Details
-
Type:
Bug
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:1
-
Epic Link:
-
Sprint:Spring 2, Spring 3, Spring 4
Description
The UCSC track data hubs to IGB quickload converter is currently not working with the newest version of IGB (10.0.0). I've confirmed that it does work with the previous version (9.1.10). Similarly, adding a public UCSC track hub to IGB from this https://bioviz.org/public-trackhubs.html webpage using the "+" button doesn't work either.
The error in both cases reads: Could not add to IGB. Please update IGB to latest version.
Attachments
Activity
Tested locally on Mac with 9.1.4 and 9.1.10 and 10.0.0, no issues found.
Change request:
- Please issue PR to a different target: branch "main" (master branch is no longer the main branch)
Thanks Karthik Raveendran!
PR is merged.
For testing, we'll need to use a new test server that I have not yet set up. I'll post here again when the testing site is ready.
Assigning this ticket to me so that it's more clear that I still need to do a thing before the new code can be tested and ticket closed.
Test server is now available.
Tested on Mac using IGB 10.0.0 early access.
The test page for bioviz.org (https://biovizubuntutest.bioviz.org/public-trackhubs.html) is working correctly, I am able to add the trackhub to IGB as a new data source.
The converter page (https://translate.bioviz.org/) will need to be updated (this page is hosted separately from bioviz.org). Looks like the change should be made here -> https://bitbucket.org/lorainelab/hub-facade/src/main/igb_trackhub/ui/static/js/manualConverter.js
Changes implement: PR Submitted https://bitbucket.org/lorainelab/hub-facade/pull-requests/32
The code change looks good.
Ready for pull request.
Proceeding to deploy changes for testing.
Deployed changes:
- Changed into ansible-playbooks directory of cloned hub-facade repository
- Updated code with:
ansible-playbook -i inventory.ini setup.yml
using inventory file:
[hub_facade_hosts] translate ansible_host=3.213.48.139 domain=translate.bioviz.org secret_key=dkasdkhjwns igb_repository=https://bitbucket.org/lorainelab/integrated-genome-browser/ igb_branch=master quickload_contents_txt=http://igbquickload.org/quickload/contents.txt stack=Prod [hub_facade_hosts:vars] ansible_ssh_common_args="-o StrictHostKeyChecking=no" ansible_python_interpreter=/usr/bin/python3
Changes should now be deployed and are ready for testing.
cc:
Testing on Mac
https://translate.bioviz.org/ - Working correctly on main-JDK21-with-javafx-no-theme and IGB 9.1.10
https://biovizubuntutest.bioviz.org/public-trackhubs.html - Working correctly on main-JDK21-with-javafx-no-theme and IGB 9.1.10
Final step is to deploy changes to bioviz.org
Tested on newly deployed https://www.bioviz.org/public-trackhubs.html - everything working correctly, able to add public hubs as new data sources to IGB on 9.1.10 and 10.0.0
Closing ticket.
When we made the changes to IGB in 9.1.10 to accept trackhub requests we added a condition to the bioviz code base to check versions: any version below 9.1.10 would send a toast to user saying, "Could not add to IGB. Please update IGB to latest version.". However, the condition was incomplete and only checked the if the last part of the version is less than 10 and disregards the rest of the version. The new changes to bioviz has the complete conditional statement for the version. See commit
As this is a small change, I have also created the PR: https://bitbucket.org/lorainelab/bioviz/pull-requests/124