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:1
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Epic Link:
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Sprint:Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar
Description
When a user opens the Xenopus tropicalis genome, several popups appear that say:
"The file contains data for too many seuence; some may not be shown."
Do not show this message.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Rank | Ranked higher |
| Sprint | Spring 3 : 17 Feb to 21 Feb [ 87 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Summary | Fix: ERROR message about two many sequences | Fix: ERROR message about too many sequences |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Thank you!
I just reviewed the changes that are made for the same in order to remove the error panel that was showing message: "The file contains data for too many sequences; some may not be shown. If this is a problem, please compress and index the file using tabix.". A logger is added instead of the error panel which is showing the same message in the console.
I have also tested it with IGB and it looks fine. Attaching screenshot for the reference.
Please submit a PR for the same.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Attachment | Screen Shot 2020-02-20 at 11.54.43 AM.png [ 14642 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Prutha Kulkarni [ prutha ] | Nowlan Freese [ nfreese ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
Merged and ready for testing.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Sprint | Spring 3 : 17 Feb to 28 Feb [ 87 ] | Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 87, 89 ] |
| Rank | Ranked higher |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Ann Loraine [ aloraine ] | Noor Zahara [ noor91zahara ] |
It works as expected. No pop-up is shown with the error but is logged on the consoled.
| Assignee | Noor Zahara [ noor91zahara ] | Nowlan Freese [ nfreese ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Branch with changes: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2270-manySeqMessage
To test:
In IGB, open Xenopus tropicalis Nov 2009. The console should log the warning:
"The file contains data for too many sequences; some may not be shown. If this is a problem, please compress and index the file using tabix."
No popups regarding the warning should occur.
I changed the handling of the issue so that instead of presenting the user with a popup it is logged to the console.
There seems to be several things going on with this issue.
1) The X tropicalis Nov 2009 refgene file (X_tropicalis_Nov_2009_refGene.bed.gz) is gzipped, but does not have a tabix index.
2) This issue is related to https://jira.transvar.org/browse/IGBF-33. However,
IGBF-33did not fully address the original issue, which was meant to be addressed by additional refactoring that never occurred (https://jira.transvar.org/browse/DB-166).