[InterMine Dev] how to define LocatedOn attribute of Location and avoid duplicate objects error

Richard Smith richard at flymine.org
Mon Mar 5 17:09:42 GMT 2012


On 05/03/2012 16:51, Dr. Intikhab Alam wrote:

>> Ah, in that case I don't know what the problem with the XML is, but the
>> error message means that two organism items have been loaded.  Is it
>> possible that more than one XML was read for one of the sources?  This
>> can happen if they are in sub-directories.
> 
> Yes, it failed again and this is probably due to subdirs, I will make sure
> these are separate now.


Descending into subdirectories isn't very obvious behaviour unfortunately.
You can also use and includes property to restrict the files each source is
loading:

<property name="src.data.dir.includes" value="file1.xml"/>

>>>> You could speed this up by creating a database copy once the dump is
>>>> loaded up, e.g.
> 
> Now that it failed and includes my cageTag tables with data and model
> updated to include my tables, can I make a copy or I need to exclude this
> duplication situation first and later make a clean copy?

You need to reload from the dump to get a clean copy then create the
backup with createdb -T.

> 
> Thanks, I now understand the Gbrowse issue, will this be fixed soon?

Hopefully tomorrow.

Regards,
Richard.

> Best Wishes,
> 
> Intikhab
>>>>
>>>> createdb -T flymine-db flymine-db-backup
>>>
>>>
> 




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