Re: [Gusdev-gusdev] UpdateGusFromXML and updating records

[Angel P. <an...@pc...>]

The GUS XML parser is not a real XML parser. The order of the columns 
matter. Put <PROTOCOL_ID> before <PROTOCOL_TYPE_ID>

angel
Kevin Murphy wrote:

> Elisabetta Manduchi wrote:
>
>> Yes, as far as I know. If the primary_key is in the xml, an update 
>> should occur. 
>
>
>
> Hmm, this record, which specifies a value for the table's primary key 
> (PROTOCOL_ID), experiences a "duplicate column name" error after an 
> attempted insert:
>
> <RAD3::Protocol>
>  <PROTOCOL_TYPE_ID>12</PROTOCOL_TYPE_ID>
>  <PROTOCOL_ID>1</PROTOCOL_ID>
>  <NAME>Spot quantification</NAME>
>  <PROTOCOL_DESCRIPTION>null</PROTOCOL_DESCRIPTION>
>  <URI>http://experimental.act.cmis.csiro.au/Spot/index.php</URI>
>  <SOFTWARE_TYPE_ID>637</SOFTWARE_TYPE_ID>
>  <SOFTWARE_DESCRIPTION>Spot</SOFTWARE_DESCRIPTION>
>  <HARDWARE_TYPE_ID>null</HARDWARE_TYPE_ID>
>  <HARDWARE_DESCRIPTION>null</HARDWARE_DESCRIPTION>
>  <BIBLIOGRAPHIC_REFERENCE_ID>15</BIBLIOGRAPHIC_REFERENCE_ID>
> </RAD3::Protocol>
>
> but this one, which doesn't try to specify a protocol_id, succeeds:
>
> <RAD3::Protocol>
>  <PROTOCOL_TYPE_ID>1650</PROTOCOL_TYPE_ID>
>  <NAME>Affymetrix GeneArray Scanner</NAME>
>  <PROTOCOL_DESCRIPTION>null</PROTOCOL_DESCRIPTION>
>  <URI>http://www.affymetrix.com</URI>
>  <SOFTWARE_TYPE_ID>null</SOFTWARE_TYPE_ID>
>  <SOFTWARE_DESCRIPTION>null</SOFTWARE_DESCRIPTION>
>  <HARDWARE_TYPE_ID>609</HARDWARE_TYPE_ID>
>  <HARDWARE_DESCRIPTION>"Designed by Agilent Technologies. Monochrome, 
> 20 5m resolution. The GeneArray Scanner is designed to measure the 
> intensity of fluorescence of lab\
> eled sample nucleic acid (RNA and DNA) bound to GeneChip probe arrays. 
> The scanner has the ability to focus the 488nm argon laser beam to a 
> spot size of less than 4 micro\
> ns."</HARDWARE_DESCRIPTION>
>  
> <BIBLIOGRAPHIC_REFERENCE_ID>null</BIBLIOGRAPHIC_REFERENCE_ID>                                                                                                            
>
> </RAD3::Protocol>
>
> Here's the full error output:
>
> sqlExec:
>    INSERT INTO RAD3.Protocol (  SOFTWARE_TYPE_ID, row_user_id, 
> user_write, group_write, NAME, PROTOCOL_DESCRIPTION, row_project_id, 
> group_read, PROTOCOL_ID, row_group_id\
> , other_read, PROTOCOL_TYPE_ID, URI, BIBLIOGRAPHIC_REFERENCE_ID, 
> SOFTWARE_DESCRIPTION, HARDWARE_TYPE_ID, HARDWARE_DESCRIPTION, 
> modification_date, protocol_id, user_read, \
> row_alg_invocation_id, other_write )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, 
> SYSDATE, ?, ?, ?, ? )
>  bindValues (637, 23, 1, 1, Spot quantification, , 1, 1, 1, 1, 1, 12, 
> http://experimental.act.cmis.csiro.au/Spot/index.php, 15, Spot, , , 
> 101, 1, 306, 0)
> DBD::Oracle::st execute failed: ORA-00957: duplicate column name (DBD 
> ERROR: error possibly near <*> indicator at char 146 in '
>    INSERT INTO RAD3.Protocol (  SOFTWARE_TYPE_ID, row_user_id, 
> user_write, group_write, NAME, PROTOCOL_DESCRIPTION, row_project_id, 
> group_read, <*>PROTOCOL_ID, row_group\
> _id, other_read, PROTOCOL_TYPE_ID, URI, BIBLIOGRAPHIC_REFERENCE_ID, 
> SOFTWARE_DESCRIPTION, HARDWARE_TYPE_ID, HARDWARE_DESCRIPTION, 
> modification_date, protocol_id, user_rea\
> d, row_alg_invocation_id, other_write )
>    VALUES   (  :p1, :p2, :p3, :p4, :p5, :p6, :p7, :p8, :p9, :p10, 
> :p11, :p12, :p13, :p14, :p15, :p16, :p17, SYSDATE, :p18, :p19, :p20, 
> :p21 ) ') [for Statement "
>    INSERT INTO RAD3.Protocol (  SOFTWARE_TYPE_ID, row_user_id, 
> user_write, group_write, NAME, PROTOCOL_DESCRIPTION, row_project_id, 
> group_read, PROTOCOL_ID, row_group_id\
> , other_read, PROTOCOL_TYPE_ID, URI, BIBLIOGRAPHIC_REFERENCE_ID, 
> SOFTWARE_DESCRIPTION, HARDWARE_TYPE_ID, HARDWARE_DESCRIPTION, 
> modification_date, protocol_id, user_read, \
> row_alg_invocation_id, other_write )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, 
> SYSDATE, ?, ?, ?, ? ) " with ParamValues: :p1='637', :p2='23', :p3=1, 
> :p4=1, :p5='Spot quantification',\
> :p6=undef, :p7='1', :p8=1, :p9='1', :p10='1', :p11=1, :p20='306', 
> :p12='12', :p21=0, 
> :p13='http://experimental.act.cmis.csiro.au/Spot/index.php', 
> :p14='15', :p15='Spot',\
> :p16=undef, :p17=undef, :p18='101', :p19=1] at 
> /checkout/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 146, <GEN0> 
> line 432.
>
> I'm continuing to investigate.  My version of UpdateGusFromXML.pm 
> seems to be 1.11, but I realize that it is dependent on a bunch of 
> other modules.
>
> Thanks,
> Kevin Murphy
>
>> ---
>>
>> On Tue, 7 Dec 2004, Kevin Murphy wrote:
>>
>>> Can UpdateGusFromXML be used for updating as well as inserting records?
>>>
>>> I was hoping that merely by including the primary key in the XML 
>>> that the plugin would take the hint and do an update on the relevant 
>>> record.  However, it doesn't seem to like this.
>>>
>>> Thanks,
>>> Kevin Murphy
>>>
>>>
>>>
>
>
>
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