Details
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Type:
Task
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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:2
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Epic Link:
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Sprint:Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15
Description
Add a button to the manual trackhub-converter page to hit the "Add Data Source" endpoint in IGB. Parameters required for the request:
1) quickloadurl (eg. https://translate.bioviz.org/api/?hubUrl=https://raw.githubusercontent.com/mhalushka/miROme/main/UCSC/hub.txt&filePath=/) and 2) quickloadname: short label in the hubUrl file (use the hubUrl in the above link to see a short label example)
Use the following endpoint: http://127.0.0.1:7085/igbDataSource for the request call.
Attachments
Issue Links
Activity
Changes are deployed to bioviz main site. Ready for testing.
Dr. [~aloraine] - Changes have been made to resolve the above issue and pull request submitted.
Pull request: https://bitbucket.org/lorainelab/bioviz/pull-requests/102
Karthik Raveendran - Can you check the commits for IGBF-3147 - https://bitbucket.org/lorainelab/bioviz/commits/
It looks like the pull request that was merged into master included a revert of the code changes?
When I test https://www.bioviz.org/public-trackhubs.html I'm not seeing the most recent changes.
Master branch is built and ready for testing.
For the manual trackhub converter page, the 'Add Data Source to IGB' button and the method has been implemented. The button appears only after the UCSC trackhub is converted and the quickload data source URL is copied from the result for the 'quickloadurl' parameter. For the 'quickloadname' parameter, the UCSC trackhub url is called and the 'shortLabel' is used. Thus, the 'add data source' endpoint URL is built.
However, when the igbDataSource endpoint is hit, I run into an error in IGB:
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: genomeVersionNamePrefix is a required field.
When sample parameters are used(like "bioviz.org" and "karthik" for quickloadurl and quickloadname respectively) right after the 'built' URL above is called, both data sources are added to IGB.
See Nowlan Freese comments in IGBF-3131 where a list of testing issues are mentioned, Issue 2 "Invalid quickload (incorrect URL that returns HTML) "
For public trackhub page, I assume that the same error will appear. A design for 'Add Data Source' button needs to finalized as well.
Tested https://www.bioviz.org/public-trackhubs.html using MacOS 12.5 with Firefox and IGB master as of August 23, 2022.
Reset IGB preferences to default and remove the .igb folder.
Tested the Add Hub to IGB and Open in IGB buttons/links on the Breast Cancer lncRNA hub. The data source was successfully added to IGB and the genome was loaded, respectively. I was able to load and view data. All other links worked correctly.
Toasts appeared when the appropriate button/link was clicked. However, I would like to improve the toast messages and have created a new ticket (
IGBF-3164).Closing ticket.