From: steve f. <sfi...@pc...> - 2003-03-26 14:49:46
|
jonathan- i few people have recently asked me a question that you can best answer. what if any is the limit to the size of primary keys? this question comes out of the observation that we are burning through primary keys when we test in non-commit mode. i have been assuming that the limit is large enough that we don't need to worry about exhausting them. steve |
From: Pjm <pj...@sa...> - 2003-03-26 17:35:23
|
steve fischer wrote: > jonathan- > > i few people have recently asked me a question that you can best answer. > > what if any is the limit to the size of primary keys? > > this question comes out of the observation that we are burning through > primary keys when we test in non-commit mode. > > i have been assuming that the limit is large enough that we don't need > to worry about exhausting them. > > steve Steve, I asked one of our DBAs (Andy) and he replied with; "It's limited by the datatype of the column it's on which, in the case of GUS, is NUMBER(10) typically. So, it will reach 9,999,999,999 and then fall over. The GO schema tables look similar. In GUS I can see an occasional composite primary key where one of the columns is NUMBER(6) (eg. AASEQUENCEKEYWORDVER), so the limit would be six digits in that case." Hope that helps. Paul. |
From: Chetna W. <ch...@ar...> - 2003-03-27 18:53:35
|
Hi guys, I havent seen this error on the mailing list hence writing to you all. I am getting following sequence of errors: 1) [chetna@mango chetna]$ ga GUS::Common::Plugin::LoadTaxon --gencode=/home/gusdev/gus3.0-checkouts/ncbi-taxonomy/gc.prt --verbose Reading properties from /home/gus_home/config/GUS-PluginMgr.prop Reading properties from /home/chetna/.gus.properties prepareAndExecute: SELECT * FROM Core.AlgorithmImplementation WHERE executable = 'GUS::Common::Plugin::LoadTaxon' AND cvs_revision = '1.24' prepareAndExecute: select * from core.algorithmimplementation where executable = 'GUS::Common::Plugin::LoadTaxon' USER ERROR: GUS::Common::Plugin::LoadTaxon has never been registered. Please use 'ga +create GUS::Common::Plugin::LoadTaxon --commit' Issuing rollback() for database handle being DESTROY'd without explicit disconnect(). 2) ---------------------- [chetna@mango chetna]$ ga +create GUS::Common::Plugin::LoadTaxon --commit Reading properties from /home/gus_home/config/GUS-PluginMgr.prop Reading properties from /home/chetna/.gus.properties 'string' is not a legal param type for option gencode. 'boolean' is not a legal param type for option commit. 'string' is not a legal param type for option group. 'integer' is not a legal param type for option algoinvo. 'string' is not a legal param type for option user. 'string' is not a legal param type for option comment. 'string' is not a legal param type for option nodes. 'string' is not a legal param type for option gusconfigfile. 'string' is not a legal param type for option names. 'int' is not a legal param type for option restart. 'string' is not a legal param type for option project. Hope to hearing from you Chetna |
From: Jonathan C. <cra...@pc...> - 2003-03-27 19:01:49
|
Chetna- I don't have much experience with the new Perl object layer yet, but perhaps the LoadTaxon plugin hasn't been updated to the new system? Either that or maybe there's a small controlled vocabulary table of parameter types that needs to be populated in the database (I think there was some e-mail traffic to this effect fairly recently.) Jonathan |
From: Chetna W. <ch...@ar...> - 2003-03-29 21:10:23
|
Hi, I am running following: [chetna@mango chetna]$ ga GUS::Common::Plugin::LoadTaxon --gencode=/home/gusdev/gus3.0-checkouts/ncbi-taxonomy/gc.prt --commit Reading properties from /home/gus_home/config/GUS-PluginMgr.prop Reading properties from /home/chetna/.gus.properties Provide the names of the names.dmp, nodes.dmp, and gencode.dmp files on the command line: ! [chetna@mango chetna]$ Now that I look into the table sres.geneticcode its empty. Same is the case with nodes.dmp and names.dmp Is there a sequence of actions to be done before running LoadTaxon? Thanks chetna |
From: Deborah F. P. <pi...@pc...> - 2003-03-30 14:47:44
|
You need to get the taxonomy files from NCBI which can be obtained from their ftp site: ftp://ftp.ncbi.nih.gov/pub/taxonomy/ The file you need to load these tables (Taxon,TaxonName, and GeneticCode) can be found there: taxdump.tar.gz You will need to tar the file before running the plug-in and put the options, --node, --name, --gencode, with the corresponding full path and name of the corresponding files on the command line. The plugin should fill all three tables. Debbie On Sat, 29 Mar 2003, Chetna Warade wrote: > Hi, > > I am running following: > > [chetna@mango chetna]$ ga GUS::Common::Plugin::LoadTaxon > --gencode=/home/gusdev/gus3.0-checkouts/ncbi-taxonomy/gc.prt --commit > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop > Reading properties from /home/chetna/.gus.properties > Provide the names of the names.dmp, nodes.dmp, and gencode.dmp files on > the command line: ! > [chetna@mango chetna]$ > > Now that I look into the table sres.geneticcode its empty. Same is the > case with nodes.dmp and names.dmp > > Is there a sequence of actions to be done before running LoadTaxon? > > Thanks > chetna > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: > The Definitive IT and Networking Event. Be There! > NetWorld+Interop Las Vegas 2003 -- Register today! > http://ads.sourceforge.net/cgi-bin/redirect.pl?keyn0001en > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |