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(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 >> >> >> -- >> >> >> 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. 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