Details
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Type:
Bug
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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 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8
Description
The track hub named "ENCODE RNA" declares that it has data for human genome version hg38 (aka H_sapiens_Dec_2013), and the Track Hub Facade creates an IGB Quickload URL for it, but when the Quickload URL is added to IGB, the data sources does not show a folder for it.
The converted URL:
To see the list of available genome versions on this hub, see:
Attachments
Issue Links
- relates to
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IGBF-2944 Update annots.xml url validation and filetype determination for trackhubs
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- Closed
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Activity
PR for IGBF-2944 submitted.
PRs are all merged and the new track hub facade back end code is deployed to the "back end" site used by BioViz.org. You can test the track hub functionality by visiting the main bioviz.org Web site and clicking the link in the middle part of the end of the page. From there, you can convert sites and try them out in the new IGB version.
Philip Badzuh - the server for https://api.wenglab.org/screen_v13/hubs/rna22/hub.txt seems to be down. Is there another example I can use for testing?
Seems to be up now.
In case it goes down again, to test the first commit any converted trackhub URL that has an unsecured/http protocol can be used e.g. this one.
The issue was that the annots.xml validation was not very robust - the presence of 'https' or 'http' was checked for in the data source URL, however, since multiple protocols are present in converted trackhub quickloads, this led to issues. Now the first and actual protocol of the data source is being checked.
Regarding the second commit, I am not sure if there are any other data files in any trackhub's annots.xml that have query parameters. You may have to catch the ENCODE RNA server being up.
I was able to test using the URL: https://translate.bioviz.org/rest_api/?hubUrl=https://api.wenglab.org/screen_v13/hubs/rna22/hub.txt&fileName=/
Note that there is an issue where the protocol is not added to the translated track hub webpage (for example the url is missing https://). This prevents IGB from correctly adding the Quickload site. There appears to be some code to handle this on bioviz.org/trackhubs, but it appears to only work for localhost.
I was able to see the quickload folder for hg38 and mm10 as well as load data for both. I was unable to see the quickload folder for hg19. When I tried to reload the quickload the translate.bioviz.org server appeared to go down.
I am going to close this issue as the primary issues have been solved.
Some problem occurs with other track hubs, including GTEx Analysis Hub.