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" <[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
