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will-moore/omero-docker-test.sh

Last active August 22, 2017 11:30
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Commands for running OMERO in Docker for testing OMERO.web
Raw
omero-docker-test.sh
# DOCKER OMERO
$ cd Desktop/OMERO-INSTALL/omero-install/
$ git fetch origin
$ git checkout origin/develop
$ cd linux/test
$ ./docker-build.sh ubuntu1604_nginx
...
+ OMEROVER=latest
+ WEBAPPS=false
+ PGVER=pg94
+ ICEVER=ice36
+ source settings.env
++ OMERO_DB_USER=db_user
++ OMERO_DB_PASS=db_password
++ OMERO_DB_NAME=omero_database
++ OMERO_ROOT_PASS=omero_root_password
++ OMERO_DATA_DIR=/OMERO
++ OMERO_WEB_PORT=80
++ export OMERO_DB_USER OMERO_DB_PASS OMERO_DB_NAME OMERO_ROOT_PASS OMERO_DATA_DIR OMERO_WEB_PORT
++ export PGPASSWORD=db_password
++ PGPASSWORD=db_password
+ bash -eux step01_ubuntu_init.sh
+ apt-get update
...
+ OMERO.server/bin/omero config set omero.web.application_server wsgi-tcp
+ OMERO.server/bin/omero web config nginx --http 80
+ cp /home/omero/OMERO.server/nginx.conf.tmp /etc/nginx/sites-available/omero-web
+ rm /etc/nginx/sites-enabled/default
+ ln -s /etc/nginx/sites-available/omero-web /etc/nginx/sites-enabled/
+ service nginx start
* Starting nginx nginx
...done.
...
# Run Docker...
$ docker run --rm -it -v /Users/wmoore/Documents/biology-data:/biology-data -p 8080:80 -p 4063:4063 -p 4064:4064 omero_install_test_ubuntu1604_nginx
root@c48890350831:/# su omero
omero@c48890350831:/$ cd /home/omero/OMERO.server/
omero@c48890350831:~/OMERO.server$ bin/omero import /biology-data/DV/PTRE/
Server: [localhost:4064]
Username: [omero]root
Password: #omero_root_password
...
# Enable PUBLIC user for OMERO.web...
omero@c48890350831:~/OMERO.server$ bin/omero config set omero.web.public.enabled True
omero@c48890350831:~/OMERO.server$ bin/omero config set omero.web.public.user root
omero@c48890350831:~/OMERO.server$ bin/omero config set omero.web.public.password omero_root_password
omero@c48890350831:~/OMERO.server$ bin/omero web stop
Stopping OMERO.web... [OK]
OMERO.web WSGI workers (PID 930) killed.
Removed stale /home/omero/OMERO.server-5.3.3-ice36-b63/var/django.pid
omero@c48890350831:~/OMERO.server$ bin/omero web start
Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'
0 static files copied to '/home/omero/OMERO.server-5.3.3-ice36-b63/lib/python/omeroweb/static', 611 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time... [OK]
Starting OMERO.web... [OK]
exit # back to root
# Test using curl (from host OS) - see https://trello.com/c/2fI9hSVQ/127-demo-internal-server-error-briefly
for ((c=1;c<=15;c++)); do curl -sL http://localhost:8080/webclient/img_detail/1/ > img_detail.html ; done;
# Checking number of processes...
root@c48890350831:/home/omero/OMERO.server# ps -aux
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
root 1 0.0 0.1 18248 2584 ? Ss 10:37 0:00 bash
postgres 29 0.0 0.1 292912 2456 ? S 10:37 0:00 /usr/lib/postgresql/9.4/bin/postgres -D /var/lib/postgresql/9.4/main -c config_file=/etc/postgresql/9.4/main/postgresql.conf
postgres 32 0.0 0.6 293180 12916 ? Ss 10:37 0:00 postgres: checkpointer process
postgres 33 0.0 0.0 292912 600 ? Ss 10:37 0:00 postgres: writer process
postgres 34 0.0 0.0 292912 1600 ? Ss 10:37 0:00 postgres: wal writer process
postgres 35 0.0 0.1 293336 2988 ? Ss 10:37 0:00 postgres: autovacuum launcher process
postgres 36 0.0 0.0 148340 856 ? Ss 10:37 0:00 postgres: stats collector process
root 48 0.0 0.0 26072 1264 ? Ss 10:37 0:00 cron
omero 571 0.0 0.1 2075612 3768 ? Sl 10:37 0:00 icegridnode --daemon --pidfile /home/omero/OMERO.server/var/master/master.pid --nochdir --Ice.Config=/home/omero/OMERO.server/etc/internal.
omero 622 0.3 0.0 755088 1416 ? Sl 10:37 0:10 python lib/python/fsDropBox.py --Ice.Config=/home/omero/OMERO.server-5.3.3-ice36-b63/var/master/servers/DropBox/config/config
omero 630 0.0 0.0 1037964 260 ? Sl 10:37 0:00 python lib/python/fsServerFS.py --Ice.Config=/home/omero/OMERO.server-5.3.3-ice36-b63/var/master/servers/FileServer/config/config
omero 631 0.1 0.0 860948 384 ? Sl 10:37 0:03 python lib/python/fsServerMS.py --Ice.Config=/home/omero/OMERO.server-5.3.3-ice36-b63/var/master/servers/MonitorServer/config/config
omero 632 2.2 17.4 3841196 356568 ? Sl 10:37 1:02 java -Xmx341m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions -Djava.awt.headless=true -Dlogback.configurationFile=etc/logback-indexi
omero 633 0.0 0.2 502648 6004 ? Sl 10:37 0:02 glacier2router --Ice.Config=/home/omero/OMERO.server-5.3.3-ice36-b63/var/master/servers/OMERO.Glacier2/config/config
omero 635 2.1 14.4 3962084 295640 ? Sl 10:37 0:58 java -Xmx512m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions -Djava.awt.headless=true -Dlogback.configurationFile=etc/logback-indexi
omero 643 0.0 0.0 547464 364 ? Sl 10:37 0:00 icebox --Ice.Config=/home/omero/OMERO.server-5.3.3-ice36-b63/var/master/servers/OMERO.IceStorm/config/config
omero 649 0.2 0.1 1027096 2880 ? Sl 10:37 0:05 python lib/python/runTables.py --Ice.Config=/home/omero/OMERO.server-5.3.3-ice36-b63/var/master/servers/Tables-0/config/config
omero 665 0.2 0.8 1685156 16444 ? Sl 10:37 0:07 python lib/python/runProcessor.py --Ice.Config=/home/omero/OMERO.server-5.3.3-ice36-b63/var/master/servers/Processor-0/config/config
postgres 803 0.0 0.4 297952 9936 ? Ss 10:37 0:00 postgres: db_user omero_database 127.0.0.1(52278) idle
postgres 806 0.1 0.5 298380 12228 ? Ss 10:37 0:04 postgres: db_user omero_database 127.0.0.1(52280) idle
root 864 0.0 0.0 125116 1380 ? Ss 10:38 0:00 nginx: master process /usr/sbin/nginx
www-data 866 0.0 0.0 125440 1704 ? S 10:38 0:00 nginx: worker process
www-data 867 0.0 0.1 125440 2556 ? S 10:38 0:00 nginx: worker process
www-data 868 0.0 0.0 125440 1704 ? S 10:38 0:00 nginx: worker process
www-data 869 0.0 0.1 125704 3148 ? S 10:38 0:00 nginx: worker process
omero 1371 3.7 30.4 4166020 622564 ? Sl 10:44 1:28 java -Xmx512m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions -Djava.awt.headless=true -Dlogback.configurationFile=etc/logback.xml -D
omero 1994 0.0 0.7 45328 14552 ? S 11:12 0:00 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.3.3-ice36-b63/var/django.pid --bind 127.0.0.1:4080 --workers 5 --t
omero 1999 0.1 4.3 629936 89308 ? S 11:12 0:01 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.3.3-ice36-b63/var/django.pid --bind 127.0.0.1:4080 --workers 5 --t
omero 2002 0.2 4.4 786776 90572 ? Sl 11:12 0:01 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.3.3-ice36-b63/var/django.pid --bind 127.0.0.1:4080 --workers 5 --t
omero 2003 0.2 4.3 630732 90040 ? S 11:12 0:01 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.3.3-ice36-b63/var/django.pid --bind 127.0.0.1:4080 --workers 5 --t
omero 2004 0.2 4.4 941836 90096 ? Sl 11:12 0:01 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.3.3-ice36-b63/var/django.pid --bind 127.0.0.1:4080 --workers 5 --t
omero 2005 0.2 4.4 631056 90632 ? S 11:12 0:01 /usr/bin/python /usr/local/bin/gunicorn -D -p /home/omero/OMERO.server-5.3.3-ice36-b63/var/django.pid --bind 127.0.0.1:4080 --workers 5 --t
postgres 2335 0.7 1.3 301432 26904 ? Ss 11:20 0:01 postgres: db_user omero_database 127.0.0.1(53206) idle
postgres 2363 0.0 0.6 295352 13916 ? Ss 11:21 0:00 postgres: db_user omero_database 127.0.0.1(53234) idle
root 2733 0.0 0.1 34428 2896 ? R+ 11:22 0:00 ps -aux
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