I've finally joined the happy throng suffering from Unicode errors. In my
particular case, running the deseq tool from the main toolshed brought down my
Galaxy server, and it wouldn't restart. The traceback in paster.log contained
this
Traceback (most recent call last):
[snip]
File
"/home/galaxy-dev/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 2903, in __init__
self._init_metadata()
File
"/home/galaxy-dev/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 3306, in _init_metadata
self.__buffer_rows()
File
"/home/galaxy-dev/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 3326, in __buffer_rows
self.__rowbuffer = collections.deque(self.cursor.fetchmany(size))
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 162:
ordinal not in range(128)
The same error occurred each time I tried to restart the galaxy server until I
restored the galaxy database from last night's postgres backup.
The problem was my galaxy database in postgres was using SQL_ASCII encoding,
which turns out to be a bad idea if you're ever going to write Unicode
characters there. (I'm quite disappointed that this is the default encoding
for postgres databases on CentOS 6.)
The fix was to dump the galaxy database, recreate it with UTF8 encoding, and
reload it. Now everything works, and that one tool doesn't crash my galaxy
server.
I thought it would be worth noting that postgres databases should be created
with UTF8 encoding on this page:
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server
I think the right thing to do is to ensure you set the default database
encoding for postgres when you run initdb. You only get one chance to get this
right. After that, a way to change the default database encoding to UTF8 is
given here:
https://gist.github.com/ffmike/877447
Scary stuff, but it worked well enough for me.
Alternatively, if you didn't think about encodings when you ran initdb, you can
think about it every time you run createdb.
Hope this helps someone.
cheers,
Simon
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