Open Microscopy Environment

Posted: **Mon Aug 22, 2011 2:53 pm**

we've been having some issues with the new server, both when accessing it from the webclient and when logging onto it as the omero user.

1. can multiple people be logged on to the webclient using the same username and password? this works on our server here (omepslid), but we've had issues where the list of datasets won't load or functionality we've programmed won't work unless only one person is logged on at a time.

2. when using omero shell from the command line, i'm unable to exit using Ctrl-D; i have to quit the terminal. i tried restarting the server and the web (using omero admin stop/start and omero web stop/start), but am still having the same issue.

3. BK found the following error in the OMERO.web log:

Code: Select all: Mon, 22 Aug 2011 15:16:07 blitz_gateway WARNING Traceback (most recent call last): File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/gateway/__init__.py", line 1011, in _closeSession self.c.killSession() File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/clients.py", line 760, in killSession s.uuid = omero.rtypes.rstring(self.getSessionId()) File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/clients.py", line 346, in getSessionId return self.getSession().ice_getIdentity().name File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/clients.py", line 335, in getSession raise omero.ClientError("No session available") ClientError: No session available Mon, 22 Aug 2011 15:16:07 blitz_gateway INFO closed connecion (uuid=None) Mon, 22 Aug 2011 15:16:07 blitz_gateway INFO created connection (uuid=77926572-ed57-4027-acd1-30e9e95280d8) Mon, 22 Aug 2011 15:16:07 blitz_gateway WARNING Traceback (most recent call last): File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/gateway/__init__.py", line 1011, in _closeSession self.c.killSession() File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/clients.py", line 760, in killSession s.uuid = omero.rtypes.rstring(self.getSessionId()) File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/clients.py", line 346, in getSessionId return self.getSession().ice_getIdentity().name File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/clients.py", line 335, in getSession raise omero.ClientError("No session available") ClientError: No session available

Posted: **Mon Aug 22, 2011 6:12 pm**

for 2.
the problem occurs after i use the command:
client=pslid.utilities.connect( server, port )

pslid.utilities.connect does the following:
client=omero.client(server,port)
client.enableKeepAlive(60)
return client

this isn't a problem on the omepslid server. is there some way that client needs to be closed or KeepAlive disabled so that i can exit omero shell normally?

thanks,
jenn

Posted: **Mon Aug 22, 2011 6:17 pm**

Related to question 1.

Now, even if there is only one person logged on, I cannot display all the projects and datasets on the left panel of the omero.web (when you click the "DATA").

BK

Posted: **Mon Aug 22, 2011 6:26 pm**

Hi Jenn,

for 2, yes. All uses of omero.client instances with the keep alive thread will need to be wrapped by a try/finally calling:

Code: Select all: client.closeSession()

As for 1, it is certainly the intent that multiple people can be logged on simultaneously. Have you ever seen this behavior via scripts? Is there any error in the web or server logs? Have you tried turning on debugging for OMERO.web?

3 may also be related to 1 since it looks like one or more omero.client objects are being closed while still active. Could you possibly wipe out your logs and reproduce with debugging turned on? What steps are needed to make the error appear?

Regards,
~Josh.

Posted: **Mon Aug 22, 2011 7:06 pm**

could you tell me how to turn on/off the debug mode?

bk

Posted: **Mon Aug 22, 2011 7:29 pm**

Hi BK,

Code: Select all: bin/omero config set omero.web.debug True

should do what you need. More configuration options for the 4.2.1 and 4.2.2 web client are available under https://www.openmicroscopy.org/site/support/omero422/server/install_web

Cheers,
~Josh

Posted: **Mon Aug 22, 2011 8:26 pm**

I did the following process.

1. I wiped out all the log files
2. I restarted the server and web.

-rw-r--r-- 1 omero omero 21366 2011-08-22 20:18 Blitz-0.log
-rw-r--r-- 1 omero omero 735 2011-08-22 20:17 DropBox.log
-rw-r--r-- 1 omero omero 114 2011-08-22 20:17 FileServer.log
-rw-r--r-- 1 omero omero 2942 2011-08-22 20:17 Indexer-0.log
-rw-r--r-- 1 omero omero 0 2011-08-22 20:17 master.err
-rw-r--r-- 1 omero omero 0 2011-08-22 20:17 master.out
-rw-r--r-- 1 omero omero 927 2011-08-22 20:17 MonitorServer.log
-rw-r--r-- 1 omero omero 10944 2011-08-22 20:20 OMEROweb-DEBUG.log
-rw-r--r-- 1 omero omero 952 2011-08-22 20:18 Processor-0.log
-rw-r--r-- 1 omero omero 583 2011-08-22 20:18 Tables-0.log

3. I login to omero.web.
I got the message from OMEROweb-DEBUG.log

on, 22 Aug 2011 21:21:19 webgateway INFO reached connector_pool_size (70), size after purge: (0)
Mon, 22 Aug 2011 21:21:19 webgateway DEBUG Traceback (most recent call last):
File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omeroweb/webgateway/views.py", line 107, in _createConnection
blitzcon = client_wrapper(username, passwd, host=host, port=port, group=None, try_super=try_super, secure=secure, useragent=useragent)
File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/__init__.py", line 19, in client_wrapper
return omero.gateway.BlitzGateway(*args, **kwargs)
File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omeroweb/webclient/webclient_gateway.py", line 79, in __init__
super(OmeroWebGateway, self).__init__(*args, **kwargs)
File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/gateway/__init__.py", line 753, in __init__
self._resetOmeroClient()
File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/gateway/__init__.py", line 1025, in _resetOmeroClient
self.c = omero.client(pmap=['--Ice.Config='+','.join(self.ice_config)])
File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/__init__.py", line 23, in client
return omero.clients.BaseClient(*args, **kwargs)
File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/clients.py", line 122, in __init__
self._initData(id)
File "/home/omero/OMERO.server-Beta-4.2.1/lib/python/omero/clients.py", line 224, in _initData
self.__ic = Ice.initialize(id)
File "/usr/lib/pymodules/python2.6/Ice.py", line 340, in initialize
communicator = IcePy.Communicator(args, data)
EndpointParseException: exception ::Ice::EndpointParseException
{
str = ssl -p 4064 -h <"omero.host" not set>
}

4. I pressed "DATA" from OMERO.web, but it does not display those projects on the left panel. Note that everytime i click the "DATA", the size of Blitz-0.log gets bigger by 10MB. note the size of the file from below.

-rw-r--r-- 1 omero omero 10233123 2011-08-22 20:24 Blitz-0.log
-rw-r--r-- 1 omero omero 735 2011-08-22 20:17 DropBox.log
-rw-r--r-- 1 omero omero 114 2011-08-22 20:17 FileServer.log
-rw-r--r-- 1 omero omero 2942 2011-08-22 20:17 Indexer-0.log
-rw-r--r-- 1 omero omero 0 2011-08-22 20:17 master.err
-rw-r--r-- 1 omero omero 0 2011-08-22 20:17 master.out
-rw-r--r-- 1 omero omero 927 2011-08-22 20:17 MonitorServer.log
-rw-r--r-- 1 omero omero 34988 2011-08-22 20:22 OMEROweb-DEBUG.log
-rw-r--r-- 1 omero omero 952 2011-08-22 20:18 Processor-0.log
-rw-r--r-- 1 omero omero 583 2011-08-22 20:18 Tables-0.log

5. interesting thing is it is "sometimes" good after I delete all the cashe from my browsers and try to log in.

BK

Posted: **Tue Aug 23, 2011 12:03 am**

thanks Josh.

to elucidate on 2:
a. is client.closeSession() required whenever a client is created or only when KeepAlive is enabled?
b. if a session is created using client.createSession(), do we need to do both session.close() and client.closeSession()?

thanks again,
jenn

Posted: **Tue Aug 23, 2011 6:50 am**

Jenn,

jennBakal wrote:to elucidate on 2:
a. is client.closeSession() required whenever a client is created or only when KeepAlive is enabled?
b. if a session is created using client.createSession(), do we need to do both session.close() and client.closeSession()?

closeSession should be called whenever createSession was successful. In other words:

Code: Select all: c = omero.client() s = c.createSession() try: # anything here, including c.enableKeepAlive() finally: c.closeSession()

s.close() is called by c.closeSession() and so is not required.

Cheers,
~Josh.

Posted: **Tue Aug 23, 2011 9:37 am**

Hi BK,

bhcho wrote:1. I wiped out all the log files
2. I restarted the server and web.
3. I login to omero.web.
4. I pressed "DATA" from OMERO.web, but it does not display those projects on the left panel. Note that everytime i click the "DATA", the size of Blitz-0.log gets bigger by 10MB. note the size of the file from below.
5. interesting thing is it is "sometimes" good after I delete all the cashe from my browsers and try to log in.

Ola just tested your branch. By commenting out the import of "pslid," she was able to start up the webclient and log in from multiple browsers. I.e. we're not seeing the same thing happen. Do you have any local code changes that haven't been committed to your branch yet? Could you perhaps share your web configuration with us? (omitting passwords, etc) Do you want to upload the compressed OMEROweb-DEBUG.log to see if we can pinpoint anything?

Cheers,
~Josh.

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