Balloon pop ups

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Balloon pop ups

Joachim Baran-3
Hello,

  Is there a way to debug why balloon pop ups do not show in my GBrowse instance?

  I changed the data source from Bio::DB::GFF to Bio::DB::SeqFeature::Store and the features themselves are rendering correctly. However, no matter what I do, I cannot get balloons to pop up.

  The balloon images are accessible via their static URIs.

  There are no errors in the JavaScript console.

  It looks like a request is never made to the server to show a pop up.

  I tried explicitly adding "balloon tips = 1" and "balloon hover = Test" to the "[GENERAL]" section, but even that does not make balloons to appear.

Thank you,
Joachim


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Re: Balloon pop ups

Scott Cain
Hi Joachim,

Strange; did you restart apache?  That's the first thing I would suggest.  Also, does it generate balloons for the configuration options on the upper left of the tracks (ie, all of the little red icons)?  If so, the debugging will probably move to BioGraphics code.

Scott



On Wed, Sep 18, 2013 at 10:47 AM, Joachim Baran <[hidden email]> wrote:
Hello,

  Is there a way to debug why balloon pop ups do not show in my GBrowse instance?

  I changed the data source from Bio::DB::GFF to Bio::DB::SeqFeature::Store and the features themselves are rendering correctly. However, no matter what I do, I cannot get balloons to pop up.

  The balloon images are accessible via their static URIs.

  There are no errors in the JavaScript console.

  It looks like a request is never made to the server to show a pop up.

  I tried explicitly adding "balloon tips = 1" and "balloon hover = Test" to the "[GENERAL]" section, but even that does not make balloons to appear.

Thank you,
Joachim


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Re: Balloon pop ups

Joachim Baran-3
Hi!

  Thanks for the quick reply!

On 18 September 2013 12:02, Scott Cain <[hidden email]> wrote:
Strange; did you restart apache?
  Yes. That is covered. I also checked that the shown contents are really being updated and not coming from a cache by adding a static description to features that I vary now and then.
 
Also, does it generate balloons for the configuration options on the upper left of the tracks (ie, all of the little red icons)?
  Yes. Balloons are shown for the little red icons as well as for the tracks in the track configuration panel.
 
If so, the debugging will probably move to BioGraphics code.
  Oh no...

Joachim


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Re: Balloon pop ups

Scott Cain
Oh, I was wrong about BioGraphics--the balloon code is all in GBrowse. 

A few more things:
* Check your apache access and error logs to see if you have any 400 errors associated with the balloons.

* Please send the GBrowse.conf and data source conf to the list.

Scott



On Wed, Sep 18, 2013 at 12:08 PM, Joachim Baran <[hidden email]> wrote:
Hi!

  Thanks for the quick reply!

On 18 September 2013 12:02, Scott Cain <[hidden email]> wrote:
Strange; did you restart apache?
  Yes. That is covered. I also checked that the shown contents are really being updated and not coming from a cache by adding a static description to features that I vary now and then.
 
Also, does it generate balloons for the configuration options on the upper left of the tracks (ie, all of the little red icons)?
  Yes. Balloons are shown for the little red icons as well as for the tracks in the track configuration panel.
 
If so, the debugging will probably move to BioGraphics code.
  Oh no...

Joachim




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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Balloon pop ups

Joachim Baran-3

On 18 September 2013 12:18, Scott Cain <[hidden email]> wrote:
Oh, I was wrong about BioGraphics--the balloon code is all in GBrowse. 
  Phew!
 
A few more things:
* Check your apache access and error logs to see if you have any 400 errors associated with the balloons.
  I do not see any errors, which I have to admit is a bit weird.
 
* Please send the GBrowse.conf and data source conf to the list.

  There might be a problem with our GBrowse/BioGraphics combo. I try to figure out which versions were installed, because I have not done that myself this time round. I think the "latest" versions were installed two/three weeks ago.

Joachim


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Re: Balloon pop ups

Scott Cain
Hi Joachim,

A few things, which may or may not be related to your balloon problem:

* Aggregators don't work with SeqFeature::Store; you should get rid of those lines.

* The "Deprecated Configuration" section at the bottom of the GBrowse.conf makes me a little concerned--I'm pretty sure you not allowed to have anything in the in the GBrowse.conf file below the data source definitions except data sources.  Of particular interest to me is that there is a "custom balloons" item there that might be causing trouble.

Scott



On Wed, Sep 18, 2013 at 12:35 PM, Joachim Baran <[hidden email]> wrote:

On 18 September 2013 12:18, Scott Cain <[hidden email]> wrote:
Oh, I was wrong about BioGraphics--the balloon code is all in GBrowse. 
  Phew!
 
A few more things:
* Check your apache access and error logs to see if you have any 400 errors associated with the balloons.
  I do not see any errors, which I have to admit is a bit weird.
 
* Please send the GBrowse.conf and data source conf to the list.

  There might be a problem with our GBrowse/BioGraphics combo. I try to figure out which versions were installed, because I have not done that myself this time round. I think the "latest" versions were installed two/three weeks ago.

Joachim




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Balloon pop ups

Joachim Baran-3
Hello,

On 18 September 2013 13:16, Scott Cain <[hidden email]> wrote:
A few things, which may or may not be related to your balloon problem:
  Okay, thank you. I will address these issues later.

  It looks like the balloon problem is related to the GBrowse version. Balloons work in our configuration with 2.43 and 2.54, but they do not work with version 2.55.

Joachim


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Re: Balloon pop ups

Scott Cain
Hi Joachim,

Do the balloons work with other data sources?  I just tried GBrowse 2.55 with the builtin yeast data sources and it works.

Scott



On Wed, Sep 18, 2013 at 2:38 PM, Joachim Baran <[hidden email]> wrote:
Hello,

On 18 September 2013 13:16, Scott Cain <[hidden email]> wrote:
A few things, which may or may not be related to your balloon problem:
  Okay, thank you. I will address these issues later.

  It looks like the balloon problem is related to the GBrowse version. Balloons work in our configuration with 2.43 and 2.54, but they do not work with version 2.55.

Joachim




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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