hello again
seen this?
ERROR something wrong with your registry:
Initializer.pm: Set at least one virtaulSchema attribute
default="1"
following the user guide my test registry look like this:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<virtualSchema name="default">
<MartDBLocation
name = "ent-lit"
displayName = "Entomology Literature"
databaseType = "postgres"
host = "localhost"
port = "3306"
database = "ent-lit"
schema = "ent_lit_mart"
user = "alexie"
password = ""
visible = "1"
default = ""
includeDatasets = ""
/>
</virtualSchema>
</MartRegistry>
is there something missing? Proceeding blindly, I tried default="1" or
default="true" but that didn't change the error message. The trace
message follows below.
Please note that this is not the first register i load to BioMart. but I
scrolled up in the instructions and it only informs of two options: a
renamed file (the command i use) and the one with the clean option.
ta
alexie
ERROR something wrong with your registry:
Initializer.pm: Set at least one virtaulSchema attribute
default="1"
Trace begun at
/usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 686
BioMart::Initializer::_loadConfigFrom('BioMart::Initializer=HASH(0x21007e0)',
'IO::File=GLOB(0x21004f0)') called at
/usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 240
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x21007e0)',
'registryFile', '/usr/software/biomart-perl/conf/myRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x21007e0)',
'registryFile', '/usr/software/biomart-perl/conf/myRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 344
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x21007e0)',
'registryFile', '/usr/software/biomart-perl/conf/myRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 184
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x21007e0)',
'registryFile', '/usr/software/biomart-perl/conf/myRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/usr/software/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/usr/software/biomart-perl/conf/myRegistry.xml', 'action', 'cached',
'mode', 'memory') called at
/usr/software/biomart-perl/bin/configureBioMart.pl line 339
eval {...} at /usr/software/biomart-perl/bin/configureBioMart.pl line 338
I also tried to re-configure using the test registryURLPointer.xml but I
got this error (with --update or --clean commands...)
ERROR something wrong with your registry:
syntax error at line 1, column 0, byte 0 at
/usr/lib/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi/XML/Parser.pm
line 187
--
Alexie Papanicolaou
Entomology
Max Planck Institute for Chemical Ecology
Hans Knoell Str 8
07745 Jena
Germany
[EMAIL PROTECTED]
