Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:2
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Epic Link:
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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
Attachments
Activity
I have made the necessary changes to quickload module for the same.
I would suggest that someone who has prior knowledge about how the genome is loaded into IGB and how annots.xml works, should pick this up for the review. This way they'll be able to figure out quickly if I have missed anything which should have been handled.
The branch code can be found at :
https://bitbucket.org/pkulka10/igb_prutha/src/IGBF-1424/
You can use "https://quickload-testing.s3.amazonaws.com/noAnnotsQL/" hosted file for testing.
Steps for testing:
1) Run IGB and open preferences.
2) Go to Data sources tab and add a new Data Source by copying "https://quickload-testing.s3.amazonaws.com/noAnnotsQL/" url to the textbox.
3) "E_unicornus" named species will appear under the Species dropdown present in the right panel in IGB. Select it.
4) Select a Genome version which is available for the species.
5) It does not have an annots.xml file still the genome will be shown with a blank screen and a co-ordinate axis on it.
I added a question about Exception handling on the fork. Please take a look Prutha Kulkarni
Prof. [~aloraine], I have replied to the comment. Moving the ticket to In progress for further modifications.
Thanks.
Prof. [~aloraine], I have made the necessary changes and pushed those to the same branch. Also, I've improved the function validateURL a bit. Could you please have a look at those changes ?
Let me know if this is what you meant.
Changes can be found at:
https://bitbucket.org/pkulka10/igb_prutha/commits/d7aea8474f55848ea9a2cd3d0909e8d77b47dc0f
Thanks.
Please see comment on your branch
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.
Please submit PR. Thank you!
[~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?
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.
Example quickload site with empty annots.xml file in A_thaliana_Jun_2009 genome directory: http://igbquickload.org/smokeTestingQuickload/