#304 Errors importing MySQL

[Anonymous]

Hi Paula,

Thanks for the reply. Would it be possible to keep characters listed on
the following mysql page in mind when doing the next release:

http://dev.mysql.com/doc/refman/5.0/en/string-syntax.html

We can fix it up on our end if need be but if it's not hard that might
make our lives easier. In the past we were able to get a successful load
fairly easily.

Regarding the Web form for support, has that been fixed or should I be
e-mailing chebi-help?

Thanks

John

On Wed, 24 Feb 2010, Paula de Matos wrote:

> Hi John,
>
> Thanks very much for your query and apologies for the late response.
>
> I can't really see whats going wrong. The only explanation I can think of is
> that we are not escaping certain special characters in MySQL. Do you have a
> list of special characters that should be excluded from MySQL.
>
> Here is an example insert statement that fails.
>
> insert into compounds (id, name, source, parent_id, chebi_accession, status,
> definition, modified_on, created_by, star) values
> ('461659','(2R)-2-{2-[(2S)-2-{2-[(2S)-2-[(2S)-2-[(2S)-2-{[(2S)
> -1-[(2S)-2-[(2S)-2-[(2S)-2-[(2S)-2-[(2S)-2-[(2S)-2-[(2S)-2-(2-amino-3-{[1-(3-{[(2S,3S,4S,6R)-3-hydroxy-2-methyl-6-{[(1S,3S)-3,5,12-trihydroxy-3-(2-hydroxyacetyl)-10-methoxy-6,11-dioxo-1,2,3
> ,4,6,11-hexahydrotetracen-1-yl]oxy}oxan-4-yl]carbamoyl}propyl)-2,5-dioxopyrrolidin-3-yl]sulfanyl}propanamido)-3-hydroxypropanamido]-5-[(diaminomethylidene)amino]pentanamido]-5-[(diaminometh
> ylidene)amino]pentanamido]propanamido]-5-[(diaminomethylidene)amino]pentanamido]-5-[(diaminomethylidene)amino]pentanamido]-3-hydroxypropanoyl]pyrrolidin-2-yl]formamido}-5-[(diaminomethylide
> ne)amino]pentanamido]-3-(1H-imidazol-4-yl)propanamido]-4-methylpentanamido]acetamido}-3-hydroxypropanamido]acetamido}-3-sulfanylpropanoic

> acid; 2,2,2-trifluoroacetic acid','ChEMBL',null,'CH
> EBI:461659','E','','','LOADER','2');
>
> Best Regards,
> Paula
>
> John Legato wrote:
>> Hello,
>>
>> We're making great use of the ChEBI data EBI provides. We have a local
>> instance that we loaded some time ago and would like to update our local
>> copy. We've run been for the last several releases(11/04/09 & 01/06/2010,
>> 02/03/2010) to get an SQL dump loaded. However we are running into errors
>> that appear to be related to quoting. It's possible that it's a MySQL
>> database quote setting but we are not certain. We're using
>> generic_dump_allstar.zip in combination with mysql_create_tables.sql both
>> dated 02/03/2010.
>>
>> The procedure we've been using is as follows is in the attached log
>> file(gzipped due to its 20MB size). We're seeing errors in compounds.sql,
>> in the past we've seen similar errors loading structure as well. Do you see
>> anything obvious that indicates what may be preventing a successful load?
>>
>> Also we've sent this query a few times using the "Contact us" web form on
>> the EBI site. We receive the auto reply, but no further follow up.
>>
>>
>> Thanks
>>
>> John

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