[IGBF-3029] CLONE - Bug when browsing genome file - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Blocker
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
- collector-b04cfbf9

Story Points:
0.5
Epic Link:
Improve IGB for users
Sprint:
Fall 9 2021 Dec 13 - Dec 24

Description

A user reported the following problem:

After click in the browse button to open a genome file the program freezes and you have to force quit (OSX - 10.15.7)

Reporter: Carlos Lax
E-mail: carlos.lax@um.es

For this task, check that it is still possible to browse and open a genome file. Also, contact the user and ask if you can get access to the genome file they were trying to open.

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igbman-852091-151221-1548-17.pdf
236 kB
15/Dec/21 10:48 AM
screenshot-1.png
97 kB
14/Dec/21 2:50 PM

Issue Links

clones

HELP-378 Bug when browsing genome file

To-Do

Activity

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Ann Loraine created issue - 14/Dec/21 11:26 AM

Ann Loraine made changes - 14/Dec/21 11:26 AM

Field	Original Value	New Value
Link		This issue clones HELP-378 [ HELP-378 ]

Ann Loraine made changes - 14/Dec/21 11:26 AM

Project	User Support [ 10740 ]	IGB [ 10840 ]
Key	~~HELP-379~~	~~IGBF-3029~~
Issue Type	Bug [ 1 ]	Task [ 3 ]

Ann Loraine made changes - 14/Dec/21 11:27 AM

Description

After click in the browse button to open a genome file the program freezes and you have to force quit (OSX - 10.15.7)

*Reporter*: Carlos Lax
*E-mail*: [mailto:carlos.lax@um.es]

A user reported the following problem:

??After click in the browse button to open a genome file the program freezes and you have to force quit (OSX - 10.15.7)

*Reporter*: Carlos Lax
*E-mail*: [mailto:carlos.lax@um.es]??

Ann Loraine made changes - 14/Dec/21 11:28 AM

Description

A user reported the following problem:

{quote}
After click in the browse button to open a genome file the program freezes and you have to force quit (OSX - 10.15.7)

*Reporter*: Carlos Lax
*E-mail*: [mailto:carlos.lax@um.es]
{quote}

For this task, check that it is still possible to browse and open a genome file. Also, contact the user and ask if you can get access to the genome file they were trying to open.

Ann Loraine made changes - 14/Dec/21 11:29 AM

Epic Link

IGBF-1765 [ 17855 ]

Ann Loraine made changes - 14/Dec/21 11:29 AM

Story Points		0.5
Priority		Blocker [ 1 ]
Sprint		Fall 9 2021 Dec 13 - Dec 24 [ 135 ]

Ann Loraine made changes - 14/Dec/21 11:29 AM

Assignee

Ann Loraine [ aloraine ]

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Ann Loraine added a comment - 14/Dec/21 11:35 AM

Contacting the reporter to ask for access to the genome file:

Hello Dr. Lax,

Thank you for letting us know about the problem!

If possible, could you let us know the file you were trying to open? If we can get a copy of it, it will help us figure out what the problem is.

Warm regards,

Ann Loraine

cc: Omkar Marne

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Ann Loraine added a comment - 14/Dec/21 11:35 AM Contacting the reporter to ask for access to the genome file: Hello Dr. Lax, Thank you for letting us know about the problem! If possible, could you let us know the file you were trying to open? If we can get a copy of it, it will help us figure out what the problem is. Warm regards, Ann Loraine cc: Omkar Marne

Ann Loraine made changes - 14/Dec/21 11:37 AM

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Ranked higher

Omkar Marne (Inactive) made changes - 14/Dec/21 1:47 PM

Assignee

Omkar Marne [ omarne ]

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Ann Loraine added a comment - 14/Dec/21 1:59 PM - edited

User appears to be attempting to open a custom genome, as per the description in this help guide page:

https://wiki.bioviz.org/confluence/pages/viewpage.action?pageId=852091

Also, see the attached PDF (igbman-852091-151221-1548-17.pdf) with the above page from the user's guide.

Show

Ann Loraine added a comment - 14/Dec/21 1:59 PM - edited User appears to be attempting to open a custom genome, as per the description in this help guide page: https://wiki.bioviz.org/confluence/pages/viewpage.action?pageId=852091 Also, see the attached PDF (igbman-852091-151221-1548-17.pdf) with the above page from the user's guide.

Omkar Marne (Inactive) made changes - 14/Dec/21 2:50 PM

Attachment

screenshot-1.png [ 17022 ]

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Omkar Marne (Inactive) added a comment - 14/Dec/21 2:55 PM - edited

I tried opening A_thaliana_Jun_2009.2bit both locally and using its url: http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit. The file opened without any delay.
The sequence data was visible immediately after hitting Load sequence button.
Please see attached screenshot.

Dr. [~aloraine] Please specify the file name which the user is opening.

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Omkar Marne (Inactive) added a comment - 14/Dec/21 2:55 PM - edited I tried opening A_thaliana_Jun_2009.2bit both locally and using its url: http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit . The file opened without any delay. The sequence data was visible immediately after hitting Load sequence button. Please see attached screenshot. Dr. [~aloraine] Please specify the file name which the user is opening.

Omkar Marne (Inactive) made changes - 14/Dec/21 2:55 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Ann Loraine added a comment - 14/Dec/21 7:55 PM

Thank you Omkar Marne for looking into it.
I have emailed the user to ask for the file - see previous comment.
Please move this back to "To-Do" while we wait.

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Ann Loraine added a comment - 14/Dec/21 7:55 PM Thank you Omkar Marne for looking into it. I have emailed the user to ask for the file - see previous comment. Please move this back to "To-Do" while we wait.

Omkar Marne (Inactive) made changes - 15/Dec/21 10:44 AM

Assignee

Omkar Marne [ omarne ]

Ann Loraine [ aloraine ]

Omkar Marne (Inactive) made changes - 15/Dec/21 10:44 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

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Ann Loraine added a comment - 15/Dec/21 10:46 AM - edited

NF notes this could be a legit bug arising from changes made in the most recent release of IGB. Notes that many of these issues come from the user trying to load the wrong file format.

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Ann Loraine added a comment - 15/Dec/21 10:46 AM - edited NF notes this could be a legit bug arising from changes made in the most recent release of IGB. Notes that many of these issues come from the user trying to load the wrong file format.

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Ann Loraine added a comment - 15/Dec/21 10:47 AM - edited

Probably the user did not try to load a 2bit but was trying to load a fasta file. So we should test a fasta file.
cc: Omkar Marne

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Ann Loraine added a comment - 15/Dec/21 10:47 AM - edited Probably the user did not try to load a 2bit but was trying to load a fasta file. So we should test a fasta file. cc: Omkar Marne

Ann Loraine made changes - 15/Dec/21 10:48 AM

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igbman-852091-151221-1548-17.pdf [ 17028 ]

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Nowlan Freese added a comment - 15/Dec/21 11:47 AM

I tested a .fasta file created from the A_thaliana_Jun_2009.2bit file. There were no issues loading it as either the .fasta or as a .fasta.gz.

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Nowlan Freese added a comment - 15/Dec/21 11:47 AM I tested a .fasta file created from the A_thaliana_Jun_2009.2bit file. There were no issues loading it as either the .fasta or as a .fasta.gz.

Ann Loraine made changes - 16/Dec/21 1:10 PM

Assignee

Ann Loraine [ aloraine ]

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Ann Loraine added a comment - 16/Dec/21 1:10 PM

Closing for now. Will re-open if and when the user gets back to us with the requested info.

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Ann Loraine added a comment - 16/Dec/21 1:10 PM Closing for now. Will re-open if and when the user gets back to us with the requested info.

Ann Loraine made changes - 16/Dec/21 1:10 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 16/Dec/21 1:10 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Ann Loraine made changes - 16/Dec/21 1:10 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]