Re: [Gusdev-gusdev] about uploading RAD data problem

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Hello Elisabetta and Sam,

I am new to RAD modules in GUS. Now we have some microarray data, which is 
available in 3 different file formats(.cel,.dat,.CHP). Which of these 3 
files can be uploaded to RAD tables. None of the tables are in text format.

Thanks in advance.

Sucheta

At 07:55 PM 11/16/2003 -0800, sam wang wrote:
>Dear Elisabetta,
>
>thank you very much for your great help! now I am trying according to your 
>suggestion, besides, it seems a little complicated :-)
>
>Thanks again,
>Sammy
>
>Elisabetta Manduchi <man...@pc...> wrote:
>Dear Sam,
>regarding the part of your question referring to the manufacturer_id
>error, if you look at schemaBrowser for RAD3.Array at
>http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=RAD3::Array&path=RAD3::Array 
>
>you should see that manufacturer_id and platform_type_id are nonnullable.
>Thus a valid manufacturer_id and a valid platform_type_id must be given
>when running the ArrayLoader plugin (see also plugin documentation at
>http://www.gusdb.org/documentation/plugins/GUS-RAD-Plugin-ArrayLoader.html).
>This means that before you can load an array, you will need to have
>entered the manufacturer in the SRes.Contact (this can be done also
>via the StudyAnnotator Contact form) and you should have in 
>RAD3.OntologyEntry
>an entry that describes the platform type. MGED has an ontology available
>that we use to populate RAD3.OntologyEntry for terms referring to
>platform types, namely the ontology for class=TechnologyType. The idea is
>that in RAD3.OntologyEntry we store the instances of this class,
>all of which have category set to 'TechnologyType". Similarly for
>SubstrateType, an array entry in RAD3.Array has a substrate_type_id that
>points to a term in RAd3.OntologyEntry describing the substrate type. For
>this we use the instances of the MGED SubstrateType class, that is we
>enter in RAD3.OntologyEntry an entry for each such instance, all having
>category set to "SubstrateType". To get the MGED instatnces (individuals)
>for TechnologyType and SubstrateType, you can go to
>http://mged.sourceforge.net/ontologies/MGEDontology.php#TechnologyType and
>http://mged.sourceforge.net/ontologies/MGEDontology.php#SubstrateType
>I believe that, even though substrate_type_id is nullable in RAD3.Array,
>the ArrayLoader might require that this value is provided in the arguments
>anyway. Junmin, cc'ed in this email, can confirm this, as he is the author
>of the ArrayLoader plugin.
>Elisabetta
>
>On Fri, 14 Nov 2003, sam wang wrote:
>
> > Dear friends,
> >
> > after I download the new version of DbiDbHandle.pm,
> > though it can go more steps, but there is no any data
> > in my database, besides, there is an error "ERROR a
> > VALID -- manufacturer_id must be on the commandline
> > manufacturer_id = 0", I don't know the meaning and if
> > it's the problem that I can't upload data? if so, how
> > can I correct it?
> >
> > Thank you very much for your help!
> > Sammy
> >
> >
> > please check the following error message:
> >
> > [oracle@GUS oracle]$ 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
> > Fri Nov 14 19:43:23 2003 ALGINVID 3
> > Fri Nov 14 19:43:23 2003 ARGS algoinvo
> > 1
> > Fri Nov 14 19:43:23 2003 ARGS cfg_file
> > /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
> > Fri Nov 14 19:43:23 2003 ARGS comment
> > Fri Nov 14 19:43:23 2003 ARGS commit
> > Fri Nov 14 19:43:23 2003 ARGS data_file
> > /home/oracle/RADDOTSdataset/assay5quan3
> > Fri Nov 14 19:43:23 2003 ARGS debug
> > Fri Nov 14 19:43:23 2003 ARGS group
> > Fri Nov 14 19:43:23 2003 ARGS gusconfigfile
> > /home/oracle/.gus.properties
> > Fri Nov 14 19:43:23 2003 ARGS
> > manufacturer_id 0
> > Fri Nov 14 19:43:23 2003 ARGS noWarning
> > Fri Nov 14 19:43:23 2003 ARGS
> > platform_type_id 0
> > Fri Nov 14 19:43:23 2003 ARGS project
> > Fri Nov 14 19:43:23 2003 ARGS protocol_id
> > Fri Nov 14 19:43:23 2003 ARGS restart
> > Fri Nov 14 19:43:23 2003 ARGS sqlVerbose
> > Fri Nov 14 19:43:23 2003 ARGS
> > substrate_type_id
> > Fri Nov 14 19:43:23 2003 ARGS testnumber
> > Fri Nov 14 19:43:23 2003 ARGS usage
> > Fri Nov 14 19:43:23 2003 ARGS user
> > Fri Nov 14 19:43:23 2003 ARGS verbose
> > Fri Nov 14 19:43:23 2003 ARGS veryVerbose
> > Fri Nov 14 19:43:23 2003 COMMIT commit off
> > Fri Nov 14 19:43:23 2003 ERROR a VALID --
> > manufacturer_id must be on the commandline
> > manufacturer_id = 0
> > Fri Nov 14 19:43:23 2003 RESULT
> > [oracle@GUS oracle]$
> >
> >
> >
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>
>--
>Elisabetta Manduchi
>
>Computational Biology and Informatics Laboratory
>Center for Bioinformatics
>University of Pennsylvania
>1428 Blockley Hall
>423 Guardian Drive
>Philadelphia, PA 19104-6021
>
>phone: 215-573-4408
>fax: 215 573-3111
>email: man...@pc...
>web: http://www.cbil.upenn.edu/~manduchi
>
>---
>
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