Details
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Type:
Bug
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:1.5
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Epic Link:
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Sprint:Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19
Description
Error in working of search subsystems. When I search for DMD in the Quick-search box it is navigating to GSDMD instead of DMD. When I checked in the 9.1.4 version, the search for DMD is working fine.
To reproduce the issue
1)Open IGB and select Homo Sapiens genome.
2)Type "DMD" in the Quick-search box.
3)IGB is navigating to GSDMD instead of DMD.
This is working fine in IGB 9.1.4
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Assignee | Ann Loraine [ aloraine ] |
| Story Points | 1.5 |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
Nowlan Freese - if you are available, could you take a look?
| Assignee | Nowlan Freese [ nfreese ] |
9.1.6 is pulling the annotation from: http://lorainelab-quickload.scidas.org/quickload/H_sapiens_Dec_2013/H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz
9.1.4 is pulling the annotation from: http://igbquickload.org/quickload/H_sapiens_Dec_2013/H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz
The 9.1.6 annotation is the human annotation from October of 2020.
The 9.1.4 annotation is the human annotation from March of 2019.
Searching for DMD works correctly when the March 2019 annotation is used.
Searching for DMD does not work when the October 2020 annotation is used.
When I compared the files there are a few differences in the gene IDs, but I did not see anything that would explain why the quick search is behaving oddly. Would need to further investigate why these two files lead to this difference.
There does not appear to be any difference in the search functionality between 9.1.6 and 9.1.4.
| Attachment | H_sapiens_Dec_2013_ncbiRefSeqCurated_MARCH-2019.bed.gz [ 14967 ] | |
| Attachment | H_sapiens_Dec_2013_ncbiRefSeqCurated_MARCH-2019.bed.gz.tbi [ 14968 ] | |
| Attachment | H_sapiens_Dec_2013_ncbiRefSeqCurated_OCTOBER-2020.bed.gz [ 14969 ] | |
| Attachment | H_sapiens_Dec_2013_ncbiRefSeqCurated_OCTOBER-2020.bed.gz.tbi [ 14970 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Attachment | H_sapiens_Dec_2013_ncbiRefSeqCurated_MARCH-2019_SMALL.bed.gz [ 14973 ] | |
| Attachment | H_sapiens_Dec_2013_ncbiRefSeqCurated_MARCH-2019_SMALL.bed.gz.tbi [ 14974 ] | |
| Attachment | H_sapiens_Dec_2013_ncbiRefSeqCurated_OCTOBER-2020_SMALL.bed.gz [ 14975 ] | |
| Attachment | H_sapiens_Dec_2013_ncbiRefSeqCurated_OCTOBER-2020_SMALL.bed.gz.tbi [ 14976 ] |
| Summary | Error in navigation for Quick-Search Box | Investigate: Error in navigation for Quick-Search Box |
Updated igbquickload.org with the latest files from the subversion repository https://svn.bioviz.org/viewvc. After that doing, we observe identical behavior with 9.1.4 and 9.1.6. Next step: Create an "investigate" ticket to determine cause.
In a nutshell, the basic problem is that when a user enters DMD in the "Quick Search" box, two options appear: "GSDMD" and "DMD". When the user selects "DMD", IGB zooms-and-scrolls to the location of GSDMD and not DMD.
Why this is happening needs to be determined. Please see attached files.
| Fix Version/s | 9.1.6 Major Release [ 10604 ] | |
| Labels | Intermediate |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Fall 5 Nov 9 - Nov 20 [ 108 ] | Fall 6 Nov 23 - Dec 4 [ 109 ] |
| Sprint | Fall 6 Nov 30 - Dec 11 [ 109 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 109, 110 ] |
| Rank | Ranked higher |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 109, 110 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 109, 110, 111 ] |
| Rank | Ranked higher |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 109, 110, 111 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 109, 110 ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 109, 110 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 2 Jan 11 - Jan 22 [ 109, 110, 112 ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 2 Jan 11 - Jan 22 [ 109, 110, 112 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5 [ 109, 110, 113 ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5 [ 109, 110, 113 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 109, 110, 113, 114 ] |
| Rank | Ranked higher |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 109, 110, 113, 114 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 109, 110, 113, 114, 115 ] |
| Rank | Ranked higher |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 109, 110, 113, 114, 115 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19 [ 109, 110, 113, 114, 116 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19 [ 109, 110, 113, 114, 116 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 1 Mar 22 - Apr 2 [ 109, 110, 113, 114, 116, 117 ] |
| Rank | Ranked higher |
| Assignee | Omkar Marne [ omarne ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Previous issues investigating search functionality in IGB:
https://jira.transvar.org/browse/IGBF-1096
https://jira.transvar.org/browse/IGBF-2032
| Rank | Ranked higher |
My observations on IGB 9.1.8:
I downloaded the attached annotation files from the ticket.
I selected Species as “Homo Sapiens” and Genome version as “H_sapien_2013”.
I unticked RefSeq curated tab under IGB Quickload in configure box menu.
I opened below files one by one.
When I selected "DMD" in quick search box for annotation files (Load mode as genome)
• H_sapiens_Dec_2013_ncbiRefSeqCurated_MARCH-2019.bed
• H_sapiens_Dec_2013_ncbiRefSeqCurated_MARCH-2019_SMALL.bed
In the advanced search box, IGB navigated to DMD as expected but
When I selected “DMD” in quick search box for annotation files (Load mode as genome)
• H_sapiens_Dec_2013_ncbiRefSeqCurated_OCTOBER-2020.bed
• H_sapiens_Dec_2013_ncbiRefSeqCurated_OCTOBER-2020_SMALL.bed
In the advanced search box, IGB navigated to GSDMD instead of DMD.
I will continue investigating in the code base of IGB quick search box for its odd behavior.
| Rank | Ranked higher |
As per Dr. Freese's guidance I investigated MapRangeBox.java file which is a code for quick search box of IGB. There are 6 search functions with different search criteria's for string . I think we can try altering those search criteria's to check if we are getting the expected results.
Dr. Loraine please suggest on the same.
| Rank | Ranked higher |
| Assignee | Omkar Marne [ omarne ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2 [ 109, 110, 113, 114, 116, 117 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 6 Mar 8 - Mar 19 [ 109, 110, 113, 114, 116 ] |
| Rank | Ranked higher |
| Rank | Ranked lower |
As per my observations I figured that ID - NM_004019.2 is unavailable in 9.1.6 for human genome.
[~aloraine] - Any suggestions?