Re: [GUSDEV] LoadTaxon tax_id null error

[Michael S. <msa...@pc...>]

I knew this sounded familiar-- Debbie's post refreshed my memory.  This is
an open issue and there is an entry in the tracker for it:

https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=45

Based on the tracker comments, this error only appears when not in commit
mode.

I've increased the priority in the tracker, and this is scheduled for
resolution in the next release.

--Mike


On 10/11/05 9:04 AM, "pi...@pc..." <pi...@pc...> wrote:

> Merges are updates to the existing db. It occurs when NCBI merges or
> transforms
> one tax_id with another and the merge file is cumulative. If this is the first
> loading of the NCBI taxon, then your db instance will have none of
> these tax id
> to merge and you'll get this message. In the future you will get fewer.
> Therefore, this is OK.
> 
> The failure you get is more serious. Did you provide the entire node.dmp file.
> It looks like you didn't get the taxon table loaded. That must occur before
> loading the taxonname table. One thought, I think you need to load with commit
> on.
> 
>                                                Deborah
> 
> 
> Quoting Weichen Wu <we...@se...>:
> 
>> My GUS 3.5 instance is complete new and I am loading NCBI Taxon data
>> files using LoadTaxon.pm plugin. I have this problem about null value
>> of tax_id. Do I need load anything else before loading taxon?
>> The log is as follows:
>> 
>> [wewu@noodle ncbi_taxon]$     ga GUS::Supported::Plugin::LoadTaxon
>> --nodes nodes.dmp --names names.dmp --gencode gencode.dmp --merged
>> merged.dmp
>> Mon Oct 10 16:37:29 2005        ARGS    algoinvo        1
>> <... skip some lines>
>> Mon Oct 10 16:37:29 2005        Doing merge and NCBI tax id '12' not
>> in database, skipping
>> <...skip many lines>
>> Mon Oct 10 16:37:33 2005        Doing merge and NCBI tax id '349635'
>> not in database, skipping
>> Mon Oct 10 16:37:33 2005        Updating and inserting SRes.GeneticCode
>> Mon Oct 10 16:37:50 2005        Number processed: 1000
>> <...skip many lines>
>> Mon Oct 10 16:54:33 2005        Number processed: 278000
>> Mon Oct 10 16:54:34 2005        Inserting and updating TaxonName
>> 
>> DBD::Pg::st execute failed: ERROR:  null value in column "taxon_id"
>> violates not-null constraint
>> ERROR:
>> SQL ERROR!! involving
>>    INSERT INTO SRes.TaxonName (  unique_name_variant, group_write,
>> other_read, group_read, name, taxon_id, user_read, row_user_id,
>> modification_date, name_class, other_write, row_alg_invocation_id,
>> row_project_id, taxon_name_id, row_group_id, user_write )
>>    VALUES   (  null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
>> Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 7, 1, 1, 1, 1
>> at /home/wewu/work/6_gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>> line 166
>> 
>> Thanks,
>> Weichen
>> 
>> 
>> 
>> ----- Original Message ----- From: "Steve Fischer" <sfi...@pc...>
>> To: "Weichen Wu" <we...@se...>
>> Cc: <gus...@li...>
>> Sent: Saturday, October 08, 2005 7:29 AM
>> Subject: Re: [GUSDEV] mapping file
>> 
>> 
>>> yes, the mapping file is required.  you can use the genbank2gus.xml
>>> file if your embl file uses features and qualifiers that conform to
>>> the genbank/embl/ddbj feature table (see
>>> http://www.ncbi.nlm.nih.gov/collab/FT/).
>>> but, you must understand that input often does not conform, or,
>>> places data into qualifiers in the wrong way.
>>> 
>>> in this case, you will need to provide your own mapping file.
>>> 
>>> here is a snip from the documentation from the plugin (i just
>>> improved the doc in latest plugin version):
>>> 
>>> --------
>>> Another way to generate a template mapping file is by using the
>>> command reportFeatureQualifiers.  This command analyzes a set of
>>> input files, and reports the feature/qualifier structure found in
>>> them.  It can output the report in simple text form, or in XML that
>>> is a template for the mapping file.
>>> --------
>>> 
>>> steve
>>> 
>>> Weichen Wu wrote:
>>> 
>>>> Hi,
>>>> 
>>>> To use InsertSequenceFeatures plugin, is the mapping file is
>>>> required? There is a genebank2gus.xml. Is there a mapping file for
>>>> EMBL format available?
>>>> 
>>>> Thanks,
>>>> Weichen
>>>> 
>>>> 
>>>> 
>>>> 
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>> 
>> 
>> 
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> 
> 
> 
> 
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