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" <[email protected]> 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 <[email protected]> >> Date: Sat, 16 Jul 2011 10:54:06 -0400 >> To: jzhang <[email protected]> >> Cc: "[email protected]" <[email protected]> >> 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 >>>[email protected] by return e-mail message and delete all copies of >>>the original communication. Thank you for your cooperation. >>> >>> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
