Open Microscopy Environment

We believe we went through all of the pre-requisite and installation steps for OMERO.server. We should be able to login via the shell command, 'bin/omero login' , using the username and password set up in the environment variables and used in the installation, right?

I would think so, yes. One issue that often occurs is which account to use where. If you think that might be the case, see

https://docs.openmicroscopy.org/omero/5.4.5/sysadmins/troubleshooting.html#which-user-account-and-password-do-i-use-where

Cheers,
~Josh

Hi fhagemei,

Could you please point us to the install instructions you followed?

Our CentOS 7 and Ice 3.6 install instructions would initialise the database with the OMERO root password defined in an env var via

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OMERO.server/bin/omero db script -f OMERO.server/db.sql --password "$OMERO_ROOT_PASS"

If the variable wasn't defined, perhaps the db script step didn't run? You can tell if the DB has been bootstrapped with:

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echo "select * from dbpatch" | psql -h localhost -U db_user omero_database

Cheers,

Kenny

Thanks, and yes, we followed those instructions so the password is in the environment. We even set the user and db to both be omero for the username and we set the omero system and omero db passwords to be the same. The SA did the install, yet we can't get omero to work. I can directly access psql and the omero database via:
psql -d omero -U omero -W
but I can't do anything via omero commands, for example:
[omero@bioimages bin]$ ./omero user add fhagemei Fred Hagemeister
Server: [localhost:4064]
Username: [omero]omero
Password:
Password check failed for 'omero'

So for the test, given I get the following which is presumably a positive result, right?

[omero@bioimages ~]$ echo "select * from dbpatch" | psql -h localhost -U omero omero
id | currentpatch | currentversion | permissions | finished | message | previouspatch | previousversion | external_id
----+--------------+----------------+-------------+----------------------------+----------------------------------------------------------------------------------------------+---------------+-----------------+-------------
1 | 0 | OMERO5.4 | -52 | 2018-05-22 10:44:34.020891 | Database ready. | 0 | OMERO5.4 |
2 | 0 | OMERO5.4 | -52 | 2018-05-22 10:45:08.599039 | DB check DBEnumCheck: done for Bio-Formats revision 34c7ca439a617601ce1ac5dcbdcdcfc6f0bfdaf1 | 0 | OMERO5.4 |
3 | 0 | OMERO5.4 | -52 | 2018-05-22 10:45:09.482224 | DB check DBMappedEnumCheck: done for OMERO version OMERO5.4__0 | 0 | OMERO5.4 |
4 | 0 | OMERO5.4 | -52 | 2018-05-22 10:45:09.48953 | DB check DBUnicodeUnitsCheck: done | 0 | OMERO5.4 |
(4 rows)

For omero diagnosticcs, I get:
[omero@bioimages bin]$ ./omero admin diagnostics

================================================================================
OMERO Diagnostics (admin) 5.4.5-ice36-b83
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.5 (/usr/bin/python)
Commands: icegridnode --version 3.6.4 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.4 (/usr/bin/icegridadmin)
Commands: psql --version 9.6.9 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 20306, enabled)
Server: DropBox active (pid = 20340, enabled)
Server: FileServer active (pid = 20346, enabled)
Server: Indexer-0 active (pid = 20369, enabled)
Server: MonitorServer active (pid = 20349, enabled)
Server: OMERO.Glacier2 active (pid = 20350, enabled)
Server: OMERO.IceStorm active (pid = 20351, enabled)
Server: PixelData-0 active (pid = 20373, enabled)
Server: Processor-0 active (pid = 20352, enabled)
Server: Tables-0 active (pid = 20357, enabled)
Server: TestDropBox inactive (enabled)

Log dir: /home/omero/OMERO.server-5.4.5-ice36-b83/var/log exists
Log files: Blitz-0.log 85.0 MB errors=0 warnings=40
Log files: DropBox.log 14.0 KB errors=0 warnings=5
Log files: FileServer.log 1.0 KB
Log files: Indexer-0.log 214.0 KB
Log files: MonitorServer.log 7.0 KB
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 3.0 KB errors=0 warnings=1
Log files: PixelData-0.log 84.0 KB
Log files: Processor-0.log 852.0 KB errors=0 warnings=5
Log files: Tables-0.log 10.0 KB errors=0 warnings=5
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB errors=1 warnings=0
Log files: master.out 0.0 KB
Log files: Total size 87.09 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/omero/.local/bin:/home/omero/bin
Environment:PYTHONPATH=(unset)
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:'/images' Exists? True Is writable? True
OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)

JVM settings: Blitz-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

Cheers,
Fred

Hi Fred,

if you have not yet added a user yet, I would expect you to be logging in as "root":

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OMERO   OMERO administrator   root   root_password


~Josh

Thanks. That must be it, but we did try that, but I guess we didn't understand the message that came from it, i.e., the message in response sounded more like an error than success.

Cheers,
Fred