On Fri, 2007-09-28 at 14:17 +0200, Matthias Hoys wrote: > Hi, > > I tried changing the names and display names but have the same error: > > ERROR something wrong with your registry: Could not retrieve valid XML > for SCHEMA: tax_ncbi DATASET: RICEBLASTMART > > In the mean time, my colleague found out that the query to Oracle is > done in the wrong schema: > > SELECT compressed_xml FROM tax_ncbi.meta_conf__xml__dm mc, > tax_ncbi.meta_conf__user__dm mu, tax_ncbi.meta_conf__interface__dm mi, > tax_ncbi.meta_conf__dataset__main main WHERE (dataset = 'RICEBLASTMART' > OR dataset = 'RICEBLASTMART') AND mu.mart_user='default' AND > mu.dataset_id_key=main.dataset_id_key AND interface = 'default' AND > main.dataset_id_key=mc.dataset_id_key AND > mc.dataset_id_key=mi.dataset_id_key > > So tax_ncbi. should be replaced by devgenmart. > > Could it be that the queries are wrongly generated ?
could possibly be as it looks, but this could be wrong because of wrong values being propagated from marteditor configuration step. would be helpful if I can have the xmls. thanks a lot. syed > > > Matthias > > > -----Original Message----- > From: Syed Haider [mailto:[EMAIL PROTECTED] > Sent: Friday, September 28, 2007 2:01 PM > To: Matthias Hoys > Subject: RE: [mart-dev] Problem with multiple MartDBLocations v0.6 > > Hi Matthias > apologies, but I meant the xmls files from marteditor xml dump. > in addition, I just discovered that the system is trying to retrieve > > 'Could not retrieve valid XML for SCHEMA: tax_ncbi DATASET: > RICEBLASTMART' > > which I guess is incorrect, it should be SCHEMA: devgenmart instead. > please try the same > perl bin/configure.pl -r conf/your_registry.xml --clean > but first change the name and displayName attributes of both > MartDBLocations and set them to unique value, which should no be causing > any trouble, but I just want to see what appears on your screen > subsequently. > > > thanks. > syed > > > On Fri, 2007-09-28 at 13:47 +0200, Matthias Hoys wrote: > > In addendum the xml file and the output. > > > > Same error without --lazyload (this is a server with only 128MB RAM). > > > > > > Matthias > > > > > > -----Original Message----- > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > Sent: Friday, September 28, 2007 1:21 PM > > To: Matthias Hoys > > Subject: RE: [mart-dev] Problem with multiple MartDBLocations v0.6 > > > > Matthias, > > please send me your xml files and please try configuring as > > perl bin/configure.pl -r conf/your_registry.xml --clean > > and ignore --lazyload option, and let me know what gets printed on > your > > display. looks to me cpan compression module Zlib is crashing. > anyways, > > lets see. > > > > thanks > > syed > > > > On Fri, 2007-09-28 at 13:17 +0200, Matthias Hoys wrote: > > > Hello Syed, > > > > > > I removed the virtualSchema tags and it still doesn't work. > > > This is the error message: > > > > > > > > > Use of uninitialized value in length at > > > /usr/lib/perl5/site_perl/5.8.5/Compress/Zlib.pm line 478. > > > > > > ERROR something wrong with your registry: Could not retrieve valid > XML > > > for SCHEMA: tax_ncbi DATASET: RICEBLASTMART > > > > > > Trace begun at > > > > > > /home/bioinf/biomart-perl/bin/../lib/BioMart/Configuration/MartDBLocatio > > > n.pm line 138 > > > > > > BioMart::Configuration::MartDBLocation::getDatasetConfigXML('BioMart::Co > > > nfiguration::MartDBLocation=HASH(0x93dfd5c)', 'd > > > efault', 'RICEBLASTMART', 'default', 1) called at > > > /home/bioinf/biomart-perl/bin/../lib/BioMart/Configurator.pm line > 177 > > > > > > BioMart::Configurator::getConfigurationTree('BioMart::Configurator=HASH( > > > 0x93dfc9c)', 'default', 'RICEBLASTMART', 'defaul > > > t', 1) called at > > > /home/bioinf/biomart-perl/bin/../lib/BioMart/Dataset/TableSet.pm > line > > > 110 > > > > > > BioMart::Dataset::TableSet::_getConfigurationTree('BioMart::Dataset::Tab > > > leSet=HASH(0x9439c3c)', 'default', 1) called at > > > /home/bioinf/biomart-perl/bin/../lib/BioMart/DatasetI.pm line 711 > > > > > > BioMart::DatasetI::getConfigurationTree('BioMart::Dataset::TableSet=HASH > > > (0x9439c3c)', 'default', 1) called at /home/bioi > > > nf/biomart-perl/bin/../lib/BioMart/Registry.pm line 1076 > > > > > > BioMart::Registry::_getConfigurationTrees('BioMart::Registry=HASH(0x93c2 > > > 1f0)') called at /home/bioinf/biomart-perl/bin/. > > > ./lib/BioMart/Registry.pm line 1002 > > > BioMart::Registry::configure('BioMart::Registry=HASH(0x93c21f0)') > > called > > > at /home/bioinf/biomart-perl/bin/../lib/BioMart > > > /Initializer.pm line 426 > > > > > > BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x935018c)', > > > 'registryFile', '/home/bioinf/biomart-perl/conf > > > /devgenDBRegistry_test.xml', 'action', 'clean', 'mode', 'lazyload') > > > called at /home/bioinf/biomart-perl/bin/../lib/BioMa > > > rt/Initializer.pm line 160 > > > BioMart::Initializer::_new('BioMart::Initializer=HASH(0x935018c)', > > > 'registryFile', '/home/bioinf/biomart-perl/conf/devge > > > nDBRegistry_test.xml', 'action', 'clean', 'mode', 'lazyload') called > > at > > > /home/bioinf/biomart-perl/bin/../lib/BioMart/Roo > > > tI.pm line 42 > > > BioMart::RootI::new('BioMart::Initializer', 'registryFile', > > > '/home/bioinf/biomart-perl/conf/devgenDBRegistry_test.xml', > > > 'action', 'clean', 'mode', 'lazyload') called at > > > /home/bioinf/biomart-perl/bin/configureBioMart.pl line 302 > > > eval {...} at /home/bioinf/biomart-perl/bin/configureBioMart.pl line > > 301 > > > > > > > > > Any ideas ? > > > > > > Matthias > > > > > > > > > -----Original Message----- > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > Sent: Friday, September 28, 2007 12:17 PM > > > To: Matthias Hoys > > > Cc: [email protected] > > > Subject: Re: [mart-dev] Problem with multiple MartDBLocations v0.6 > > > > > > Hi Mattias, > > > we use more than one martDBLocations all the time, and it should > work. > > > Could you please set visible=1 in the following line, > > > <virtualSchema name="default" visible="0"> or better would be to > > > completely remove virtualSchema tags. > > > cheers > > > syed > > > > > > > > > On Fri, 2007-09-28 at 11:37 +0200, Matthias Hoys wrote: > > > > Hello, > > > > > > > > > > > > > > > > I'm trying to configure BioMart 0.6 to work with two > MartDBLocations > > > > (both connecting to a different Oracle schema), but I can't get it > > to > > > > work. > > > > > > > > During the configuration, it looks like datasets from the second > > > > schema are incorrectly looked up in the first schema (but of > course > > > > nothing is found). > > > > > > > > The configuration runs fine with only 1 MartDBLocation (I tried > both > > > > individually and they work). Could there be a bug in the parsing > of > > > > the MartRegistry code when there is more than 1 MartDBLocation ? > > > > > > > > > > > > > > > > This is my registry xml file, I think the syntax is fine: > > > > > > > > > > > > > > > > <?xml version="1.0" encoding="UTF-8"?> > > > > > > > > <!DOCTYPE MartRegistry> > > > > > > > > <MartRegistry> > > > > > > > > <virtualSchema name="default" visible="0"> > > > > > > > > <MartDBLocation name = "TAX_NCBI" > > > > > > > > displayName = "TAX_NCBI" > > > > > > > > databaseType = "oracle" > > > > > > > > host = "host1" > > > > > > > > port = "1521" > > > > > > > > database = "db1" > > > > > > > > schema = "tax_ncbi" > > > > > > > > user = "tax_ncbi" > > > > > > > > password = "xxx" > > > > > > > > visible = "1" > > > > > > > > includeDatasets = "" > > > > > > > > martUser = "" > > > > > > > > default = "0" > > > > > > > > /> > > > > > > > > <MartDBLocation > > > > > > > > name = "MART" > > > > > > > > displayName = "MART" > > > > > > > > databaseType = "oracle" > > > > > > > > host = "host1" > > > > > > > > port = "1521" > > > > > > > > database = "db1" > > > > > > > > schema = "mart" > > > > > > > > user = "mart" > > > > > > > > password = "xxx" > > > > > > > > visible = "1" > > > > > > > > includeDatasets = "" > > > > > > > > martUser = "" > > > > > > > > default = "1" > > > > > > > > /> > > > > > > > > </virtualSchema> > > > > > > > > </MartRegistry> > > > > > > > > > > > > > > > > > > > > > > > > Thanks, > > > > > > > > Matthias > > > > > > > > > > > > > > > > > > > > > >
