Re: [BioMart Users] Biomart Perl API Problem

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Re: [BioMart Users] Biomart Perl API Problem

Arek Kasprzyk
Hi Manjula,
I am forwarding your email to the [hidden email]. The developers there will be able to help you

a


On Mon, Jul 11, 2011 at 11:45 AM, Manjula Dharmawardhana <[hidden email]> wrote:
Dear Arek,
You must be getting thousands of eMails like this and hope I am not annoying you with this.
I am Biomedical Informatics Student in Sri Lanka learning perl and trying to use Biomart to access COSMIC. I will be grateful if you can tell me;
  • Is it possible to use the perl API in Windows?
The Linux command 'cp' used in the Initializer.pm (Line 127) is not working in windows.
  • If not, is there a workaround for this?

Thanking you in Advance,
Manjula Dharmawardhana

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Re: [BioMart Users] Biomart Perl API Problem

Junjun Zhang
Re: [BioMart Users] Biomart Perl API Problem Dear Manjula,

For Windows, you may try to first install Cygwin (http://www.cygwin.com/) then install BioMart 0.7.

Let us know how it goes, feel free to let us know if you encounter any problems.

Best regards,

Junjun


On 11-07-11 8:19 PM, "Arek Kasprzyk" <arek.kasprzyk@...> wrote:

Hi Manjula,
I am forwarding your email to the users@.... The developers there will be able to help you

a


On Mon, Jul 11, 2011 at 11:45 AM, Manjula Dharmawardhana <manjulapra@...> wrote:
Dear Arek,
You must be getting thousands of eMails like this and hope I am not annoying you with this.
I am Biomedical Informatics Student in Sri Lanka learning perl and trying to use Biomart to access COSMIC. I will be grateful if you can tell me;
  • Is it possible to use the perl API in Windows?
The Linux command 'cp' used in the Initializer.pm (Line 127) is not working in windows.
  • If not, is there a workaround for this?

Thanking you in Advance,
Manjula Dharmawardhana

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Re: [BioMart Users] Biomart Perl API Problem

manjulapra
Hi Junjun and other users,
Thank you very much for the quick and prompt reply, and for helping out newbies like me!

I have installed cygwin and added it to the path. Selected cygwin as interpreter type in my EPIC settings in Eclipse.
But, when running, it gives this error, which does not give any information!

"An internal error occurred during: "Launching Q1.pl".
java.lang.NullPointerException"

My coding and Registry file can be found in this page,

http://biostar.stackexchange.com/questions/10159/biomart-perl-api-in-windows

I don't know whether you can help with this error, but any help in greatly appreciated.

Thanks in advance,

Manjula


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Re: [BioMart Users] Biomart Perl API Problem

Junjun Zhang
Dear Manjula,

Under Windows environment, you can use Eclipse to write your Perl code, but it may be problematic to run BioMart Perl code under Eclipse. You may need to run it under cygwin. When your Perl script is ready to run, start cygwin (make sure Perl is installed under cygwin), then 'cd' into where your perl code is located, just run it as 'perl <name_of_the_perl_code>'.

At the beginning of your perl script, you may need to add a line after 'use strict' something like:

use lib '/path/to/your/BioMart/installation/lib';

This will make Perl know where to load BioMart modules.

Junjun


From: Manjula Dharmawardhana <[hidden email]>
Date: Tue, 12 Jul 2011 01:19:04 -0400
To: jzhang <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] Biomart Perl API Problem

Hi Junjun and other users,
Thank you very much for the quick and prompt reply, and for helping out newbies like me!

I have installed cygwin and added it to the path. Selected cygwin as interpreter type in my EPIC settings in Eclipse.
But, when running, it gives this error, which does not give any information!

"An internal error occurred during: "Launching Q1.pl".
java.lang.NullPointerException"

My coding and Registry file can be found in this page,

http://biostar.stackexchange.com/questions/10159/biomart-perl-api-in-windows

I don't know whether you can help with this error, but any help in greatly appreciated.

Thanks in advance,

Manjula


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Re: [BioMart Users] Biomart Perl API Problem

manjulapra
Thank you Junjun and all,
I have got it right. I changed the interpreter to normal from Cygwin in eclipse preferences and now it's working but giving a "Could not connect to Database" error which I suspect due to something wrong in my Registry file. Thank you all for the help.

Regards,
Manjula


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Re: [BioMart Users] Biomart Perl API Problem

Junjun Zhang
Re: [BioMart Users] Biomart Perl API Problem Hi Manjula,

Are you using the registry file shown in the following page?

http://biostar.stackexchange.com/questions/10159/biomart-perl-api-in-windows

I don’t think the database in the registry file exists any more.

For testing purpose, you can try the vega database using the following settings:

   host         = "martdb.ensembl.org"
    port         = "5316"
    database     = "vega_mart_63"
    schema       = "vega_mart_63"
    user         = "anonymous"
    password     = ""

Best regards,

Junjun


On 11-07-13 1:12 PM, "Manjula Dharmawardhana" <manjulapra@...> wrote:

Thank you Junjun and all,
I have got it right. I changed the interpreter to normal from Cygwin in eclipse preferences and now it's working but giving a "Could not connect to Database" error which I suspect due to something wrong in my Registry file. Thank you all for the help.

Regards,
Manjula


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Re: [BioMart Users] Biomart Perl API Problem

manjulapra
Thank you all,

Yes Junjun it is the same coding, but I have changed the Registry file, Here is the new one

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
     <MartURLLocation
         database="cosp"
         default="1"
         displayName="COSMIC (SANGER UK)"
         host="www.sanger.ac.uk"
         includeDatasets=""
         martUser=""
         name="CosmicMart"
         path="/genetics/CGP/cosmic/biomart/martservice"
        port="80"
         redirect="1"
         serverVirtualSchema="default"
         visible="1"
     />
 </MartRegistry>

Here is what I get at the console;

cygwin warning:
  MS-DOS style path detected: C:/Users/Manjula/workspace/TestMart/registry_DOM_XML
  Preferred POSIX equivalent is: /cygdrive/c/Users/Manjula/workspace/TestMart/registry_DOM_XML
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames

Connection parameters of [COSMIC (SANGER UK)]    [ OK ]

Use of uninitialized value in lc at C:/Perl64/lib/BioMart/Initializer.pm line 1135.
could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"


Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x162da60)', 'BioMart::Dataset::Vary: Accept-Encoding') called at C:\Perl64\lib\BioMart\Initializer.pm line 1162
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x162da60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x162da60)', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x162da60)', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 144
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x162da60)', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\site\lib\BioMart\RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Users\Manjula\workspace\TestMart\Q1.pl line 22

When I change the path to the registry file as "/cygdrive/c/......" I get a con not find the file error.

Strange thing is that, If I give the relative path to the registry file, I get a different error. i.e;

Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 114.
Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 116.
Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 123.
Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 125.
Use of uninitialized value in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 134.
Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 143.

Connection parameters of [COSMIC (SANGER UK)]    [ OK ]

Use of uninitialized value in lc at C:/Perl64/lib/BioMart/Initializer.pm line 1135.
could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"


Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x38da60)', 'BioMart::Dataset::Vary: Accept-Encoding') called at C:\Perl64\lib\BioMart\Initializer.pm line 1162
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x38da60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x38da60)', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x38da60)', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 144
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x38da60)', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\site\lib\BioMart\RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Users\Manjula\workspace\TestMart\Q1.pl line 22


Any help is greatly appreciated!

Thank you!

Regards,
Manjula


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Re: [BioMart Users] Biomart Perl API Problem

Junjun Zhang
Hi Manjula,

Sorry for not be able to response you sooner due to recent travels.

We had experienced similar problem as you showed below. It was caused by some unusual response from the remote server. We have fixed it in the BioMart SVN repository.

You can checkout the code at: https://code.oicr.on.ca/svn/biomart/biomart-perl/trunk/. I just tried it with you registry file. It worked!

Please give it a try, let me know how it goes.

Cheers,
Junjun


From: Manjula Dharmawardhana <[hidden email]>
Date: Sat, 16 Jul 2011 10:54:06 -0400
To: jzhang <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] Biomart Perl API Problem

Thank you all,

Yes Junjun it is the same coding, but I have changed the Registry file, Here is the new one

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
     <MartURLLocation
         database="cosp"
         default="1"
         displayName="COSMIC (SANGER UK)"
         host="www.sanger.ac.uk"
         includeDatasets=""
         martUser=""
         name="CosmicMart"
         path="/genetics/CGP/cosmic/biomart/martservice"
        port="80"
         redirect="1"
         serverVirtualSchema="default"
         visible="1"
     />
 </MartRegistry>

Here is what I get at the console;

cygwin warning:
  MS-DOS style path detected: C:/Users/Manjula/workspace/TestMart/registry_DOM_XML
  Preferred POSIX equivalent is: /cygdrive/c/Users/Manjula/workspace/TestMart/registry_DOM_XML
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames

Connection parameters of [COSMIC (SANGER UK)]    [ OK ]

Use of uninitialized value in lc at C:/Perl64/lib/BioMart/Initializer.pm line 1135.
could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"


Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x162da60)', 'BioMart::Dataset::Vary: Accept-Encoding') called at C:\Perl64\lib\BioMart\Initializer.pm line 1162
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x162da60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x162da60)', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x162da60)', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 144
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x162da60)', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\site\lib\BioMart\RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Users\Manjula\workspace\TestMart\Q1.pl line 22

When I change the path to the registry file as "/cygdrive/c/......" I get a con not find the file error.

Strange thing is that, If I give the relative path to the registry file, I get a different error. i.e;

Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 114.
Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 116.
Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 123.
Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 125.
Use of uninitialized value in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 134.
Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 143.

Connection parameters of [COSMIC (SANGER UK)]    [ OK ]

Use of uninitialized value in lc at C:/Perl64/lib/BioMart/Initializer.pm line 1135.
could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"


Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x38da60)', 'BioMart::Dataset::Vary: Accept-Encoding') called at C:\Perl64\lib\BioMart\Initializer.pm line 1162
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x38da60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x38da60)', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x38da60)', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 144
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x38da60)', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\site\lib\BioMart\RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Users\Manjula\workspace\TestMart\Q1.pl line 22


Any help is greatly appreciated!

Thank you!

Regards,
Manjula


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This communication (including any attachments) is intended for the use of the intended recipient only and may contain information that is confidential, privileged or legally protected. Any unauthorized use or dissemination of this communication is strictly prohibited. If you have received this communication in error, please immediately notify [hidden email] by return e-mail message and delete all copies of the original communication. Thank you for your cooperation.



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Re: [BioMart Users] Biomart Perl API Problem

Fields, Christopher J
Just curious, but will the perl API be supported long-term?  I know of a few users who would like BioMart accessibility within BioPerl (for instance), but it doesn't make much sense to write up anything if the perl API is not being actively developed; we could put more effort to the Java-based API instead.

chris

On Jul 21, 2011, at 11:51 AM, Junjun Zhang wrote:

> Hi Manjula,
>
> Sorry for not be able to response you sooner due to recent travels.
>
> We had experienced similar problem as you showed below. It was caused by some unusual response from the remote server. We have fixed it in the BioMart SVN repository.
>
> You can checkout the code at: https://code.oicr.on.ca/svn/biomart/biomart-perl/trunk/. I just tried it with you registry file. It worked!
>
> Please give it a try, let me know how it goes.
>
> Cheers,
> Junjun
>
>
> From: Manjula Dharmawardhana <[hidden email]>
> Date: Sat, 16 Jul 2011 10:54:06 -0400
> To: jzhang <[hidden email]>
> Cc: "[hidden email]" <[hidden email]>
> Subject: Re: [BioMart Users] Biomart Perl API Problem
>
>> Thank you all,
>>
>> Yes Junjun it is the same coding, but I have changed the Registry file, Here is the new one
>>
>> <?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE MartRegistry>
>> <MartRegistry>
>>      <MartURLLocation
>>          database="cosp"
>>          default="1"
>>          displayName="COSMIC (SANGER UK)"
>>          host="www.sanger.ac.uk"
>>          includeDatasets=""
>>          martUser=""
>>          name="CosmicMart"
>>          path="/genetics/CGP/cosmic/biomart/martservice"
>>         port="80"
>>          redirect="1"
>>          serverVirtualSchema="default"
>>          visible="1"
>>      />
>>  </MartRegistry>
>>
>> Here is what I get at the console;
>>
>> cygwin warning:
>>   MS-DOS style path detected: C:/Users/Manjula/workspace/TestMart/registry_DOM_XML
>>   Preferred POSIX equivalent is: /cygdrive/c/Users/Manjula/workspace/TestMart/registry_DOM_XML
>>   CYGWIN environment variable option "nodosfilewarning" turns off this warning.
>>   Consult the user's guide for more details about POSIX paths:
>>     http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
>>
>> Connection parameters of [COSMIC (SANGER UK)]    [ OK ]
>>
>> Use of uninitialized value in lc at C:/Perl64/lib/BioMart/Initializer.pm line 1135.
>> could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"
>>
>>
>> Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
>> BioMart::Root::loadModule('BioMart::Initializer=HASH(0x162da60)', 'BioMart::Dataset::Vary: Accept-Encoding') called at C:\Perl64\lib\BioMart\Initializer.pm line 1162
>> BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x162da60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
>> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x162da60)', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 377
>> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x162da60)', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 144
>> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x162da60)', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\site\lib\BioMart\RootI.pm line 64
>> BioMart::RootI::new('BioMart::Initializer', 'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean') called at C:\Users\Manjula\workspace\TestMart\Q1.pl line 22
>>
>> When I change the path to the registry file as "/cygdrive/c/......" I get a con not find the file error.
>>
>> Strange thing is that, If I give the relative path to the registry file, I get a different error. i.e;
>>
>> Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 114.
>> Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 116.
>> Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 123.
>> Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 125.
>> Use of uninitialized value in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 134.
>> Use of uninitialized value $1 in concatenation (.) or string at C:/Perl64/lib/BioMart/Initializer.pm line 143.
>>
>> Connection parameters of [COSMIC (SANGER UK)]    [ OK ]
>>
>> Use of uninitialized value in lc at C:/Perl64/lib/BioMart/Initializer.pm line 1135.
>> could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"
>>
>>
>> Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
>> BioMart::Root::loadModule('BioMart::Initializer=HASH(0x38da60)', 'BioMart::Dataset::Vary: Accept-Encoding') called at C:\Perl64\lib\BioMart\Initializer.pm line 1162
>> BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x38da60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
>> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x38da60)', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 377
>> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x38da60)', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 144
>> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x38da60)', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Perl64\site\lib\BioMart\RootI.pm line 64
>> BioMart::RootI::new('BioMart::Initializer', 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at C:\Users\Manjula\workspace\TestMart\Q1.pl line 22
>>
>>
>> Any help is greatly appreciated!
>>
>> Thank you!
>>
>> Regards,
>> Manjula
>>
>>
>> --
>>
>>
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Re: [BioMart Users] Biomart Perl API Problem

Junjun Zhang
Hi Chris,

Thanks for raising this important point.

No, at this time, we don't have any plan for supporting Perl API in the
BioMart 0.8. It is encouraged to use REST API for remote access BioMart
data sources.

Perl API needs to be rewritten in order to work with BioMart 0.8 (and
later versions). Basically, it would be a wrapper of the REST API, just
like how 'biomaRt' R package works.

Cheers,
Junjun



On 11-07-21 1:00 PM, "Chris Fields" <[hidden email]> wrote:

>Just curious, but will the perl API be supported long-term?  I know of a
>few users who would like BioMart accessibility within BioPerl (for
>instance), but it doesn't make much sense to write up anything if the
>perl API is not being actively developed; we could put more effort to the
>Java-based API instead.
>
>chris
>
>On Jul 21, 2011, at 11:51 AM, Junjun Zhang wrote:
>
>> Hi Manjula,
>>
>> Sorry for not be able to response you sooner due to recent travels.
>>
>> We had experienced similar problem as you showed below. It was caused
>>by some unusual response from the remote server. We have fixed it in the
>>BioMart SVN repository.
>>
>> You can checkout the code at:
>>https://code.oicr.on.ca/svn/biomart/biomart-perl/trunk/. I just tried it
>>with you registry file. It worked!
>>
>> Please give it a try, let me know how it goes.
>>
>> Cheers,
>> Junjun
>>
>>
>> From: Manjula Dharmawardhana <[hidden email]>
>> Date: Sat, 16 Jul 2011 10:54:06 -0400
>> To: jzhang <[hidden email]>
>> Cc: "[hidden email]" <[hidden email]>
>> Subject: Re: [BioMart Users] Biomart Perl API Problem
>>
>>> Thank you all,
>>>
>>> Yes Junjun it is the same coding, but I have changed the Registry
>>>file, Here is the new one
>>>
>>> <?xml version="1.0" encoding="UTF-8"?>
>>> <!DOCTYPE MartRegistry>
>>> <MartRegistry>
>>>      <MartURLLocation
>>>          database="cosp"
>>>          default="1"
>>>          displayName="COSMIC (SANGER UK)"
>>>          host="www.sanger.ac.uk"
>>>          includeDatasets=""
>>>          martUser=""
>>>          name="CosmicMart"
>>>          path="/genetics/CGP/cosmic/biomart/martservice"
>>>         port="80"
>>>          redirect="1"
>>>          serverVirtualSchema="default"
>>>          visible="1"
>>>      />
>>>  </MartRegistry>
>>>
>>> Here is what I get at the console;
>>>
>>> cygwin warning:
>>>   MS-DOS style path detected:
>>>C:/Users/Manjula/workspace/TestMart/registry_DOM_XML
>>>   Preferred POSIX equivalent is:
>>>/cygdrive/c/Users/Manjula/workspace/TestMart/registry_DOM_XML
>>>   CYGWIN environment variable option "nodosfilewarning" turns off this
>>>warning.
>>>   Consult the user's guide for more details about POSIX paths:
>>>     http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
>>>
>>> Connection parameters of [COSMIC (SANGER UK)]    [ OK ]
>>>
>>> Use of uninitialized value in lc at
>>>C:/Perl64/lib/BioMart/Initializer.pm line 1135.
>>> could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax
>>>error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"
>>>
>>>
>>> Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
>>> BioMart::Root::loadModule('BioMart::Initializer=HASH(0x162da60)',
>>>'BioMart::Dataset::Vary: Accept-Encoding') called at
>>>C:\Perl64\lib\BioMart\Initializer.pm line 1162
>>>
>>>BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x162
>>>da60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
>>> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x162da60)',
>>>'registryFile',
>>>'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action',
>>>'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 377
>>>
>>>BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x162da60)',
>>> 'registryFile',
>>>'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action',
>>>'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 144
>>> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x162da60)',
>>>'registryFile',
>>>'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action',
>>>'clean') called at C:\Perl64\site\lib\BioMart\RootI.pm line 64
>>> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
>>>'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action',
>>>'clean') called at C:\Users\Manjula\workspace\TestMart\Q1.pl line 22
>>>
>>> When I change the path to the registry file as "/cygdrive/c/......" I
>>>get a con not find the file error.
>>>
>>> Strange thing is that, If I give the relative path to the registry
>>>file, I get a different error. i.e;
>>>
>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>C:/Perl64/lib/BioMart/Initializer.pm line 114.
>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>C:/Perl64/lib/BioMart/Initializer.pm line 116.
>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>C:/Perl64/lib/BioMart/Initializer.pm line 123.
>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>C:/Perl64/lib/BioMart/Initializer.pm line 125.
>>> Use of uninitialized value in concatenation (.) or string at
>>>C:/Perl64/lib/BioMart/Initializer.pm line 134.
>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>C:/Perl64/lib/BioMart/Initializer.pm line 143.
>>>
>>> Connection parameters of [COSMIC (SANGER UK)]    [ OK ]
>>>
>>> Use of uninitialized value in lc at
>>>C:/Perl64/lib/BioMart/Initializer.pm line 1135.
>>> could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax
>>>error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"
>>>
>>>
>>> Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
>>> BioMart::Root::loadModule('BioMart::Initializer=HASH(0x38da60)',
>>>'BioMart::Dataset::Vary: Accept-Encoding') called at
>>>C:\Perl64\lib\BioMart\Initializer.pm line 1162
>>>
>>>BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x38d
>>>a60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
>>> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x38da60)',
>>>'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at
>>>C:\Perl64\lib\BioMart\Initializer.pm line 377
>>>
>>>BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x38da60)',
>>>'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at
>>>C:\Perl64\lib\BioMart\Initializer.pm line 144
>>> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x38da60)',
>>>'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at
>>>C:\Perl64\site\lib\BioMart\RootI.pm line 64
>>> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
>>>'cosmicRegistry.xml', 'action', 'clean') called at
>>>C:\Users\Manjula\workspace\TestMart\Q1.pl line 22
>>>
>>>
>>> Any help is greatly appreciated!
>>>
>>> Thank you!
>>>
>>> Regards,
>>> Manjula
>>>
>>>
>>> --
>>>
>>>
>>> This communication (including any attachments) is intended for the use
>>>of the intended recipient only and may contain information that is
>>>confidential, privileged or legally protected. Any unauthorized use or
>>>dissemination of this communication is strictly prohibited. If you have
>>>received this communication in error, please immediately notify
>>>[hidden email] by return e-mail message and delete all copies of
>>>the original communication. Thank you for your cooperation.
>>>
>>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>

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Re: [BioMart Users] Biomart Perl API Problem

Fields, Christopher J
Okay, makes sense to me (and is the easiest solution).  thanks!

chris

On Jul 21, 2011, at 12:10 PM, Junjun Zhang wrote:

> Hi Chris,
>
> Thanks for raising this important point.
>
> No, at this time, we don't have any plan for supporting Perl API in the
> BioMart 0.8. It is encouraged to use REST API for remote access BioMart
> data sources.
>
> Perl API needs to be rewritten in order to work with BioMart 0.8 (and
> later versions). Basically, it would be a wrapper of the REST API, just
> like how 'biomaRt' R package works.
>
> Cheers,
> Junjun
>
>
>
> On 11-07-21 1:00 PM, "Chris Fields" <[hidden email]> wrote:
>
>> Just curious, but will the perl API be supported long-term?  I know of a
>> few users who would like BioMart accessibility within BioPerl (for
>> instance), but it doesn't make much sense to write up anything if the
>> perl API is not being actively developed; we could put more effort to the
>> Java-based API instead.
>>
>> chris
>>
>> On Jul 21, 2011, at 11:51 AM, Junjun Zhang wrote:
>>
>>> Hi Manjula,
>>>
>>> Sorry for not be able to response you sooner due to recent travels.
>>>
>>> We had experienced similar problem as you showed below. It was caused
>>> by some unusual response from the remote server. We have fixed it in the
>>> BioMart SVN repository.
>>>
>>> You can checkout the code at:
>>> https://code.oicr.on.ca/svn/biomart/biomart-perl/trunk/. I just tried it
>>> with you registry file. It worked!
>>>
>>> Please give it a try, let me know how it goes.
>>>
>>> Cheers,
>>> Junjun
>>>
>>>
>>> From: Manjula Dharmawardhana <[hidden email]>
>>> Date: Sat, 16 Jul 2011 10:54:06 -0400
>>> To: jzhang <[hidden email]>
>>> Cc: "[hidden email]" <[hidden email]>
>>> Subject: Re: [BioMart Users] Biomart Perl API Problem
>>>
>>>> Thank you all,
>>>>
>>>> Yes Junjun it is the same coding, but I have changed the Registry
>>>> file, Here is the new one
>>>>
>>>> <?xml version="1.0" encoding="UTF-8"?>
>>>> <!DOCTYPE MartRegistry>
>>>> <MartRegistry>
>>>>     <MartURLLocation
>>>>         database="cosp"
>>>>         default="1"
>>>>         displayName="COSMIC (SANGER UK)"
>>>>         host="www.sanger.ac.uk"
>>>>         includeDatasets=""
>>>>         martUser=""
>>>>         name="CosmicMart"
>>>>         path="/genetics/CGP/cosmic/biomart/martservice"
>>>>        port="80"
>>>>         redirect="1"
>>>>         serverVirtualSchema="default"
>>>>         visible="1"
>>>>     />
>>>> </MartRegistry>
>>>>
>>>> Here is what I get at the console;
>>>>
>>>> cygwin warning:
>>>>  MS-DOS style path detected:
>>>> C:/Users/Manjula/workspace/TestMart/registry_DOM_XML
>>>>  Preferred POSIX equivalent is:
>>>> /cygdrive/c/Users/Manjula/workspace/TestMart/registry_DOM_XML
>>>>  CYGWIN environment variable option "nodosfilewarning" turns off this
>>>> warning.
>>>>  Consult the user's guide for more details about POSIX paths:
>>>>    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
>>>>
>>>> Connection parameters of [COSMIC (SANGER UK)]    [ OK ]
>>>>
>>>> Use of uninitialized value in lc at
>>>> C:/Perl64/lib/BioMart/Initializer.pm line 1135.
>>>> could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax
>>>> error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"
>>>>
>>>>
>>>> Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
>>>> BioMart::Root::loadModule('BioMart::Initializer=HASH(0x162da60)',
>>>> 'BioMart::Dataset::Vary: Accept-Encoding') called at
>>>> C:\Perl64\lib\BioMart\Initializer.pm line 1162
>>>>
>>>> BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x162
>>>> da60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
>>>> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x162da60)',
>>>> 'registryFile',
>>>> 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action',
>>>> 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 377
>>>>
>>>> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x162da60)',
>>>> 'registryFile',
>>>> 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action',
>>>> 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 144
>>>> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x162da60)',
>>>> 'registryFile',
>>>> 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action',
>>>> 'clean') called at C:\Perl64\site\lib\BioMart\RootI.pm line 64
>>>> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
>>>> 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action',
>>>> 'clean') called at C:\Users\Manjula\workspace\TestMart\Q1.pl line 22
>>>>
>>>> When I change the path to the registry file as "/cygdrive/c/......" I
>>>> get a con not find the file error.
>>>>
>>>> Strange thing is that, If I give the relative path to the registry
>>>> file, I get a different error. i.e;
>>>>
>>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>> C:/Perl64/lib/BioMart/Initializer.pm line 114.
>>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>> C:/Perl64/lib/BioMart/Initializer.pm line 116.
>>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>> C:/Perl64/lib/BioMart/Initializer.pm line 123.
>>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>> C:/Perl64/lib/BioMart/Initializer.pm line 125.
>>>> Use of uninitialized value in concatenation (.) or string at
>>>> C:/Perl64/lib/BioMart/Initializer.pm line 134.
>>>> Use of uninitialized value $1 in concatenation (.) or string at
>>>> C:/Perl64/lib/BioMart/Initializer.pm line 143.
>>>>
>>>> Connection parameters of [COSMIC (SANGER UK)]    [ OK ]
>>>>
>>>> Use of uninitialized value in lc at
>>>> C:/Perl64/lib/BioMart/Initializer.pm line 1135.
>>>> could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax
>>>> error at (eval 103) line 1, near "require BioMart::Dataset::Vary:"
>>>>
>>>>
>>>> Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
>>>> BioMart::Root::loadModule('BioMart::Initializer=HASH(0x38da60)',
>>>> 'BioMart::Dataset::Vary: Accept-Encoding') called at
>>>> C:\Perl64\lib\BioMart\Initializer.pm line 1162
>>>>
>>>> BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x38d
>>>> a60)') called at C:\Perl64\lib\BioMart\Initializer.pm line 228
>>>> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x38da60)',
>>>> 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at
>>>> C:\Perl64\lib\BioMart\Initializer.pm line 377
>>>>
>>>> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x38da60)',
>>>> 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at
>>>> C:\Perl64\lib\BioMart\Initializer.pm line 144
>>>> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x38da60)',
>>>> 'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at
>>>> C:\Perl64\site\lib\BioMart\RootI.pm line 64
>>>> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
>>>> 'cosmicRegistry.xml', 'action', 'clean') called at
>>>> C:\Users\Manjula\workspace\TestMart\Q1.pl line 22
>>>>
>>>>
>>>> Any help is greatly appreciated!
>>>>
>>>> Thank you!
>>>>
>>>> Regards,
>>>> Manjula
>>>>
>>>>
>>>> --
>>>>
>>>>
>>>> This communication (including any attachments) is intended for the use
>>>> of the intended recipient only and may contain information that is
>>>> confidential, privileged or legally protected. Any unauthorized use or
>>>> dissemination of this communication is strictly prohibited. If you have
>>>> received this communication in error, please immediately notify
>>>> [hidden email] by return e-mail message and delete all copies of
>>>> the original communication. Thank you for your cooperation.
>>>>
>>>>
>>> _______________________________________________
>>> Users mailing list
>>> [hidden email]
>>> https://lists.biomart.org/mailman/listinfo/users
>>
>

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