[ome-users] Problem running omero configuration

Leon Kolchinsky lkolchin at gmail.com
Fri Aug 19 01:44:03 BST 2011 

Hi,

Sure, thanks for asking.
I've just moved to a separate version of python - python2.6 which
specifically installed for omero user.

Cheers,
Leon Kolchinsky



On Fri, Aug 19, 2011 at 00:08, Josh Moore <josh at glencoesoftware.com> wrote:

> 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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