Open Microscopy Environment

Hi

I have installed omero4.1.1 server on a mac and I think that I installed everything right following Janek and Kenneth guide. Omero webadmin gives me the attached issue when logging-in.

I looked and the posts: CLOSED: OMERO.webadmin - "Error ConnectionRefusedException", and Beta 4.2 & web issue; but I'm still having trouble

Please help

The problem is that the web server cannot read and write to the SQLite database file. Based on your log file this will be located here at /Library/Omero/Current/lib/python/omero/db.sqlite3. You have multiple options including changing the permissions on that file to allow the Apache user to read and write to it, moving its location, etc. You can also upgrade to 4.2.0 which does not use the db.sqlite3 SQLite database file at all.

Hi
I cleaned /var/lib -removed weblog and webdb- and then re-ran web settings. I got the following, which I thought is good:

Code: Select all

Database synchronization...
Creating table django_admin_log
Creating table auth_permission
Creating table auth_group
Creating table auth_user
Creating table auth_message
Creating table django_content_type
Creating table django_session
Creating table django_site
Creating table feedback_emailtemplate
Creating table webadmin_gateway
Installing custom SQL for feedback.EmailTemplate model
Installing index for admin.LogEntry model
Installing index for auth.Permission model
Installing index for auth.Message model
Installing json fixture 'initial_data' from absolute path.
Installed 2 object(s) from 1 fixture(s)
OMERO.web was configured successful. Please start the application.


Then I gave _www ownership and read and write permissions to weblog and webdb directories, however Omero webadmin still gives me the error I posted above. I have attached the weblog message below

Have you started the server? The log is telling you that it cannot connect to a server on localhost.

I had started the server, below is the server diagnostics:

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================================================================================
OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================
       
Commands:   java -version                  1.6.0     (/usr/bin/java)
Commands:   python -V                      2.6.1     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/Library/Ice/3.3/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/Library/Ice/3.3/bin/icegridadmin)
Commands:   psql --version                 8.4.2     (/Library/PostgreSQL/8.4/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 69046, enabled)
Server:     DropBox                        active (pid = 69081, enabled)
Server:     FSServer                       active (pid = 69048, enabled)
Server:     Indexer-0                      active (pid = 69049, enabled)
Server:     OMERO.Glacier2                 active (pid = 69050, enabled)
Server:     OMERO.IceStorm                 active (pid = 69051, enabled)
Server:     Processor-0                    active (pid = 69052, enabled)
Server:     Tables-0                       active (pid = 69053, enabled)
Server:     TestDropBox                    inactive (enabled)
Server:     Web                            inactive (enabled)

Log dir:    /Library/Omero/Versions/4.1.1/var/log exists

Log files:  Blitz-0.log                    6.0 MB        errors=11   warnings=9   
Log files:  DropBox.log                    13.0 KB       errors=11   warnings=10 
Log files:  FSServer.log                   3.0 KB        errors=1    warnings=2   
Log files:  Indexer-0.log                  306.0 KB      errors=35   warnings=62 
Log files:  OMEROweb.log                   0.0 KB        errors=1    warnings=0   
Log files:  OMEROweb.log.2010-07-26        0.0 KB        errors=2    warnings=0   
Log files:  Processor-0.log                249.0 KB      errors=65   warnings=477
Log files:  Processor-0.log.1              4.0 MB        errors=1347 warnings=9630
Log files:  Tables-0.log                   256.0 KB      errors=66   warnings=505
Log files:  Tables-0.log.1                 4.0 MB        errors=1346 warnings=9522
Log files:  TestDropBox.log                n/a
Log files:  master.err                     13.0 KB     
Log files:  master.out                     0.0 KB       
Log files:  Total size                     17.13 MB


Are you trying to use OMERO.web with mod_python or with the standalone server? Where are your web log and web database directories and what are their permissions?

it worked!
I am using OMERO.web with mod_python. web log directory: /var/lib/omero/weblog, web db directory: /var/lib/omero/webdb. I had given the apache user permissions on the db.sqlite3 file inside the webdb directory, but now I gave the apache user permissions on the webdb directory itself.

thanks a lot!

That's great! Glad we could get you up and running.