[InterMine Dev] loading interpro.xml (Solved)

Joe Carlson jwcarlson at lbl.gov
Thu Dec 10 17:09:42 GMT 2015


Sorry. This was an error in my codebase.

We were trying out an alternate db server that was alledged to be a 
postgres compliant one the other week. It was not, and I was trying a 
couple of tweaks to make it work before I gave up. But I forgot to 
rollback my changes.


-------- Forwarded Message --------
Subject: 	loading interpro.xml
Date: 	Wed, 9 Dec 2015 21:16:53 -0800
From: 	Joe Carlson <jwcarlson at lbl.gov>
To: 	dev at intermine.org


Don’t you just hate it when code that you’ve been using for a year or so 
suddenly breaks?

I’ve just updated my version of interpro.xml (to 53.0) and am using your 
vanilla interpro data loader. I’m getting error messages because there 
are non-UTF8 characters:
> [integrate] Caused by: java.sql.SQLException: Error writing to 
> database, running statement COPY Attribute (name, intermine_value, 
> itemId) FROM STDIN;
> [integrate] , data size = 2682870
> [integrate]     at 
> org.intermine.sql.writebatch.FlushJobPostgresCopyImpl.flush(FlushJobPostgresCopyImpl.java:56) 
> [integrate]     at 
> org.intermine.sql.writebatch.Batch$BatchFlusher.run(Batch.java:461)
> [integrate]     at java.lang.Thread.run(Thread.java:745)
> [integrate] Caused by: org.postgresql.util.PSQLException: ERROR: 
> invalid byte sequence for encoding "UTF8": 0xfd
> [integrate]   Where: COPY attribute, line 42945
> [integrate]     at 
> org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161) 
> [integrate]     at 
> org.postgresql.core.v3.QueryExecutorImpl.processCopyResults(QueryExecutorImpl.java:966) 
> [integrate]     at 
> org.postgresql.core.v3.QueryExecutorImpl.endCopy(QueryExecutorImpl.java:828) 
> [integrate]     at 
> org.postgresql.core.v3.CopyInImpl.endCopy(CopyInImpl.java:59)
> [integrate]     at 
> org.postgresql.copy.CopyManager.copyIn(CopyManager.java:181)
> [integrate]     at 
> org.postgresql.copy.CopyManager.copyIn(CopyManager.java:161)
> [integrate]     at 
> org.intermine.sql.writebatch.FlushJobPostgresCopyImpl.flush(FlushJobPostgresCopyImpl.java:51) 
> [integrate]     ... 2 more
>      [null] Exiting 
> /global/u1/j/jcarlson/src/intermine/bio/sources/interpro/build.xml.

The header of interpro.xml says it has encoding ISO-8859-1. I’ve looked 
at it and it does have some naughty characters in it

My server encoding is UTF8. I’ve tried playing around with iconv to make 
the xml UTF8, but nothing has helped (so far). I’d rather not resort to 
hand edits.

Which version of interpro.xml do you load in flymine? Did you have this 
problem? Or, should I open a ticket?



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