Details
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Type:
New Feature
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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:None
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Story Points:1
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Epic Link:
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Sprint:Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24
Description
A method for determining whether or not a UCSC genome name can be mapped to an IGB genome version is needed in order to decide which genome versions in the trackhub table UI can be made to have the option of utilizing IGB's 'open genome' endpoint located at http://localhost:7085/IGBControl?version=GENOME. Since this functionality may be needed in future services, an endpoint can be added to the trackhub facade API that returns the primary IGB genome version name corresponding to the provided UCSC genome version. This can be accomplished by searching the master synonyms.txt in an attempt to find an entry that matches the UCSC genome name. The first entry of the corresponding row would then be returned as the primary IGB genome version name.
It may be useful to extend IGB's endpoint to also include an 'species' query parameter, which could allow users to open converted trackhubs whose genome versions do not map to those associated with an IGB-supported organism.
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Activity
Please review the changes linked to in my previous comment.
Changes are good! Please submit PR.
Great! Please see PR here.
Merged and deployed to back end site for testing: https://translate.bioviz.org. Ready for testing.
After performing the testing instructions from the read me the file I am getting the expected output.
While executing the URL I had to install Postman app desktop agent to display the POST method result on the localhost.
Please see screenshot 2.
Closing the ticket.
I started by implementing the endpoint to take a single UCSC genome and return the IGB equivalent, however, this would require many requests that would increase latency for the front-end.
As a second version, I updated the endpoint to take multiple UCSC genome versions for conversion.
In testing, there was a CORS issue, so I configured our django server to allow requests from all origins in the browser. We can update this to limit it to bioviz.org, if you see this as an issue, [~aloraine].