Re: [Gusdev-gusdev] Taxonomy plugin hanging

[Deborah F. P. <pi...@pc...>]

Hi Juan,

I ran the current version of LoadTaxon 2 weeks ago without this problem so 
I wonder if there is something different about your schema. Specifically, 
you may be missing an index that we have. Our Taxon table has the 
following indexes: taxon_id, 
ncbi_tax_id,genetic_code_id,mitochondrial_genetic_code_id, and parent_id. 
For example, the subroutine that inserts rows into TaxonName, queries the 
Taxon table using ncbi_tax_id and without an index, each taxonname record 
would require a full table scan of the taxon table.

Could you check for this? Does anyone else have an idea?

                                                        Debbie


On Tue, 20 Jul 2004, Juan Perin wrote:

> I assumed it was doing work, as you said, it appeared to be wrapping things
> up, although I let it sit for over 24 hours in this state, and nothing
> happened.  This is the only reason I killed it, and it seems to do that
> every time I run the plugin.  Perhaps, something is wrong with our
> configuration, although so far no other database upload has had errors.  We
> still have a few more to go though.
>
> THANKS
>
>> Hi,
>>
>> You appear to have cancelled the plugin as it was entering data into
>> dots.TaxonName which it does after filling dots.Taxon. It was actually
>> doing work and not just hanging. The plugin should probably be modified to
>> have some intermittent output giving the status of the operation so that
>> the operator is aware that it isn't just hanging. I will look into doing
>> that.
>>
>> The last update I did took about 1.25 hours but that will vary with your
>> servers and how busy the database is. I don't have the numbers for the
>> initial entry.
>>
>>                                                     Debbie
>>
>>
>>
>> On Tue, 20 Jul 2004, Juan Perin wrote:
>>
>>> When initially populating the Taxonomy database, the population of the
>>> tables with taxon_id's runs until what appears to be the last entry and
>>> hangs indefinitely.  The following is the output after Ctrl-c 'ing to try to
>>> escape.  After checking the tables, they seem to be populated fine, and the
>>> number of entries seems consistent with the number of entries given in the
>>> taxonomy database.
>>>
>>> DBD::Oracle::db commit failed: ORA-01013: user requested cancel of current
>>> operation (DBD ERROR: OCITransCommit) at
>>> /checkout/GUS/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 479, <NODES> line
>>> 225327.
>>> DBD::Oracle::st execute failed: ORA-01013: user requested cancel of current
>>> operation (DBD ERROR: OCIStmtExecute) [for Statement "select
>>> SRes.TaxonName_SQ.NEXTVAL from DUAL"] at
>>> /checkout/GUS/lib/perl/GUS/ObjRelP/DbiTable.pm line 555, <NODES> line
>>> 225327.
>>>
>>> Also... How long should this initial process take?  The first run took well
>>> over 24 hours, but subsequent runs ran over about 20 minutes...
>>>
>>> -Juan Perin
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by BEA Weblogic Workshop
>>> FREE Java Enterprise J2EE developer tools!
>>> Get your free copy of BEA WebLogic Workshop 8.1 today.
>>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by BEA Weblogic Workshop
>> FREE Java Enterprise J2EE developer tools!
>> Get your free copy of BEA WebLogic Workshop 8.1 today.
>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>