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hadim / docker-omero

Set of Dockerfile to build a ready-to-use OMERO server
MIT License
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login failed, admin diagnostics error: OMERO.web not installed! and Django not installed! #10

Closed maxgittelman closed 6 years ago

maxgittelman commented 6 years ago

I have a two part question. First, this is what my terminal reads when I launch docker.

mgitt@mgpc:~/workspace/omero/docker-omero$ sudo docker-compose up
[sudo] password for mgitt: 
Starting omero-data ... 
Starting omero-data ... done
Starting omero-db ... 
Starting omero-db ... done
Starting omero-server ... 
Starting omero-server ... done
Starting omero-web ... 
Starting omero-web ... done
Attaching to omero-data, omero-db, omero-server, omero-web
omero-db        | LOG:  database system was interrupted; last known up at 2017-10-06 15:43:16 UTC
omero-data exited with code 0
omero-server    | Waiting for database server to be up.
omero-web       | 2017-10-10 13:20:03,557 CRIT Supervisor running as root (no user in config file)
omero-db        | FATAL:  the database system is starting up
omero-web       | 2017-10-10 13:20:03,559 INFO supervisord started with pid 1
omero-db        | LOG:  database system was not properly shut down; automatic recovery in progress
omero-db        | LOG:  record with zero length at 0/208C630
omero-db        | LOG:  redo is not required
omero-db        | LOG:  MultiXact member wraparound protections are now enabled
omero-db        | LOG:  database system is ready to accept connections
omero-db        | LOG:  autovacuum launcher started
omero-web       | 2017-10-10 13:20:04,561 INFO spawned: 'nginx' with pid 9
omero-web       | 2017-10-10 13:20:04,563 INFO spawned: 'omero_web' with pid 10
omero-web       | 2017-10-10 13:20:06,429 INFO success: nginx entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-10 13:20:06,430 INFO success: omero_web entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-10 13:20:07,328 INFO exited: omero_web (exit status 96; not expected)
omero-server    | ln: failed to create symbolic link 'lib/scripts/custom_scripts/omero_scripts': File exists
omero-web       | 2017-10-10 13:20:08,329 INFO spawned: 'omero_web' with pid 42
omero-web       | 2017-10-10 13:20:10,082 INFO success: omero_web entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-10 13:20:10,849 INFO exited: omero_web (exit status 0; expected)
omero-web       | 2017-10-10 13:20:10,888 INFO reaped unknown pid 64
omero-web       | 2017-10-10 13:20:10,888 INFO reaped unknown pid 65
omero-server    | No descriptor given. Using etc/grid/default.xml
omero-db        | LOG:  unexpected EOF on client connection with an open transaction

The first natural question is whether I should be worried that a symbolic link failed to be made (9th to last line), and that an unexpected end-of-file was logged on the last line. If we ignore that problem and open up a browser to localhost, I am unable to login via root and password. I entered dockers env to see if I could log in manually but got this:

omero@1d45a4fc662e:/omero/OMERO.server$ bin/omero login
Server: [localhost:4064]
Username: [omero]
Password:
internal server error

Do you have an equivalent settings.env file in docker as the OME Ubuntu setup. I do not know what the username and password are and am unable to login.

I proceeded to run a diagnostic check bin/omero admin diagnostics and maybe this is my issue:

omero@1d45a4fc662e:/omero/OMERO.server$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics 5.2.7-ice35-b40
================================================================================

ERROR:omero.util.UpgradeCheck:<urlopen error timed out>
Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      2.7.12    (/usr/bin/python)
Commands:   icegridnode --version          3.5.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.5.5     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        inactive (disabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 541, enabled)
Server:     Indexer-0                      inactive (disabled)
Server:     MonitorServer                  active (pid = 438, enabled)
Server:     OMERO.Glacier2                 active (pid = 479, enabled)
Server:     OMERO.IceStorm                 active (pid = 488, enabled)
Server:     PixelData-0                    inactive (disabled)
Server:     Processor-0                    activation timed out (pid = 11834, enabled)
Server:     Tables-0                       activation timed out (pid = 11835, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /omero/OMERO.server/var/log    exists
Log files:  Blitz-0.log                    51.0 KB       errors=9    warnings=1   
Log files:  DropBox.log                    1.0 KB        errors=2    warnings=1   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  3.0 KB        errors=1    warnings=0   
Log files:  MonitorServer.log              0.0 KB       
Log files:  OMEROweb.log                   n/a
Log files:  PixelData-0.log                4.0 KB        errors=1    warnings=0   
Log files:  Processor-0.log                652.0 KB      errors=372  warnings=186 
Log files:  Tables-0.log                   696.0 KB      errors=372  warnings=186 
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB        errors=0    warnings=3   
Log files:  master.out                     0.0 KB       
Log files:  Total size                     1.41 MB

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

JVM settings: Blitz-${index}                -Xmx2495m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx1663m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx2495m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx1663m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web not installed!
Django not installed!

Recapping my 2 part question:

  1. As I am new to docker, I cannot say I know where python is installed within the environment. Should I simply pip install Django from within docker to fix the problem?
  2. To login via omero where is the settings.env file. What is the password?