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OMERO.server creation questions

General user discussion about using the OMERO platform to its fullest. Please ask new questions at https://forum.image.sc/tags/omero
Please note:
Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

There are workflow guides for various OMERO functions on our help site - http://help.openmicroscopy.org

You should find answers to any basic questions about using the clients there.
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Re: OMERO.server creation questions

Postby shaneklumpp » Thu Dec 22, 2016 5:09 pm

Thanks for the link to installing webtagging. When i followed the guide and everything worked I believe. When i try and start OMERO.web i get a long debug/error message:

omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero config get
omero.data.dir=OMERO
omero.db.name=omero_database
omero.db.pass=omeropass
omero.db.user=EACRIuser
omero.web.application_server=development
omero.web.apps=["autotag", "tagsearch"]
omero.web.debug=True
omero.web.ui.center_plugins=[["Auto Tag", "autotag/auto_tag_init.js.html", "auto_tag_panel"]]
omero.web.ui.top_links=[["Data", "webindex", {"title": "Browse Data via Projects, Tags etc"}], ["History", "history", {"title": "History"}], ["Help", "http://help.openmicroscopy.org/", {"target": "new", "title": "Open OMERO user guide in a new tab"}], ["Tag Search", "tagsearch"]]
omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero admin restart
Waiting on shutdown. Use CTRL-C to exit
.No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero web start
INFO:__main__:Application Starting...
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
DEBUG:omeroweb.settings:ADMINS = [] (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER = 'development' (source:omero.web.application_server)
DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '127.0.0.1' (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 0 (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = 4080 (source:default)
DEBUG:omeroweb.settings:ADDITIONAL_APPS = [u'autotag', u'tagsearch'] (source:omero.web.apps)
DEBUG:omeroweb.settings:CACHES = {u'default': {u'BACKEND': u'django.core.cache.backends.dummy.DummyCache'}} (source:default)
DEBUG:omeroweb.settings:CHUNK_SIZE = 1048576 (source:default)
DEBUG:omeroweb.settings:DATABASES = {} (source:default)
DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:LOGDIR = '/home/omero/OMERO.server-5.2.6-ice35-b35/var/log' (source:default)
DEBUG:omeroweb.settings:LOGIN_LOGO = None (source:default)
DEBUG:omeroweb.settings:LOGIN_REDIRECT = {} (source:default)
DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (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:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:default)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x7f46ab8d5510> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SECRET_KEY = u'********************' (source:default)
DEBUG:omeroweb.settings:SECURE_PROXY_SSL_HEADER = [] (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'localhost', 4064, u'omero']] (source:default)
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 = 'omeroweb.filesessionstore' (source:default)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_ROOT = '/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/omeroweb/static' (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 = [[u'Auto Tag', u'autotag/auto_tag_init.js.html', u'auto_tag_panel']] (source:omero.web.ui.center_plugins)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/includes/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclient/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'}], [u'Tag Search', u'tagsearch']] (source:omero.web.ui.top_links)
DEBUG:omeroweb.settings:USE_X_FORWARDED_HOST = False (source:default)
DEBUG:omeroweb.settings:VIEWER_VIEW = 'omeroweb.webclient.views.image_viewer' (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:WSGI_ARGS = None (source:default)
DEBUG:omeroweb.settings:WSGI_TIMEOUT = 60 (source:default)
DEBUG:omeroweb.settings:WSGI_WORKERS = 5 (source:default)
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: autotag
DEBUG:omeroweb.settings:Couldn't import settings from app: autotag
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: tagsearch
DEBUG:omeroweb.settings:Couldn't import settings from app: tagsearch
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.contrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient', 'omeroweb.webgateway', 'omeroweb.webredirect', 'pipeline', u'autotag', u'tagsearch')]
Traceback (most recent call last):
File "manage.py", line 56, in <module>
execute_from_command_line(sys.argv)
File "/usr/local/lib/python2.7/dist-packages/django/core/management/__init__.py", line 354, in execute_from_command_line
utility.execute()
File "/usr/local/lib/python2.7/dist-packages/django/core/management/__init__.py", line 328, in execute
django.setup()
File "/usr/local/lib/python2.7/dist-packages/django/__init__.py", line 18, in setup
apps.populate(settings.INSTALLED_APPS)
File "/usr/local/lib/python2.7/dist-packages/django/apps/registry.py", line 85, in populate
app_config = AppConfig.create(entry)
File "/usr/local/lib/python2.7/dist-packages/django/apps/config.py", line 86, in create
module = import_module(entry)
File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
ImportError: No module named autotag
omero@ip-172-31-18-162:~/OMERO.server/bin$


How do i fix this?
Last edited by shaneklumpp on Thu Dec 22, 2016 5:29 pm, edited 1 time in total.
shaneklumpp
 
Posts: 38
Joined: Tue Aug 16, 2016 10:07 pm
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Re: OMERO.server creation questions

Postby kennethgillen » Thu Dec 22, 2016 5:27 pm

shaneklumpp wrote:How do i fix this?


It very much sounds like the folder you've placed the web extension is -not- in your server's $PYTHONPATH env var.

Code: Select all
bin/omero admin diagnostics
will print out the server's PYTHONPATH - so you can check it there.

For example:

Code: Select all

[omero-os-user@servername ~]$ echo $PYTHONPATH
/opt/omero/omero/web-extensions

12 [omero-os-user@servername ~]$ cd /opt/omero/omero/web-extensions/
11 [omero-os-user@servername web-extensions]$ ls -alhrt
10 total 28K
  9 drwxr-xr-x.  7 omero-os-user omero 4.0K Nov 27  2015 figure-1.2.0
  8 drwxr-xr-x.  4 omero-os-user omero 4.0K Apr 19  2016 webtagging-2.0.0
  7 lrwxrwxrwx.  1 omero-os-user omero   26 May  9  2016 tagsearch -> webtagging-2.0.0/tagsearch
  6 lrwxrwxrwx.  1 omero-os-user omero   24 May  9  2016 autotag -> webtagging-2.0.0/autotag
  5 -rwxr-xr-x.  1 omero-os-user omero  531 May  9  2016 UPGRADE-webtagging
  4 -rwxr-xr-x.  1 omero-os-user omero 1.5K May 25  2016 UPGRADE-figure
  3 lrwxrwxrwx.  1 omero-os-user omero   12 May 25  2016 figure -> figure-1.2.1
  2 drwxr-xr-x.  5 omero-os-user omero 4.0K May 25  2016 .
  1 drwxr-xr-x.  7 omero-os-user omero 4.0K May 25  2016 figure-1.2.1
13  drwxr-xr-x. 19 omero-os-user omero 4.0K Dec 14 11:11 ..
kennethgillen
 
Posts: 254
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Re: OMERO.server creation questions

Postby shaneklumpp » Thu Dec 22, 2016 5:42 pm

Alright so the problem is with the $PYTHONPATH then.

when i run:
omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero admin diagnostics
i get

Environment:PYTHONPATH=(unset)


which shows my PYTHONPATH is unset i believe.

when i followed the instructions for installing webtagging I ran:
export PYTHONPATH=~/Checkout/webtagging:$PYTHONPATH

which should've added it to my path I believe but obviously didnt...

Also when i run:
omero@ip-172-31-18-162:~$ echo $PYTHONPATH

i get nothing
shaneklumpp
 
Posts: 38
Joined: Tue Aug 16, 2016 10:07 pm
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Re: OMERO.server creation questions

Postby jmoore » Thu Dec 22, 2016 7:14 pm

Hi Shane,

perhaps the issue is that you'll need to run

Code: Select all
export PYTHONPATH=~/Checkout/webtagging:$PYTHONPATH


in each shell/terminal that you open. So best would be to start a new terminal, then run:

Code: Select all
~/OMERO.server/bin$ export PYTHONPATH=~/Checkout/webtagging:$PYTHONPATH
~/OMERO.server/bin$ ./omero admin restart
~/OMERO.server/bin$ ./omero admin diagnostics


all one after the other.

Cheers,
~Josh
User avatar
jmoore
Site Admin
 
Posts: 1591
Joined: Fri May 22, 2009 1:29 pm
Location: Germany
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Re: OMERO.server creation questions

Postby shaneklumpp » Thu Dec 22, 2016 10:22 pm

Thanks that worked. Python path now includes PYTHONPATH=~/Checkout/webtagging:$PYTHONPATH

When I run ./omero web restart i get

Stopping OMERO.web... DEVELOPMENT: You will have to kill processes by hand!


When i run ./omero start i get a series of debug messages but i dont see any errors. Does this okay?

omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero web start
INFO:__main__:Application Starting...
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
DEBUG:omeroweb.settings:ADMINS = [] (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER = 'development' (source:omero.web.application_server)
DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '127.0.0.1' (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 0 (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = 4080 (source:default)
DEBUG:omeroweb.settings:ADDITIONAL_APPS = [u'autotag', u'tagsearch'] (source:omero.web.apps)
DEBUG:omeroweb.settings:CACHES = {u'default': {u'BACKEND': u'django.core.cache.backends.dummy.DummyCache'}} (source:default)
DEBUG:omeroweb.settings:CHUNK_SIZE = 1048576 (source:default)
DEBUG:omeroweb.settings:DATABASES = {} (source:default)
DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:LOGDIR = '/home/omero/OMERO.server-5.2.6-ice35-b35/var/log' (source:default)
DEBUG:omeroweb.settings:LOGIN_LOGO = None (source:default)
DEBUG:omeroweb.settings:LOGIN_REDIRECT = {} (source:default)
DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (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:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:default)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x7f30cb498510> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SECRET_KEY = u'********************' (source:default)
DEBUG:omeroweb.settings:SECURE_PROXY_SSL_HEADER = [] (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'localhost', 4064, u'omero']] (source:default)
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 = 'omeroweb.filesessionstore' (source:default)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_ROOT = '/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/omeroweb/static' (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 = [[u'Auto Tag', u'autotag/auto_tag_init.js.html', u'auto_tag_panel']] (source:omero.web.ui.center_plugins)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/includes/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclient/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'}], [u'Tag Search', u'tagsearch']] (source:omero.web.ui.top_links)
DEBUG:omeroweb.settings:USE_X_FORWARDED_HOST = False (source:default)
DEBUG:omeroweb.settings:VIEWER_VIEW = 'omeroweb.webclient.views.image_viewer' (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:WSGI_ARGS = None (source:default)
DEBUG:omeroweb.settings:WSGI_TIMEOUT = 60 (source:default)
DEBUG:omeroweb.settings:WSGI_WORKERS = 5 (source:default)
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: autotag
INFO:root:Processing custom settings for module autotag.settings
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: tagsearch
DEBUG:omeroweb.settings:Couldn't import settings from app: tagsearch
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.contrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient', 'omeroweb.webgateway', 'omeroweb.webredirect', 'pipeline', u'autotag', u'tagsearch')]
/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/pipeline/utils.py:11: RemovedInDjango19Warning: django.utils.importlib will be removed in Django 1.9.
from django.utils import importlib

Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'

0 static files copied to '/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/omeroweb/static', 650 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time... INFO:__main__:Application Starting...
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
DEBUG:omeroweb.settings:ADMINS = [] (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER = 'development' (source:omero.web.application_server)
DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '127.0.0.1' (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 0 (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = 4080 (source:default)
DEBUG:omeroweb.settings:ADDITIONAL_APPS = [u'autotag', u'tagsearch'] (source:omero.web.apps)
DEBUG:omeroweb.settings:CACHES = {u'default': {u'BACKEND': u'django.core.cache.backends.dummy.DummyCache'}} (source:default)
DEBUG:omeroweb.settings:CHUNK_SIZE = 1048576 (source:default)
DEBUG:omeroweb.settings:DATABASES = {} (source:default)
DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:LOGDIR = '/home/omero/OMERO.server-5.2.6-ice35-b35/var/log' (source:default)
DEBUG:omeroweb.settings:LOGIN_LOGO = None (source:default)
DEBUG:omeroweb.settings:LOGIN_REDIRECT = {} (source:default)
DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (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:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:default)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x7fe0048e0510> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SECRET_KEY = u'********************' (source:default)
DEBUG:omeroweb.settings:SECURE_PROXY_SSL_HEADER = [] (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'localhost', 4064, u'omero']] (source:default)
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 = 'omeroweb.filesessionstore' (source:default)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_ROOT = '/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/omeroweb/static' (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 = [[u'Auto Tag', u'autotag/auto_tag_init.js.html', u'auto_tag_panel']] (source:omero.web.ui.center_plugins)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/includes/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclient/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'}], [u'Tag Search', u'tagsearch']] (source:omero.web.ui.top_links)
DEBUG:omeroweb.settings:USE_X_FORWARDED_HOST = False (source:default)
DEBUG:omeroweb.settings:VIEWER_VIEW = 'omeroweb.webclient.views.image_viewer' (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:WSGI_ARGS = None (source:default)
DEBUG:omeroweb.settings:WSGI_TIMEOUT = 60 (source:default)
DEBUG:omeroweb.settings:WSGI_WORKERS = 5 (source:default)
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: autotag
INFO:root:Processing custom settings for module autotag.settings
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: tagsearch
DEBUG:omeroweb.settings:Couldn't import settings from app: tagsearch
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.contrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient', 'omeroweb.webgateway', 'omeroweb.webredirect', 'pipeline', u'autotag', u'tagsearch')]
[OK]
Starting OMERO.web... [FAILED] OMERO.web already started. /home/omero/OMERO.server-5.2.6-ice35-b35/var/django.pid exists (PID: 2176)! Use 'web stop or restart' first.
shaneklumpp
 
Posts: 38
Joined: Tue Aug 16, 2016 10:07 pm
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Re: OMERO.server creation questions

Postby jmoore » Fri Dec 23, 2016 9:17 am

Hi Shane,

Code: Select all
Starting OMERO.web... [FAILED] OMERO.web already started. /home/omero/OMERO.server-5.2.6-ice35-b35/var/django.pid exists (PID: 2176)! Use 'web stop or restart' first.


A previous hard-restart likely left this file dangling. First, check that no OMERO.web is running:

Code: Select all
ps auxw -H | grep django.pid


If not, then delete the django.pid by hand. After that, your `omero web start` command should succeed.

Note: you have omero.web.application_server=development set which means you are currently working under https://www.openmicroscopy.org/site/support/omero5.2/developers/Web/Deployment.html?highlight=application_server. Before rolling out OMERO.web more widely, we'd very much suggest you switch this value back to the default of "wsgi-tcp" and follow the production instructions under https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/unix/install-web.html.

All the best for the holidays,
~Josh
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Re: OMERO.server creation questions

Postby shaneklumpp » Fri Dec 23, 2016 6:04 pm

Thanks and a happy holidays to everyone here too!

I will make the changes.

Shane
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Posts: 38
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Re: OMERO.server creation questions

Postby shaneklumpp » Wed Dec 28, 2016 5:57 pm

I have two quesetions. When I use the command: ps auxw -H | grep django.pid

I get several django.pid "hits" do i need to delete every one?

What I get:

root@ip-172-31-18-162:~# ps auxw -H | grep django.pid
root 23644 0.0 0.0 10464 932 pts/0 S+ 17:49 0:00 grep --color=auto django.pid
omero 2176 0.0 0.2 50216 11308 ? S Dec06 3:46 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.2.6-ice35-b35/var/django.pid --bind 127.0.0.1:4080 --workers 5 --threads 1 --timeout 60 --max-requests 0 omeroweb.wsgi:application
omero 2181 0.0 2.6 1762196 107160 ? Sl Dec06 0:40 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.2.6-ice35-b35/var/django.pid --bind 127.0.0.1:4080 --workers 5 --threads 1 --timeout 60 --max-requests 0 omeroweb.wsgi:application
omero 2182 0.0 2.6 1885444 107724 ? Sl Dec06 0:39 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.2.6-ice35-b35/var/django.pid --bind 127.0.0.1:4080 --workers 5 --threads 1 --timeout 60 --max-requests 0 omeroweb.wsgi:application
omero 2183 0.0 3.2 2107104 132816 ? Sl Dec06 0:41 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.2.6-ice35-b35/var/django.pid --bind 127.0.0.1:4080 --workers 5 --threads 1 --timeout 60 --max-requests 0 omeroweb.wsgi:application
omero 2188 0.0 3.2 1589864 130008 ? Sl Dec06 0:39 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.2.6-ice35-b35/var/django.pid --bind 127.0.0.1:4080 --workers 5 --threads 1 --timeout 60 --max-requests 0 omeroweb.wsgi:application
omero 2191 0.0 3.2 1908776 131736 ? Sl Dec06 0:41 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.2.6-ice35-b35/var/django.pid --bind 127.0.0.1:4080 --workers 5 --threads 1 --timeout 60 --max-requests 0 omeroweb.wsgi:application


I deleted one Django.pid (in the /home/omero/OMERO.server-5.2.6-ice35-b35/var/ directory) and re ran ./omero web start again:

omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero web start
INFO:__main__:Application Starting...
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
DEBUG:omeroweb.settings:ADMINS = [] (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER = 'development' (source:omero.web.application_server)
DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '127.0.0.1' (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 0 (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = 4080 (source:default)
DEBUG:omeroweb.settings:ADDITIONAL_APPS = [u'autotag', u'tagsearch'] (source:omero.web.apps)
DEBUG:omeroweb.settings:CACHES = {u'default': {u'BACKEND': u'django.core.cache.backends.dummy.DummyCache'}} (source:default)
DEBUG:omeroweb.settings:CHUNK_SIZE = 1048576 (source:default)
DEBUG:omeroweb.settings:DATABASES = {} (source:default)
DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:LOGDIR = '/home/omero/OMERO.server-5.2.6-ice35-b35/var/log' (source:default)
DEBUG:omeroweb.settings:LOGIN_LOGO = None (source:default)
DEBUG:omeroweb.settings:LOGIN_REDIRECT = {} (source:default)
DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (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:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:default)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x7f1cd3ddb510> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SECRET_KEY = u'********************' (source:default)
DEBUG:omeroweb.settings:SECURE_PROXY_SSL_HEADER = [] (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'localhost', 4064, u'omero']] (source:default)
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 = 'omeroweb.filesessionstore' (source:default)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_ROOT = '/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/omeroweb/static' (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 = [[u'Auto Tag', u'autotag/auto_tag_init.js.html', u'auto_tag_panel']] (source:omero.web.ui.center_plugins)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/includes/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclient/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'}], [u'Tag Search', u'tagsearch']] (source:omero.web.ui.top_links)
DEBUG:omeroweb.settings:USE_X_FORWARDED_HOST = False (source:default)
DEBUG:omeroweb.settings:VIEWER_VIEW = 'omeroweb.webclient.views.image_viewer' (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:WSGI_ARGS = None (source:default)
DEBUG:omeroweb.settings:WSGI_TIMEOUT = 60 (source:default)
DEBUG:omeroweb.settings:WSGI_WORKERS = 5 (source:default)
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: autotag
INFO:root:Processing custom settings for module autotag.settings
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: tagsearch
DEBUG:omeroweb.settings:Couldn't import settings from app: tagsearch
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.contrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient', 'omeroweb.webgateway', 'omeroweb.webredirect', 'pipeline', u'autotag', u'tagsearch')]
/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/pipeline/utils.py:11: RemovedInDjango19Warning: django.utils.importlib will be removed in Django 1.9.
from django.utils import importlib

Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'

0 static files copied to '/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/omeroweb/static', 650 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time... INFO:__main__:Application Starting...
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
DEBUG:omeroweb.settings:ADMINS = [] (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER = 'development' (source:omero.web.application_server)
DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '127.0.0.1' (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 0 (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = 4080 (source:default)
DEBUG:omeroweb.settings:ADDITIONAL_APPS = [u'autotag', u'tagsearch'] (source:omero.web.apps)
DEBUG:omeroweb.settings:CACHES = {u'default': {u'BACKEND': u'django.core.cache.backends.dummy.DummyCache'}} (source:default)
DEBUG:omeroweb.settings:CHUNK_SIZE = 1048576 (source:default)
DEBUG:omeroweb.settings:DATABASES = {} (source:default)
DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:LOGDIR = '/home/omero/OMERO.server-5.2.6-ice35-b35/var/log' (source:default)
DEBUG:omeroweb.settings:LOGIN_LOGO = None (source:default)
DEBUG:omeroweb.settings:LOGIN_REDIRECT = {} (source:default)
DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (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:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:default)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x7f33f23a5510> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SECRET_KEY = u'********************' (source:default)
DEBUG:omeroweb.settings:SECURE_PROXY_SSL_HEADER = [] (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'localhost', 4064, u'omero']] (source:default)
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 = 'omeroweb.filesessionstore' (source:default)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_ROOT = '/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/omeroweb/static' (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 = [[u'Auto Tag', u'autotag/auto_tag_init.js.html', u'auto_tag_panel']] (source:omero.web.ui.center_plugins)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/includes/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclient/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'}], [u'Tag Search', u'tagsearch']] (source:omero.web.ui.top_links)
DEBUG:omeroweb.settings:USE_X_FORWARDED_HOST = False (source:default)
DEBUG:omeroweb.settings:VIEWER_VIEW = 'omeroweb.webclient.views.image_viewer' (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:WSGI_ARGS = None (source:default)
DEBUG:omeroweb.settings:WSGI_TIMEOUT = 60 (source:default)
DEBUG:omeroweb.settings:WSGI_WORKERS = 5 (source:default)
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: autotag
INFO:root:Processing custom settings for module autotag.settings
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: tagsearch
DEBUG:omeroweb.settings:Couldn't import settings from app: tagsearch
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.contrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient', 'omeroweb.webgateway', 'omeroweb.webredirect', 'pipeline', u'autotag', u'tagsearch')]
[OK]
Starting OMERO.web... INFO:__main__:Application Starting...
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
DEBUG:omeroweb.settings:ADMINS = [] (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER = 'development' (source:omero.web.application_server)
DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '127.0.0.1' (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 0 (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = 4080 (source:default)
DEBUG:omeroweb.settings:ADDITIONAL_APPS = [u'autotag', u'tagsearch'] (source:omero.web.apps)
DEBUG:omeroweb.settings:CACHES = {u'default': {u'BACKEND': u'django.core.cache.backends.dummy.DummyCache'}} (source:default)
DEBUG:omeroweb.settings:CHUNK_SIZE = 1048576 (source:default)
DEBUG:omeroweb.settings:DATABASES = {} (source:default)
DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:LOGDIR = '/home/omero/OMERO.server-5.2.6-ice35-b35/var/log' (source:default)
DEBUG:omeroweb.settings:LOGIN_LOGO = None (source:default)
DEBUG:omeroweb.settings:LOGIN_REDIRECT = {} (source:default)
DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (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:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:default)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x7fd50151a510> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SECRET_KEY = u'********************' (source:default)
DEBUG:omeroweb.settings:SECURE_PROXY_SSL_HEADER = [] (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'localhost', 4064, u'omero']] (source:default)
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 = 'omeroweb.filesessionstore' (source:default)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_ROOT = '/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/omeroweb/static' (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 = [[u'Auto Tag', u'autotag/auto_tag_init.js.html', u'auto_tag_panel']] (source:omero.web.ui.center_plugins)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/includes/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclient/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'}], [u'Tag Search', u'tagsearch']] (source:omero.web.ui.top_links)
DEBUG:omeroweb.settings:USE_X_FORWARDED_HOST = False (source:default)
DEBUG:omeroweb.settings:VIEWER_VIEW = 'omeroweb.webclient.views.image_viewer' (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:WSGI_ARGS = None (source:default)
DEBUG:omeroweb.settings:WSGI_TIMEOUT = 60 (source:default)
DEBUG:omeroweb.settings:WSGI_WORKERS = 5 (source:default)
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: autotag
INFO:root:Processing custom settings for module autotag.settings
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: tagsearch
DEBUG:omeroweb.settings:Couldn't import settings from app: tagsearch
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.contrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient', 'omeroweb.webgateway', 'omeroweb.webredirect', 'pipeline', u'autotag', u'tagsearch')]
Performing system checks...

System check identified no issues (1 silenced).
December 28, 2016 - 19:36:55
Django version 1.8.17, using settings 'omeroweb.settings'
Starting development server at http://127.0.0.1:4080/
Quit the server with CONTROL-C.
Error: That port is already in use.


Do i need to reset all the django.pid? i could only find one

Shane
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Posts: 38
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Re: OMERO.server creation questions

Postby jmoore » Wed Jan 04, 2017 4:19 pm

Hi Shane,

shaneklumpp wrote:I have two quesetions. When I use the command: ps auxw -H | grep django.pid

I get several django.pid "hits" do i need to delete every one?


It's less important to delete the pid files than it is to kill the processes that are listed in those pid files. For example, `kill -TERM 2176`. Until you see no gunicorn processes, you likely won't be able to start a new OMERO.web due to:

Error: That port is already in use.


Cheers,
~Josh
User avatar
jmoore
Site Admin
 
Posts: 1591
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Re: OMERO.server creation questions

Postby shaneklumpp » Thu Jan 05, 2017 9:30 pm

Thanks for the reply.

I did what you said Josh by switching the application from development to wsgi-tcp by following this link:
https://www.openmicroscopy.org/site/sup ... l-web.html

my error message including omero web status

omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero web startINFO:__main__:Application Starting...
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
INFO:root:Processing custom settings for module omeroweb.settings
DEBUG:omeroweb.settings:ADMINS = [] (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER = 'wsgi-tcp' (source:omero.web.application_server)
DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '127.0.0.1' (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 0 (source:default)
DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = 4080 (source:default)
DEBUG:omeroweb.settings:ADDITIONAL_APPS = [u'autotag', u'tagsearch'] (source:omero.web.apps)
DEBUG:omeroweb.settings:CACHES = {u'default': {u'BACKEND': u'django.core.cache.backends.dummy.DummyCache'}} (source:default)
DEBUG:omeroweb.settings:CHUNK_SIZE = 1048576 (source:default)
DEBUG:omeroweb.settings:DATABASES = {} (source:default)
DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
DEBUG:omeroweb.settings:LOGDIR = '/home/omero/OMERO.server-5.2.6-ice35-b35/var/log' (source:default)
DEBUG:omeroweb.settings:LOGIN_LOGO = 'http://oregon.providence.org/~/media/Images/Providence%20OR/EACRI/eacrilogo.jpg' (source:omero.web.login_logo)
DEBUG:omeroweb.settings:LOGIN_REDIRECT = {} (source:default)
DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (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:default)
DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
DEBUG:omeroweb.settings:PUBLIC_PASSWORD = u'********************' (source:default)
DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object at 0x7f8863d62510> (source:default)
DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
DEBUG:omeroweb.settings:SECRET_KEY = u'********************' (source:default)
DEBUG:omeroweb.settings:SECURE_PROXY_SSL_HEADER = [] (source:default)
DEBUG:omeroweb.settings:SERVER_LIST = [[u'localhost', 4064, u'omero']] (source:default)
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 = 'omeroweb.filesessionstore' (source:default)
DEBUG:omeroweb.settings:SESSION_EXPIRE_AT_BROWSER_CLOSE = True (source:default)
DEBUG:omeroweb.settings:STATIC_ROOT = '/home/omero/OMERO.server-5.2.6-ice35-b35/lib/python/omeroweb/static' (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 = [[u'Auto Tag', u'autotag/auto_tag_init.js.html', u'auto_tag_panel']] (source:omero.web.ui.center_plugins)
DEBUG:omeroweb.settings:RIGHT_PLUGINS = [[u'Acquisition', u'webclient/data/includes/right_plugin.acquisition.js.html', u'metadata_tab'], [u'Preview', u'webclient/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'}], [u'Tag Search', u'tagsearch']] (source:omero.web.ui.top_links)
DEBUG:omeroweb.settings:USE_X_FORWARDED_HOST = False (source:default)
DEBUG:omeroweb.settings:VIEWER_VIEW = 'omeroweb.webclient.views.image_viewer' (source:default)
DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
DEBUG:omeroweb.settings:WSGI_ARGS = None (source:default)
DEBUG:omeroweb.settings:WSGI_TIMEOUT = 60 (source:default)
DEBUG:omeroweb.settings:WSGI_WORKERS = 5 (source:default)
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: autotag
DEBUG:omeroweb.settings:Couldn't import settings from app: autotag
DEBUG:omeroweb.settings:Attempting to import additional app settings for app: tagsearch
DEBUG:omeroweb.settings:Couldn't import settings from app: tagsearch
DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles', 'django.contrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin', 'omeroweb.webclient', 'omeroweb.webgateway', 'omeroweb.webredirect', 'pipeline', u'autotag', u'tagsearch')]
Traceback (most recent call last):
File "manage.py", line 56, in <module>
execute_from_command_line(sys.argv)
File "/usr/local/lib/python2.7/dist-packages/django/core/management/__init__.py", line 354, in execute_from_command_line
utility.execute()
File "/usr/local/lib/python2.7/dist-packages/django/core/management/__init__.py", line 328, in execute
django.setup()
File "/usr/local/lib/python2.7/dist-packages/django/__init__.py", line 18, in setup
apps.populate(settings.INSTALLED_APPS)
File "/usr/local/lib/python2.7/dist-packages/django/apps/registry.py", line 85, in populate
app_config = AppConfig.create(entry)
File "/usr/local/lib/python2.7/dist-packages/django/apps/config.py", line 86, in create
module = import_module(entry)
File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
ImportError: No module named autotag
omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero web status
OMERO.web status... [NOT STARTED]


When i re ran omero admin diagnostics I noticed my PYTHON PATH was unset again.
I reset it using
Code: Select all
CODE: SELECT ALL
~/OMERO.server/bin$ export PYTHONPATH=~/Checkout/webtagging:$PYTHONPATH
~/OMERO.server/bin$ ./omero admin restart
~/OMERO.server/bin$ ./omero admin diagnostics


Then restarted omero.admin and omero.web and it worked. Everything started up.

Am i going to have to do this every time I change something? Is there a way to save my python path?
shaneklumpp
 
Posts: 38
Joined: Tue Aug 16, 2016 10:07 pm
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