    Updated:
                    Resolved: