[Gmod-ajax] capability equivalent to remote feature track in Gbrowse?

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[Gmod-ajax] capability equivalent to remote feature track in Gbrowse?

dmgood11
Hi All,

  We're in the middle of converting our GBrowse installations to JBrowse, and need to retain our ability to show user BLAST results in the genome browser.  We currently do that in GBrowse with remote feature tracks, configured as:

[UserBlast]
stranded = 1
remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid') ;return "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
balloon hover =
link =


This searches a user- and session-specific directory for BLAST output files, converts them to GFF on the fly, and displays them in the track UserBlast.  

Is there an equivalent capability in JBrowse, assuming we had already converted our BLAST results to JSON?

thx,

-David


David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley


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Re: capability equivalent to remote feature track in Gbrowse?

Suzanna Lewis
Hi David,

Would BLAT be an acceptable substitute? We've got that working for Apollo and it shouldn't require too much effort to push back into the main branch of JBrowse.

-S

On Nov 7, 2013, at 10:03 PM, David M. Goodstein <[hidden email]> wrote:

Hi All,

  We're in the middle of converting our GBrowse installations to JBrowse, and need to retain our ability to show user BLAST results in the genome browser.  We currently do that in GBrowse with remote feature tracks, configured as:

[UserBlast]
stranded = 1
remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid') ;return "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
balloon hover =
link =


This searches a user- and session-specific directory for BLAST output files, converts them to GFF on the fly, and displays them in the track UserBlast.  

Is there an equivalent capability in JBrowse, assuming we had already converted our BLAST results to JSON?

thx,

-David


David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
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techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
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from the latest Intel processors and coprocessors. See abstracts and register
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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Robert Buels-2
Hi David,

Did you write this to the gmod-ajax mailing list?  I didn't see it come
through there, or I would have responded more quickly.

Option 1:
   You can definitely serve BLAST results through the JBrowse REST API,
see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.

Option 2:
   Or you might also be able to just use the existing web service if
it's just returning small bits of GFF3 (is it?).  JBrowse has a data
backend that can read GFF3 directly, also.  The track configuration
would probably be something like (not tested):

{ "label": "blast_gff3_test",
   "type": "JBrowse/View/Track/CanvasFeatures",
   "storeClass": "JBrowse/Store/SeqFeature/GFF3",
   "urlTemplate":
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
}

and that configuration could in turn either be served by a server-side
script and included with an "include" statement in the JBrowse
configuration, or injected into a running JBrowse on the client side
(with APIs that I still haven't documented very well), something like:

   JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
configuration objects ]);


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/08/2013 01:15 PM, Suzanna Lewis wrote:

> Hi David,
>
> Would BLAT be an acceptable substitute? We've got that working for
> Apollo and it shouldn't require too much effort to push back into the
> main branch of JBrowse.
>
> -S
>
> On Nov 7, 2013, at 10:03 PM, David M. Goodstein <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Hi All,
>>
>>   We're in the middle of converting our GBrowse installations to
>> JBrowse, and need to retain our ability to show user BLAST results in
>> the genome browser.  We currently do that in GBrowse with remote
>> feature tracks, configured as:
>>
>> [UserBlast]
>> stranded = 1
>> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
>> ;return
>> "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>> balloon hover =
>> link =
>>
>>
>> This searches a user- and session-specific directory for BLAST output
>> files, converts them to GFF on the fly, and displays them in the track
>> UserBlast.
>>
>> Is there an equivalent capability in JBrowse, assuming we had already
>> converted our BLAST results to JSON?
>>
>> thx,
>>
>> -David
>>
>>
>> David M. Goodstein, Ph.D.
>> Phytozome Group Lead
>> Plant and Computational Genomics Group
>> Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S.
>> Dept. of Energy
>> Center for Integrative Genomics - UC Berkeley
>>
>> ------------------------------------------------------------------------------
>> November Webinars for C, C++, Fortran Developers
>> Accelerate application performance with scalable programming models.
>> Explore
>> techniques for threading, error checking, porting, and tuning. Get the
>> most
>> from the latest Intel processors and coprocessors. See abstracts and
>> register
>> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
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Re: capability equivalent to remote feature track in Gbrowse?

dmgood11
In reply to this post by Suzanna Lewis
Hi Suzanna,
  We need this capability (remote feature tracks tied to specific users) in general:  for BLAT, BLAST, exonerate, etc.  
thx,

-David

On Nov 8, 2013, at 10:15 AM, Suzanna Lewis wrote:

Hi David,

Would BLAT be an acceptable substitute? We've got that working for Apollo and it shouldn't require too much effort to push back into the main branch of JBrowse.

-S

On Nov 7, 2013, at 10:03 PM, David M. Goodstein <[hidden email]> wrote:

Hi All,

  We're in the middle of converting our GBrowse installations to JBrowse, and need to retain our ability to show user BLAST results in the genome browser.  We currently do that in GBrowse with remote feature tracks, configured as:

[UserBlast]
stranded = 1
remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid') ;return "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
balloon hover =
link =


This searches a user- and session-specific directory for BLAST output files, converts them to GFF on the fly, and displays them in the track UserBlast.  

Is there an equivalent capability in JBrowse, assuming we had already converted our BLAST results to JSON?

thx,

-David


David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley


------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Richard Hayes
In reply to this post by Robert Buels-2
Excellent, thanks. I'll give these options a try.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]> wrote:
Hi David,

Did you write this to the gmod-ajax mailing list?  I didn't see it come
through there, or I would have responded more quickly.

Option 1:
   You can definitely serve BLAST results through the JBrowse REST API,
see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.

Option 2:
   Or you might also be able to just use the existing web service if
it's just returning small bits of GFF3 (is it?).  JBrowse has a data
backend that can read GFF3 directly, also.  The track configuration
would probably be something like (not tested):

{ "label": "blast_gff3_test",
   "type": "JBrowse/View/Track/CanvasFeatures",
   "storeClass": "JBrowse/Store/SeqFeature/GFF3",
   "urlTemplate":
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
}

and that configuration could in turn either be served by a server-side
script and included with an "include" statement in the JBrowse
configuration, or injected into a running JBrowse on the client side
(with APIs that I still haven't documented very well), something like:

   JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
configuration objects ]);


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
> Hi David,
>
> Would BLAT be an acceptable substitute? We've got that working for
> Apollo and it shouldn't require too much effort to push back into the
> main branch of JBrowse.
>
> -S
>
> On Nov 7, 2013, at 10:03 PM, David M. Goodstein <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Hi All,
>>
>>   We're in the middle of converting our GBrowse installations to
>> JBrowse, and need to retain our ability to show user BLAST results in
>> the genome browser.  We currently do that in GBrowse with remote
>> feature tracks, configured as:
>>
>> [UserBlast]
>> stranded = 1
>> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
>> ;return
>> "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>> balloon hover =
>> link =
>>
>>
>> This searches a user- and session-specific directory for BLAST output
>> files, converts them to GFF on the fly, and displays them in the track
>> UserBlast.
>>
>> Is there an equivalent capability in JBrowse, assuming we had already
>> converted our BLAST results to JSON?
>>
>> thx,
>>
>> -David
>>
>>
>> David M. Goodstein, Ph.D.
>> Phytozome Group Lead
>> Plant and Computational Genomics Group
>> Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S.
>> Dept. of Energy
>> Center for Integrative Genomics - UC Berkeley
>>
>> ------------------------------------------------------------------------------
>> November Webinars for C, C++, Fortran Developers
>> Accelerate application performance with scalable programming models.
>> Explore
>> techniques for threading, error checking, porting, and tuning. Get the
>> most
>> from the latest Intel processors and coprocessors. See abstracts and
>> register
>> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
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------------------------------------------------------------------------------
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Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

dmgood11
Thanks Rob, we'll take a look.  We'll likely have some questions as to how to tie this to user and session (for the server-side option).

-David

On Nov 8, 2013, at 11:04 AM, Richard Hayes wrote:

Excellent, thanks. I'll give these options a try.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]> wrote:
Hi David,

Did you write this to the gmod-ajax mailing list?  I didn't see it come
through there, or I would have responded more quickly.

Option 1:
   You can definitely serve BLAST results through the JBrowse REST API,
see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.

Option 2:
   Or you might also be able to just use the existing web service if
it's just returning small bits of GFF3 (is it?).  JBrowse has a data
backend that can read GFF3 directly, also.  The track configuration
would probably be something like (not tested):

{ "label": "blast_gff3_test",
   "type": "JBrowse/View/Track/CanvasFeatures",
   "storeClass": "JBrowse/Store/SeqFeature/GFF3",
   "urlTemplate":
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
}

and that configuration could in turn either be served by a server-side
script and included with an "include" statement in the JBrowse
configuration, or injected into a running JBrowse on the client side
(with APIs that I still haven't documented very well), something like:

   JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
configuration objects ]);


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
> Hi David,
>
> Would BLAT be an acceptable substitute? We've got that working for
> Apollo and it shouldn't require too much effort to push back into the
> main branch of JBrowse.
>
> -S
>
> On Nov 7, 2013, at 10:03 PM, David M. Goodstein <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Hi All,
>>
>>   We're in the middle of converting our GBrowse installations to
>> JBrowse, and need to retain our ability to show user BLAST results in
>> the genome browser.  We currently do that in GBrowse with remote
>> feature tracks, configured as:
>>
>> [UserBlast]
>> stranded = 1
>> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
>> ;return
>> "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>> balloon hover =
>> link =
>>
>>
>> This searches a user- and session-specific directory for BLAST output
>> files, converts them to GFF on the fly, and displays them in the track
>> UserBlast.
>>
>> Is there an equivalent capability in JBrowse, assuming we had already
>> converted our BLAST results to JSON?
>>
>> thx,
>>
>> -David
>>
>>
>> David M. Goodstein, Ph.D.
>> Phytozome Group Lead
>> Plant and Computational Genomics Group
>> Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S.
>> Dept. of Energy
>> Center for Integrative Genomics - UC Berkeley
>>
>> ------------------------------------------------------------------------------
>> November Webinars for C, C++, Fortran Developers
>> Accelerate application performance with scalable programming models.
>> Explore
>> techniques for threading, error checking, porting, and tuning. Get the
>> most
>> from the latest Intel processors and coprocessors. See abstracts and
>> register
>> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley


------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Suzanna Lewis
Rob's always on top of things like this :)

I'll have to stop in next week and see how it's going.

-S

On Nov 8, 2013, at 11:30 AM, "David M. Goodstein" <[hidden email]> wrote:

Thanks Rob, we'll take a look.  We'll likely have some questions as to how to tie this to user and session (for the server-side option).

-David

On Nov 8, 2013, at 11:04 AM, Richard Hayes wrote:

Excellent, thanks. I'll give these options a try.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]> wrote:
Hi David,

Did you write this to the gmod-ajax mailing list?  I didn't see it come
through there, or I would have responded more quickly.

Option 1:
   You can definitely serve BLAST results through the JBrowse REST API,
see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.

Option 2:
   Or you might also be able to just use the existing web service if
it's just returning small bits of GFF3 (is it?).  JBrowse has a data
backend that can read GFF3 directly, also.  The track configuration
would probably be something like (not tested):

{ "label": "blast_gff3_test",
   "type": "JBrowse/View/Track/CanvasFeatures",
   "storeClass": "JBrowse/Store/SeqFeature/GFF3",
   "urlTemplate":
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
}

and that configuration could in turn either be served by a server-side
script and included with an "include" statement in the JBrowse
configuration, or injected into a running JBrowse on the client side
(with APIs that I still haven't documented very well), something like:

   JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
configuration objects ]);


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
> Hi David,
>
> Would BLAT be an acceptable substitute? We've got that working for
> Apollo and it shouldn't require too much effort to push back into the
> main branch of JBrowse.
>
> -S
>
> On Nov 7, 2013, at 10:03 PM, David M. Goodstein <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Hi All,
>>
>>   We're in the middle of converting our GBrowse installations to
>> JBrowse, and need to retain our ability to show user BLAST results in
>> the genome browser.  We currently do that in GBrowse with remote
>> feature tracks, configured as:
>>
>> [UserBlast]
>> stranded = 1
>> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
>> ;return
>> "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>> balloon hover =
>> link =
>>
>>
>> This searches a user- and session-specific directory for BLAST output
>> files, converts them to GFF on the fly, and displays them in the track
>> UserBlast.
>>
>> Is there an equivalent capability in JBrowse, assuming we had already
>> converted our BLAST results to JSON?
>>
>> thx,
>>
>> -David
>>
>>
>> David M. Goodstein, Ph.D.
>> Phytozome Group Lead
>> Plant and Computational Genomics Group
>> Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S.
>> Dept. of Energy
>> Center for Integrative Genomics - UC Berkeley
>>
>> ------------------------------------------------------------------------------
>> November Webinars for C, C++, Fortran Developers
>> Accelerate application performance with scalable programming models.
>> Explore
>> techniques for threading, error checking, porting, and tuning. Get the
>> most
>> from the latest Intel processors and coprocessors. See abstracts and
>> register
>> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-ajax mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax


David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
Gmod-ajax mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Robert Buels-2
In reply to this post by dmgood11
On 11/08/2013 02:30 PM, David M. Goodstein wrote:
> Thanks Rob, we'll take a look.  We'll likely have some questions as to
> how to tie this to user and session (for the server-side option).

There isn't explicit support in JBrowse 1 for users and sessions.  But,
if JBrowse is running on the same server as the other stuff, any cookies
that other code sets in the user's browser will be provided by with the
requests that JBrowse makes to your backend APIs.

So, if you use a session cookie, and JBrowse is running on the same
server, the session cookie should just be passed through, and things
*should* just work.  I think.


--
Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Jillian Rowe
Since Jbrowse is html/javascript you can toss it into any web framework
and do your authentication through that. If you don't need any role
based access I've tried it out with apache and ldap and it was fine.

Role based access we do with the perl catalyst framework and a mysql
database that gets the user, finds their roles, gets the tracks for
those roles, and spits out the json data to tracklist.json (or whatever
the file name is).

Best,
Jillian


On 11/08/2013 11:34 PM, Robert Buels wrote:

> On 11/08/2013 02:30 PM, David M. Goodstein wrote:
>> Thanks Rob, we'll take a look.  We'll likely have some questions as to
>> how to tie this to user and session (for the server-side option).
> There isn't explicit support in JBrowse 1 for users and sessions.  But,
> if JBrowse is running on the same server as the other stuff, any cookies
> that other code sets in the user's browser will be provided by with the
> requests that JBrowse makes to your backend APIs.
>
> So, if you use a session cookie, and JBrowse is running on the same
> server, the session cookie should just be passed through, and things
> *should* just work.  I think.
>
>
> --
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Richard Hayes
In reply to this post by Robert Buels-2
Hi Rob,

Following up on this, I am trying to add a track via URL querystring to load GFF3 returned directly by a CGI script. Various attempts with the following are close, but aren't fully working.

I have addTracks=[ {"track" : "BlastResults",
                                "key" : "User Blast Results",
                                "type" : "CanvasFeatures",
                                "glyph" : "JBrowse/View/FeatureGlyph/Segments",
                               "feature" : [ "match:BLAST" ],
                               "subParts" : "match_part",
                               "style" : { "color" : "deepskyblue" },
                               "store" : "userblast"
} ]

and addStores=[ { "userblast" : {
                            "type" : "JBrowse/Store/SeqFeature/GFF3",
                            "urlTemplate" : "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST" }
}]

These are cobbled together from several other email threads. Do I have the right mix of parameters in each one? There is no wiki documentation for addStores. The actual query string has whitespace removed and is urlecoded. This is still behind a firewall on our dev server, but this is the link I'm attempting on an otherwise empty cache other than generating a blast result on our frontend website:

http://zome-dev.phytozome.net/jbrowse/index.html?data=genomes%2FAcoerulea&loc=scaffold_1%3A1112664..1119856&tracks=BlastResults%2CTranscripts%2CAlt_Transcripts%2CPASA_assembly&addTracks=%5B%7B%22label%22%3A%22User%20Blast%20Results%22%2C%22type%22%3A%22CanvasFeatures%22%2C%22glyph%22%3A%22JBrowse%2FView%2FFeatureGlyph%2FSegments%22%2C%22feature%22%3A%5B%22match%3ABLAST%22%5D%2C%22subParts%22%3A%22match_part%22%2C%22style%22%3A%7B%22color%22%3A%22deepskyblue%22%7D%2C%22store%22%20%3A%20%22userblast%22%7D%5D&addStores=%5B%7B%20%22userblast%22%20%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FGFF3%22%2C%22urlTemplate%22%3A%22http%3A%2F%2Fzome-dev.phytozome.net%2Fcgi-bin%2FreturnBLASTgff.pl%3Fsource%3Daquilegia%26zuid%3D52cbbda135582%26type%3Dmatch%3ABLAST%22%7D%20%7D%5D

The urlTemplate link above is also behind the firewall, but returns GFF3 directly. The zuid parameter matches with a user session cookie from our frontend when links like these will be generated.

I can get the track to show up on the track list only if I wrap both strings in square brackets (as shown), but it remains unselected despite being in the tracks list. When I click to turn it on, I get the error:

store 'userblast' not found

I feel that I'm close, but unsure what is missing or not otherwise correct.

Thanks!

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]> wrote:
Hi David,

Did you write this to the gmod-ajax mailing list?  I didn't see it come
through there, or I would have responded more quickly.

Option 1:
   You can definitely serve BLAST results through the JBrowse REST API,
see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.

Option 2:
   Or you might also be able to just use the existing web service if
it's just returning small bits of GFF3 (is it?).  JBrowse has a data
backend that can read GFF3 directly, also.  The track configuration
would probably be something like (not tested):

{ "label": "blast_gff3_test",
   "type": "JBrowse/View/Track/CanvasFeatures",
   "storeClass": "JBrowse/Store/SeqFeature/GFF3",
   "urlTemplate":
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
}

and that configuration could in turn either be served by a server-side
script and included with an "include" statement in the JBrowse
configuration, or injected into a running JBrowse on the client side
(with APIs that I still haven't documented very well), something like:

   JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
configuration objects ]);


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
> Hi David,
>
> Would BLAT be an acceptable substitute? We've got that working for
> Apollo and it shouldn't require too much effort to push back into the
> main branch of JBrowse.
>
> -S
>
> On Nov 7, 2013, at 10:03 PM, David M. Goodstein <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Hi All,
>>
>>   We're in the middle of converting our GBrowse installations to
>> JBrowse, and need to retain our ability to show user BLAST results in
>> the genome browser.  We currently do that in GBrowse with remote
>> feature tracks, configured as:
>>
>> [UserBlast]
>> stranded = 1
>> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
>> ;return
>> "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>> balloon hover =
>> link =
>>
>>
>> This searches a user- and session-specific directory for BLAST output
>> files, converts them to GFF on the fly, and displays them in the track
>> UserBlast.
>>
>> Is there an equivalent capability in JBrowse, assuming we had already
>> converted our BLAST results to JSON?
>>
>> thx,
>>
>> -David
>>
>>
>> David M. Goodstein, Ph.D.
>> Phytozome Group Lead
>> Plant and Computational Genomics Group
>> Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S.
>> Dept. of Energy
>> Center for Integrative Genomics - UC Berkeley
>>
>> ------------------------------------------------------------------------------
>> November Webinars for C, C++, Fortran Developers
>> Accelerate application performance with scalable programming models.
>> Explore
>> techniques for threading, error checking, porting, and tuning. Get the
>> most
>> from the latest Intel processors and coprocessors. See abstracts and
>> register
>> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Robert Buels-2
"track" and "feature" are biodb-to-json.pl things.  "features" doensj't
do anything in JBrowse itself, and you probably want "label" instead of
"track".  Try using this addTracks:

addTracks=[{
   "label" : "BlastResults",
   "key" : "User Blast Results",
   "type" : "CanvasFeatures",
   "glyph" : "JBrowse/View/FeatureGlyph/Segments",
   "subParts" : "match_part",
   "style" : { "color" : "deepskyblue" },
   "store" : "userblast"
}]

Does that work?

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/07/2014 01:58 PM, Richard Hayes wrote:

> Hi Rob,
>
> Following up on this, I am trying to add a track via URL querystring to
> load GFF3 returned directly by a CGI script. Various attempts with the
> following are close, but aren't fully working.
>
> I have addTracks=[ {"track" : "BlastResults",
>                                  "key" : "User Blast Results",
>                                  "type" : "CanvasFeatures",
>                                  "glyph" :
> "JBrowse/View/FeatureGlyph/Segments",
>                                 "feature" : [ "match:BLAST" ],
>                                 "subParts" : "match_part",
>                                 "style" : { "color" : "deepskyblue" },
>                                 "store" : "userblast"
> } ]
>
> and addStores=[ { "userblast" : {
>                              "type" : "JBrowse/Store/SeqFeature/GFF3",
>                              "urlTemplate" :
> "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST"
> }
> }]
>
> These are cobbled together from several other email threads. Do I have
> the right mix of parameters in each one? There is no wiki documentation
> for addStores. The actual query string has whitespace removed and is
> urlecoded. This is still behind a firewall on our dev server, but this
> is the link I'm attempting on an otherwise empty cache other than
> generating a blast result on our frontend website:
>
> http://zome-dev.phytozome.net/jbrowse/index.html?data=genomes%2FAcoerulea&loc=scaffold_1%3A1112664..1119856&tracks=BlastResults%2CTranscripts%2CAlt_Transcripts%2CPASA_assembly&addTracks=%5B%7B%22label%22%3A%22User%20Blast%20Results%22%2C%22type%22%3A%22CanvasFeatures%22%2C%22glyph%22%3A%22JBrowse%2FView%2FFeatureGlyph%2FSegments%22%2C%22feature%22%3A%5B%22match%3ABLAST%22%5D%2C%22subParts%22%3A%22match_part%22%2C%22style%22%3A%7B%22color%22%3A%22deepskyblue%22%7D%2C%22store%22%20%3A%20%22userblast%22%7D%5D&addStores=%5B%7B%20%22userblast%22%20%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FGFF3%22%2C%22urlTemplate%22%3A%22http%3A%2F%2Fzome-dev.phytozome.net%2Fcgi-bin%2FreturnBLASTgff.pl%3Fsource%3Daquilegia%26zuid%3D52cbbda135582%26type%3Dmatch%3ABLAST%22%7D%20%7D%5D
>
> The urlTemplate link above is also behind the firewall, but returns GFF3
> directly. The zuid parameter matches with a user session cookie from our
> frontend when links like these will be generated.
>
> I can get the track to show up on the track list only if I wrap both
> strings in square brackets (as shown), but it remains unselected despite
> being in the tracks list. When I click to turn it on, I get the error:
>
> store 'userblast' not found
>
> I feel that I'm close, but unsure what is missing or not otherwise correct.
>
> Thanks!
>
> Richard D. Hayes, Ph.D.
> Joint Genome Institute / Lawrence Berkeley National Lab
> http://www.phytozome.net
>
>
> On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi David,
>
>     Did you write this to the gmod-ajax mailing list?  I didn't see it come
>     through there, or I would have responded more quickly.
>
>     Option 1:
>         You can definitely serve BLAST results through the JBrowse REST API,
>     see
>     http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.
>
>     Option 2:
>         Or you might also be able to just use the existing web service if
>     it's just returning small bits of GFF3 (is it?).  JBrowse has a data
>     backend that can read GFF3 directly, also.  The track configuration
>     would probably be something like (not tested):
>
>     { "label": "blast_gff3_test",
>         "type": "JBrowse/View/Track/CanvasFeatures",
>         "storeClass": "JBrowse/Store/SeqFeature/GFF3",
>         "urlTemplate":
>     "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
>     }
>
>     and that configuration could in turn either be served by a server-side
>     script and included with an "include" statement in the JBrowse
>     configuration, or injected into a running JBrowse on the client side
>     (with APIs that I still haven't documented very well), something like:
>
>         JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
>     configuration objects ]);
>
>
>     Robert Buels
>     Lead Developer
>     JBrowse - http://jbrowse.org
>
>     On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
>      > Hi David,
>      >
>      > Would BLAT be an acceptable substitute? We've got that working for
>      > Apollo and it shouldn't require too much effort to push back into the
>      > main branch of JBrowse.
>      >
>      > -S
>      >
>      > On Nov 7, 2013, at 10:03 PM, David M. Goodstein
>     <[hidden email] <mailto:[hidden email]>
>      > <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>      >
>      >> Hi All,
>      >>
>      >>   We're in the middle of converting our GBrowse installations to
>      >> JBrowse, and need to retain our ability to show user BLAST
>     results in
>      >> the genome browser.  We currently do that in GBrowse with remote
>      >> feature tracks, configured as:
>      >>
>      >> [UserBlast]
>      >> stranded = 1
>      >> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
>      >> ;return
>      >>
>     "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>      >> balloon hover =
>      >> link =
>      >>
>      >>
>      >> This searches a user- and session-specific directory for BLAST
>     output
>      >> files, converts them to GFF on the fly, and displays them in the
>     track
>      >> UserBlast.
>      >>
>      >> Is there an equivalent capability in JBrowse, assuming we had
>     already
>      >> converted our BLAST results to JSON?
>      >>
>      >> thx,
>      >>
>      >> -David
>      >>
>      >>
>      >> David M. Goodstein, Ph.D.
>      >> Phytozome Group Lead
>      >> Plant and Computational Genomics Group
>      >> Joint Genome Institute - Lawrence Berkeley National Laboratory -
>     U.S.
>      >> Dept. of Energy
>      >> Center for Integrative Genomics - UC Berkeley
>      >>
>      >>
>     ------------------------------------------------------------------------------
>      >> November Webinars for C, C++, Fortran Developers
>      >> Accelerate application performance with scalable programming models.
>      >> Explore
>      >> techniques for threading, error checking, porting, and tuning.
>     Get the
>      >> most
>      >> from the latest Intel processors and coprocessors. See abstracts and
>      >> register
>      >>
>     http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
>      >> Gmod-ajax mailing list
>      >> [hidden email]
>     <mailto:[hidden email]>
>      >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>      >
>
>     ------------------------------------------------------------------------------
>     November Webinars for C, C++, Fortran Developers
>     Accelerate application performance with scalable programming models.
>     Explore
>     techniques for threading, error checking, porting, and tuning. Get
>     the most
>     from the latest Intel processors and coprocessors. See abstracts and
>     register
>     http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
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>
>

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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Robert Buels-2
In reply to this post by Richard Hayes
Oh, also the addStores should not be in an arrayref:

addStores={ "userblast" : {
                             "type" : "JBrowse/Store/SeqFeature/GFF3",
                             "urlTemplate" :
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST"
}
}

I added it to the wiki just now, thanks for pointing that out:
http://gmod.org/wiki/JBrowse_Configuration_Guide#addStores

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/07/2014 01:58 PM, Richard Hayes wrote:

> Hi Rob,
>
> Following up on this, I am trying to add a track via URL querystring to
> load GFF3 returned directly by a CGI script. Various attempts with the
> following are close, but aren't fully working.
>
> I have addTracks=[ {"track" : "BlastResults",
>                                  "key" : "User Blast Results",
>                                  "type" : "CanvasFeatures",
>                                  "glyph" :
> "JBrowse/View/FeatureGlyph/Segments",
>                                 "feature" : [ "match:BLAST" ],
>                                 "subParts" : "match_part",
>                                 "style" : { "color" : "deepskyblue" },
>                                 "store" : "userblast"
> } ]
>
> and addStores=[ { "userblast" : {
>                              "type" : "JBrowse/Store/SeqFeature/GFF3",
>                              "urlTemplate" :
> "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST"
> }
> }]
>
> These are cobbled together from several other email threads. Do I have
> the right mix of parameters in each one? There is no wiki documentation
> for addStores. The actual query string has whitespace removed and is
> urlecoded. This is still behind a firewall on our dev server, but this
> is the link I'm attempting on an otherwise empty cache other than
> generating a blast result on our frontend website:
>
> http://zome-dev.phytozome.net/jbrowse/index.html?data=genomes%2FAcoerulea&loc=scaffold_1%3A1112664..1119856&tracks=BlastResults%2CTranscripts%2CAlt_Transcripts%2CPASA_assembly&addTracks=%5B%7B%22label%22%3A%22User%20Blast%20Results%22%2C%22type%22%3A%22CanvasFeatures%22%2C%22glyph%22%3A%22JBrowse%2FView%2FFeatureGlyph%2FSegments%22%2C%22feature%22%3A%5B%22match%3ABLAST%22%5D%2C%22subParts%22%3A%22match_part%22%2C%22style%22%3A%7B%22color%22%3A%22deepskyblue%22%7D%2C%22store%22%20%3A%20%22userblast%22%7D%5D&addStores=%5B%7B%20%22userblast%22%20%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FGFF3%22%2C%22urlTemplate%22%3A%22http%3A%2F%2Fzome-dev.phytozome.net%2Fcgi-bin%2FreturnBLASTgff.pl%3Fsource%3Daquilegia%26zuid%3D52cbbda135582%26type%3Dmatch%3ABLAST%22%7D%20%7D%5D
>
> The urlTemplate link above is also behind the firewall, but returns GFF3
> directly. The zuid parameter matches with a user session cookie from our
> frontend when links like these will be generated.
>
> I can get the track to show up on the track list only if I wrap both
> strings in square brackets (as shown), but it remains unselected despite
> being in the tracks list. When I click to turn it on, I get the error:
>
> store 'userblast' not found
>
> I feel that I'm close, but unsure what is missing or not otherwise correct.
>
> Thanks!
>
> Richard D. Hayes, Ph.D.
> Joint Genome Institute / Lawrence Berkeley National Lab
> http://www.phytozome.net
>
>
> On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi David,
>
>     Did you write this to the gmod-ajax mailing list?  I didn't see it come
>     through there, or I would have responded more quickly.
>
>     Option 1:
>         You can definitely serve BLAST results through the JBrowse REST API,
>     see
>     http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.
>
>     Option 2:
>         Or you might also be able to just use the existing web service if
>     it's just returning small bits of GFF3 (is it?).  JBrowse has a data
>     backend that can read GFF3 directly, also.  The track configuration
>     would probably be something like (not tested):
>
>     { "label": "blast_gff3_test",
>         "type": "JBrowse/View/Track/CanvasFeatures",
>         "storeClass": "JBrowse/Store/SeqFeature/GFF3",
>         "urlTemplate":
>     "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
>     }
>
>     and that configuration could in turn either be served by a server-side
>     script and included with an "include" statement in the JBrowse
>     configuration, or injected into a running JBrowse on the client side
>     (with APIs that I still haven't documented very well), something like:
>
>         JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
>     configuration objects ]);
>
>
>     Robert Buels
>     Lead Developer
>     JBrowse - http://jbrowse.org
>
>     On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
>      > Hi David,
>      >
>      > Would BLAT be an acceptable substitute? We've got that working for
>      > Apollo and it shouldn't require too much effort to push back into the
>      > main branch of JBrowse.
>      >
>      > -S
>      >
>      > On Nov 7, 2013, at 10:03 PM, David M. Goodstein
>     <[hidden email] <mailto:[hidden email]>
>      > <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>      >
>      >> Hi All,
>      >>
>      >>   We're in the middle of converting our GBrowse installations to
>      >> JBrowse, and need to retain our ability to show user BLAST
>     results in
>      >> the genome browser.  We currently do that in GBrowse with remote
>      >> feature tracks, configured as:
>      >>
>      >> [UserBlast]
>      >> stranded = 1
>      >> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
>      >> ;return
>      >>
>     "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>      >> balloon hover =
>      >> link =
>      >>
>      >>
>      >> This searches a user- and session-specific directory for BLAST
>     output
>      >> files, converts them to GFF on the fly, and displays them in the
>     track
>      >> UserBlast.
>      >>
>      >> Is there an equivalent capability in JBrowse, assuming we had
>     already
>      >> converted our BLAST results to JSON?
>      >>
>      >> thx,
>      >>
>      >> -David
>      >>
>      >>
>      >> David M. Goodstein, Ph.D.
>      >> Phytozome Group Lead
>      >> Plant and Computational Genomics Group
>      >> Joint Genome Institute - Lawrence Berkeley National Laboratory -
>     U.S.
>      >> Dept. of Energy
>      >> Center for Integrative Genomics - UC Berkeley
>      >>
>      >>
>     ------------------------------------------------------------------------------
>      >> November Webinars for C, C++, Fortran Developers
>      >> Accelerate application performance with scalable programming models.
>      >> Explore
>      >> techniques for threading, error checking, porting, and tuning.
>     Get the
>      >> most
>      >> from the latest Intel processors and coprocessors. See abstracts and
>      >> register
>      >>
>     http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
>      >> Gmod-ajax mailing list
>      >> [hidden email]
>     <mailto:[hidden email]>
>      >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>      >
>
>     ------------------------------------------------------------------------------
>     November Webinars for C, C++, Fortran Developers
>     Accelerate application performance with scalable programming models.
>     Explore
>     techniques for threading, error checking, porting, and tuning. Get
>     the most
>     from the latest Intel processors and coprocessors. See abstracts and
>     register
>     http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
>     _______________________________________________
>     Gmod-ajax mailing list
>     [hidden email] <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Richard Hayes
Success!

I do get this error on the console if I don't supply a full path to "type", e.g.
"type" : "JBrowse/View/Track/CanvasFeatures"

  1. GET http://zome-dev.phytozome.net/jbrowse/CanvasFeatures.js 404 (Not Found)


Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Tue, Jan 7, 2014 at 11:42 AM, Robert Buels <[hidden email]> wrote:
Oh, also the addStores should not be in an arrayref:


addStores={ "userblast" : {
                            "type" : "JBrowse/Store/SeqFeature/GFF3",
                            "urlTemplate" : "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST" }
}

I added it to the wiki just now, thanks for pointing that out:
http://gmod.org/wiki/JBrowse_Configuration_Guide#addStores


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/07/2014 01:58 PM, Richard Hayes wrote:
Hi Rob,

Following up on this, I am trying to add a track via URL querystring to
load GFF3 returned directly by a CGI script. Various attempts with the
following are close, but aren't fully working.

I have addTracks=[ {"track" : "BlastResults",
                                 "key" : "User Blast Results",
                                 "type" : "CanvasFeatures",
                                 "glyph" :
"JBrowse/View/FeatureGlyph/Segments",
                                "feature" : [ "match:BLAST" ],
                                "subParts" : "match_part",
                                "style" : { "color" : "deepskyblue" },
                                "store" : "userblast"
} ]

and addStores=[ { "userblast" : {
                             "type" : "JBrowse/Store/SeqFeature/GFF3",
                             "urlTemplate" :
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST"
}
}]

These are cobbled together from several other email threads. Do I have
the right mix of parameters in each one? There is no wiki documentation
for addStores. The actual query string has whitespace removed and is
urlecoded. This is still behind a firewall on our dev server, but this
is the link I'm attempting on an otherwise empty cache other than
generating a blast result on our frontend website:

http://zome-dev.phytozome.net/jbrowse/index.html?data=genomes%2FAcoerulea&loc=scaffold_1%3A1112664..1119856&tracks=BlastResults%2CTranscripts%2CAlt_Transcripts%2CPASA_assembly&addTracks=%5B%7B%22label%22%3A%22User%20Blast%20Results%22%2C%22type%22%3A%22CanvasFeatures%22%2C%22glyph%22%3A%22JBrowse%2FView%2FFeatureGlyph%2FSegments%22%2C%22feature%22%3A%5B%22match%3ABLAST%22%5D%2C%22subParts%22%3A%22match_part%22%2C%22style%22%3A%7B%22color%22%3A%22deepskyblue%22%7D%2C%22store%22%20%3A%20%22userblast%22%7D%5D&addStores=%5B%7B%20%22userblast%22%20%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FGFF3%22%2C%22urlTemplate%22%3A%22http%3A%2F%2Fzome-dev.phytozome.net%2Fcgi-bin%2FreturnBLASTgff.pl%3Fsource%3Daquilegia%26zuid%3D52cbbda135582%26type%3Dmatch%3ABLAST%22%7D%20%7D%5D

The urlTemplate link above is also behind the firewall, but returns GFF3
directly. The zuid parameter matches with a user session cookie from our
frontend when links like these will be generated.

I can get the track to show up on the track list only if I wrap both
strings in square brackets (as shown), but it remains unselected despite
being in the tracks list. When I click to turn it on, I get the error:

store 'userblast' not found

I feel that I'm close, but unsure what is missing or not otherwise correct.

Thanks!

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi David,

    Did you write this to the gmod-ajax mailing list?  I didn't see it come
    through there, or I would have responded more quickly.

    Option 1:
        You can definitely serve BLAST results through the JBrowse REST API,
    see
    http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.

    Option 2:
        Or you might also be able to just use the existing web service if
    it's just returning small bits of GFF3 (is it?).  JBrowse has a data
    backend that can read GFF3 directly, also.  The track configuration
    would probably be something like (not tested):

    { "label": "blast_gff3_test",
        "type": "JBrowse/View/Track/CanvasFeatures",
        "storeClass": "JBrowse/Store/SeqFeature/GFF3",
        "urlTemplate":
    "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
    }

    and that configuration could in turn either be served by a server-side
    script and included with an "include" statement in the JBrowse
    configuration, or injected into a running JBrowse on the client side
    (with APIs that I still haven't documented very well), something like:

        JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
    configuration objects ]);


    Robert Buels
    Lead Developer
    JBrowse - http://jbrowse.org

    On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
     > Hi David,
     >
     > Would BLAT be an acceptable substitute? We've got that working for
     > Apollo and it shouldn't require too much effort to push back into the
     > main branch of JBrowse.
     >
     > -S
     >
     > On Nov 7, 2013, at 10:03 PM, David M. Goodstein
    <[hidden email] <mailto:[hidden email]>
     > <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
     >
     >> Hi All,
     >>
     >>   We're in the middle of converting our GBrowse installations to
     >> JBrowse, and need to retain our ability to show user BLAST
    results in
     >> the genome browser.  We currently do that in GBrowse with remote
     >> feature tracks, configured as:
     >>
     >> [UserBlast]
     >> stranded = 1
     >> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
     >> ;return
     >>
    "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
     >> balloon hover =
     >> link =
     >>
     >>
     >> This searches a user- and session-specific directory for BLAST
    output
     >> files, converts them to GFF on the fly, and displays them in the
    track
     >> UserBlast.
     >>
     >> Is there an equivalent capability in JBrowse, assuming we had
    already
     >> converted our BLAST results to JSON?
     >>
     >> thx,
     >>
     >> -David
     >>
     >>
     >> David M. Goodstein, Ph.D.
     >> Phytozome Group Lead
     >> Plant and Computational Genomics Group
     >> Joint Genome Institute - Lawrence Berkeley National Laboratory -
    U.S.
     >> Dept. of Energy
     >> Center for Integrative Genomics - UC Berkeley
     >>
     >>
    ------------------------------------------------------------------------------
     >> November Webinars for C, C++, Fortran Developers
     >> Accelerate application performance with scalable programming models.
     >> Explore
     >> techniques for threading, error checking, porting, and tuning.
    Get the
     >> most
     >> from the latest Intel processors and coprocessors. See abstracts and
     >> register
     >>
    http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
     >> Gmod-ajax mailing list
     >> [hidden email]
    <mailto:[hidden email]>

     >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
     >

    ------------------------------------------------------------------------------
    November Webinars for C, C++, Fortran Developers
    Accelerate application performance with scalable programming models.
    Explore
    techniques for threading, error checking, porting, and tuning. Get
    the most
    from the latest Intel processors and coprocessors. See abstracts and
    register
    http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
    _______________________________________________
    Gmod-ajax mailing list
    [hidden email] <mailto:[hidden email]>
    https://lists.sourceforge.net/lists/listinfo/gmod-ajax




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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Richard Hayes
What level of persistence should we expect for tracks added via URL addTracks and addStores parameters? In my now working example above, if I switch datasources back and forth, the added track on the original datasource is currently lost.

I think this might be part of a larger issue with multi-dataset installations, where the cookie storage of selected tracks appears to be a global value. I've seen other cases where:
1) I turn on TrackA in SpeciesX
2) I switch to SpeciesY from the datasource dorp down menu. SpeciesY doesn't have TrackA.
3) I switch back to SpeciesX, but TrackA is no longer selected.

Thanks,

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Tue, Jan 7, 2014 at 12:11 PM, Richard Hayes <[hidden email]> wrote:
Success!

I do get this error on the console if I don't supply a full path to "type", e.g.
"type" : "JBrowse/View/Track/CanvasFeatures"

  1. GET http://zome-dev.phytozome.net/jbrowse/CanvasFeatures.js 404 (Not Found)


Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Tue, Jan 7, 2014 at 11:42 AM, Robert Buels <[hidden email]> wrote:
Oh, also the addStores should not be in an arrayref:


addStores={ "userblast" : {
                            "type" : "JBrowse/Store/SeqFeature/GFF3",
                            "urlTemplate" : "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST" }
}

I added it to the wiki just now, thanks for pointing that out:
http://gmod.org/wiki/JBrowse_Configuration_Guide#addStores


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/07/2014 01:58 PM, Richard Hayes wrote:
Hi Rob,

Following up on this, I am trying to add a track via URL querystring to
load GFF3 returned directly by a CGI script. Various attempts with the
following are close, but aren't fully working.

I have addTracks=[ {"track" : "BlastResults",
                                 "key" : "User Blast Results",
                                 "type" : "CanvasFeatures",
                                 "glyph" :
"JBrowse/View/FeatureGlyph/Segments",
                                "feature" : [ "match:BLAST" ],
                                "subParts" : "match_part",
                                "style" : { "color" : "deepskyblue" },
                                "store" : "userblast"
} ]

and addStores=[ { "userblast" : {
                             "type" : "JBrowse/Store/SeqFeature/GFF3",
                             "urlTemplate" :
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST"
}
}]

These are cobbled together from several other email threads. Do I have
the right mix of parameters in each one? There is no wiki documentation
for addStores. The actual query string has whitespace removed and is
urlecoded. This is still behind a firewall on our dev server, but this
is the link I'm attempting on an otherwise empty cache other than
generating a blast result on our frontend website:

http://zome-dev.phytozome.net/jbrowse/index.html?data=genomes%2FAcoerulea&loc=scaffold_1%3A1112664..1119856&tracks=BlastResults%2CTranscripts%2CAlt_Transcripts%2CPASA_assembly&addTracks=%5B%7B%22label%22%3A%22User%20Blast%20Results%22%2C%22type%22%3A%22CanvasFeatures%22%2C%22glyph%22%3A%22JBrowse%2FView%2FFeatureGlyph%2FSegments%22%2C%22feature%22%3A%5B%22match%3ABLAST%22%5D%2C%22subParts%22%3A%22match_part%22%2C%22style%22%3A%7B%22color%22%3A%22deepskyblue%22%7D%2C%22store%22%20%3A%20%22userblast%22%7D%5D&addStores=%5B%7B%20%22userblast%22%20%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FGFF3%22%2C%22urlTemplate%22%3A%22http%3A%2F%2Fzome-dev.phytozome.net%2Fcgi-bin%2FreturnBLASTgff.pl%3Fsource%3Daquilegia%26zuid%3D52cbbda135582%26type%3Dmatch%3ABLAST%22%7D%20%7D%5D

The urlTemplate link above is also behind the firewall, but returns GFF3
directly. The zuid parameter matches with a user session cookie from our
frontend when links like these will be generated.

I can get the track to show up on the track list only if I wrap both
strings in square brackets (as shown), but it remains unselected despite
being in the tracks list. When I click to turn it on, I get the error:

store 'userblast' not found

I feel that I'm close, but unsure what is missing or not otherwise correct.

Thanks!

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi David,

    Did you write this to the gmod-ajax mailing list?  I didn't see it come
    through there, or I would have responded more quickly.

    Option 1:
        You can definitely serve BLAST results through the JBrowse REST API,
    see
    http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.

    Option 2:
        Or you might also be able to just use the existing web service if
    it's just returning small bits of GFF3 (is it?).  JBrowse has a data
    backend that can read GFF3 directly, also.  The track configuration
    would probably be something like (not tested):

    { "label": "blast_gff3_test",
        "type": "JBrowse/View/Track/CanvasFeatures",
        "storeClass": "JBrowse/Store/SeqFeature/GFF3",
        "urlTemplate":
    "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
    }

    and that configuration could in turn either be served by a server-side
    script and included with an "include" statement in the JBrowse
    configuration, or injected into a running JBrowse on the client side
    (with APIs that I still haven't documented very well), something like:

        JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
    configuration objects ]);


    Robert Buels
    Lead Developer
    JBrowse - http://jbrowse.org

    On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
     > Hi David,
     >
     > Would BLAT be an acceptable substitute? We've got that working for
     > Apollo and it shouldn't require too much effort to push back into the
     > main branch of JBrowse.
     >
     > -S
     >
     > On Nov 7, 2013, at 10:03 PM, David M. Goodstein
    <[hidden email] <mailto:[hidden email]>
     > <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
     >
     >> Hi All,
     >>
     >>   We're in the middle of converting our GBrowse installations to
     >> JBrowse, and need to retain our ability to show user BLAST
    results in
     >> the genome browser.  We currently do that in GBrowse with remote
     >> feature tracks, configured as:
     >>
     >> [UserBlast]
     >> stranded = 1
     >> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
     >> ;return
     >>
    "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
     >> balloon hover =
     >> link =
     >>
     >>
     >> This searches a user- and session-specific directory for BLAST
    output
     >> files, converts them to GFF on the fly, and displays them in the
    track
     >> UserBlast.
     >>
     >> Is there an equivalent capability in JBrowse, assuming we had
    already
     >> converted our BLAST results to JSON?
     >>
     >> thx,
     >>
     >> -David
     >>
     >>
     >> David M. Goodstein, Ph.D.
     >> Phytozome Group Lead
     >> Plant and Computational Genomics Group
     >> Joint Genome Institute - Lawrence Berkeley National Laboratory -
    U.S.
     >> Dept. of Energy
     >> Center for Integrative Genomics - UC Berkeley
     >>
     >>
    ------------------------------------------------------------------------------
     >> November Webinars for C, C++, Fortran Developers
     >> Accelerate application performance with scalable programming models.
     >> Explore
     >> techniques for threading, error checking, porting, and tuning.
    Get the
     >> most
     >> from the latest Intel processors and coprocessors. See abstracts and
     >> register
     >>
    http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
     >> Gmod-ajax mailing list
     >> [hidden email]
    <mailto:[hidden email]>

     >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
     >

    ------------------------------------------------------------------------------
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    Accelerate application performance with scalable programming models.
    Explore
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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Robert Buels-2
There isn't any persistence for URL tracks right now.  I think this is
probably best.

And yes, cookie storage of selected tracks is a global value for the
installation.  That, in contrast, should probably be changed to be keyed
to the dataset_id. https://github.com/GMOD/jbrowse/issues/410

Currently assigned to 1.11.2.  I'm afraid that's going to come out after
PAG though.  Unless of course that causes you a super-big problem, in
which case I will do it faster.

Are you and/or David going to PAG?  I am.  For like the ... I think 9th
year in a row?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/07/2014 04:30 PM, Richard Hayes wrote:

> What level of persistence should we expect for tracks added via URL
> addTracks and addStores parameters? In my now working example above, if
> I switch datasources back and forth, the added track on the original
> datasource is currently lost.
>
> I think this might be part of a larger issue with multi-dataset
> installations, where the cookie storage of selected tracks appears to be
> a global value. I've seen other cases where:
> 1) I turn on TrackA in SpeciesX
> 2) I switch to SpeciesY from the datasource dorp down menu. SpeciesY
> doesn't have TrackA.
> 3) I switch back to SpeciesX, but TrackA is no longer selected.
>
> Thanks,
>
> Richard D. Hayes, Ph.D.
> Joint Genome Institute / Lawrence Berkeley National Lab
> http://www.phytozome.net
>
>
> On Tue, Jan 7, 2014 at 12:11 PM, Richard Hayes <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Success!
>
>     I do get this error on the console if I don't supply a full path to
>     "type", e.g.
>     "type" : "JBrowse/View/Track/CanvasFeatures"
>
>      1. GET http://zome-dev.phytozome.net/jbrowse/CanvasFeatures.js 404
>         (Not Found)
>
>
>
>     Richard D. Hayes, Ph.D.
>     Joint Genome Institute / Lawrence Berkeley National Lab
>     http://www.phytozome.net
>
>
>     On Tue, Jan 7, 2014 at 11:42 AM, Robert Buels <[hidden email]
>     <mailto:[hidden email]>> wrote:
>
>         Oh, also the addStores should not be in an arrayref:
>
>
>         addStores={ "userblast" : {
>                                      "type" :
>         "JBrowse/Store/SeqFeature/__GFF3",
>                                      "urlTemplate" :
>         "http://zome-dev.phytozome.__net/cgi-bin/returnBLASTgff.pl?__source=aquilegia&zuid=__52cbbda135582&type=match:BLAST
>         <http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST>__"
>         }
>         }
>
>         I added it to the wiki just now, thanks for pointing that out:
>         http://gmod.org/wiki/JBrowse___Configuration_Guide#addStores
>         <http://gmod.org/wiki/JBrowse_Configuration_Guide#addStores>
>
>
>         Robert Buels
>         Lead Developer
>         JBrowse - http://jbrowse.org
>
>         On 01/07/2014 01:58 PM, Richard Hayes wrote:
>
>             Hi Rob,
>
>             Following up on this, I am trying to add a track via URL
>             querystring to
>             load GFF3 returned directly by a CGI script. Various
>             attempts with the
>             following are close, but aren't fully working.
>
>             I have addTracks=[ {"track" : "BlastResults",
>                                               "key" : "User Blast Results",
>                                               "type" : "CanvasFeatures",
>                                               "glyph" :
>             "JBrowse/View/FeatureGlyph/__Segments",
>                                              "feature" : [ "match:BLAST" ],
>                                              "subParts" : "match_part",
>                                              "style" : { "color" :
>             "deepskyblue" },
>                                              "store" : "userblast"
>             } ]
>
>             and addStores=[ { "userblast" : {
>                                           "type" :
>             "JBrowse/Store/SeqFeature/__GFF3",
>                                           "urlTemplate" :
>             "http://zome-dev.phytozome.__net/cgi-bin/returnBLASTgff.pl?__source=aquilegia&zuid=__52cbbda135582&type=match:BLAST
>             <http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST>__"
>             }
>             }]
>
>             These are cobbled together from several other email threads.
>             Do I have
>             the right mix of parameters in each one? There is no wiki
>             documentation
>             for addStores. The actual query string has whitespace
>             removed and is
>             urlecoded. This is still behind a firewall on our dev
>             server, but this
>             is the link I'm attempting on an otherwise empty cache other
>             than
>             generating a blast result on our frontend website:
>
>             <a href="http://zome-dev.phytozome.net/__jbrowse/index.html?data=__genomes%2FAcoerulea&loc=__scaffold_1%3A1112664..1119856&__tracks=BlastResults%__2CTranscripts%2CAlt___Transcripts%2CPASA_assembly&__addTracks=%5B%7B%22label%22%__3A%22User%20Blast%20Results%__22%2C%22type%22%3A%__22CanvasFeatures%22%2C%__22glyph%22%3A%22JBrowse%__2FView%2FFeatureGlyph%__2FSegments%22%2C%22feature%22%__3A%5B%22match%3ABLAST%22%5D%__2C%22subParts%22%3A%22match___part%22%2C%22style%22%3A%7B%__22color%22%3A%22deepskyblue%__22%7D%2C%22store%22%20%3A%20%__22userblast%22%7D%5D&__addStores=%5B%7B%20%__22userblast%22%20%3A%20%7B%20%__22type%22%3A%20%22JBrowse%__2FStore%2FSeqFeature%2FGFF3%__22%2C%22urlTemplate%22%3A%__22http%3A%2F%2Fzome-dev.__phytozome.net%2Fcgi-bin%__2FreturnBLASTgff.pl%3Fsource%__3Daquilegia%26zuid%__3D52cbbda135582%26type%__3Dmatch%3ABLAST%22%7D%20%7D%5D">http://zome-dev.phytozome.net/__jbrowse/index.html?data=__genomes%2FAcoerulea&loc=__scaffold_1%3A1112664..1119856&__tracks=BlastResults%__2CTranscripts%2CAlt___Transcripts%2CPASA_assembly&__addTracks=%5B%7B%22label%22%__3A%22User%20Blast%20Results%__22%2C%22type%22%3A%__22CanvasFeatures%22%2C%__22glyph%22%3A%22JBrowse%__2FView%2FFeatureGlyph%__2FSegments%22%2C%22feature%22%__3A%5B%22match%3ABLAST%22%5D%__2C%22subParts%22%3A%22match___part%22%2C%22style%22%3A%7B%__22color%22%3A%22deepskyblue%__22%7D%2C%22store%22%20%3A%20%__22userblast%22%7D%5D&__addStores=%5B%7B%20%__22userblast%22%20%3A%20%7B%20%__22type%22%3A%20%22JBrowse%__2FStore%2FSeqFeature%2FGFF3%__22%2C%22urlTemplate%22%3A%__22http%3A%2F%2Fzome-dev.__phytozome.net%2Fcgi-bin%__2FreturnBLASTgff.pl%3Fsource%__3Daquilegia%26zuid%__3D52cbbda135582%26type%__3Dmatch%3ABLAST%22%7D%20%7D%5D
>             <http://zome-dev.phytozome.net/jbrowse/index.html?data=genomes%2FAcoerulea&loc=scaffold_1%3A1112664..1119856&tracks=BlastResults%2CTranscripts%2CAlt_Transcripts%2CPASA_assembly&addTracks=%5B%7B%22label%22%3A%22User%20Blast%20Results%22%2C%22type%22%3A%22CanvasFeatures%22%2C%22glyph%22%3A%22JBrowse%2FView%2FFeatureGlyph%2FSegments%22%2C%22feature%22%3A%5B%22match%3ABLAST%22%5D%2C%22subParts%22%3A%22match_part%22%2C%22style%22%3A%7B%22color%22%3A%22deepskyblue%22%7D%2C%22store%22%20%3A%20%22userblast%22%7D%5D&addStores=%5B%7B%20%22userblast%22%20%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FGFF3%22%2C%22urlTemplate%22%3A%22http%3A%2F%2Fzome-dev.phytozome.net%2Fcgi-bin%2FreturnBLASTgff.pl%3Fsource%3Daquilegia%26zuid%3D52cbbda135582%26type%3Dmatch%3ABLAST%22%7D%20%7D%5D>
>
>             The urlTemplate link above is also behind the firewall, but
>             returns GFF3
>             directly. The zuid parameter matches with a user session
>             cookie from our
>             frontend when links like these will be generated.
>
>             I can get the track to show up on the track list only if I
>             wrap both
>             strings in square brackets (as shown), but it remains
>             unselected despite
>             being in the tracks list. When I click to turn it on, I get
>             the error:
>
>             store 'userblast' not found
>
>             I feel that I'm close, but unsure what is missing or not
>             otherwise correct.
>
>             Thanks!
>
>             Richard D. Hayes, Ph.D.
>             Joint Genome Institute / Lawrence Berkeley National Lab
>             http://www.phytozome.net
>
>
>             On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels
>             <[hidden email] <mailto:[hidden email]>
>             <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>                  Hi David,
>
>                  Did you write this to the gmod-ajax mailing list?  I
>             didn't see it come
>                  through there, or I would have responded more quickly.
>
>                  Option 1:
>                      You can definitely serve BLAST results through the
>             JBrowse REST API,
>                  see
>             http://gmod.org/wiki/JBrowse___Configuration_Guide#Writing___JBrowse-compatible_Web___Services
>             <http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services>.
>
>                  Option 2:
>                      Or you might also be able to just use the existing
>             web service if
>                  it's just returning small bits of GFF3 (is it?).
>               JBrowse has a data
>                  backend that can read GFF3 directly, also.  The track
>             configuration
>                  would probably be something like (not tested):
>
>                  { "label": "blast_gff3_test",
>                      "type": "JBrowse/View/Track/__CanvasFeatures",
>                      "storeClass": "JBrowse/Store/SeqFeature/__GFF3",
>                      "urlTemplate":
>
>             "http://zome-dev.phytozome.__net/cgi-bin/returnBLASTgff.pl?__source=maize&zuid=$zuid&type=__match:BLAST
>             <http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST>"
>                  }
>
>                  and that configuration could in turn either be served
>             by a server-side
>                  script and included with an "include" statement in the
>             JBrowse
>                  configuration, or injected into a running JBrowse on
>             the client side
>                  (with APIs that I still haven't documented very well),
>             something like:
>
>                      JBrowse.publish('/jbrowse/v1/__c/tracks/new', [
>             zero or more track
>                  configuration objects ]);
>
>
>                  Robert Buels
>                  Lead Developer
>                  JBrowse - http://jbrowse.org
>
>                  On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
>                   > Hi David,
>                   >
>                   > Would BLAT be an acceptable substitute? We've got
>             that working for
>                   > Apollo and it shouldn't require too much effort to
>             push back into the
>                   > main branch of JBrowse.
>                   >
>                   > -S
>                   >
>                   > On Nov 7, 2013, at 10:03 PM, David M. Goodstein
>                  <[hidden email] <mailto:[hidden email]>
>             <mailto:[hidden email] <mailto:[hidden email]>>
>                   > <mailto:[hidden email]
>             <mailto:[hidden email]> <mailto:[hidden email]
>             <mailto:[hidden email]>>>> wrote:
>                   >
>                   >> Hi All,
>                   >>
>                   >>   We're in the middle of converting our GBrowse
>             installations to
>                   >> JBrowse, and need to retain our ability to show
>             user BLAST
>                  results in
>                   >> the genome browser.  We currently do that in
>             GBrowse with remote
>                   >> feature tracks, configured as:
>                   >>
>                   >> [UserBlast]
>                   >> stranded = 1
>                   >> remote feature = sub{my $q = CGI->new;my $zuid=
>             $q->cookie('zuid')
>                   >> ;return
>                   >>
>
>             "http://zome-dev.phytozome.__net/cgi-bin/returnBLASTgff.pl?__source=maize&zuid=$zuid&type=__match:BLAST
>             <http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST>";}
>                   >> balloon hover =
>                   >> link =
>                   >>
>                   >>
>                   >> This searches a user- and session-specific
>             directory for BLAST
>                  output
>                   >> files, converts them to GFF on the fly, and
>             displays them in the
>                  track
>                   >> UserBlast.
>                   >>
>                   >> Is there an equivalent capability in JBrowse,
>             assuming we had
>                  already
>                   >> converted our BLAST results to JSON?
>                   >>
>                   >> thx,
>                   >>
>                   >> -David
>                   >>
>                   >>
>                   >> David M. Goodstein, Ph.D.
>                   >> Phytozome Group Lead
>                   >> Plant and Computational Genomics Group
>                   >> Joint Genome Institute - Lawrence Berkeley National
>             Laboratory -
>                  U.S.
>                   >> Dept. of Energy
>                   >> Center for Integrative Genomics - UC Berkeley
>                   >>
>                   >>
>
>             ------------------------------__------------------------------__------------------
>                   >> November Webinars for C, C++, Fortran Developers
>                   >> Accelerate application performance with scalable
>             programming models.
>                   >> Explore
>                   >> techniques for threading, error checking, porting,
>             and tuning.
>                  Get the
>                   >> most
>                   >> from the latest Intel processors and coprocessors.
>             See abstracts and
>                   >> register
>                   >>
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>             <mailto:[hidden email]>
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>             <mailto:[hidden email]>>
>
>                   >>
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>             <https://lists.sourceforge.net/lists/listinfo/gmod-ajax>
>                   >
>
>
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>                  Accelerate application performance with scalable
>             programming models.
>                  Explore
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>             tuning. Get
>                  the most
>                  from the latest Intel processors and coprocessors. See
>             abstracts and
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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Richard Hayes
In reply to this post by Richard Hayes
Hi,

Looking at this topic some more, I am testing out including the blast results track in the config files, rather than relying on adding the track and it's custom store via the browser querystring.

I'm including this in my tracks.conf, attempting a function callback for urlTemplate to alter the URL according to a cookie set by our frontend codebase.

[tracks.UserBlastResults]
key = User Blast Results                                                                                                                               
type = JBrowse/View/Track/CanvasFeatures
glyph = JBrowse/View/FeatureGlyph/Segments
subParts = match_part
style.color = deepskyblue
storeClass = JBrowse/Store/SeqFeature/GFF3
urlTemplate = function( track, feature ) {
                  var zuid = getCookie('zuid');
                  if (zuid !="") {
                      console.log('zuid='+zuid);
                      return '<a href="http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&amp;zuid=&#39;+zuid+&#39;&amp;type=match:BLAST">http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid='+zuid+'&type=match:BLAST';
                  }
                  else {
                      console.log('no zuid cookie');
                      return '';
                  }
          }

I must have the function declaration wrong, as this complains in the console:
Uncaught TypeError: Object function ( track, feature ) { var zuid = getCookie('zuid'); if (zuid !="") { console.log('zuid='+zuid); return 'http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid='+zuid+'&type=match:BLAST'; } else { console.log('no zuid cookie'); return ''; } } has no method 'match'

Tests with a known cookie value hardcoded in tracks.conf as
are working, so it's a matter of figuring out the correct syntax for a urlTemplate callback function.



Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Tue, Jan 7, 2014 at 10:58 AM, Richard Hayes <[hidden email]> wrote:
Hi Rob,

Following up on this, I am trying to add a track via URL querystring to load GFF3 returned directly by a CGI script. Various attempts with the following are close, but aren't fully working.

I have addTracks=[ {"track" : "BlastResults",
                                "key" : "User Blast Results",
                                "type" : "CanvasFeatures",
                                "glyph" : "JBrowse/View/FeatureGlyph/Segments",
                               "feature" : [ "match:BLAST" ],
                               "subParts" : "match_part",
                               "style" : { "color" : "deepskyblue" },
                               "store" : "userblast"
} ]

and addStores=[ { "userblast" : {
                            "type" : "JBrowse/Store/SeqFeature/GFF3",
                            "urlTemplate" : "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST" }
}]

These are cobbled together from several other email threads. Do I have the right mix of parameters in each one? There is no wiki documentation for addStores. The actual query string has whitespace removed and is urlecoded. This is still behind a firewall on our dev server, but this is the link I'm attempting on an otherwise empty cache other than generating a blast result on our frontend website:

http://zome-dev.phytozome.net/jbrowse/index.html?data=genomes%2FAcoerulea&loc=scaffold_1%3A1112664..1119856&tracks=BlastResults%2CTranscripts%2CAlt_Transcripts%2CPASA_assembly&addTracks=%5B%7B%22label%22%3A%22User%20Blast%20Results%22%2C%22type%22%3A%22CanvasFeatures%22%2C%22glyph%22%3A%22JBrowse%2FView%2FFeatureGlyph%2FSegments%22%2C%22feature%22%3A%5B%22match%3ABLAST%22%5D%2C%22subParts%22%3A%22match_part%22%2C%22style%22%3A%7B%22color%22%3A%22deepskyblue%22%7D%2C%22store%22%20%3A%20%22userblast%22%7D%5D&addStores=%5B%7B%20%22userblast%22%20%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FGFF3%22%2C%22urlTemplate%22%3A%22http%3A%2F%2Fzome-dev.phytozome.net%2Fcgi-bin%2FreturnBLASTgff.pl%3Fsource%3Daquilegia%26zuid%3D52cbbda135582%26type%3Dmatch%3ABLAST%22%7D%20%7D%5D

The urlTemplate link above is also behind the firewall, but returns GFF3 directly. The zuid parameter matches with a user session cookie from our frontend when links like these will be generated.

I can get the track to show up on the track list only if I wrap both strings in square brackets (as shown), but it remains unselected despite being in the tracks list. When I click to turn it on, I get the error:

store 'userblast' not found

I feel that I'm close, but unsure what is missing or not otherwise correct.

Thanks!

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]> wrote:
Hi David,

Did you write this to the gmod-ajax mailing list?  I didn't see it come
through there, or I would have responded more quickly.

Option 1:
   You can definitely serve BLAST results through the JBrowse REST API,
see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.

Option 2:
   Or you might also be able to just use the existing web service if
it's just returning small bits of GFF3 (is it?).  JBrowse has a data
backend that can read GFF3 directly, also.  The track configuration
would probably be something like (not tested):

{ "label": "blast_gff3_test",
   "type": "JBrowse/View/Track/CanvasFeatures",
   "storeClass": "JBrowse/Store/SeqFeature/GFF3",
   "urlTemplate":
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
}

and that configuration could in turn either be served by a server-side
script and included with an "include" statement in the JBrowse
configuration, or injected into a running JBrowse on the client side
(with APIs that I still haven't documented very well), something like:

   JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
configuration objects ]);


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
> Hi David,
>
> Would BLAT be an acceptable substitute? We've got that working for
> Apollo and it shouldn't require too much effort to push back into the
> main branch of JBrowse.
>
> -S
>
> On Nov 7, 2013, at 10:03 PM, David M. Goodstein <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Hi All,
>>
>>   We're in the middle of converting our GBrowse installations to
>> JBrowse, and need to retain our ability to show user BLAST results in
>> the genome browser.  We currently do that in GBrowse with remote
>> feature tracks, configured as:
>>
>> [UserBlast]
>> stranded = 1
>> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
>> ;return
>> "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>> balloon hover =
>> link =
>>
>>
>> This searches a user- and session-specific directory for BLAST output
>> files, converts them to GFF on the fly, and displays them in the track
>> UserBlast.
>>
>> Is there an equivalent capability in JBrowse, assuming we had already
>> converted our BLAST results to JSON?
>>
>> thx,
>>
>> -David
>>
>>
>> David M. Goodstein, Ph.D.
>> Phytozome Group Lead
>> Plant and Computational Genomics Group
>> Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S.
>> Dept. of Energy
>> Center for Integrative Genomics - UC Berkeley
>>
>> ------------------------------------------------------------------------------
>> November Webinars for C, C++, Fortran Developers
>> Accelerate application performance with scalable programming models.
>> Explore
>> techniques for threading, error checking, porting, and tuning. Get the
>> most
>> from the latest Intel processors and coprocessors. See abstracts and
>> register
>> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Richard Hayes
Sorry, I realized that I pasted from a config file with an incomplete function, since getCookie doesn't actually exist (I've been cobbling this together from a javascript cookie tutorial). The full function that should work is:

urlTemplate = function( track, feature ) {
                  var zuid = "";
                  var ca = document.cookie.split(';');
                  for (var i=0; i<ca.length; i++) {
                      var c = ca[i].trim();
                      if (c.indexOf("zuid=")==0) zuid = c.substring(5,c.length);
                  }
                  if (zuid != "") {
                      console.log("zuid="+zuid);
                      return "http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid="+zuid+"&type=match:BLAST";
                  }
                  else {
                      console.log("no zuid cookie");
                      return "";
                  }
              }

However, trying just:
urlTemplate = function( track, feature ) {
                  return "http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid=3213496843103&type=match:BLAST";
                  }
gives me:
Uncaught TypeError: Object function ( track, feature ) { return "http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid=3213496843103&type=match:BLAST"; } has no method 'match'

leading me to think urlTemplate doesn't yet accept callbacks. has no method 'match' seems to indicate that the function is not getting interpreted as a callback, or I'm not returning a value that is seen as a string.


Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Fri, Jan 31, 2014 at 3:20 PM, Richard Hayes <[hidden email]> wrote:
Hi,

Looking at this topic some more, I am testing out including the blast results track in the config files, rather than relying on adding the track and it's custom store via the browser querystring.

I'm including this in my tracks.conf, attempting a function callback for urlTemplate to alter the URL according to a cookie set by our frontend codebase.

[tracks.UserBlastResults]
key = User Blast Results                                                                                                                               
type = JBrowse/View/Track/CanvasFeatures
glyph = JBrowse/View/FeatureGlyph/Segments
subParts = match_part
style.color = deepskyblue
storeClass = JBrowse/Store/SeqFeature/GFF3
urlTemplate = function( track, feature ) {
                  var zuid = getCookie('zuid');
                  if (zuid !="") {
                      console.log('zuid='+zuid);
                      return '<a href="http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&amp;zuid=&#39;+zuid+&#39;&amp;type=match:BLAST" target="_blank">http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid='+zuid+'&type=match:BLAST';
                  }
                  else {
                      console.log('no zuid cookie');
                      return '';
                  }
          }

I must have the function declaration wrong, as this complains in the console:
Uncaught TypeError: Object function ( track, feature ) { var zuid = getCookie('zuid'); if (zuid !="") { console.log('zuid='+zuid); return 'http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid='+zuid+'&type=match:BLAST'; } else { console.log('no zuid cookie'); return ''; } } has no method 'match'

Tests with a known cookie value hardcoded in tracks.conf as
are working, so it's a matter of figuring out the correct syntax for a urlTemplate callback function.



Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Tue, Jan 7, 2014 at 10:58 AM, Richard Hayes <[hidden email]> wrote:
Hi Rob,

Following up on this, I am trying to add a track via URL querystring to load GFF3 returned directly by a CGI script. Various attempts with the following are close, but aren't fully working.

I have addTracks=[ {"track" : "BlastResults",
                                "key" : "User Blast Results",
                                "type" : "CanvasFeatures",
                                "glyph" : "JBrowse/View/FeatureGlyph/Segments",
                               "feature" : [ "match:BLAST" ],
                               "subParts" : "match_part",
                               "style" : { "color" : "deepskyblue" },
                               "store" : "userblast"
} ]

and addStores=[ { "userblast" : {
                            "type" : "JBrowse/Store/SeqFeature/GFF3",
                            "urlTemplate" : "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST" }
}]

These are cobbled together from several other email threads. Do I have the right mix of parameters in each one? There is no wiki documentation for addStores. The actual query string has whitespace removed and is urlecoded. This is still behind a firewall on our dev server, but this is the link I'm attempting on an otherwise empty cache other than generating a blast result on our frontend website:

http://zome-dev.phytozome.net/jbrowse/index.html?data=genomes%2FAcoerulea&loc=scaffold_1%3A1112664..1119856&tracks=BlastResults%2CTranscripts%2CAlt_Transcripts%2CPASA_assembly&addTracks=%5B%7B%22label%22%3A%22User%20Blast%20Results%22%2C%22type%22%3A%22CanvasFeatures%22%2C%22glyph%22%3A%22JBrowse%2FView%2FFeatureGlyph%2FSegments%22%2C%22feature%22%3A%5B%22match%3ABLAST%22%5D%2C%22subParts%22%3A%22match_part%22%2C%22style%22%3A%7B%22color%22%3A%22deepskyblue%22%7D%2C%22store%22%20%3A%20%22userblast%22%7D%5D&addStores=%5B%7B%20%22userblast%22%20%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FGFF3%22%2C%22urlTemplate%22%3A%22http%3A%2F%2Fzome-dev.phytozome.net%2Fcgi-bin%2FreturnBLASTgff.pl%3Fsource%3Daquilegia%26zuid%3D52cbbda135582%26type%3Dmatch%3ABLAST%22%7D%20%7D%5D

The urlTemplate link above is also behind the firewall, but returns GFF3 directly. The zuid parameter matches with a user session cookie from our frontend when links like these will be generated.

I can get the track to show up on the track list only if I wrap both strings in square brackets (as shown), but it remains unselected despite being in the tracks list. When I click to turn it on, I get the error:

store 'userblast' not found

I feel that I'm close, but unsure what is missing or not otherwise correct.

Thanks!

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]> wrote:
Hi David,

Did you write this to the gmod-ajax mailing list?  I didn't see it come
through there, or I would have responded more quickly.

Option 1:
   You can definitely serve BLAST results through the JBrowse REST API,
see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.

Option 2:
   Or you might also be able to just use the existing web service if
it's just returning small bits of GFF3 (is it?).  JBrowse has a data
backend that can read GFF3 directly, also.  The track configuration
would probably be something like (not tested):

{ "label": "blast_gff3_test",
   "type": "JBrowse/View/Track/CanvasFeatures",
   "storeClass": "JBrowse/Store/SeqFeature/GFF3",
   "urlTemplate":
"http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
}

and that configuration could in turn either be served by a server-side
script and included with an "include" statement in the JBrowse
configuration, or injected into a running JBrowse on the client side
(with APIs that I still haven't documented very well), something like:

   JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or more track
configuration objects ]);


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
> Hi David,
>
> Would BLAT be an acceptable substitute? We've got that working for
> Apollo and it shouldn't require too much effort to push back into the
> main branch of JBrowse.
>
> -S
>
> On Nov 7, 2013, at 10:03 PM, David M. Goodstein <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Hi All,
>>
>>   We're in the middle of converting our GBrowse installations to
>> JBrowse, and need to retain our ability to show user BLAST results in
>> the genome browser.  We currently do that in GBrowse with remote
>> feature tracks, configured as:
>>
>> [UserBlast]
>> stranded = 1
>> remote feature = sub{my $q = CGI->new;my $zuid= $q->cookie('zuid')
>> ;return
>> "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>> balloon hover =
>> link =
>>
>>
>> This searches a user- and session-specific directory for BLAST output
>> files, converts them to GFF on the fly, and displays them in the track
>> UserBlast.
>>
>> Is there an equivalent capability in JBrowse, assuming we had already
>> converted our BLAST results to JSON?
>>
>> thx,
>>
>> -David
>>
>>
>> David M. Goodstein, Ph.D.
>> Phytozome Group Lead
>> Plant and Computational Genomics Group
>> Joint Genome Institute - Lawrence Berkeley National Laboratory - U.S.
>> Dept. of Energy
>> Center for Integrative Genomics - UC Berkeley
>>
>> ------------------------------------------------------------------------------
>> November Webinars for C, C++, Fortran Developers
>> Accelerate application performance with scalable programming models.
>> Explore
>> techniques for threading, error checking, porting, and tuning. Get the
>> most
>> from the latest Intel processors and coprocessors. See abstracts and
>> register
>> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

------------------------------------------------------------------------------
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Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
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Re: [apollo-dev] capability equivalent to remote feature track in Gbrowse?

Robert Buels-2
urlTemplate variables don't support callbacks right now.  It's not super
hard to add support for it though.  Maybe we can go over how to do it in
IRC on Monday?  The code to start looking at would be
src/JBrowse/Store/SeqFeature/NCList.js


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/31/2014 03:55 PM, Richard Hayes wrote:

> Sorry, I realized that I pasted from a config file with an incomplete
> function, since getCookie doesn't actually exist (I've been cobbling
> this together from a javascript cookie tutorial). The full function that
> should work is:
>
> urlTemplate = function( track, feature ) {
>                    var zuid = "";
>                    var ca = document.cookie.split(';');
>                    for (var i=0; i<ca.length; i++) {
>                        var c = ca[i].trim();
>                        if (c.indexOf("zuid=")==0) zuid =
> c.substring(5,c.length);
>                    }
>                    if (zuid != "") {
>                        console.log("zuid="+zuid);
>                        return
> "http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid="+zuid+"&type=match:BLAST";
>                    }
>                    else {
>                        console.log("no zuid cookie");
>                        return "";
>                    }
>                }
>
> However, trying just:
> urlTemplate = function( track, feature ) {
>                    return
> "http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid=3213496843103&type=match:BLAST";
>                    }
> gives me:
> Uncaught TypeError: Object function ( track, feature ) { return
> "http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid=3213496843103&type=match:BLAST";
> } has no method 'match'
>
> leading me to think urlTemplate doesn't yet accept callbacks. has no
> method 'match' seems to indicate that the function is not getting
> interpreted as a callback, or I'm not returning a value that is seen as
> a string.
>
>
> Richard D. Hayes, Ph.D.
> Joint Genome Institute / Lawrence Berkeley National Lab
> http://www.phytozome.net
>
>
> On Fri, Jan 31, 2014 at 3:20 PM, Richard Hayes <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi,
>
>     Looking at this topic some more, I am testing out including the
>     blast results track in the config files, rather than relying on
>     adding the track and it's custom store via the browser querystring.
>
>     I'm including this in my tracks.conf, attempting a function callback
>     for urlTemplate to alter the URL according to a cookie set by our
>     frontend codebase.
>
>     [tracks.UserBlastResults]
>     key = User Blast Results
>     type = JBrowse/View/Track/CanvasFeatures
>     glyph = JBrowse/View/FeatureGlyph/Segments
>     subParts = match_part
>     style.color = deepskyblue
>     storeClass = JBrowse/Store/SeqFeature/GFF3
>     urlTemplate = function( track, feature ) {
>                        var zuid = getCookie('zuid');
>                        if (zuid !="") {
>                            console.log('zuid='+zuid);
>                            return
>     'http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid='+zuid+'&type=match:BLAST';
>                        }
>                        else {
>                            console.log('no zuid cookie');
>                            return '';
>                        }
>                }
>
>     I must have the function declaration wrong, as this complains in the
>     console:
>     Uncaught TypeError: Object function ( track, feature ) { var zuid =
>     getCookie('zuid'); if (zuid !="") { console.log('zuid='+zuid);
>     return
>     'http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid='+zuid+'&type=match:BLAST
>     <http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid=%27+zuid+%27&type=match:BLAST>';
>     } else { console.log('no zuid cookie'); return ''; } } has no method
>     'match'
>
>     Tests with a known cookie value hardcoded in tracks.conf as
>     urlTemplate =
>     http://gpweb20.nersc.gov:8081/cgi-bin/returnBLASTgff.pl?source=poplar&zuid=3213496843103&type=match:BLAST
>
>     are working, so it's a matter of figuring out the correct syntax for
>     a urlTemplate callback function.
>
>
>
>     Richard D. Hayes, Ph.D.
>     Joint Genome Institute / Lawrence Berkeley National Lab
>     http://www.phytozome.net
>
>
>     On Tue, Jan 7, 2014 at 10:58 AM, Richard Hayes <[hidden email]
>     <mailto:[hidden email]>> wrote:
>
>         Hi Rob,
>
>         Following up on this, I am trying to add a track via URL
>         querystring to load GFF3 returned directly by a CGI script.
>         Various attempts with the following are close, but aren't fully
>         working.
>
>         I have addTracks=[ {"track" : "BlastResults",
>                                          "key" : "User Blast Results",
>                                          "type" : "CanvasFeatures",
>                                          "glyph" :
>         "JBrowse/View/FeatureGlyph/Segments",
>                                         "feature" : [ "match:BLAST" ],
>                                         "subParts" : "match_part",
>                                         "style" : { "color" :
>         "deepskyblue" },
>                                         "store" : "userblast"
>         } ]
>
>         and addStores=[ { "userblast" : {
>                                      "type" :
>         "JBrowse/Store/SeqFeature/GFF3",
>                                      "urlTemplate" :
>         "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=aquilegia&zuid=52cbbda135582&type=match:BLAST"
>         }
>         }]
>
>         These are cobbled together from several other email threads. Do
>         I have the right mix of parameters in each one? There is no wiki
>         documentation for addStores. The actual query string has
>         whitespace removed and is urlecoded. This is still behind a
>         firewall on our dev server, but this is the link I'm attempting
>         on an otherwise empty cache other than generating a blast result
>         on our frontend website:
>
>         http://zome-dev.phytozome.net/jbrowse/index.html?data=genomes%2FAcoerulea&loc=scaffold_1%3A1112664..1119856&tracks=BlastResults%2CTranscripts%2CAlt_Transcripts%2CPASA_assembly&addTracks=%5B%7B%22label%22%3A%22User%20Blast%20Results%22%2C%22type%22%3A%22CanvasFeatures%22%2C%22glyph%22%3A%22JBrowse%2FView%2FFeatureGlyph%2FSegments%22%2C%22feature%22%3A%5B%22match%3ABLAST%22%5D%2C%22subParts%22%3A%22match_part%22%2C%22style%22%3A%7B%22color%22%3A%22deepskyblue%22%7D%2C%22store%22%20%3A%20%22userblast%22%7D%5D&addStores=%5B%7B%20%22userblast%22%20%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FGFF3%22%2C%22urlTemplate%22%3A%22http%3A%2F%2Fzome-dev.phytozome.net%2Fcgi-bin%2FreturnBLASTgff.pl%3Fsource%3Daquilegia%26zuid%3D52cbbda135582%26type%3Dmatch%3ABLAST%22%7D%20%7D%5D
>
>         The urlTemplate link above is also behind the firewall, but
>         returns GFF3 directly. The zuid parameter matches with a user
>         session cookie from our frontend when links like these will be
>         generated.
>
>         I can get the track to show up on the track list only if I wrap
>         both strings in square brackets (as shown), but it remains
>         unselected despite being in the tracks list. When I click to
>         turn it on, I get the error:
>
>         store 'userblast' not found
>
>         I feel that I'm close, but unsure what is missing or not
>         otherwise correct.
>
>         Thanks!
>
>         Richard D. Hayes, Ph.D.
>         Joint Genome Institute / Lawrence Berkeley National Lab
>         http://www.phytozome.net
>
>
>         On Fri, Nov 8, 2013 at 10:33 AM, Robert Buels <[hidden email]
>         <mailto:[hidden email]>> wrote:
>
>             Hi David,
>
>             Did you write this to the gmod-ajax mailing list?  I didn't
>             see it come
>             through there, or I would have responded more quickly.
>
>             Option 1:
>                 You can definitely serve BLAST results through the
>             JBrowse REST API,
>             see
>             http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services.
>
>             Option 2:
>                 Or you might also be able to just use the existing web
>             service if
>             it's just returning small bits of GFF3 (is it?).  JBrowse
>             has a data
>             backend that can read GFF3 directly, also.  The track
>             configuration
>             would probably be something like (not tested):
>
>             { "label": "blast_gff3_test",
>                 "type": "JBrowse/View/Track/CanvasFeatures",
>                 "storeClass": "JBrowse/Store/SeqFeature/GFF3",
>                 "urlTemplate":
>             "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST"
>             }
>
>             and that configuration could in turn either be served by a
>             server-side
>             script and included with an "include" statement in the JBrowse
>             configuration, or injected into a running JBrowse on the
>             client side
>             (with APIs that I still haven't documented very well),
>             something like:
>
>                 JBrowse.publish('/jbrowse/v1/c/tracks/new', [ zero or
>             more track
>             configuration objects ]);
>
>
>             Robert Buels
>             Lead Developer
>             JBrowse - http://jbrowse.org
>
>             On 11/08/2013 01:15 PM, Suzanna Lewis wrote:
>              > Hi David,
>              >
>              > Would BLAT be an acceptable substitute? We've got that
>             working for
>              > Apollo and it shouldn't require too much effort to push
>             back into the
>              > main branch of JBrowse.
>              >
>              > -S
>              >
>              > On Nov 7, 2013, at 10:03 PM, David M. Goodstein
>             <[hidden email] <mailto:[hidden email]>
>              > <mailto:[hidden email]
>             <mailto:[hidden email]>>> wrote:
>              >
>              >> Hi All,
>              >>
>              >>   We're in the middle of converting our GBrowse
>             installations to
>              >> JBrowse, and need to retain our ability to show user
>             BLAST results in
>              >> the genome browser.  We currently do that in GBrowse
>             with remote
>              >> feature tracks, configured as:
>              >>
>              >> [UserBlast]
>              >> stranded = 1
>              >> remote feature = sub{my $q = CGI->new;my $zuid=
>             $q->cookie('zuid')
>              >> ;return
>              >>
>             "http://zome-dev.phytozome.net/cgi-bin/returnBLASTgff.pl?source=maize&zuid=$zuid&type=match:BLAST";}
>              >> balloon hover =
>              >> link =
>              >>
>              >>
>              >> This searches a user- and session-specific directory for
>             BLAST output
>              >> files, converts them to GFF on the fly, and displays
>             them in the track
>              >> UserBlast.
>              >>
>              >> Is there an equivalent capability in JBrowse, assuming
>             we had already
>              >> converted our BLAST results to JSON?
>              >>
>              >> thx,
>              >>
>              >> -David
>              >>
>              >>
>              >> David M. Goodstein, Ph.D.
>              >> Phytozome Group Lead
>              >> Plant and Computational Genomics Group
>              >> Joint Genome Institute - Lawrence Berkeley National
>             Laboratory - U.S.
>              >> Dept. of Energy
>              >> Center for Integrative Genomics - UC Berkeley
>              >>
>              >>
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