Re: [Gusdev-gusdev] how to upload dataset of 'RAD' and 'DoTS' ? many thanks in advance!

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dear sam-

see below.

steve

sam wang wrote:

>Dear friends,
>
>I have installed GUS successfully and registed 'ga'
>and 'SubmitRow' plugin. now I want to upload data of
>'RAD' and 'DoTS'. but when I use 'ga' to upload data
>of 'RAD', I met the following problem,
>first, I don't know if I need register 'ArrayLoader'
>plugin. when I tried to register it using the
>following command, I got the errors as follow:
>
>
>[oracle@GUS perl]$ ga +create
>GUS::RAD::Plugin:ArrayLoader --verbose
>
i believe the syntax error it is referring to is that you are missing a 
':'  in the line above, after 'Plugin:'

>Reading properties from
>/opt/gus/gus_home/config/GUS-PluginMgr.prop
>Reading properties from /home/oracle/.gus.properties
>DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
>::st are not setup, RootClass ignored at
>/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
>DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
>::st are not setup, RootClass ignored at
>/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
>DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
>::st are not setup, RootClass ignored at
>/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
> 
>ERROR: syntax error at (eval 3) line 1, near "require
>GUS::RAD::Plugin:"
> 
> 
>--------------------------- STACK TRACE
>-------------------------
>       
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','syntax
>error at (eval 3) line 1, near "require
>GUS::RAD::Plug...') called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 248
>       
>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 664
>       
>GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x804d00c)',0,'GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 456
>       
>GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 283
>       
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 192
>       
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060680)')
>called at /opt/gus/gus_home/bin/ga line 11
>
>
>
>
>if I ignore this error and try to upload data file,
>then I got the following errors:
>[oracle@GUS perl]$ ga GUS::RAD::Plugin:ArrayLoader
>--cfg_file
>/opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
>--data_file /home/oracle/RADDOTSdataset/assay5quan3
>Reading properties from
>/opt/gus/gus_home/config/GUS-PluginMgr.prop
> 
>ERROR: syntax error at (eval 1) line 1, near "require
>GUS::RAD::Plugin:"
> 
> 
>--------------------------- STACK TRACE
>-------------------------
>       
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','syntax
>error at (eval 1) line 1, near "require
>GUS::RAD::Plug...') called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 248
>       
>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 377
>       
>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 283
>       
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 192
>       
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060680)')
>called at /opt/gus/gus_home/bin/ga line 11
>
>
>sorry for the long error information. in a word, I
>don't know how can I upload 'RAD' data even though I
>found there several plugins for uploading 'RAD'
>dataset. besides, I don't know if I should use
>'ArrayLoader' plugin to upload dataset download from
>the following webpage:
>http://www.cbil.upenn.edu/RAD3/php/download.php#study5
>because I saw there are totally six differents plugins
>in 'RAD'. I don't know which plugin should upload
>which data, in fact, I just find the above link about
>RAD dataset. and I don't know if there are some other
>datasets that can be downloaded from the website.
>
>as for 'DoTS', it seems worse than 'RAD', because I
>can't find any plugin to upload the dataset to GUS. 
>
>does anyone upload dataset of 'RAD' and 'DoTS' before?
>or does any document about how to upload dataset about
>'RAD' and 'DoTS'? any hint will be greatly appreciate!
>
>best wishes!
>Sammy
>
>
>
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