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

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

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]$
> 
> 
> 
> __________________________________
> Do you Yahoo!?
> Protect your identity with Yahoo! Mail AddressGuard
> http://antispam.yahoo.com/whatsnewfree
> 
> 
> -------------------------------------------------------
> This SF. Net email is sponsored by: GoToMyPC
> GoToMyPC is the fast, easy and secure way to access your computer from
> any Web browser or wireless device. Click here to Try it Free!
> https://www.gotomypc.com/tr/OSDN/AW/Q4_2003/t/g22lp?Target=mm/g22lp.tmpl
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

-- 
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

---

---------------------------------
Do you Yahoo!?
Protect your identity with Yahoo! Mail AddressGuard