[BioMart Users] BioMart Central Portal

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[BioMart Users] BioMart Central Portal

Isaac cano
Dear BioMart users,

I've recently known about the BioMart Central Portal and I was wondering if it is available as a mart so we can import the complete central portal as a source into martconfigurator. Is this possible?!

Thanks,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: (+34)932 275 400, ext. 4182\4523
Mobile: (+34) 666 186 748
Fax: (+34) 932 275 455


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Re: [BioMart Users] BioMart Central Portal

Arek Kasprzyk
Hi Isaac,
yes it is possible. The config should be available from the 'registry' directory in rc6 but if not Junjun Zhang (cc'ed on this email) will be able to make this configuraiton available to you. I believe that Nuria (cc'ed on this email) is also interested in this config.
a

On Wed, Dec 21, 2011 at 11:26 AM, Isaac cano <[hidden email]> wrote:
Dear BioMart users,

I've recently known about the BioMart Central Portal and I was wondering if it is available as a mart so we can import the complete central portal as a source into martconfigurator. Is this possible?!

Thanks,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455


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Re: [BioMart Users] BioMart Central Portal

Isaac cano

Thanks a lot Arek, I'll check the registry directory first.
I have to say that Nuria is now in another professional situation but I think she continues being interested.
Thanks,
Isaac

El 21/12/2011 18:46, "Arek Kasprzyk" <[hidden email]> escribió:
Hi Isaac,
yes it is possible. The config should be available from the 'registry' directory in rc6 but if not Junjun Zhang (cc'ed on this email) will be able to make this configuraiton available to you. I believe that Nuria (cc'ed on this email) is also interested in this config.
a

On Wed, Dec 21, 2011 at 11:26 AM, Isaac cano <[hidden email]> wrote:
Dear BioMart users,

I've recently known about the BioMart Central Portal and I was wondering if it is available as a mart so we can import the complete central portal as a source into martconfigurator. Is this possible?!

Thanks,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455


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Re: [BioMart Users] BioMart Central Portal

Junjun Zhang
Junjun

From: Isaac cano <[hidden email]>
Date: Wed, 21 Dec 2011 13:08:16 -0500
To: Arek Kasprzyk <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, jzhang <[hidden email]>, BioMart Users <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Thanks a lot Arek, I'll check the registry directory first.
I have to say that Nuria is now in another professional situation but I think she continues being interested.
Thanks,
Isaac

El 21/12/2011 18:46, "Arek Kasprzyk" <[hidden email]> escribió:
Hi Isaac,
yes it is possible. The config should be available from the 'registry' directory in rc6 but if not Junjun Zhang (cc'ed on this email) will be able to make this configuraiton available to you. I believe that Nuria (cc'ed on this email) is also interested in this config.
a

On Wed, Dec 21, 2011 at 11:26 AM, Isaac cano <[hidden email]> wrote:
Dear BioMart users,

I've recently known about the BioMart Central Portal and I was wondering if it is available as a mart so we can import the complete central portal as a source into martconfigurator. Is this possible?!

Thanks,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455


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[hidden email]
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Re: [BioMart Users] BioMart Central Portal

Isaac cano

Thanks Junjun!
Isaac

El 21/12/2011 20:07, "Junjun Zhang" <[hidden email]> escribió:
Junjun

From: Isaac cano <[hidden email]>
Date: Wed, 21 Dec 2011 13:08:16 -0500
To: Arek Kasprzyk <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, jzhang <[hidden email]>, BioMart Users <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Thanks a lot Arek, I'll check the registry directory first.
I have to say that Nuria is now in another professional situation but I think she continues being interested.
Thanks,
Isaac

El 21/12/2011 18:46, "Arek Kasprzyk" <[hidden email]> escribió:
Hi Isaac,
yes it is possible. The config should be available from the 'registry' directory in rc6 but if not Junjun Zhang (cc'ed on this email) will be able to make this configuraiton available to you. I believe that Nuria (cc'ed on this email) is also interested in this config.
a

On Wed, Dec 21, 2011 at 11:26 AM, Isaac cano <[hidden email]> wrote:
Dear BioMart users,

I've recently known about the BioMart Central Portal and I was wondering if it is available as a mart so we can import the complete central portal as a source into martconfigurator. Is this possible?!

Thanks,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455


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[BioMart Users] Plugin development

Mariette
In reply to this post by Isaac cano
Hi everyone,

I want my plugin to run some basic command, to do so I implemented a processor. However I cannot figure out
how I can catch up parameters I send to the processor.
As example:
the request would be:

http://localhost:9000/martservice/results?query=<!DOCTYPE Query><Query client="webbrowser" processor="MyProcessor" limit="-1" header="0"><Dataset name="mart_db" config="mart_config"><Attribute name="mart__contig__main__dna"/></Dataset></Query>

MyProcessor write the dna value in fasta format and run a command that will format the data to be vizualised into biomart. However, I'd like to provide some other parameters to MyProcessor. I'd like to add some params:

http://localhost:9000/martservice/results?test=test_value&query=<!DOCTYPE Query><Query client="webbrowser" processor="MyProcessor" limit="-1" header="0"><Dataset name="mart_db" config="mart_config"><Attribute name="mart__contig__main__dna"/></Dataset></Query>

and catch the test value within my processor. How can I do so ?
Maybe I shouldn't use a processor, there is any other way to compute some calculation on the server side ?

thanks for your answer,
Jerome

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Re: [BioMart Users] BioMart Central Portal

Isaac cano
In reply to this post by Junjun Zhang
Dear JunJun,

I'm trying to open the CentralPortal.xml registry file but martconfigurator is not able to open it. I get no logs so just command line output that first says something regarding password encryption (see password.png screenshot attached) and then some other outputs (see martconfigurator_output.txt attached). 

I'm using proxy server so I've set it properly and I've tried to open the icgc7.xml registry file and it worked. Any idea why I cannot get opened the CentralPortal.xml registry file??!

Thanks!!

Isaac   

2011/12/21 Junjun Zhang <[hidden email]>
Junjun

From: Isaac cano <[hidden email]>
Date: Wed, 21 Dec 2011 13:08:16 -0500
To: Arek Kasprzyk <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, jzhang <[hidden email]>, BioMart Users <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Thanks a lot Arek, I'll check the registry directory first.
I have to say that Nuria is now in another professional situation but I think she continues being interested.
Thanks,
Isaac

El 21/12/2011 18:46, "Arek Kasprzyk" <[hidden email]> escribió:
Hi Isaac,
yes it is possible. The config should be available from the 'registry' directory in rc6 but if not Junjun Zhang (cc'ed on this email) will be able to make this configuraiton available to you. I believe that Nuria (cc'ed on this email) is also interested in this config.
a

On Wed, Dec 21, 2011 at 11:26 AM, Isaac cano <[hidden email]> wrote:
Dear BioMart users,

I've recently known about the BioMart Central Portal and I was wondering if it is available as a mart so we can import the complete central portal as a source into martconfigurator. Is this possible?!

Thanks,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users





--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: (+34)932 275 400, ext. 4182\4523
Mobile: (+34) 666 186 748
Fax: (+34) 932 275 455


_______________________________________________
Users mailing list
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martconfigurator_output.txt (23K) Download Attachment
password.png (195K) Download Attachment
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Re: [BioMart Users] BioMart Central Portal

Isaac cano
Dear JunJun,

After a long long time trying martconfigurator to open the central portal registry file I've got an out of memory error: GC overhead limit exceed.

Is this really that I should increase the system's physical RAM memory of maybe the Java heap??!!

Thanks!

Isaac

2011/12/22 Isaac cano <[hidden email]>
Dear JunJun,

I'm trying to open the CentralPortal.xml registry file but martconfigurator is not able to open it. I get no logs so just command line output that first says something regarding password encryption (see password.png screenshot attached) and then some other outputs (see martconfigurator_output.txt attached). 

I'm using proxy server so I've set it properly and I've tried to open the icgc7.xml registry file and it worked. Any idea why I cannot get opened the CentralPortal.xml registry file??!

Thanks!!

Isaac   


2011/12/21 Junjun Zhang <[hidden email]>
Junjun

From: Isaac cano <[hidden email]>
Date: Wed, 21 Dec 2011 13:08:16 -0500
To: Arek Kasprzyk <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, jzhang <[hidden email]>, BioMart Users <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Thanks a lot Arek, I'll check the registry directory first.
I have to say that Nuria is now in another professional situation but I think she continues being interested.
Thanks,
Isaac

El 21/12/2011 18:46, "Arek Kasprzyk" <[hidden email]> escribió:
Hi Isaac,
yes it is possible. The config should be available from the 'registry' directory in rc6 but if not Junjun Zhang (cc'ed on this email) will be able to make this configuraiton available to you. I believe that Nuria (cc'ed on this email) is also interested in this config.
a

On Wed, Dec 21, 2011 at 11:26 AM, Isaac cano <[hidden email]> wrote:
Dear BioMart users,

I've recently known about the BioMart Central Portal and I was wondering if it is available as a mart so we can import the complete central portal as a source into martconfigurator. Is this possible?!

Thanks,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users





--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455




--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: (+34)932 275 400, ext. 4182\4523
Mobile: (+34) 666 186 748
Fax: (+34) 932 275 455


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Re: [BioMart Users] BioMart Central Portal

Junjun Zhang
Dear Isaac,

Yes, you need a lot of memory in order to open this registry, it's large.

After compilation with ant, please edit the following file:

dist/scripts/martconfigurator.sh

So that the following line looks like:

$JAVA -Xmx8g -Xms3g -cp $TMP_CLASSPATH org.biomart.configurator.test.MartConfigurator $@

Hope this helps,

Junjun



From: Isaac cano <[hidden email]>
Date: Thu, 22 Dec 2011 07:17:04 -0500
To: jzhang <[hidden email]>, Arek Kasprzyk <[hidden email]>
Cc: BioMart Users <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Dear JunJun,

After a long long time trying martconfigurator to open the central portal registry file I've got an out of memory error: GC overhead limit exceed.

Is this really that I should increase the system's physical RAM memory of maybe the Java heap??!!

Thanks!

Isaac

2011/12/22 Isaac cano <[hidden email]>
Dear JunJun,

I'm trying to open the CentralPortal.xml registry file but martconfigurator is not able to open it. I get no logs so just command line output that first says something regarding password encryption (see password.png screenshot attached) and then some other outputs (see martconfigurator_output.txt attached). 

I'm using proxy server so I've set it properly and I've tried to open the icgc7.xml registry file and it worked. Any idea why I cannot get opened the CentralPortal.xml registry file??!

Thanks!!

Isaac   


2011/12/21 Junjun Zhang <[hidden email]>
Junjun

From: Isaac cano <[hidden email]>
Date: Wed, 21 Dec 2011 13:08:16 -0500
To: Arek Kasprzyk <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, jzhang <[hidden email]>, BioMart Users <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Thanks a lot Arek, I'll check the registry directory first.
I have to say that Nuria is now in another professional situation but I think she continues being interested.
Thanks,
Isaac

El 21/12/2011 18:46, "Arek Kasprzyk" <[hidden email]> escribió:
Hi Isaac,
yes it is possible. The config should be available from the 'registry' directory in rc6 but if not Junjun Zhang (cc'ed on this email) will be able to make this configuraiton available to you. I believe that Nuria (cc'ed on this email) is also interested in this config.
a

On Wed, Dec 21, 2011 at 11:26 AM, Isaac cano <[hidden email]> wrote:
Dear BioMart users,

I've recently known about the BioMart Central Portal and I was wondering if it is available as a mart so we can import the complete central portal as a source into martconfigurator. Is this possible?!

Thanks,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users





--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455




--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: (+34)932 275 400, ext. 4182\4523
Mobile: (+34) 666 186 748
Fax: (+34) 932 275 455


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] BioMart Central Portal

Isaac cano

Thanks Junjun, I'll try that.
Isaac

El 22/12/2011 19:56, "Junjun Zhang" <[hidden email]> escribió:
Dear Isaac,

Yes, you need a lot of memory in order to open this registry, it's large.

After compilation with ant, please edit the following file:

dist/scripts/martconfigurator.sh

So that the following line looks like:

$JAVA -Xmx8g -Xms3g -cp $TMP_CLASSPATH org.biomart.configurator.test.MartConfigurator $@

Hope this helps,

Junjun



From: Isaac cano <[hidden email]>
Date: Thu, 22 Dec 2011 07:17:04 -0500
To: jzhang <[hidden email]>, Arek Kasprzyk <[hidden email]>
Cc: BioMart Users <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Dear JunJun,

After a long long time trying martconfigurator to open the central portal registry file I've got an out of memory error: GC overhead limit exceed.

Is this really that I should increase the system's physical RAM memory of maybe the Java heap??!!

Thanks!

Isaac

2011/12/22 Isaac cano <[hidden email]>
Dear JunJun,

I'm trying to open the CentralPortal.xml registry file but martconfigurator is not able to open it. I get no logs so just command line output that first says something regarding password encryption (see password.png screenshot attached) and then some other outputs (see martconfigurator_output.txt attached). 

I'm using proxy server so I've set it properly and I've tried to open the icgc7.xml registry file and it worked. Any idea why I cannot get opened the CentralPortal.xml registry file??!

Thanks!!

Isaac   


2011/12/21 Junjun Zhang <[hidden email]>
Junjun

From: Isaac cano <[hidden email]>
Date: Wed, 21 Dec 2011 13:08:16 -0500
To: Arek Kasprzyk <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, jzhang <[hidden email]>, BioMart Users <[hidden email]>
Subject: Re: [BioMart Users] BioMart Central Portal

Thanks a lot Arek, I'll check the registry directory first.
I have to say that Nuria is now in another professional situation but I think she continues being interested.
Thanks,
Isaac

El 21/12/2011 18:46, "Arek Kasprzyk" <[hidden email]> escribió:
Hi Isaac,
yes it is possible. The config should be available from the 'registry' directory in rc6 but if not Junjun Zhang (cc'ed on this email) will be able to make this configuraiton available to you. I believe that Nuria (cc'ed on this email) is also interested in this config.
a

On Wed, Dec 21, 2011 at 11:26 AM, Isaac cano <[hidden email]> wrote:
Dear BioMart users,

I've recently known about the BioMart Central Portal and I was wondering if it is available as a mart so we can import the complete central portal as a source into martconfigurator. Is this possible?!

Thanks,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users





--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455




--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: <a href="tel:%28%2B34%29932%20275%20400%2C%20ext.%204182" value="+34932275400" target="_blank">(+34)932 275 400, ext. 4182\4523
Mobile: <a href="tel:%28%2B34%29%20666%20186%20748" value="+34666186748" target="_blank">(+34) 666 186 748
Fax: <a href="tel:%28%2B34%29%20932%20275%20455" value="+34932275455" target="_blank">(+34) 932 275 455


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Re: [BioMart Users] Plugin development

Syed Haider
In reply to this post by Mariette
Hi Jerome,

the ?query request wont accept addition params. A good way to instruct
your Processor to do something dynamic:

1- in the Processor file (eg. TSV.java) retrieve some params from local
variables or file

2- pass in an additional attribtue in query that is mapped against a
database column which contains this dynamic information. And when the
data is returned in the Processor, use these values to carry out your
desired operations.

HTH,
Syed

On 22/12/2011 10:16, Mariette wrote:

> Hi everyone,
>
> I want my plugin to run some basic command, to do so I implemented a processor. However I cannot figure out
> how I can catch up parameters I send to the processor.
> As example:
> the request would be:
>
> http://localhost:9000/martservice/results?query=<!DOCTYPE Query><Query client="webbrowser" processor="MyProcessor" limit="-1" header="0"><Dataset name="mart_db" config="mart_config"><Attribute name="mart__contig__main__dna"/></Dataset></Query>
>
> MyProcessor write the dna value in fasta format and run a command that will format the data to be vizualised into biomart. However, I'd like to provide some other parameters to MyProcessor. I'd like to add some params:
>
> http://localhost:9000/martservice/results?test=test_value&query=<!DOCTYPE Query><Query client="webbrowser" processor="MyProcessor" limit="-1" header="0"><Dataset name="mart_db" config="mart_config"><Attribute name="mart__contig__main__dna"/></Dataset></Query>
>
> and catch the test value within my processor. How can I do so ?
> Maybe I shouldn't use a processor, there is any other way to compute some calculation on the server side ?
>
> thanks for your answer,
> Jerome
>
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