Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Minor
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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 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16, Spring 6 2022 Mar 14 - Mar 25
Description
A lot of Web sites are configured to redirect http to https for most URLs.
However, it is not clear how IGB handles this when accessing Quickload URLs.
For example, what happens if IGB tries to contact a site added to IGB as Quickload URL "http://example.com/quickload" and the server is configured to redirect request to "https://example.com/quickload" ?
Can IGB properly handle the redirect?
Please investigate.
Possible strategy:
- Add an all-new testing Quickload site to BioViz.org (e.g., http://bioviz.org/example_quickload), submit PR for the example and wait for it to merged and deployed
- Confirm that the redirection is working by opening the "contents.txt" URL in a browser (http://bioviz.org/example_quickload/contents.txt)
- Deactivate all current Quickload sites in IGB and then re-start IGB
- Next, add this new Quickload testing URL to IGB using protocol "http" as the quickload address
- Then try to open the genome from the testing site in IGB
- Report any errors observed.
Does IGB appear to be reading and using the testing quickload meta-data files to configure the genome?
Report on any errors.
Attachments
Issue Links
Activity
Please review or search the commit history of the bioviz.org git repository: https://bitbucket.org/lorainelab/bioviz/src/master/
Hello Dr. Loraine, I have created a sample example_quickload. Please find my PR : https://bitbucket.org/lorainelab/bioviz/pull-requests/86/igbf-2669-example-quicload
Change requests:
1) Change "example_genome" directory name to A_thaliana_Jun_2009
2) Move "example_quickload" to "htdocs/quickload"
3) Change name of "example_quickload" to "example"
4) Edit "annots.xml" to include only one file tag
5) Squash commits on the branch so that only the smaller version of annots.xml file does will get merged in
Hello Dr. [~aloraine] Please see the requested changes below.
https://bitbucket.org/lorainelab/bioviz/pull-requests/86/igbf-2669
Please get rid of initial commit that added enormous xml file to repo.
Hello Dr. Loraine
Please find my new pull request : https://bitbucket.org/lorainelab/bioviz/pull-requests/87/igbf-2669-new-sample-quickload
Thanks - looks good. Proceeding to merge.
New example quickload is deployed to https://www.bioviz.org/quickload/example/
Moving back to "to-do" for Omkar Marne to use the new quickload to test as noted in the Description.
New example quickload is deployed to https://www.bioviz.org/quickload/example/
Moving back to "to-do" for Omkar Marne to use the new quickload to test as noted in the Description.
Test results after adding above quickload as data source:
IGB won't allow http protocol as data source as the server is set to automatically redirect from http to https. If the user uses the http quickload url then IGB won't follow the redirect and the quickload will not be added.
Testing on a quickload hosted on bitbucket (which redirects from http to https as tested using Google Chrome and the contents.txt file) also fails to work in IGB if the quickload URL is set to http. Along with Omkar's testing it would appear that IGB does not follow the redirect from http to https for Quickloads.
Console logs:
10:18:29.900 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.0/
10:18:30.036 WARN o.l.i.quickload.util.QuickloadUtils - Could not read contents.txt from: http://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.0/contents.txt
10:18:30.037 WARN o.l.i.q.QuickloadDataProvider - Missing required quickload file, or could not reach source. This quickloak source will be disabled for this session.
10:18:30.069 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.0/synonyms.txt
10:18:30.101 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.0/species.txt
I have created a new ticket (IGBF-3103) to address the redirect issue.
Closing ticket.
Dr. [~aloraine] Do you have the reference links or previous tickets of adding new quickload site to bioviz.org?