Open Microscopy Environment

Setup:
2008 64bit
IIS w/IASPI w/32bit app enabled and IASPI_WSGI
Postgress v9.0.4 x64
Ice v3.3.1 VC80
ActivePython v2.5.6.10 x32
Java JDK v6u27 x32
PIL v1.1.7 for py2.5
MatLib v1.0.1 for py2.5
PyTables v2.1.2

Successfully initiated DB
Successfully populated DB
Successfully sent Admin Start

Successfully set all Omero.web settings

Successfully ran bin/omero web iis

Failed bin/omero web syncmedia

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   trace ends with:    apps = map(lambda x: x.startswith('omeroweb.') and x[9:] or x, settings.INSTALLED_APPS)
                               NameError: global name 'settigns' is not defined

If I run omero diagnostics, suceeds all the way down to web status:

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

OMERO Diagnostics 4.3.2-8fc94b85-b2882
===============================================================================


Commands:   java -version                  1.6.0     (C:\Windows\system32\java.EXE)
Commands:   python -V                      2.5.6     (C:\apps\Python25\python.EXE)
Commands:   icegridnode --version          3.3.1     (c:\apps\ice-3.3.1\bin\icegridnode.EXE)
Commands:   icegridadmin --version         3.3.1     (c:\apps\ice-3.3.1\bin\icegridadmin.EXE)
Commands:   psql --version                 not found

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 2228, enabled)
Server:     DropBox                        active (pid = 2052, enabled)
Server:     FileServer                     active (pid = 1340, enabled)
Server:     Indexer-0                      active (pid = 2600, enabled)
Server:     MonitorServer                  active (pid = 2152, enabled)
Server:     OMERO.Glacier2                 active (pid = 3180, enabled)
Server:     OMERO.IceStorm                 active (pid = 3192, enabled)
Server:     PixelData-0                    active (pid = 2092, enabled)
Server:     Processor-0                    active (pid = 2920, enabled)
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

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

Log files:  Blitz-0.log                    140.0 KB      errors=2    warnings=3

Log files:  DropBox.log                    6.0 KB        errors=0    warnings=2

Log files:  FileServer.log                 0.0 KB
Log files:  Indexer-0.log                  54.0 KB       errors=1    warnings=0

Log files:  MonitorServer.log              3.0 KB        errors=0    warnings=2

Log files:  OMEROweb.log                   42.0 KB       errors=63   warnings=0

Log files:  PixelData-0.log                6.0 KB        errors=0    warnings=1

Log files:  Processor-0.log                4.0 KB        errors=0    warnings=2

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                     0.26 MB

Parsing Blitz-0.log:[line:107] => Server restarted <=
Parsing Blitz-0.log:[line:715] => Server restarted <=
Parsing Blitz-0.log:[line:873] => Server restarted <=

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=C:\apps\Python25\;C:\Windows\system32;C:\Windows;C:\Windows\Sys
tem32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;c:\apps\ice-3.3.1\bin
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... Traceback (most recent call last):
  File "C:\apps\omero_dist\bin\\omero", line 123, in <module>
    rv = omero.cli.argv()
  File "C:\apps\omero_dist\lib\python\omero\cli.py", line 1172, in argv
    cli.invoke(args[1:])
  File "C:\apps\omero_dist\lib\python\omero\cli.py", line 722, in invoke
    stop = self.onecmd(line, previous_args)
  File "C:\apps\omero_dist\lib\python\omero\cli.py", line 791, in onecmd
    self.execute(line, previous_args)
  File "C:\apps\omero_dist\lib\python\omero\cli.py", line 871, in execute
    args.func(args)
  File "C:\apps\omero_dist\lib\python\omero\plugins\prefs.py", line 67, in open_
and_close_config
    return func(*args, **kwargs)
  File "C:\apps\omero_dist\lib\python\omero\plugins\admin.py", line 780, in diag
nostics
    WebControl().status(args)
  File "C:\apps\omero_dist\lib\python\omero\plugins\web.py", line 391, in status

    import omeroweb.settings as settings
  File "C:\apps\omero_dist\lib\python\omeroweb\settings.py", line 76, in <module
>
    CONFIG_XML = omero.config.ConfigXml(CONFIG_XML)
  File "C:\apps\omero_dist\lib\python\omero\config.py", line 58, in __init__
    portalocker.lock(self.lock, portalocker.LOCK_NB|portalocker.LOCK_EX)
  File "C:\apps\omero_dist\lib\python\portalocker.py", line 93, in lock
    raise LockException(LockException.LOCK_FAILED, exc_value[2])
portalocker.LockException: (1, 'The process cannot access the file because anoth
er process has locked a portion of the file.')

.... not sure where to go from here. Were some errors/warnings listed in logs, will parse them, but any help would be appreciated. Not sure if the psql --version "not found" statement in diag is bad either.

Not finding psql on Windows is not a problem. It will usually only be on your PATH if you open the psql console from the Start menu. Could you send the entire trace that's printed from "web syncmedia"?

Thanks,
~Josh

full syncmedia output:

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Traceback (most recent call last):
  File "C:\path1\omeroinstdir\bin\\omero", line 123, in <module>
    rv = omero.cli.argv()
  File "C:\path1\omeroinstdir\lib\python\omero\cli.py", line 1172, in argv
    cli.invoke(args[1:])
  File "C:\path1\omeroinstdir\lib\python\omero\cli.py", line 722, in invoke
    stop = self.onecmd(line, previous_args)
  File "C:\path1\omeroinstdir\lib\python\omero\cli.py", line 791, in onecmd
    self.execute(line, previous_args)
  File "C:\path1\omeroinstdir\lib\python\omero\cli.py", line 871, in execute
    args.func(args)
  File "C:\path1\omeroinstdir\lib\python\omero\plugins\web.py", line 200, in syncmedia
    apps = map(lambda x: x.startswith('omeroweb.') and x[9:] or x, settings.INSTALLED_APPS)
NameError: global name 'settings' is not defined

\path1\omeroinstdir\ replaced actual path.

Odd double wack (\\ after \bin in the first line path). Both cli.py and web.py are present at stated paths.

OK, slowly went back through the web config and I found that I had entered a value into the config.xml (via omero config set) with syntax that Omero didn't like. I also miss-understood the instructions about what values were default vs required... After removing all but the required, web start completed.

That being said, on some of the 'optional' settings, I'm still confused on syntax of the value's, specifically where the examples utilize ' " [ . If I type in exactly as the example does for the omero.web.admins setting:

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omero config set omero.web.admins '[["Dave", "dave@example.com"], ["Bob", "bob@example.com"]]'

... as given, I get the following err:

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usage: C:\apps\omero_dist\bin\\omero config set [-h] KEY [VALUE]
C:\apps\omero_dist\bin\\omero config set: error: unrecognized arguments: dave@example.com], [Bob, bob@example.com]]'

Similar type error for the omero.web.server_list. Anyway, just in case anyone is searching for similar issue, the bare minium output I needed to get to the web console was:

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C:\apps\omero_dist\bin>omero config get
omero.data.dir=c:\\datadir
omero.db.name=dbname
omero.db.pass=mypwd
omero.db.user=myuser
omero.web.application_host=http://server.dept.domain.edu:80/
omero.web.application_server=fastcgi-tcp
omero.web.cache_backend=file://C:/windows/temp/
omero.web.email_host=pop.domain.edu
omero.web.server_email=me@domain.edu
omero.web.session_engine=django.contrib.sessions.backends.cache


also... even though I can get to the webadmin page and login, if I do the omero admin diagnostic command now, all goes through except OMERO.web status .... [NOT STARTED]

assuming an oddity with IIS, but thought worth noting.

leejb wrote:That being said, on some of the 'optional' settings, I'm still confused on syntax of the value's, specifically where the examples utilize ' " [ . If I type in exactly as the example does for the omero.web.admins setting:

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omero config set omero.web.admins '[["Dave", "dave@example.com"], ["Bob", "bob@example.com"]]'

... as given, I get the following err:

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usage: C:\apps\omero_dist\bin\\omero config set [-h] KEY [VALUE]
C:\apps\omero_dist\bin\\omero config set: error: unrecognized arguments: dave@example.com], [Bob, bob@example.com]]'

This is an issue with quotation handling differences between Linux and Windows. I've added ticket 6866 for us to improve the documentation. Under Linux, the outer single quotes produce a single argument. For Windows, you'll need to use different escaping, like that explained under http://stackoverflow.com/questions/562038/escaping-double-quotes-in-batch-script for example.

Alternatively, you can use:

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bin\omero config edit


which will open notepad.exe for you to make the modifications.

Cheers,
~Josh

leejb wrote:also... even though I can get to the webadmin page and login, if I do the omero admin diagnostic command now, all goes through except OMERO.web status .... [NOT STARTED]

assuming an oddity with IIS, but thought worth noting.

Right. Under Windows,

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bin\omero web start | stop | status

all do nothing. For example, if you run "bin\omero web start", you'll just receive an error message. This is because IIS takes care of starting and stopping the process itself. If you would like, you can change the following property:

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bin\omero config set omero.web.application_server development


in which case, bin\omero admin diagnostics will tell you that it knows nothing about web.

Sorry for the confusion.
~Josh.