Open Microscopy Environment

Hi everybody,
when screening the forum and regarding the installation of OMERO via homebrew on MAC OS X it seems the web deployment is not a "standard" for macintosh based systems (the latest posts are three years old and the web deployment on mac has two lines of code for a development server). Has anybody here have some experience with that, especially with OME5 web deployment on a Mavericks (OSX 10.9) system? Nevertheless this is just one part of my question. The other part concerns the possibility to host the web service on a windows machine while the omero sever itself is situated on a mac. Can this be realised, is this just a theoretical possibility or is this impossible.

Best regards and thanks for your answers.

Benjamin

Hi Benjamin

The instructions for setting up OMERO.web are the same for OS X and Linux, see:
http://www.openmicroscopy.org/site/supp ... l-web.html

It's possible to run OMERO on one server and OMERO.web on another including Windows, see:
http://www.openmicroscopy.org/site/supp ... stallation
http://www.openmicroscopy.org/site/supp ... l-web.html

Note we don't generally test OMERO.web on Windows, so if you can suggest any improvements to our documentation we'd be grateful for them.

Best wishes

Simon

Thanks for your reply Simon,
I'll have a look into it. If I run into some problems which I cannot solve myself, I'll post another reply.

Best regards

Benjamin

Hi,
so i followed the Windows steps to get the web deployment running in Windows. The problem is when i do
>>omero web iis
it says
<<0 static files copied, 818 unmodified.
<<Configured virtual directory: /omero
<<Configured virtual directory: /static
<<Installation complete.
but if then i add
>>omero web status
i get
<<OMERO.web status... NOT STARTED
Development Server starts and does connect to omero.server, even to the omero.server hosted on a diffrent machine. The clients do connect. Nevertheless when I try to load the website I just get HTTP error 500. The web.log does show any to me obvious error.

Best regards

Benjamin

Lipplab wrote:Hi,
so i followed the Windows steps to get the web deployment running in Windows. The problem is when i do
>>omero web iis
it says
<<0 static files copied, 818 unmodified.
<<Configured virtual directory: /omero
<<Configured virtual directory: /static
<<Installation complete.
but if then i add
>>omero web status
i get
<<OMERO.web status... NOT STARTED

Hi Benjamin,
I'm at a similar point in the IIS OMERO.web deployment. What happens when you execute the code

Code: Select all

bin\omero web start

?

Kyle

Hi Kyle,
the server asks me wether I really want to do this and that i should not be using omero web start on windows.
Then some errors from omero.util.TempFileManager concerning tmp file in the local user directories.

Best Regards

Benjamin

Lipplab wrote:the server asks me wether I really want to do this and that i should not be using omero web start on windows.
Then some errors from omero.util.TempFileManager concerning tmp file in the local user directories.

OK, then we are having the same issue then at the exact same place in the OMERO.web deployment. I also get the Error 500-Internal server error when I try to access OMERO.web from a browser.

I'm not sure if the omero web start command is required on IIS, but I also get a similar output when I run that command. See my previous post: http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7486

Let me know if you find out anything!
Kyle

Ok to add some more detail,
the fast-cgi-tcp server with iis tells me there is a problem with _omero_web_iis.dll but does not specify this.
Any idea?

At Kyle,
I saw your thread but somehow I was not able to make this connection we had the same error. Sorry

Best
Benjamin

EDIT: So the Error displayed 800700c1 would tell in windows that the application is not a valid win32 application. Since I'm running everything in win7 64Bit and enabled the 32Bit support I do not get the message.

EDIT2 I disabled 32 Bit support now website is hosted but i cannot login
EDIT3 I removed the omero.web.session_engine now it works.

Hi Benjamin,
I also disabled 32 bit support. Specifically, I went to Start -> Administrator Tools -> Internet Information Services (IIS) Manager. I clicked my server in the left-hand pane, then selected "Application Pools" beneath it. I right-clicked DefaultAppPool and selected "Advanced Settings..." from the menu. In the new menu, I disabled the 32 bit support.

As a result, I can see the OMERO.web login page now as well. I can log in via the web interface as 'root' or as a user I created.

It's really strange, but thanks for finding a solution!

Kyle

Dear all,

I just updated our omero web server (win7 64 bit) from 5.0.2 to 5.1.4.
I enabled the 32 bit application in IIS and I did all the steps from here:
http://www.openmicroscopy.org/site/supp ... #using-iis
and here:
http://www.openmicroscopy.org/site/supp ... l-web.html
http://www.openmicroscopy.org/site/supp ... grade.html

I tried to get the web server started but i still give some error message.
So, i don't have any clue how to get the web server running again.

Code: Select all

DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (source:default)
DEBUG:omeroweb.settings:OPEN_ASTEX_MAX_SIDE = 400 (source:default)
DEBUG:omeroweb.settings:OPEN_ASTEX_MAX_VOXELS = 27000000 (source:default)
DEBUG:omeroweb.settings:OPEN_ASTEX_MIN_SIDE = 20 (source:default)
DEBUG:omeroweb.settings:PAGE = 200 (source:default)
DEBUG:omeroweb.settings:PING_INTERVAL = 60000 (source:default)
DEBUG:omeroweb.settings:PIPELINE_CSS_COMPRESSOR = None (source:default)
DEBUG:omeroweb.settings:PIPELINE_JS_COMPRESSOR = None (source:default)
DEBUG:omeroweb.settings:STATICFILES_STORAGE = 'pipeline.storage.PipelineStorage'
(source:default)
DEBUG:omeroweb.settings:FORCE_SCRIPT_NAME = None (source:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_KEY = u'********************' (source:defau
lt)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:defaul
t)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x000000
00060ED9B0> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'134.96.155.200', 4064, u'ome-www'], [u
'localhost', 4064, u'omeroTest']] (source:omero.web.server_list)
DEBUG:omeroweb.settings:SESSION_COOKIE_AGE = 86400 (source:default)
DEBUG:omeroweb.settings:SESSION_COOKIE_DOMAIN = None (source:default)
DEBUG:omeroweb.settings:SESSION_COOKIE_NAME = None (source:default)
DEBUG:omeroweb.settings:SESSION_ENGINE = 'django.contrib.sessions.backends.cache
' (source:omero.web.session_engine)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_URL = '/static/' (source:default)
DEBUG:omeroweb.settings:STATICFILES_DIRS = [] (source:default)
DEBUG:omeroweb.settings:TEMPLATE_DIRS = [] (source:default)
DEBUG:omeroweb.settings:CENTER_PLUGINS = [] (source:default)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/inclu
des/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclien
t/data/includes/right_plugin.preview.js.html', u'preview_tab']] (source:default)

DEBUG:omeroweb.settings:TOP_LINKS = [[u'Data', u'webindex', {u'title': u'Browse
Data via Projects, Tags etc'}], [u'History', u'history', {u'title': u'History'}]
, [u'Help', u'http://help.openmicroscopy.org/', {u'target': u'new', u'title': u'
Open OMERO user guide in a new tab'}]] (source:default)
DEBUG:omeroweb.settings:USE_X_FORWARDED_HOST = False (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.c
ontrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.
contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient',
'omeroweb.webgateway', 'omeroweb.webredirect', 'omeroweb.webstart', 'pipeline')]

[OK]
WARNING: FastCGI support is deprecated and will be removed in OMERO 5.2. Install
Gunicorn and update config.
Starting OMERO.web...
WARNING: Unless you **really** know what you are doing you should NOT be
using bin\omero web start on Windows with FastCGI.

[OK]
ERROR:omero.util.TempFileManager:rmtree error: remove('C:\Users\Administrator\Ap
pData\Roaming\omero\tmp\omero_Administrator\4608\.lock') => [Error 32] The proce
ss cannot access the file because it is being used by another process: u'C:\\Use
rs\\Administrator\\AppData\\Roaming\\omero\\tmp\\omero_Administrator\\4608\\.loc
k'
ERROR:omero.util.TempFileManager:rmtree error: rmdir('C:\Users\Administrator\App
Data\Roaming\omero\tmp\omero_Administrator\4608') => [Error 145] The directory i
s not empty: u'C:\\Users\\Administrator\\AppData\\Roaming\\omero\\tmp\\omero_Adm
inistrator\\4608'

C:\OMERO.server\bin>omero web status
OMERO.web status... WARNING: FastCGI support is deprecated and will be removed i
n OMERO 5.2. Install Gunicorn and update config.
[NOT STARTED]

My configurations are

Code: Select all

C:\OMERO.server\bin>omero config get --hide-password
omero.data.dir=C:\\OMERO
omero.db.name=omeroDB
omero.db.pass=********
omero.db.user=omeroDBuser
omero.web.application_server=fastcgi-tcp
omero.web.debug=True
omero.web.server_list=[["134.96.155.200",4064,"ome-www"],["localhost",4064,"omer
oTest"]]

and omero admin diagnostics:

Code: Select all

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

OMERO Diagnostics 5.1.4-ice34-b55
================================================================================


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          3.4.2     (C:\Ice-3.4.2\bin\x64\icegr
idnode.EXE -- 2 others)
Commands:   icegridadmin --version         3.4.2     (C:\Ice-3.4.2\bin\x64\icegr
idadmin.EXE -- 2 others)
Commands:   psql --version                 9.3.10    (C:\Program Files\PostgreSQ
L\9.3\bin\psql.EXE)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 3076, enabled)
Server:     DropBox                        active (pid = 2420, enabled)
Server:     FileServer                     active (pid = 2912, enabled)
Server:     Indexer-0                      active (pid = 5116, enabled)
Server:     MonitorServer                  active (pid = 1432, enabled)
Server:     OMERO.Glacier2                 active (pid = 2116, enabled)
Server:     OMERO.IceStorm                 active (pid = 2252, enabled)
Server:     PixelData-0                    active (pid = 2720, enabled)
Server:     Processor-0                    active (pid = 4796, enabled)
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)
Server:     OMERO.master                   active (running as LocalSystem)

Log dir:    C:\OMERO.server\var\log        exists

Log files:  Blitz-0.log                    483.0 MB      errors=471  warnings=11
6
Log files:  Blitz-0.log.1                  524.0 MB      errors=205  warnings=95

Log files:  DropBox.log                    184.0 KB      errors=80   warnings=78

Log files:  FileServer.log                 16.0 KB
Log files:  Indexer-0.log                  423.0 KB      errors=97   warnings=93

Log files:  MonitorServer.log              53.0 KB
Log files:  OMEROweb.log                   2.0 MB        errors=310  warnings=15
8
Log files:  OMEROweb.log.1                 5.0 MB        errors=2    warnings=2

Log files:  OMEROweb.log.2                 5.0 MB
Log files:  OMEROweb.log.3                 5.0 MB
Log files:  OMEROweb.log.4                 5.0 MB
Log files:  OMEROweb.log.5                 5.0 MB
Log files:  OMEROweb_brokenrequest.log     0.0 KB
Log files:  OMEROweb_request.log           0.0 KB        errors=0    warnings=3

Log files:  PixelData-0.log                302.0 KB      errors=62   warnings=87

Log files:  Processor-0.log                766.0 KB      errors=187  warnings=97

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                     1037.96 MB
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=c:\Python26;C:\Windows\system32;C:\Windows;C:\Windows\System32
Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\ZeroC\I
e-3.4.2\bin;c:\Python26;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem
C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Ice-3.4.2\bin\x64;C:\Ice-3.4.2\b
n\;C:\Program Files\PostgreSQL\9.3\bin\;c:\Python26;C:\Windows\system32;C:\Wind
ws;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Prog
am Files (x86)\ZeroC\Ice-3.4.2\bin;c:\Python26;C:\Windows\system32;C:\Windows;C
\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Ice-3.4.2
bin\x64;C:\Ice-3.4.2\bin\;C:\Program Files\PostgreSQL\9.3\bin\;C:\Python26;C:\P
thon26\Scripts;C:\Programm Files\PostgreSQL\9.1\bin
Environment:PYTHONPATH=C:\Ice-3.4.2\python\x64
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'C:\\OMERO'                    Exists? True      Is writable? Tr
e
OMERO temp dir:'C:\Users\Administrator\AppData\Roaming\omero\tmp' Exists? True
Is writable? True   (Size: 0)

JVM settings: Blitz                         -Xmx1268m -XX:MaxPermSize=1g -XX:+I
noreUnrecognizedVMOptions
JVM settings: Indexer                       -Xmx845m -XX:MaxPermSize=1g -XX:+Ig
oreUnrecognizedVMOptions
JVM settings: Pixeldata                     -Xmx1268m -XX:MaxPermSize=1g -XX:+I
noreUnrecognizedVMOptions
JVM settings: Repository                    -Xmx845m -XX:MaxPermSize=1g -XX:+Ig
oreUnrecognizedVMOptions

OMERO.web status... WARNING: FastCGI support is deprecated and will be removed
n OMERO 5.2. Install Gunicorn and update config.
[NOT STARTED]

Has anyone any idea?
Many Thanks Julia