Mouse hover/mouse click doesn't work for certain tracks

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Mouse hover/mouse click doesn't work for certain tracks

Prem Anand
HI

We recently upgraded our gbrowse version from 2.38 to 2.54, with fcgi enabled.

We used to link out some of our tracks to external sites (eg: RefSeq) ie when we mouse hover, we display the title with name: start..end and upon clicking the same track, we link out to external site. 

We noticed that this is not working for certain tracks after the upgrade.  In our configuration file, we have defined the feature type:source definition as 'feature = processed_transcript:RefSeq ' and as we also wanted to exclude certain feature types from our search results (ie don't show in the search result if the type is processed_transcript), we have added 'exclude types = processed_transcript' in our database definition file.

Reading through the change logs,  exclude types ([foo:database] exclude types = type1 type2 type3) was introduced in version 2.29. In v2.44 the way the Imagemap is generated was changed, 'time-consuming callbacks are only executed when mouse hovers or clicks on the feature'.

Had a look at the modules/logs and on mouse hover/mouse click the search routines are called correctly, fetches the results, and I guess at the end it was filtering for the features that we have excluded  (at RegionSearch.pm's filter_features routine). So we are not getting any result back and the links doesn't work. We can also restore to original behaviour by setting the "inline imagemap" to true for the tracks that we add 'exclude type' and the links on mouse hover/mouse clink works by doing so.

So my hunch is that call backs failure on mouse hover/mouse click for tracks that have "exclude type" defined in database_definition file is a side effect of the new feature introduced in v2.44. I may be wrong as well. Kindly excuse if so.

Wondering if anyone has had any similar issues and is it possible to have the links working without adding the inline imagemap option (for excluded types)?

Thanks
Prem



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Re: Mouse hover/mouse click doesn't work for certain tracks

Ioannis Kirmitzoglou
Hi Prem,

I recently upgraded from 2.38 to 2.55 and faced similar issues with mouse over and clicking on remote tracks. Apparently from 2.44 they changed the behavior of mouse over events, it uses AJAX now, and I found it to cause issues. The documentation says you can use inline_imagemaps =  1 to enable the old behavior but I still couldn't make it work. After many days of debugging and out of frustration I tried using the config flag without the underscore, so I used "inline imagemaps = 1" under the [TRACK DEFAULTS] section. Magically all my problems were gone. 

Cheers, 

Ioannis 

On 26 January 2015 at 17:20, Premanand Achuthan <[hidden email]> wrote:
HI

We recently upgraded our gbrowse version from 2.38 to 2.54, with fcgi enabled.

We used to link out some of our tracks to external sites (eg: RefSeq) ie when we mouse hover, we display the title with name: start..end and upon clicking the same track, we link out to external site. 

We noticed that this is not working for certain tracks after the upgrade.  In our configuration file, we have defined the feature type:source definition as 'feature = processed_transcript:RefSeq ' and as we also wanted to exclude certain feature types from our search results (ie don't show in the search result if the type is processed_transcript), we have added 'exclude types = processed_transcript' in our database definition file.

Reading through the change logs,  exclude types ([foo:database] exclude types = type1 type2 type3) was introduced in version 2.29. In v2.44 the way the Imagemap is generated was changed, 'time-consuming callbacks are only executed when mouse hovers or clicks on the feature'.

Had a look at the modules/logs and on mouse hover/mouse click the search routines are called correctly, fetches the results, and I guess at the end it was filtering for the features that we have excluded  (at RegionSearch.pm's filter_features routine). So we are not getting any result back and the links doesn't work. We can also restore to original behaviour by setting the "inline imagemap" to true for the tracks that we add 'exclude type' and the links on mouse hover/mouse clink works by doing so.

So my hunch is that call backs failure on mouse hover/mouse click for tracks that have "exclude type" defined in database_definition file is a side effect of the new feature introduced in v2.44. I may be wrong as well. Kindly excuse if so.

Wondering if anyone has had any similar issues and is it possible to have the links working without adding the inline imagemap option (for excluded types)?

Thanks
Prem



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Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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--
Ioannis Kirmitzoglou, PhD
Bioinformatician
Postdoctoral Researcher at the Vector Immunogenomics and Infection Laboratory (VigiLab)
Imperial College London
Sir Alexander Fleming Building South, Kensington Campus, London SW7 2AZ, UK 
www.vigilab.org, www.vectorbase.org

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hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: Mouse hover/mouse click doesn't work for certain tracks

Prem Anand
Thanks Loannis.   I also noticed other issues because of this new feature from 2.44.  When you randomly mousehover the tracks, lots of AJAX requests are fired and if you are behind a firewall, the requests may be blocked .

Glad it is working for you.  Yes, inline imagemap=1 or inline imagemaps=1 should work as mentioned in change logs 

Cheers
Prem

On Tue, Jan 27, 2015 at 12:10 PM, Ioannis Kirmitzoglou <[hidden email]> wrote:
Hi Prem,

I recently upgraded from 2.38 to 2.55 and faced similar issues with mouse over and clicking on remote tracks. Apparently from 2.44 they changed the behavior of mouse over events, it uses AJAX now, and I found it to cause issues. The documentation says you can use inline_imagemaps =  1 to enable the old behavior but I still couldn't make it work. After many days of debugging and out of frustration I tried using the config flag without the underscore, so I used "inline imagemaps = 1" under the [TRACK DEFAULTS] section. Magically all my problems were gone. 

Cheers, 

Ioannis 

On 26 January 2015 at 17:20, Premanand Achuthan <[hidden email]> wrote:
HI

We recently upgraded our gbrowse version from 2.38 to 2.54, with fcgi enabled.

We used to link out some of our tracks to external sites (eg: RefSeq) ie when we mouse hover, we display the title with name: start..end and upon clicking the same track, we link out to external site. 

We noticed that this is not working for certain tracks after the upgrade.  In our configuration file, we have defined the feature type:source definition as 'feature = processed_transcript:RefSeq ' and as we also wanted to exclude certain feature types from our search results (ie don't show in the search result if the type is processed_transcript), we have added 'exclude types = processed_transcript' in our database definition file.

Reading through the change logs,  exclude types ([foo:database] exclude types = type1 type2 type3) was introduced in version 2.29. In v2.44 the way the Imagemap is generated was changed, 'time-consuming callbacks are only executed when mouse hovers or clicks on the feature'.

Had a look at the modules/logs and on mouse hover/mouse click the search routines are called correctly, fetches the results, and I guess at the end it was filtering for the features that we have excluded  (at RegionSearch.pm's filter_features routine). So we are not getting any result back and the links doesn't work. We can also restore to original behaviour by setting the "inline imagemap" to true for the tracks that we add 'exclude type' and the links on mouse hover/mouse clink works by doing so.

So my hunch is that call backs failure on mouse hover/mouse click for tracks that have "exclude type" defined in database_definition file is a side effect of the new feature introduced in v2.44. I may be wrong as well. Kindly excuse if so.

Wondering if anyone has had any similar issues and is it possible to have the links working without adding the inline imagemap option (for excluded types)?

Thanks
Prem



------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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--
Ioannis Kirmitzoglou, PhD
Bioinformatician
Postdoctoral Researcher at the Vector Immunogenomics and Infection Laboratory (VigiLab)
Imperial College London
Sir Alexander Fleming Building South, Kensington Campus, London SW7 2AZ, UK 
www.vigilab.org, www.vectorbase.org



--
Favorite Quote:
"We all have two choices: We can make a living or we can design a life."

------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: Mouse hover/mouse click doesn't work for certain tracks

Ioannis Kirmitzoglou
Thanks Prem,

I was following the documentation instructions (http://gmod.org/wiki/GBrowse_2.0_HOWTO#Computed_Options) which says inline_imagemaps. If someone from the GMOD team is watching, please fix this.

Cheers,
Ioannis

On 27 January 2015 at 12:20, Premanand Achuthan <[hidden email]> wrote:
Thanks Loannis.   I also noticed other issues because of this new feature from 2.44.  When you randomly mousehover the tracks, lots of AJAX requests are fired and if you are behind a firewall, the requests may be blocked .

Glad it is working for you.  Yes, inline imagemap=1 or inline imagemaps=1 should work as mentioned in change logs 

Cheers
Prem

On Tue, Jan 27, 2015 at 12:10 PM, Ioannis Kirmitzoglou <[hidden email]> wrote:
Hi Prem,

I recently upgraded from 2.38 to 2.55 and faced similar issues with mouse over and clicking on remote tracks. Apparently from 2.44 they changed the behavior of mouse over events, it uses AJAX now, and I found it to cause issues. The documentation says you can use inline_imagemaps =  1 to enable the old behavior but I still couldn't make it work. After many days of debugging and out of frustration I tried using the config flag without the underscore, so I used "inline imagemaps = 1" under the [TRACK DEFAULTS] section. Magically all my problems were gone. 

Cheers, 

Ioannis 

On 26 January 2015 at 17:20, Premanand Achuthan <[hidden email]> wrote:
HI

We recently upgraded our gbrowse version from 2.38 to 2.54, with fcgi enabled.

We used to link out some of our tracks to external sites (eg: RefSeq) ie when we mouse hover, we display the title with name: start..end and upon clicking the same track, we link out to external site. 

We noticed that this is not working for certain tracks after the upgrade.  In our configuration file, we have defined the feature type:source definition as 'feature = processed_transcript:RefSeq ' and as we also wanted to exclude certain feature types from our search results (ie don't show in the search result if the type is processed_transcript), we have added 'exclude types = processed_transcript' in our database definition file.

Reading through the change logs,  exclude types ([foo:database] exclude types = type1 type2 type3) was introduced in version 2.29. In v2.44 the way the Imagemap is generated was changed, 'time-consuming callbacks are only executed when mouse hovers or clicks on the feature'.

Had a look at the modules/logs and on mouse hover/mouse click the search routines are called correctly, fetches the results, and I guess at the end it was filtering for the features that we have excluded  (at RegionSearch.pm's filter_features routine). So we are not getting any result back and the links doesn't work. We can also restore to original behaviour by setting the "inline imagemap" to true for the tracks that we add 'exclude type' and the links on mouse hover/mouse clink works by doing so.

So my hunch is that call backs failure on mouse hover/mouse click for tracks that have "exclude type" defined in database_definition file is a side effect of the new feature introduced in v2.44. I may be wrong as well. Kindly excuse if so.

Wondering if anyone has had any similar issues and is it possible to have the links working without adding the inline imagemap option (for excluded types)?

Thanks
Prem



------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Ioannis Kirmitzoglou, PhD
Bioinformatician
Postdoctoral Researcher at the Vector Immunogenomics and Infection Laboratory (VigiLab)
Imperial College London
Sir Alexander Fleming Building South, Kensington Campus, London SW7 2AZ, UK 
www.vigilab.org, www.vectorbase.org



--
Favorite Quote:
"We all have two choices: We can make a living or we can design a life."



--
Ioannis Kirmitzoglou, PhD
Bioinformatician
Postdoctoral Researcher at the Vector Immunogenomics and Infection Laboratory (VigiLab)
Imperial College London
Sir Alexander Fleming Building South, Kensington Campus, London SW7 2AZ, UK 
www.vigilab.org, www.vectorbase.org

------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse