submitter_plugin.conf

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submitter_plugin.conf

Sofia Robb-4
Hello,

I was wondering if there is a standard set of "keywords" to use in the submitter_plugin.conf.  For example, I see that if one uses

seq_label = someLabel

you will get the sequence of the rubberbanded region labeled someLabel.

What I really want to pass on to a custom cgi script via the submitter is the name of the selected region, eg., Chr1:1...60000. But, it would be nice to know what other default "keywords" are available. 


Thanks,
Sofia
--
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Wessler and Stajich Laboratories
University of California Riverside


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Re: submitter_plugin.conf

Scott Cain
Hi Sofia,

I've not configured the submitter plugin myself (only used what other people have set up), but I think you can do whatever you want.  That is, the seq_label in your example above is what is passed to the external cgi as a key in a parameter list, ie http://zaaa.com/?.....&seq_label=someLabel&.....   Since you have control of the cgi you're passing to as well, you can make up parameter names as needed.

Of course, please let me know if I'm wrong, because I haven't really examined any code to verify this feeling :-)

Scott



On Mon, Dec 9, 2013 at 10:28 PM, Sofia Robb <[hidden email]> wrote:
Hello,

I was wondering if there is a standard set of "keywords" to use in the submitter_plugin.conf.  For example, I see that if one uses

seq_label = someLabel

you will get the sequence of the rubberbanded region labeled someLabel.

What I really want to pass on to a custom cgi script via the submitter is the name of the selected region, eg., Chr1:1...60000. But, it would be nice to know what other default "keywords" are available. 


Thanks,
Sofia
--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside


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

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Re: submitter_plugin.conf

Sofia Robb-4
Hi Scott,

It seems that seq_label is special, because it takes the value on the right, uses it as the cgi key and puts actual sequence as the value, seq_lab is never used in the key/value pairs passed on (somelabel=ATGC). While the others are just as you said, PROGRAM   = blastn (resulting in url.com?ROGRAM=blastn)

I want to pass the name of the region on, not the sequence. Chr1:1...10 . This comes into the submitter on the url. 


I tried using this, even though I thought it probably wouldn't work,

 my $name = param(name);
 [MY_DUMPER]
            confirm = 1
            url       = http://myURL/script.pl
            name      = $name

I also tried, and failed, to use name_label = REGION, hoping, that in the spirit of seq_label= SEQ results in SEQ=ATGCCGTTT that it would result in REGION=Chr1:1.10

Thanks,
Sofia


On Mon, Dec 9, 2013 at 9:19 PM, Scott Cain <[hidden email]> wrote:
Hi Sofia,

I've not configured the submitter plugin myself (only used what other people have set up), but I think you can do whatever you want.  That is, the seq_label in your example above is what is passed to the external cgi as a key in a parameter list, ie http://zaaa.com/?.....&seq_label=someLabel&.....   Since you have control of the cgi you're passing to as well, you can make up parameter names as needed.

Of course, please let me know if I'm wrong, because I haven't really examined any code to verify this feeling :-)

Scott



On Mon, Dec 9, 2013 at 10:28 PM, Sofia Robb <[hidden email]> wrote:
Hello,

I was wondering if there is a standard set of "keywords" to use in the submitter_plugin.conf.  For example, I see that if one uses

seq_label = someLabel

you will get the sequence of the rubberbanded region labeled someLabel.

What I really want to pass on to a custom cgi script via the submitter is the name of the selected region, eg., Chr1:1...60000. But, it would be nice to know what other default "keywords" are available. 


Thanks,
Sofia
--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside


------------------------------------------------------------------------------
Sponsored by Intel(R) XDK
Develop, test and display web and hybrid apps with a single code base.
Download it for free now!
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside


------------------------------------------------------------------------------
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organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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Re: submitter_plugin.conf

Sofia Robb-4
Hah!! I got it!! i had to add code to Submitter.pm 

I found all the lines with seq_label and added new ones for region_label. Except, I did not make the region_label required. 

I would like to add this the official code (which I have never done before). I will now look into how to do that :)

Thanks!!
Sofia


On Tue, Dec 10, 2013 at 9:19 AM, Sofia Robb <[hidden email]> wrote:
Hi Scott,

It seems that seq_label is special, because it takes the value on the right, uses it as the cgi key and puts actual sequence as the value, seq_lab is never used in the key/value pairs passed on (somelabel=ATGC). While the others are just as you said, PROGRAM   = blastn (resulting in url.com?ROGRAM=blastn)

I want to pass the name of the region on, not the sequence. Chr1:1...10 . This comes into the submitter on the url. 


I tried using this, even though I thought it probably wouldn't work,

 my $name = param(name);
 [MY_DUMPER]
            confirm = 1
            url       = http://myURL/script.pl
            name      = $name

I also tried, and failed, to use name_label = REGION, hoping, that in the spirit of seq_label= SEQ results in SEQ=ATGCCGTTT that it would result in REGION=Chr1:1.10

Thanks,
Sofia


On Mon, Dec 9, 2013 at 9:19 PM, Scott Cain <[hidden email]> wrote:
Hi Sofia,

I've not configured the submitter plugin myself (only used what other people have set up), but I think you can do whatever you want.  That is, the seq_label in your example above is what is passed to the external cgi as a key in a parameter list, ie http://zaaa.com/?.....&seq_label=someLabel&.....   Since you have control of the cgi you're passing to as well, you can make up parameter names as needed.

Of course, please let me know if I'm wrong, because I haven't really examined any code to verify this feeling :-)

Scott



On Mon, Dec 9, 2013 at 10:28 PM, Sofia Robb <[hidden email]> wrote:
Hello,

I was wondering if there is a standard set of "keywords" to use in the submitter_plugin.conf.  For example, I see that if one uses

seq_label = someLabel

you will get the sequence of the rubberbanded region labeled someLabel.

What I really want to pass on to a custom cgi script via the submitter is the name of the selected region, eg., Chr1:1...60000. But, it would be nice to know what other default "keywords" are available. 


Thanks,
Sofia
--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside


------------------------------------------------------------------------------
Sponsored by Intel(R) XDK
Develop, test and display web and hybrid apps with a single code base.
Download it for free now!
http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside




--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
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Re: submitter_plugin.conf

Fields, Christopher J
Sofia,

All the code is on github:


I would make a fork of the repository and add your fixes, then submit a pull request.

chris


On Dec 10, 2013, at 11:56 AM, Sofia Robb <[hidden email]> wrote:

Hah!! I got it!! i had to add code to Submitter.pm 

I found all the lines with seq_label and added new ones for region_label. Except, I did not make the region_label required. 

I would like to add this the official code (which I have never done before). I will now look into how to do that :)

Thanks!!
Sofia


On Tue, Dec 10, 2013 at 9:19 AM, Sofia Robb <[hidden email]> wrote:
Hi Scott,

It seems that seq_label is special, because it takes the value on the right, uses it as the cgi key and puts actual sequence as the value, seq_lab is never used in the key/value pairs passed on (somelabel=ATGC). While the others are just as you said, PROGRAM   = blastn (resulting in url.com?ROGRAM=blastn)

I want to pass the name of the region on, not the sequence. Chr1:1...10 . This comes into the submitter on the url. 


I tried using this, even though I thought it probably wouldn't work,

 my $name = param(name);
 [MY_DUMPER]
            confirm = 1
            url       = http://myURL/script.pl
            name      = $name

I also tried, and failed, to use name_label = REGION, hoping, that in the spirit of seq_label= SEQ results in SEQ=ATGCCGTTT that it would result in REGION=Chr1:1.10

Thanks,
Sofia


On Mon, Dec 9, 2013 at 9:19 PM, Scott Cain <[hidden email]> wrote:
Hi Sofia,

I've not configured the submitter plugin myself (only used what other people have set up), but I think you can do whatever you want.  That is, the seq_label in your example above is what is passed to the external cgi as a key in a parameter list, ie http://zaaa.com/?.....&seq_label=someLabel&.....   Since you have control of the cgi you're passing to as well, you can make up parameter names as needed.

Of course, please let me know if I'm wrong, because I haven't really examined any code to verify this feeling :-)

Scott



On Mon, Dec 9, 2013 at 10:28 PM, Sofia Robb <[hidden email]> wrote:
Hello,

I was wondering if there is a standard set of "keywords" to use in the submitter_plugin.conf.  For example, I see that if one uses

seq_label = someLabel

you will get the sequence of the rubberbanded region labeled someLabel.

What I really want to pass on to a custom cgi script via the submitter is the name of the selected region, eg., Chr1:1...60000. But, it would be nice to know what other default "keywords" are available. 


Thanks,
Sofia
--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside


------------------------------------------------------------------------------
Sponsored by Intel(R) XDK
Develop, test and display web and hybrid apps with a single code base.
Download it for free now!
http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside




--
Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk_______________________________________________
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------------------------------------------------------------------------------
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organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
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