OMERO.server creation questions

[jmoore]

Sounds like it's running. You should be able to login from the CLI:

Code: Select all

bin/omero login root@localhost


Cheers,
~Josh.

[rleigh]

See https://www.openmicroscopy.org/site/sup ... iagnostics

[shaneklumpp]

Alright perfect thanks for the help!

When I run Service Postgresql Start, Service nginx start, ./omero web start and ./omero admin start everything is working.

However I cannot connect through http://localhost:4080 on my web browser. I have this OMERO setup on Amazon Web services on an elastic IP (although it is Static and doesn't change...). Is there any help that I can receive to connect?

Looking through the firewall settings, do I need to open up ports 4064/443/80?

I also ran admin diagnostics and some Environment variables were not set. Are these okay to have not set at this point in time?

omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero admin diagnostics | more

================================================================================
OMERO Diagnostics 5.2.6-ice35-b35
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.6 (/usr/bin/python)
Commands: icegridnode --version 3.5.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.5.1 (/usr/bin/icegridadmin)
Commands: psql --version 9.4.10 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 3282, enabled)
Server: DropBox active (pid = 3294, enabled)
Server: FileServer active (pid = 3302, enabled)
Server: Indexer-0 active (pid = 3297, enabled)
Server: MonitorServer active (pid = 3307, enabled)
Server: OMERO.Glacier2 active (pid = 3315, enabled)
Server: OMERO.IceStorm active (pid = 3304, enabled)
Server: PixelData-0 active (pid = 3306, enabled)
Server: Processor-0 active (pid = 3299, enabled)
Server: Tables-0 active (pid = 3308, enabled)
Server: TestDropBox inactive (enabled)

Log dir: /home/omero/OMERO.server-5.2.6-ice35-b35/var/log exists
Log files: Blitz-0.log 1.0 MB errors=37 warnings=1

Log files: DropBox.log 9.0 KB errors=6 warnings=4

Log files: FileServer.log 1.0 KB
Log files: Indexer-0.log 10.0 KB errors=0 warnings=4

Log files: MonitorServer.log 3.0 KB
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 1.0 KB errors=0 warnings=5

Log files: OMEROweb_brokenrequest.lock 0.0 KB
Log files: OMEROweb_brokenrequest.log 0.0 KB
Log files: PixelData-0.log 12.0 KB
Log files: Processor-0.log 151.0 KB errors=50 warnings=11

Log files: Tables-0.log 126.0 KB errors=64 warnings=32

Log files: TestDropBox.log n/a
Log files: master.err 3.0 KB errors=6 warnings=11

Log files: master.out 1.0 KB errors=5 warnings=0

Log files: Total size 1.87 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:/bin:/usr/local/games:/usr/games
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:'OMERO' Exists? True Is writable? Tru
e
OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? Tru
e (Size: 12483)

JVM settings: Blitz-${index} -Xmx621m -XX:MaxPermSize=512m -XX:+I
gnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx414m -XX:MaxPermSize=512m -XX:+I
gnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx621m -XX:MaxPermSize=512m -XX:+I
gnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx414m -XX:MaxPermSize=512m -XX:+I
gnoreUnrecognizedVMOptions

OMERO.web status... [RUNNING] (PID 2176)
Django version: 1.8.17

[rleigh]

It's absolutely fine for these environment variables to be unset. They are optional. They are reported because they can affect the server behaviour and so are useful for diagnosing problems in case they are set incorrectly.

[atarkowska]

However I cannot connect through http://localhost:4080 on my web browser.

You shouldn't be connecting to 4080. You have to install nginx reverse proxy. Make sure you follow http://www.openmicroscopy.org/site/supp ... nginx.html

Please look at some suggestions about deployment in AWS in viewtopic.php?f=4&t=8151&p=17605&hilit=amazon#p17612

Ola

[shaneklumpp]

Alright I've got connectivity to OMERO.web through AWS I believe.

Creating users to login with do I follow these instructions? They're from an older version of OMERO but I assume they're the same

https://www.openmicroscopy.org/site/sup ... group.html

[jmoore]

See also https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/cli/usergroup.html

Nothing significant should have changed in creating users/groups from the CLI.

Cheers,
~Josh

[shaneklumpp]

Alright I have some very important questions that I can hopefully have answered. I am not exactly sure what is wrong but I'll explain my situations.

We have our OMERO.server on AWS connected to our IP address.

When I go to IPaddress/omero it gives a "404 page not found on server. Go back to OMERO.web?" when I click on OMERO.web it brings me to the IPaddress/web-client page.

does this mean that our OMERO.server is accessible from this webclient?

When I try using the username "root" and password "omero" I cannot connect... am I doing something wrong?
(Username: root, password: omero,
Username: omero, password: root,
Username: omero, password: omero,
do not work either)

when I use the user add command what type of users am I creating exactly? Am i creating users that can login through OMERO.web?

when I run through the command I get this:

omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero user add test TE ST -P password --admin
Server: [localhost:4064]
Username: [omero]
Password:
Password check failed for 'omero': []
Password:
Password check failed for 'omero': []
Password:
3 incorrect password attempts

even when I know that I am typing in the omero password correctly (I set it as just "test")

very confused and lost here.

[shaneklumpp]

Some more information: I have followed

http://www.openmicroscopy.org/site/supp ... li/db.html

and set my root password as "root"

[atarkowska]

Did you copy and paste exactly:

Code: Select all

$ bin/omero db script --password secretpassword

Your password will be secretpassword

Ola