[InterMine Dev] Fetch data from DB while parsing in custom source (II)
norbert.auer at boku.ac.at
Wed Mar 13 16:52:27 GMT 2013
Dear dev team,
I`m now working with Intermine for approximate a week.
I have a similar problem like described in http://mail.intermine.org/pipermail/dev/2011-August/001040.html .
I have created two custom sources Cellbank and Fermentation. Fermentation has a reference field linked to Cellbank. Loading the Cellbank data source work fine, but loading the Fermentation source give me an error:
org.intermine.objectstore.ObjectStoreException: Duplicate objects found for pk org.intermine.model.bio.Cellbank.key_identifier
These are the contents of the two additional files:
And this is the Converter file:
public void process(Reader reader) throws Exception
Iterator lineIter = FormattedTextParser.parseDelimitedReader(reader,',');
// Loop through csv lines
String line = (String) lineIter.next();
// Create organism if not already in database
Item ferm = createItem("Fermentation");
Item cb = createItem("Cellbank");
// primaryIdentifier already in the database
For both sources the keys.properties file include:
I still do not understand how to get the id of an object which is already in the database. If I create the referenced object new and store it like in the code above then a get the duplicate objects error even though I have set the integration key for cbId.
Thanks for any help!
DI (FH) Norbert Auer
Department of Biotechnology
University of Natural Resources and Applied Life Sciences,
Muthgasse 18, A-1190 Vienna, Austria
Tel: +43 1 47654 6837
Fax: +43 1 36006 1249
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