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From: sam w. <gus...@ya...> - 2003-11-08 06:18:50
|
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
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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|
|
From: Steve F. <st...@pc...> - 2003-11-08 18:12:19
|
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
>
>
>
>__________________________________
>Do you Yahoo!?
>Protect your identity with Yahoo! Mail AddressGuard
>http://antispam.yahoo.com/whatsnewfree
>
>
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>
|
|
From: sam w. <gus...@ya...> - 2003-11-09 04:20:44
|
Hi, friends, does there anyone who know how to upload dataset of 'RAD' and 'DoTS' into database? when I first want to upload dataset using ArrayLoader plugin of 'RAD', I got the error information that I didn't register it. so I tried register ArrayLoader plugin of 'RAD' according to the command suggestion. but I got the error information of: DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup. but I don't know what's that meaning, and how should I setup that parameters. please check the error information in detail at the bottom of this email, besides, do you know how can I upload DoTS dataset to database? thank you very much for your great help in advance! Sammy the following is the error information: [oracle@GUS perl]$ ga GUS::RAD::Plugin::ArrayLoader --cfg_file /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg --data_file /home/oracle/RADDOTSdataset/assay5quan3 --manufacturer_id 0 --platform_type_id 0 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 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 USER ERROR: GUS::RAD::Plugin::ArrayLoader has never been registered. Please use 'ga +create GUS::RAD::Plugin::ArrayLoader --commit' Issuing rollback() for database handle being DESTROY'd without explicit disconnect(). [oracle@GUS perl]$ ga +create GUS::RAD::Plugin::ArrayLoader --commit 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 Sat Nov 8 23:46:18 2003 INFO Plugin GUS::RAD::Plugin::ArrayLoader registered with cvs revision '1.4' and cvs tag ' ' [oracle@GUS perl]$ __________________________________ Do you Yahoo!? Protect your identity with Yahoo! Mail AddressGuard http://antispam.yahoo.com/whatsnewfree |
|
From: Elisabetta M. <man...@pc...> - 2003-11-08 18:28:10
|
Dear Sam, regarding your question on RAD data loading: > 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. the RAD pipeline for how data should be loaded is summarized at the bottom of this email. NOTE 1: We are currently working on a plugin that will enable batch loading for step 6. NOTE 2: The RAD Study-Annotator is available from a tarball that includes a README file and various dumps (see http://www.cbil.upenn.edu/RAD/RAD-installation.htm) and proper usage of the forms is described in a suite of tutorials at https://www.cbil.upenn.edu/RAD/tutorial/index.html. NOTE 3: individual plugin documentation is at the gusdb website. --- RAD Data Loading Pipeline (as of October 2003) 1. Array is loaded via ArrayLoader.pm, if not already in RAD. 2. User creates a new Study in RAD using the appropriate Study form in the StudyAnnotator. 3. Images and quantified data files are provided via CD or ftp. These files are archived on in appropriate directories for the study of interest. 4. A file on our web server mapping studies to their uris for images and quantified data is updated, with the info for this study. This file is subsequently used in the StudyAnnotator to link acquisitions and quantifications to the archived files. 5. Annotation for this study is done via the StudyAnnotator. 6. The quantified data are loaded into RAD via ArrayResultLoader.pm, after appropriate parsing. 7. At this point, if available, files with preprocessed (e.g. normalized, averaged, etc.) data can be loaded in RAD via (possibly repeated uses of) ProcessedResultLoader.pm. 8. If available, analysis result files are loaded via AnalysisResultLoader.pm. New views of RAD3::AnalysisResultImp can be created to accomodate new analysis protocols. --- |
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