Open Microscopy Environment

Dears,

after installing my Omero server (on Windows XP) I have this output from bin\omero admin diagnostics:

C:\omero_dist>bin\omero admin diagnostics
Error loading: C:\omero_dist\lib\python\omero\plugins\perf.py
Traceback (most recent call last):
File "C:\omero_dist\lib\python\omero\cli.py", line 1127, in loadpath
execfile( str(pathobj), loc )
File "C:\omero_dist\lib\python\omero\plugins\perf.py", line 17, in <module>
import omero.install.perf_test as perf_test
File "C:\omero_dist\lib\python\omero\install\perf_test.py", line 22, in <modul
e>
import omero.util.temp_files
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 322, in <module
>
manager = TempFileManager()
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 58, in __init__

if not self.create(self.userdir) and not self.access(self.userdir):
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 219, in access
dir = str(dir)
UnicodeEncodeError: 'ascii' codec can't encode character u'\xed' in position 49:
ordinal not in range(128)

================================================================================

OMERO Diagnostics 4.4.0-RC2-ice33-b3016
================================================================================


ERROR:omero.util.UpgradeCheck:<urlopen error [Errno 11001] getaddrinfo failed>
Commands: java -version 1.7.0 (C:\WINDOWS\system32\java.E
XE)
Commands: python -V 2.6.6 (C:\Python26\python.EXE)
Commands: icegridnode --version 3.3.1 (C:\Ice-3.3.1\bin\icegridno
de.EXE)
Commands: icegridadmin --version 3.3.1 (C:\Ice-3.3.1\bin\icegridad
min.EXE)
Commands: psql --version 8.3.18 (C:\Program Files\PostgreSQ
L\8.3\bin\psql.EXE)

Server: icegridnode running
Server: Blitz-0 active (pid = 3204, enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 2868, enabled)
Server: Indexer-0 active (pid = 3968, enabled)
Server: MonitorServer active (pid = 2908, enabled)
Server: OMERO.Glacier2 active (pid = 2012, enabled)
Server: OMERO.IceStorm active (pid = 2964, enabled)
Server: PixelData-0 active (pid = 3952, enabled)
Server: Processor-0 inactive (disabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)

Log dir: C:\omero_dist\var\log exists

Log files: Blitz-0.log 321.0 KB errors=19 warnings=31

Log files: DropBox.log n/a
Log files: FileServer.log 3.0 KB
Log files: Indexer-0.log 478.0 KB errors=18 warnings=31

Log files: MonitorServer.log 4.0 KB errors=1 warnings=0

Log files: OMEROweb.log 114.0 KB errors=92 warnings=0

Log files: OMEROweb_request.log 109.0 KB errors=46 warnings=0

Log files: PixelData-0.log 5.0 MB errors=1614 warnings=42
6
Log files: Processor-0.log n/a
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 6.18 MB

Parsing Blitz-0.log:[line:2175] => Server restarted <=

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:Error printing text
PATH=C:\Python26\;C:\Python26\Scripts;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\
System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Ice-3.3.1\bin;C:\Pro
gram Files\PostgreSQL\8.3\bin;%APPDATA%\Python\Scripts

Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO.web status... DEVELOPMENT: You will have to check status by hand!

C:\omero_dist>



Thanks for any troubleshooting ideas!

Zoner

That's an issue with RC2 that will be fixed in the final release of 4.4.0.

and after installing Omero server v.4.3.4:
Microsoft Windows XP [Verze 5.1.2600]
(C) Copyright 1985-2001 Microsoft Corp.

C:\Documents and Settings\Microscopy>cd c:\omero_dist

C:\omero_dist> bin\omero admin diagnostics
Error loading: C:\omero_dist\lib\python\omero\plugins\perf.py
Traceback (most recent call last):
File "C:\omero_dist\lib\python\omero\cli.py", line 1115, in loadpath
execfile( str(pathobj), loc )
File "C:\omero_dist\lib\python\omero\plugins\perf.py", line 17, in <module>
import omero.install.perf_test as perf_test
File "C:\omero_dist\lib\python\omero\install\perf_test.py", line 22, in <modul
e>
import omero.util.temp_files
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 322, in <module
>
manager = TempFileManager()
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 58, in __init__

if not self.create(self.userdir) and not self.access(self.userdir):
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 219, in access
dir = str(dir)
UnicodeEncodeError: 'ascii' codec can't encode character u'\xed' in position 49:
ordinal not in range(128)

================================================================================

OMERO Diagnostics 4.3.4-dbcbce5a-b4
================================================================================


Commands: java -version 1.7.0 (C:\WINDOWS\system32\java.E
XE)
Commands: python -V 2.6.6 (C:\Python26\python.EXE)
Commands: icegridnode --version 3.3.1 (C:\Ice-3.3.1\bin\icegridno
de.EXE)
Commands: icegridadmin --version 3.3.1 (C:\Ice-3.3.1\bin\icegridad
min.EXE)
Commands: psql --version 8.3.18 (C:\Program Files\PostgreSQ
L\8.3\bin\psql.EXE)

Server: icegridnode not started

Log dir: C:\omero_dist\var\log exists

Log files: Blitz-0.log 23.0 KB errors=1 warnings=0

Log files: DropBox.log n/a
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 52.0 KB errors=0 warnings=6

Log files: MonitorServer.log 0.0 KB
Log files: OMEROweb.log 0.0 KB errors=1 warnings=0

Log files: PixelData-0.log 2.0 KB
Log files: Processor-0.log n/a
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 0.08 MB

Parsing Blitz-0.log:[line:118] Did you create your omero.data.dir? E.g. /OMERO

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:Error printing text
PATH=C:\Python26\;C:\Python26\Scripts;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\
System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Ice-3.3.1\bin;C:\Pro
gram Files\PostgreSQL\8.3\bin;%APPDATA%\Python\Scripts

Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO.web status... [NOT STARTED]

C:\omero_dist>

Zoner

It's fine to ignore that first error, the issue you have now is that nothing is started.

And after command bin\omero admin startasync:


C:\omero_dist> bin\omero admin startasync
Error loading: C:\omero_dist\lib\python\omero\plugins\perf.py
Traceback (most recent call last):
File "C:\omero_dist\lib\python\omero\cli.py", line 1115, in loadpath
execfile( str(pathobj), loc )
File "C:\omero_dist\lib\python\omero\plugins\perf.py", line 17, in <module>
import omero.install.perf_test as perf_test
File "C:\omero_dist\lib\python\omero\install\perf_test.py", line 22, in <modul
e>
import omero.util.temp_files
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 322, in <module
>
manager = TempFileManager()
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 58, in __init__

if not self.create(self.userdir) and not self.access(self.userdir):
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 219, in access
dir = str(dir)
UnicodeEncodeError: 'ascii' codec can't encode character u'\xed' in position 49:
ordinal not in range(128)
No descriptor given. Using etc\grid\windefault.xml
[SC] CreateService SUCCESS


SERVICE_NAME: OMERO.master
TYPE : 10 WIN32_OWN_PROCESS
STATE : 2 START_PENDING
(NOT_STOPPABLE,NOT_PAUSABLE,IGNORES_SHUTDOWN)
WIN32_EXIT_CODE : 0 (0x0)
SERVICE_EXIT_CODE : 0 (0x0)
CHECKPOINT : 0x1
WAIT_HINT : 0x7d0
PID : 3300
FLAGS :


C:\omero_dist> bin\omero admin diagnostics
Error loading: C:\omero_dist\lib\python\omero\plugins\perf.py
Traceback (most recent call last):
File "C:\omero_dist\lib\python\omero\cli.py", line 1115, in loadpath
execfile( str(pathobj), loc )
File "C:\omero_dist\lib\python\omero\plugins\perf.py", line 17, in <module>
import omero.install.perf_test as perf_test
File "C:\omero_dist\lib\python\omero\install\perf_test.py", line 22, in <modul
e>
import omero.util.temp_files
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 322, in <module
>
manager = TempFileManager()
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 58, in __init__

if not self.create(self.userdir) and not self.access(self.userdir):
File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 219, in access
dir = str(dir)
UnicodeEncodeError: 'ascii' codec can't encode character u'\xed' in position 49:
ordinal not in range(128)

================================================================================

OMERO Diagnostics 4.3.4-dbcbce5a-b4
================================================================================


Commands: java -version 1.7.0 (C:\WINDOWS\system32\java.E
XE)
Commands: python -V 2.6.6 (C:\Python26\python.EXE)
Commands: icegridnode --version 3.3.1 (C:\Ice-3.3.1\bin\icegridno
de.EXE)
Commands: icegridadmin --version 3.3.1 (C:\Ice-3.3.1\bin\icegridad
min.EXE)
Commands: psql --version 8.3.18 (C:\Program Files\PostgreSQ
L\8.3\bin\psql.EXE)

Server: icegridnode running
Server: Blitz-0 activating (enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 4056, enabled)
Server: Indexer-0 activating (enabled)
Server: MonitorServer active (pid = 5348, enabled)
Server: OMERO.Glacier2 active (pid = 5444, enabled)
Server: OMERO.IceStorm active (pid = 3952, enabled)
Server: PixelData-0 activating (enabled)
Server: Processor-0 inactive (disabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)

Log dir: C:\omero_dist\var\log exists

Log files: Blitz-0.log 23.0 KB errors=1 warnings=0

Log files: DropBox.log n/a
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 52.0 KB errors=0 warnings=6

Log files: MonitorServer.log 0.0 KB
Log files: OMEROweb.log 0.0 KB errors=2 warnings=0

Log files: PixelData-0.log 2.0 KB
Log files: Processor-0.log n/a
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 0.08 MB

Parsing Blitz-0.log:[line:118] Did you create your omero.data.dir? E.g. /OMERO

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:Error printing text
PATH=C:\Python26\;C:\Python26\Scripts;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\
System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Ice-3.3.1\bin;C:\Pro
gram Files\PostgreSQL\8.3\bin;%APPDATA%\Python\Scripts

Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO.web status... [NOT STARTED]

C:\omero_dist\


Thank you

Zoner

Yep, there's nothing wrong with that output. You can safely ignore the UnicodeEncodeError: 'ascii' codec can't encode character u'\xed' in position 49: ordinal not in range(128) message.

Is that all you're concerned about?

Thank you for a quick reply and explanation. OMERO.insight works fine but I have a problem to access the OMERO.webadmin adminstration interface on http://localhost:4080/webadmin. Intern Omero Webserver is running. In the window of my browser (Internet Explorer) I see this message:

Traceback (most recent call last):

File "C:\omero_dist\lib\python\django\core\servers\basehttp.py", line 279, in run
self.result = application(self.environ, self.start_response)

File "C:\omero_dist\lib\python\django\core\servers\basehttp.py", line 651, in __call__
return self.application(environ, start_response)

File "C:\omero_dist\lib\python\django\core\handlers\wsgi.py", line 241, in __call__
response = self.get_response(request)

File "C:\omero_dist\lib\python\django\core\handlers\base.py", line 73, in get_response
response = middleware_method(request)

File "C:\omero_dist\lib\python\django\middleware\common.py", line 57, in process_request
_is_valid_path("%s/" % request.path_info)):

File "C:\omero_dist\lib\python\django\middleware\common.py", line 142, in _is_valid_path
urlresolvers.resolve(path)

File "C:\omero_dist\lib\python\django\core\urlresolvers.py", line 303, in resolve
return get_resolver(urlconf).resolve(path)

File "C:\omero_dist\lib\python\django\core\urlresolvers.py", line 218, in resolve
sub_match = pattern.resolve(new_path)

File "C:\omero_dist\lib\python\django\core\urlresolvers.py", line 216, in resolve
for pattern in self.url_patterns:

File "C:\omero_dist\lib\python\django\core\urlresolvers.py", line 245, in _get_url_patterns
patterns = getattr(self.urlconf_module, "urlpatterns", self.urlconf_module)

File "C:\omero_dist\lib\python\django\core\urlresolvers.py", line 240, in _get_urlconf_module
self._urlconf_module = import_module(self.urlconf_name)

File "C:\omero_dist\lib\python\django\utils\importlib.py", line 35, in import_module
__import__(name)

File "C:\omero_dist\lib\python\omeroweb\webadmin\urls.py", line 30, in <module>
from omeroweb.webadmin import views

File "C:\omero_dist\lib\python\omeroweb\webadmin\views.py", line 58, in <module>
from webclient.webclient_gateway import OmeroWebGateway

File "C:\omero_dist\lib\python\omeroweb\webclient\webclient_gateway.py", line 50, in <module>
import omero.scripts

File "C:\omero_dist\lib\python\omero\scripts.py", line 29, in <module>
import omero.util.temp_files

File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 322, in <module>
manager = TempFileManager()

File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 58, in __init__
if not self.create(self.userdir) and not self.access(self.userdir):

File "C:\omero_dist\lib\python\omero\util\temp_files.py", line 219, in access
dir = str(dir)

UnicodeEncodeError: 'ascii' codec can't encode character u'\xed' in position 49: ordinal not in range(128)

Thank you

Zoner

Sorry, on troubleshooting page I found info: "Windows XP does not run 'Development Server' version of OMERO.web".

Kind regards

Zoner