Omero 5.6.3 error

Usage & Issues
#1

I have omero in a docker-compose and it was working fine with version 5.6.3 but somehow it started to have problems. I was restarting all the time (checked by docker-compose ps)
and it had the following error:
omero-server | certificates created: /OMERO/certs/server.pem /OMERO/certs/server.p12
omero-server | Traceback (most recent call last):
omero-server | File “/opt/omero/server/venv3/bin/omero”, line 11, in
omero-server | sys.exit(main())
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/main.py”, line 125, in main
omero-server | rv = omero.cli.argv()
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py”, line 1784, in argv
omero-server | cli.invoke(args[1:])
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py”, line 1222, in invoke
omero-server | stop = self.onecmd(line, previous_args)
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py”, line 1299, in onecmd
omero-server | self.execute(line, previous_args)
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py”, line 1381, in execute
omero-server | args.func(args)
omero-server | File “/opt/omero/server/venv3/lib/python3.6/site-packages/omero/plugins/basics.py”, line 121, in call
omero-server | self._load_filehandle(fh, args.keep_going)
omero-server | File “/opt/omero/server/venv3/lib/python3.6/site-packages/omero/plugins/basics.py”, line 96, in _load_filehandle
omero-server | for line in fh:
omero-server | File “/usr/lib64/python3.6/encodings/ascii.py”, line 26, in decode
omero-server | return codecs.ascii_decode(input, self.errors)[0]
omero-server | UnicodeDecodeError: ‘ascii’ codec can’t decode byte 0xe2 in position 184: ordinal not in range(128)
omero-server | Traceback (most recent call last):
omero-server | File “/startup/50-config.py”, line 15, in
omero-server | assert rc == 0
omero-server | AssertionError

I only managed to fix by deleting the image of 5.6.3 and downgrading to 5.6.1
Was there any recent upgrade on the 5.6.3?
Regards

Joao Miguel

#2

Hi Joao,

can you confirm which docker image you are using? I recently needed to re-release 5.6.3. 5.6.3-1 has digest sha256:1947bf3cb3a92171455193c970b6d98cc50027d2f40363b1a94a839c126280f2 while 5.6.3-0 has digest sha256:bc563bf255266e59c433c167c952546881f861d8f4875d25737dc2d5d692c98e. You want 5.6.3-1.

Otherwise, this is certainly an odd error. Have you installed any other packages in the docker?

~Josh

How to pass configuration commands to omero inside a docker
#3

Ok, I will try to provide as much as I can:
Docker version 20.10.2, build 2291f61
docker-compose version 1.28.0, build d02a7b1a

Inside docker compose i am using a modified version fro CRS4 (Luca Lianas) .yml with:

  • postgres:12.5-alpine
  • redis:6.0.10-alpine
  • openmicroscopy/omero-server:5.6.1
  • crs4/ome_seadragon-web:0.7.0-ome5.8.1
  • crs4/ome_seadragon-nginx:0.7.0-ome5.8.1
  • crs4/ome_seadragon_gw-web:0.1.3
  • jwilder/nginx-proxy
  • crs4/ome_seadragon_gw-nginx:0.1.3
  • jrcs/letsencrypt-nginx-proxy-companion

The admin diagnostics is:

================================================================================
OMERO Diagnostics (admin) 5.6.2
================================================================================
        
Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      3.6.8     (/opt/omero/server/venv3/bin/python -- 2 others)
Commands:   icegridnode --version          3.6.5     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.6.5     (/usr/bin/icegridadmin)
Commands:   psql --version                 11.7      (/usr/bin/psql)
Commands:   openssl version                1.0.2     (/usr/bin/openssl)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 432, enabled)
Server:     DropBox                        active (pid = 441, enabled)
Server:     FileServer                     active (pid = 855, enabled)
Server:     Indexer-0                      active (pid = 461, enabled)
Server:     MonitorServer                  active (pid = 939, enabled)
Server:     OMERO.Glacier2                 active (pid = 487, enabled)
Server:     OMERO.IceStorm                 active (pid = 513, enabled)
Server:     PixelData-0                    active (pid = 604, enabled)
Server:     Processor-0                    active (pid = 658, enabled)
Server:     Tables-0                       active (pid = 761, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /opt/omero/server/OMERO.server/var/log exists
Log files:  Blitz-0.log                    95.1 MB       errors=0    warnings=91  
Log files:  DropBox.log                    18.8 KB       errors=4    warnings=9   
Log files:  FileServer.log                 1.8 KB        errors=0    warnings=2   
Log files:  Indexer-0.log                  113.0 KB      errors=0    warnings=22  
Log files:  MonitorServer.log              13.6 KB       errors=0    warnings=4   
Log files:  PixelData-0.log                48.6 KB       errors=0    warnings=22  
Log files:  Processor-0.log                771.9 KB      errors=0    warnings=2   
Log files:  Tables-0.log                   13.4 KB       errors=0    warnings=3   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     269.8 KB      errors=3    warnings=0   
Log files:  master.out                     empty
Log files:  Total size                     96.36 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERODIR=/opt/omero/server/OMERO.server/ 
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)          
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/opt/omero/server/venv3/bin:/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:'/OMERO'                       Exists? True	Is writable? True
OMERO temp dir:'/opt/omero/server/omero/tmp'  Exists? True	Is writable? True   (Size: 11514)

JVM settings: Blitz-${index}                -Xmx8405m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx5043m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx8405m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx5043m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
j

The changes in memory were entered manually after reboot.

I am currently unable to shut it down for long as there are colleagues using the files but I can try a different image if you suggest

I hope that helps

Joao MIguel

#4

I gave a trial to 5.6.3-1 and all seems fine with omero. It accepted the configs from both server and web.
Hurray!!
Thanks Josh
Joao Miguel

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