Reporting a number of issues

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Reporting a number of issues

kkarimi

Hi,

 

While trying to load a number of very small (10 to 20 lines) gff3 files into WebApollo 1.0.2, I noticed the following problems:

 

1)      If I load the file to display “WebApollo Features” (the default), it would show “loading” on the tracks but nothing would happen after that. The problem is that the code seems to fail to parse gff3 comments. I made the file load and display successfully by removing all comments except for the ubiquitous “##gff-version 3” comment. It would be great if the code could handle comment lines.

2)      If I loaded the file to display “WebApollo Sequences” (or anything other than features), nothing would display. The file name would be added to the local tracks list, but nothing would show up in the track area. The “Open files” window would not close either. Because the tack was not displayed, it is not possible to remove these tracks (the mechanism to delete a track depends on the track appearing in the right hand side track area, so a drop down menu is displayed with a “delete” option). This problem exists even after removing comment lines.

3)      If a track is deleted from the list of local tracks, the number of local tracks is not decreased.

 

I’ve attached one of the gff3 files to this email (contains the offending comment lines), and also included a snapshot to help make the report clearer.

 

 

 

-Kamran

 


tropsox6aa.gff3 (1K) Download Attachment
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Re: Reporting a number of issues

nathandunn

Thanks for reporting these.  Looks like they were all pre-existing errors (pre-1.0.2) as far as I can tell..  

> On Dec 2, 2014, at 1:59 PM, Kamran Karimi <[hidden email]> wrote:
>
> Hi,
>  
> While trying to load a number of very small (10 to 20 lines) gff3 files into WebApollo 1.0.2, I noticed the following problems:
>  
> 1)      If I load the file to display “WebApollo Features” (the default), it would show “loading” on the tracks but nothing would happen after that. The problem is that the code seems to fail to parse gff3 comments. I made the file load and display successfully by removing all comments except for the ubiquitous “##gff-version 3” comment. It would be great if the code could handle comment lines.

https://github.com/GMOD/Apollo/issues/98


> 2)      If I loaded the file to display “WebApollo Sequences” (or anything other than features), nothing would display. The file name would be added to the local tracks list, but nothing would show up in the track area. The “Open files” window would not close either. Because the tack was not displayed, it is not possible to remove these tracks (the mechanism to delete a track depends on the track appearing in the right hand side track area, so a drop down menu is displayed with a “delete” option). This problem exists even after removing comment lines.

https://github.com/GMOD/Apollo/issues/99

> 3)      If a track is deleted from the list of local tracks, the number of local tracks is not decreased.
>  
> I’ve attached one of the gff3 files to this email (contains the offending comment lines), and also included a snapshot to help make the report clearer.

https://github.com/GMOD/Apollo/issues/100

This may be a byproduct of the previous 2 bugs, not sure.  Not sure.  

Nathan

>  
> <image002.jpg>
>  
>  
> -Kamran
>  
> <tropsox6aa.gff3>


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Re: Reporting a number of issues

nathandunn

Kamran,

Fro eh GFF3 Import failure, if you have a specific use-case where this is failing, if you could attach it to this bug, that would be great.

e.g., Open as Web Apollo Feature  with a GFF3 (please add an attachment).


Thanks,

Nathan

On Dec 2, 2014, at 2:35 PM, Nathan Dunn <[hidden email]> wrote:


Thanks for reporting these.  Looks like they were all pre-existing errors (pre-1.0.2) as far as I can tell..  

On Dec 2, 2014, at 1:59 PM, Kamran Karimi <[hidden email]> wrote:

Hi,

While trying to load a number of very small (10 to 20 lines) gff3 files into WebApollo 1.0.2, I noticed the following problems:

1)      If I load the file to display “WebApollo Features” (the default), it would show “loading” on the tracks but nothing would happen after that. The problem is that the code seems to fail to parse gff3 comments. I made the file load and display successfully by removing all comments except for the ubiquitous “##gff-version 3” comment. It would be great if the code could handle comment lines.

https://github.com/GMOD/Apollo/issues/98


2)      If I loaded the file to display “WebApollo Sequences” (or anything other than features), nothing would display. The file name would be added to the local tracks list, but nothing would show up in the track area. The “Open files” window would not close either. Because the tack was not displayed, it is not possible to remove these tracks (the mechanism to delete a track depends on the track appearing in the right hand side track area, so a drop down menu is displayed with a “delete” option). This problem exists even after removing comment lines.

https://github.com/GMOD/Apollo/issues/99

3)      If a track is deleted from the list of local tracks, the number of local tracks is not decreased.

I’ve attached one of the gff3 files to this email (contains the offending comment lines), and also included a snapshot to help make the report clearer.

https://github.com/GMOD/Apollo/issues/100

This may be a byproduct of the previous 2 bugs, not sure.  Not sure.  

Nathan


<image002.jpg>


-Kamran

<tropsox6aa.gff3>