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: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
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Attachment | Screenshot 2024-01-24 at 16.08.11.png [ 18182 ] |
| Attachment | Screenshot 2024-01-24 at 16.08.25.png [ 18183 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Assignee | Paige Kulzer [ pkulzer ] |
Tested locally on Mac with 9.1.4 and 9.1.10 and 10.0.0, no issues found.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Karthik Raveendran [ karthik ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Change request:
- Please issue PR to a different target: branch "main" (master branch is no longer the main branch)
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
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.
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Spring 2 [ 186 ] | Spring 2, Spring 3 [ 186, 187 ] |
| Rank | Ranked higher |
Test server is now available.
| Assignee | Ann Loraine [ aloraine ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
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
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Changes implement: PR Submitted https://bitbucket.org/lorainelab/hub-facade/pull-requests/32
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
The code change looks good.
Ready for pull request.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Karthik Raveendran [ karthik ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Comment |
[ PR is merged.
To deploy, run playbooks with inventory file: {code} [hub_facade_hosts] prodhub1 ansible_host=54.145.113.158 domain=translate.bioviz.org secret_key=dkasdkhjwns igb_repository=https://bitbucket.org/lorainelab/integrated-genome-browser igb_branch=master quickload_contents_txt=http://www.igbquickload.org/quickload/contents.txt stack=Prod [hub_facade_hosts:vars] ansible_ssh_common_args="-o StrictHostKeyChecking=no" ansible_python_interpreter=/usr/bin/python3 ansible_ssh_user=ubuntu {code} ] |
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:
| Sprint | Spring 2, Spring 3 [ 186, 187 ] | Spring 2, Spring 3, Spring 4 [ 186, 187, 188 ] |
| Rank | Ranked higher |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
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
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Ann Loraine [ aloraine ] | Nowlan Freese [ nfreese ] |
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.
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
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