[ome-users] Problem running omero configuration

Josh Moore josh at glencoesoftware.com
Thu Aug 18 15:08:08 BST 2011 

Hi Leon,

did your recent reconfiguration of Python solve this issue?

Cheers,
~Josh.

On Aug 5, 2011, at 7:20 AM, Leon Kolchinsky wrote:

> Hello,
> 
> I've installed all prerequisits for omero according to
> http://www.openmicroscopy.org/site/support/omero4/server/installation
> 
> Please see below output of - /srv/omeroserver/bin/omero config set
> omero.db.name 'omero'
> 
> Ice installed using yum according to
> http://www.zeroc.com/download_3_3_1.html.
> 
> I'm running RHEL5.7
> 
> Any help greatly appreciated.
> 
> [omero at vera143 ~]$ echo $PATH
> /usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/lib64/python2.4/site-packages/Ice/:/usr/lib64/python2.4/site-packages/tables:/srv/PostgresPlus/9.0SS/bin/:/srv/PostgresPlus/9.0SS/pgAdmin3/bin:/srv/omeroserver/bin
> 
> [omero at vera143 ~]$ export
> PYTHONPATH=/usr/lib64/python2.4:/usr/lib64/python2.4/site-packages/Ice/:/usr/lib64/python2.4/site-packages/tables
> 
> [omero at vera143 ~]$ /srv/omeroserver/bin/omero config set omero.db.name'omero'
> Error loading: /srv/omeroserver/lib/python/omero/plugins/prefs.py
> Traceback (most recent call last):
>  File "/srv/omeroserver/lib/python/omero/cli.py", line 1115, in loadpath
>    execfile( str(pathobj), loc )
>  File "/srv/omeroserver/lib/python/omero/plugins/prefs.py", line 22, in ?
>    from omero.config import ConfigXml
>  File "/srv/omeroserver/lib/python/omero/config.py", line 31, in ?
>    from elementtree.ElementTree import XML, Element, SubElement, Comment,
> ElementTree, tostring
>  File "/usr/lib/python2.4/site-packages/elementtree/ElementTree.py", line
> 755, in ?
>    _escape = re.compile(eval(r'u"[&<>\"\u0080-\uffff]+"'))
>  File "/usr/lib64/python2.4/sre.py", line 180, in compile
>    return _compile(pattern, flags)
>  File "/usr/lib64/python2.4/sre.py", line 225, in _compile
>    p = sre_compile.compile(pattern, flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 500, in compile
>    code = _code(p, flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 484, in _code
>    _compile(code, p.data, flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 77, in _compile
>    _compile(code, av[2], flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 52, in _compile
>    _compile_charset(av, flags, code, fixup)
>  File "/usr/lib64/python2.4/sre_compile.py", line 178, in _compile_charset
>    for op, av in _optimize_charset(charset, fixup):
>  File "/usr/lib64/python2.4/sre_compile.py", line 221, in _optimize_charset
>    return _optimize_unicode(charset, fixup)
>  File "/usr/lib64/python2.4/sre_compile.py", line 341, in _optimize_unicode
>    mapping = array.array('b', mapping).tostring()
> AttributeError: 'module' object has no attribute 'array'
> Error loading: /srv/omeroserver/lib/python/omero/plugins/node.py
> Traceback (most recent call last):
>  File "/srv/omeroserver/lib/python/omero/cli.py", line 1115, in loadpath
>    execfile( str(pathobj), loc )
>  File "/srv/omeroserver/lib/python/omero/plugins/node.py", line 17, in ?
>    from omero.plugins.admin import AdminControl
>  File "/srv/omeroserver/lib/python/omero/plugins/admin.py", line 27, in ?
>    import omero.config
>  File "/srv/omeroserver/lib/python/omero/config.py", line 31, in ?
>    from elementtree.ElementTree import XML, Element, SubElement, Comment,
> ElementTree, tostring
>  File "/usr/lib/python2.4/site-packages/elementtree/ElementTree.py", line
> 755, in ?
>    _escape = re.compile(eval(r'u"[&<>\"\u0080-\uffff]+"'))
>  File "/usr/lib64/python2.4/sre.py", line 180, in compile
>    return _compile(pattern, flags)
>  File "/usr/lib64/python2.4/sre.py", line 225, in _compile
>    p = sre_compile.compile(pattern, flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 500, in compile
>    code = _code(p, flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 484, in _code
>    _compile(code, p.data, flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 77, in _compile
>    _compile(code, av[2], flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 52, in _compile
>    _compile_charset(av, flags, code, fixup)
>  File "/usr/lib64/python2.4/sre_compile.py", line 178, in _compile_charset
>    for op, av in _optimize_charset(charset, fixup):
>  File "/usr/lib64/python2.4/sre_compile.py", line 221, in _optimize_charset
>    return _optimize_unicode(charset, fixup)
>  File "/usr/lib64/python2.4/sre_compile.py", line 341, in _optimize_unicode
>    mapping = array.array('b', mapping).tostring()
> AttributeError: 'module' object has no attribute 'array'
> Error loading: /srv/omeroserver/lib/python/omero/plugins/admin.py
> Traceback (most recent call last):
>  File "/srv/omeroserver/lib/python/omero/cli.py", line 1115, in loadpath
>    execfile( str(pathobj), loc )
>  File "/srv/omeroserver/lib/python/omero/plugins/admin.py", line 27, in ?
>    import omero.config
>  File "/srv/omeroserver/lib/python/omero/config.py", line 31, in ?
>    from elementtree.ElementTree import XML, Element, SubElement, Comment,
> ElementTree, tostring
>  File "/usr/lib/python2.4/site-packages/elementtree/ElementTree.py", line
> 755, in ?
>    _escape = re.compile(eval(r'u"[&<>\"\u0080-\uffff]+"'))
>  File "/usr/lib64/python2.4/sre.py", line 180, in compile
>    return _compile(pattern, flags)
>  File "/usr/lib64/python2.4/sre.py", line 225, in _compile
>    p = sre_compile.compile(pattern, flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 500, in compile
>    code = _code(p, flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 484, in _code
>    _compile(code, p.data, flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 77, in _compile
>    _compile(code, av[2], flags)
>  File "/usr/lib64/python2.4/sre_compile.py", line 52, in _compile
>    _compile_charset(av, flags, code, fixup)
>  File "/usr/lib64/python2.4/sre_compile.py", line 178, in _compile_charset
>    for op, av in _optimize_charset(charset, fixup):
>  File "/usr/lib64/python2.4/sre_compile.py", line 221, in _optimize_charset
>    return _optimize_unicode(charset, fixup)
>  File "/usr/lib64/python2.4/sre_compile.py", line 341, in _optimize_unicode
>    mapping = array.array('b', mapping).tostring()
> AttributeError: 'module' object has no attribute 'array'
> usage: /srv/omeroserver/bin/omero [-h] [-v] [-d DEBUG] [--path PATH] [-C]
>                                  [-s SERVER] [-p PORT] [-g GROUP] [-u USER]
>                                  [-w PASSWORD] [-k KEY]
>                                  <subcommand> ...
> /srv/omeroserver/bin/omero: error: argument <subcommand>: invalid choice:
> 'config'
> 
> choose from:
>        cecog, db, delete, download, export, group, help, hql, import,
>        ldap, load, login, logout, perf, quit, script, server, sessions,
>        shell, testengine, upload, user, version, web
> 
> 
> Cheers,
> Leon Kolchinsky

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