Re: [Gusdev-gusdev] Taxonomy plugin hanging

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

Hi,

It is possible that even if you have all the indexes, your statistics may 
need to be updated.

By the way, here is a list of our create indexes for Taxon:

create index SRES.TAXON_IND01 on sres.Taxon (NCBI_TAX_ID)  TABLESPACE 
INDX;
create index SRES.TAXON_IND02 on sres.Taxon (GENETIC_CODE_ID)  TABLESPACE 
INDX;
create index SRES.TAXON_IND03 on sres.Taxon 
(MITOCHONDRIAL_GENETIC_CODE_ID)  TABLESPACE INDX;
create index SRES.TAXON_IND04 on sres.Taxon (PARENT_ID)  TABLESPACE INDX;

You can run the plugin without --commit and with --sqlVerbose to see all 
the sql output the plugin is executing. You could also run it with --debug 
to turn debugging on.


                                                         Debbie




On Wed, 21 Jul 2004, Deborah F. Pinney wrote:

> 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
>>>> 
>>>> 
>>>> 
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>>> 
>>> 
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>> 
>
>
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