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]<mailto:[email protected]>> Date: Sat, 16 Jul 2011 10:54:06 -0400 To: jzhang <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[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<http://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 -- [http://www.linkedin.com/img/webpromo/btn_myprofile_160x33.png]<http://lk.linkedin.com/in/manjulapra> 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]<mailto:[email protected]> by return e-mail message and delete all copies of the original communication. Thank you for your cooperation.
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