Skip to content

Instantly share code, notes, and snippets.

@atarkowska

atarkowska/gist:7b890bfc69ec38d8ba9ff615f0ca4328

Created December 21, 2016 10:15
Show Gist options
  • Save atarkowska/7b890bfc69ec38d8ba9ff615f0ca4328 to your computer and use it in GitHub Desktop.
Save atarkowska/7b890bfc69ec38d8ba9ff615f0ca4328 to your computer and use it in GitHub Desktop.
Download ZIP
omero-test
Raw
gistfile1.txt
+ docker-compose -f test/docker-compose.yml up --build --abort-on-container-exit
WARNING: The SKIP_UPGRADE_CHECK variable is not set. Defaulting to a blank string.
WARNING: The OMEROBUILD variable is not set. Defaulting to a blank string.
Building omeroserver
Step 1 : FROM openmicroscopy/omero-ssh-daemon-c7:0.1.1
---> 02e6d0e5628d
Step 2 : MAINTAINER [email protected]
---> Using cache
---> 4408ec196df0
Step 3 : RUN yum install -y epel-release && yum clean all
---> Using cache
---> 6e8053301cd9
Step 4 : RUN yum install -y wget unzip git && yum clean all
---> Using cache
---> a3abde21e9cd
Step 5 : RUN yum install -y java-1.8.0-openjdk-devel && yum clean all
---> Using cache
---> 644211999710
Step 6 : RUN yum install -y python-pip python-virtualenv python-virtualenvwrapper python-devel numpy scipy python-pillow python-matplotlib python-tables && yum clean all
---> Using cache
---> d474fc6ccef8
Step 7 : RUN cd /etc/yum.repos.d && wget https://zeroc.com/download/rpm/zeroc-ice-el7.repo
---> Using cache
---> f029b6d76ade
Step 8 : RUN yum install -y gcc gcc-c++ libdb-utils openssl-devel bzip2-devel expat-devel && yum clean all
---> Using cache
---> 3cd2825db6bf
Step 9 : RUN cd /etc/yum.repos.d && yum install -y ice-all-runtime ice-all-devel
---> Using cache
---> 2f0ce52bb2cd
Step 10 : RUN yum -y install http://yum.postgresql.org/9.5/redhat/rhel-7-x86_64/pgdg-centos95-9.5-3.noarch.rpm && yum clean all
---> Using cache
---> 5e0bd113aae7
Step 11 : RUN yum -y install postgresql95 && yum clean all
---> Using cache
---> a128d08546a6
Step 12 : ADD ./install /tmp/install
---> Using cache
---> 661b383941ed
Step 13 : RUN chmod a+r -R /tmp/install
---> Using cache
---> f19a1c0469d0
Step 14 : RUN chmod a+x /tmp/install/*.sh
---> Using cache
---> d185f16818ad
Step 15 : USER omero
---> Using cache
---> 86e6c58533e5
Step 16 : ENV HOME /home/omero
---> Using cache
---> ae695cb1de7b
Step 17 : ENV COMPONENT server
---> Using cache
---> fb9f5321a1c2
Step 18 : ENV OMERO_DB_HOST postgres
---> Using cache
---> 324b4955233c
Step 19 : ENV OMERO_DB_PORT 5432
---> Using cache
---> bcaa540e780d
Step 20 : ENV OMERO_DB_USER postgres
---> Using cache
---> bc1d38f270f0
Step 21 : ENV OMERO_DB_NAME omero
---> Using cache
---> 45614a7e5f74
Step 22 : ENV OMERO_ROOT_PASS omero
---> Using cache
---> e3c4241be20a
Step 23 : ENV SKIP_UPGRADE_CHECK false
---> Using cache
---> de57cee6700f
Step 24 : ENV RUNSCRIPT $COMPONENT
---> Using cache
---> 0f71e0d181ce
Step 25 : EXPOSE 4063 4064
---> Using cache
---> 5b79a70855bc
Step 26 : WORKDIR $HOME
---> Using cache
---> 92cb400cda00
Step 27 : ENTRYPOINT /tmp/install/docker-entrypoint.sh
---> Using cache
---> 50f096a35605
Successfully built 50f096a35605
Building omeropy
Step 1 : FROM openmicroscopy/omero-ssh-daemon-c7:0.1.1
---> 02e6d0e5628d
Step 2 : MAINTAINER [email protected]
---> Using cache
---> 4408ec196df0
Step 3 : RUN yum install -y epel-release && yum clean all
---> Using cache
---> 6e8053301cd9
Step 4 : RUN yum install -y wget unzip git && yum clean all
---> Using cache
---> a3abde21e9cd
Step 5 : RUN yum install -y java-1.8.0-openjdk-devel && yum clean all
---> Using cache
---> 644211999710
Step 6 : RUN yum install -y python-pip python-virtualenv python-virtualenvwrapper python-devel numpy scipy python-pillow python-matplotlib python-tables && yum clean all
---> Using cache
---> d474fc6ccef8
Step 7 : RUN cd /etc/yum.repos.d && wget https://zeroc.com/download/rpm/zeroc-ice-el7.repo
---> Using cache
---> f029b6d76ade
Step 8 : RUN yum install -y gcc gcc-c++ libdb-utils openssl-devel bzip2-devel expat-devel && yum clean all
---> Using cache
---> 3cd2825db6bf
Step 9 : RUN cd /etc/yum.repos.d && yum install -y ice-all-runtime ice-all-devel
---> Using cache
---> 2f0ce52bb2cd
Step 10 : RUN yum -y install http://yum.postgresql.org/9.5/redhat/rhel-7-x86_64/pgdg-centos95-9.5-3.noarch.rpm && yum clean all
---> Using cache
---> 5e0bd113aae7
Step 11 : RUN yum -y install postgresql95 && yum clean all
---> Using cache
---> a128d08546a6
Step 12 : ADD ./install /tmp/install
---> Using cache
---> 661b383941ed
Step 13 : RUN chmod a+r -R /tmp/install
---> Using cache
---> f19a1c0469d0
Step 14 : RUN chmod a+x /tmp/install/*.sh
---> Using cache
---> d185f16818ad
Step 15 : USER omero
---> Using cache
---> 86e6c58533e5
Step 16 : ENV HOME /home/omero
---> Using cache
---> ae695cb1de7b
Step 17 : ENV COMPONENT server
---> Using cache
---> fb9f5321a1c2
Step 18 : ENV OMERO_DB_HOST postgres
---> Using cache
---> 324b4955233c
Step 19 : ENV OMERO_DB_PORT 5432
---> Using cache
---> bcaa540e780d
Step 20 : ENV OMERO_DB_USER postgres
---> Using cache
---> bc1d38f270f0
Step 21 : ENV OMERO_DB_NAME omero
---> Using cache
---> 45614a7e5f74
Step 22 : ENV OMERO_ROOT_PASS omero
---> Using cache
---> e3c4241be20a
Step 23 : ENV SKIP_UPGRADE_CHECK false
---> Using cache
---> de57cee6700f
Step 24 : ENV RUNSCRIPT $COMPONENT
---> Using cache
---> 0f71e0d181ce
Step 25 : EXPOSE 4063 4064
---> Using cache
---> 5b79a70855bc
Step 26 : WORKDIR $HOME
---> Using cache
---> 92cb400cda00
Step 27 : ENTRYPOINT /tmp/install/docker-entrypoint.sh
---> Using cache
---> 50f096a35605
Successfully built 50f096a35605
Building omeropyserver
Step 1 : FROM openmicroscopy/omero-ssh-daemon-c7:0.1.1
---> 02e6d0e5628d
Step 2 : MAINTAINER [email protected]
---> Using cache
---> 4408ec196df0
Step 3 : RUN yum install -y epel-release && yum clean all
---> Using cache
---> 6e8053301cd9
Step 4 : RUN yum install -y wget unzip git && yum clean all
---> Using cache
---> a3abde21e9cd
Step 5 : RUN yum install -y java-1.8.0-openjdk-devel && yum clean all
---> Using cache
---> 644211999710
Step 6 : RUN yum install -y python-pip python-virtualenv python-virtualenvwrapper python-devel numpy scipy python-pillow python-matplotlib python-tables && yum clean all
---> Using cache
---> d474fc6ccef8
Step 7 : RUN cd /etc/yum.repos.d && wget https://zeroc.com/download/rpm/zeroc-ice-el7.repo
---> Using cache
---> f029b6d76ade
Step 8 : RUN yum install -y gcc gcc-c++ libdb-utils openssl-devel bzip2-devel expat-devel && yum clean all
---> Using cache
---> 3cd2825db6bf
Step 9 : RUN cd /etc/yum.repos.d && yum install -y ice-all-runtime ice-all-devel
---> Using cache
---> 2f0ce52bb2cd
Step 10 : RUN yum -y install http://yum.postgresql.org/9.5/redhat/rhel-7-x86_64/pgdg-centos95-9.5-3.noarch.rpm && yum clean all
---> Using cache
---> 5e0bd113aae7
Step 11 : RUN yum -y install postgresql95 && yum clean all
---> Using cache
---> a128d08546a6
Step 12 : ADD ./install /tmp/install
---> Using cache
---> 661b383941ed
Step 13 : RUN chmod a+r -R /tmp/install
---> Using cache
---> f19a1c0469d0
Step 14 : RUN chmod a+x /tmp/install/*.sh
---> Using cache
---> d185f16818ad
Step 15 : USER omero
---> Using cache
---> 86e6c58533e5
Step 16 : ENV HOME /home/omero
---> Using cache
---> ae695cb1de7b
Step 17 : ENV COMPONENT server
---> Using cache
---> fb9f5321a1c2
Step 18 : ENV OMERO_DB_HOST postgres
---> Using cache
---> 324b4955233c
Step 19 : ENV OMERO_DB_PORT 5432
---> Using cache
---> bcaa540e780d
Step 20 : ENV OMERO_DB_USER postgres
---> Using cache
---> bc1d38f270f0
Step 21 : ENV OMERO_DB_NAME omero
---> Using cache
---> 45614a7e5f74
Step 22 : ENV OMERO_ROOT_PASS omero
---> Using cache
---> e3c4241be20a
Step 23 : ENV SKIP_UPGRADE_CHECK false
---> Using cache
---> de57cee6700f
Step 24 : ENV RUNSCRIPT $COMPONENT
---> Using cache
---> 0f71e0d181ce
Step 25 : EXPOSE 4063 4064
---> Using cache
---> 5b79a70855bc
Step 26 : WORKDIR $HOME
---> Using cache
---> 92cb400cda00
Step 27 : ENTRYPOINT /tmp/install/docker-entrypoint.sh
---> Using cache
---> 50f096a35605
Successfully built 50f096a35605
Creating test_postgres_1
Creating test_omeroserver_1
Creating test_omeropy_1
Creating test_omeropyserver_1
Attaching to test_postgres_1, test_omeroserver_1, test_omeropy_1, test_omeropyserver_1
postgres_1 | The files belonging to this database system will be owned by user "postgres".
postgres_1 | This user must also own the server process.
postgres_1 |
omeropy_1 | + OMEROBUILD=
omeropy_1 | + COMPONENT=py
omeropy_1 | + RUNSCRIPT=py
omeropy_1 | + OMEROPATH=/home/omero/OMERO.py
omeropy_1 | + sudo pip install -r /tmp/install/requirements.txt
postgres_1 | The database cluster will be initialized with locale "en_US.utf8".
omeroserver_1 | + OMEROBUILD=
postgres_1 | The default database encoding has accordingly been set to "UTF8".
omeropyserver_1 | + OMEROBUILD=
omeroserver_1 | + COMPONENT=server
postgres_1 | The default text search configuration will be set to "english".
omeropyserver_1 | + COMPONENT=server
omeroserver_1 | + RUNSCRIPT=server
postgres_1 |
omeropyserver_1 | + RUNSCRIPT=py
omeroserver_1 | + OMEROPATH=/home/omero/OMERO.server
postgres_1 | Data page checksums are disabled.
omeropyserver_1 | + OMEROPATH=/home/omero/OMERO.server
omeroserver_1 | + sudo pip install -r /tmp/install/requirements.txt
postgres_1 |
omeropyserver_1 | + sudo pip install -r /tmp/install/requirements.txt
postgres_1 | fixing permissions on existing directory /var/lib/postgresql/data ... ok
postgres_1 | creating subdirectories ... ok
postgres_1 | selecting default max_connections ... 100
postgres_1 | selecting default shared_buffers ... 128MB
postgres_1 | selecting dynamic shared memory implementation ... posix
postgres_1 | creating configuration files ... ok
postgres_1 | running bootstrap script ... ok
postgres_1 | performing post-bootstrap initialization ... ok
postgres_1 | syncing data to disk ...
postgres_1 | WARNING: enabling "trust" authentication for local connections
postgres_1 | You can change this by editing pg_hba.conf or using the option -A, or
postgres_1 | --auth-local and --auth-host, the next time you run initdb.
postgres_1 | ok
postgres_1 |
postgres_1 | Success. You can now start the database server using:
postgres_1 |
postgres_1 | pg_ctl -D /var/lib/postgresql/data -l logfile start
postgres_1 |
postgres_1 | ****************************************************
postgres_1 | WARNING: No password has been set for the database.
postgres_1 | This will allow anyone with access to the
postgres_1 | Postgres port to access your database. In
postgres_1 | Docker's default configuration, this is
postgres_1 | effectively any other container on the same
postgres_1 | system.
postgres_1 |
postgres_1 | Use "-e POSTGRES_PASSWORD=password" to set
postgres_1 | it in "docker run".
postgres_1 | ****************************************************
omeropy_1 | You are using pip version 7.1.0, however version 9.0.1 is available.
omeropy_1 | You should consider upgrading via the 'pip install --upgrade pip' command.
omeroserver_1 | You are using pip version 7.1.0, however version 9.0.1 is available.
omeroserver_1 | You should consider upgrading via the 'pip install --upgrade pip' command.
omeropyserver_1 | You are using pip version 7.1.0, however version 9.0.1 is available.
omeropyserver_1 | You should consider upgrading via the 'pip install --upgrade pip' command.
omeroserver_1 | Collecting omego (from -r /tmp/install/requirements.txt (line 1))
omeropy_1 | Collecting omego (from -r /tmp/install/requirements.txt (line 1))
omeropyserver_1 | Collecting omego (from -r /tmp/install/requirements.txt (line 1))
postgres_1 | waiting for server to start....LOG: database system was shut down at 2016-12-21 10:08:13 UTC
postgres_1 | LOG: MultiXact member wraparound protections are now enabled
postgres_1 | LOG: autovacuum launcher started
postgres_1 | LOG: database system is ready to accept connections
omeroserver_1 | Downloading omego-0.4.2.tar.gz
omeropy_1 | Downloading omego-0.4.2.tar.gz
omeropyserver_1 | Downloading omego-0.4.2.tar.gz
omeroserver_1 | Collecting zeroc-ice<3.7,>3.5 (from -r /tmp/install/requirements.txt (line 2))
omeropy_1 | Collecting zeroc-ice<3.7,>3.5 (from -r /tmp/install/requirements.txt (line 2))
omeropyserver_1 | Collecting zeroc-ice<3.7,>3.5 (from -r /tmp/install/requirements.txt (line 2))
omeroserver_1 | Downloading zeroc-ice-3.6.3.tar.gz (1.1MB)
omeropy_1 | Downloading zeroc-ice-3.6.3.tar.gz (1.1MB)
omeropyserver_1 | Downloading zeroc-ice-3.6.3.tar.gz (1.1MB)
postgres_1 | done
postgres_1 | server started
postgres_1 | ALTER ROLE
postgres_1 |
postgres_1 |
postgres_1 | /docker-entrypoint.sh: ignoring /docker-entrypoint-initdb.d/*
postgres_1 |
postgres_1 | LOG: received fast shutdown request
postgres_1 | LOG: aborting any active transactions
postgres_1 | LOG: autovacuum launcher shutting down
postgres_1 | waiting for server to shut down....LOG: shutting down
postgres_1 | LOG: database system is shut down
omeroserver_1 | Collecting yaclifw>=0.1.1 (from omego->-r /tmp/install/requirements.txt (line 1))
omeropy_1 | Collecting yaclifw>=0.1.1 (from omego->-r /tmp/install/requirements.txt (line 1))
omeropyserver_1 | Collecting yaclifw>=0.1.1 (from omego->-r /tmp/install/requirements.txt (line 1))
omeropyserver_1 | Downloading yaclifw-0.1.2.tar.gz
omeropy_1 | Downloading yaclifw-0.1.2.tar.gz
omeroserver_1 | Downloading yaclifw-0.1.2.tar.gz
omeropyserver_1 | Collecting argparse (from yaclifw>=0.1.1->omego->-r /tmp/install/requirements.txt (line 1))
omeropy_1 | Collecting argparse (from yaclifw>=0.1.1->omego->-r /tmp/install/requirements.txt (line 1))
omeroserver_1 | Collecting argparse (from yaclifw>=0.1.1->omego->-r /tmp/install/requirements.txt (line 1))
omeropyserver_1 | Downloading argparse-1.4.0-py2.py3-none-any.whl
omeroserver_1 | Downloading argparse-1.4.0-py2.py3-none-any.whl
omeropy_1 | Downloading argparse-1.4.0-py2.py3-none-any.whl
omeroserver_1 | Installing collected packages: argparse, yaclifw, omego, zeroc-ice
omeropyserver_1 | Installing collected packages: argparse, yaclifw, omego, zeroc-ice
omeropy_1 | Installing collected packages: argparse, yaclifw, omego, zeroc-ice
omeroserver_1 | Running setup.py install for yaclifw
omeropyserver_1 | Running setup.py install for yaclifw
omeropy_1 | Running setup.py install for yaclifw
postgres_1 | done
postgres_1 | server stopped
postgres_1 |
postgres_1 | PostgreSQL init process complete; ready for start up.
postgres_1 |
postgres_1 | LOG: database system was shut down at 2016-12-21 10:08:14 UTC
omeropyserver_1 | Running setup.py install for omego
omeropy_1 | Running setup.py install for omego
omeroserver_1 | Running setup.py install for omego
postgres_1 | LOG: MultiXact member wraparound protections are now enabled
postgres_1 | LOG: database system is ready to accept connections
postgres_1 | LOG: autovacuum launcher started
omeropyserver_1 | Running setup.py install for zeroc-ice
omeroserver_1 | Running setup.py install for zeroc-ice
omeropy_1 | Running setup.py install for zeroc-ice
omeropyserver_1 | Successfully installed argparse-1.4.0 omego-0.4.2 yaclifw-0.1.2 zeroc-ice-3.6.3
omeroserver_1 | Successfully installed argparse-1.4.0 omego-0.4.2 yaclifw-0.1.2 zeroc-ice-3.6.3
omeropyserver_1 | + echo 'Downloading OMERO.server...'
omeropyserver_1 | + ARGS=
omeropyserver_1 | Downloading OMERO.server...
omeropyserver_1 | + '[' -n '' ']'
omeropyserver_1 | + cd /tmp
omeropyserver_1 | + omego download --ice 3.6 server
omeroserver_1 | + echo 'Downloading OMERO.server...'
omeroserver_1 | + ARGS=
omeroserver_1 | + '[' -n '' ']'
omeroserver_1 | Downloading OMERO.server...
omeroserver_1 | + cd /tmp
omeroserver_1 | + omego download --ice 3.6 server
omeropy_1 | Successfully installed argparse-1.4.0 omego-0.4.2 yaclifw-0.1.2 zeroc-ice-3.6.3
omeropy_1 | + echo 'Downloading OMERO.py...'
omeropy_1 | + ARGS=
omeropy_1 | + '[' -n '' ']'
omeropy_1 | Downloading OMERO.py...
omeropy_1 | + cd /tmp
omeropy_1 | + omego download --ice 3.6 py
omeropy_1 | 2016-12-21 10:12:40,261 [omego.artifa] INFO Checking http://downloads.openmicroscopy.org/omero/5.2.7/./artifacts/OMERO.py-5.2.7-ice36-b40.zip
omeropyserver_1 | 2016-12-21 10:12:40,261 [omego.artifa] INFO Checking http://downloads.openmicroscopy.org/omero/5.2.7/./artifacts/OMERO.server-5.2.7-ice36-b40.zip
omeropy_1 | 2016-12-21 10:12:40,262 [omego.fileut] INFO Downloading http://downloads.openmicroscopy.org/omero/5.2.7/./artifacts/OMERO.py-5.2.7-ice36-b40.zip
omeropyserver_1 | 2016-12-21 10:12:40,262 [omego.fileut] INFO Downloading http://downloads.openmicroscopy.org/omero/5.2.7/./artifacts/OMERO.server-5.2.7-ice36-b40.zip
omeroserver_1 | 2016-12-21 10:12:40,342 [omego.artifa] INFO Checking http://downloads.openmicroscopy.org/omero/5.2.7/./artifacts/OMERO.server-5.2.7-ice36-b40.zip
omeroserver_1 | 2016-12-21 10:12:40,342 [omego.fileut] INFO Downloading http://downloads.openmicroscopy.org/omero/5.2.7/./artifacts/OMERO.server-5.2.7-ice36-b40.zip
omeropy_1 | 2016-12-21 10:12:43,748 [omego.artifa] INFO Unzipping OMERO.py-5.2.7-ice36-b40.zip
omeropy_1 | ++ ls /tmp/OMERO.py-5.2.7-ice36-b40.zip
omeropy_1 | + omegozip=/tmp/OMERO.py-5.2.7-ice36-b40.zip
omeropy_1 | + omerodist=/tmp/OMERO.py-5.2.7-ice36-b40
omeropy_1 | + rm -f /tmp/OMERO.py-5.2.7-ice36-b40.zip
omeropy_1 | + mv /tmp/OMERO.py-5.2.7-ice36-b40 /home/omero/OMERO.py
omeropy_1 | + /tmp/install/py.sh
omeropy_1 | + COMPONENT=py
omeropy_1 | + OMEROPATH=/home/omero/OMERO.py
omeropy_1 | + '[' '' = true ']'
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:12:46.403 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:12:57.007 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:13:07.673 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:13:18.251 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:13:28.829 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:13:39.408 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropyserver_1 | 2016-12-21 10:13:45,478 [omego.artifa] INFO Unzipping OMERO.server-5.2.7-ice36-b40.zip
omeroserver_1 | 2016-12-21 10:13:46,353 [omego.artifa] INFO Unzipping OMERO.server-5.2.7-ice36-b40.zip
omeropyserver_1 | ++ ls /tmp/OMERO.server-5.2.7-ice36-b40.zip
omeropyserver_1 | + omegozip=/tmp/OMERO.server-5.2.7-ice36-b40.zip
omeropyserver_1 | + omerodist=/tmp/OMERO.server-5.2.7-ice36-b40
omeropyserver_1 | + rm -f /tmp/OMERO.server-5.2.7-ice36-b40.zip
omeropyserver_1 | + mv /tmp/OMERO.server-5.2.7-ice36-b40 /home/omero/OMERO.server
omeropyserver_1 | + /tmp/install/py.sh
omeropyserver_1 | + COMPONENT=server
omeropyserver_1 | + OMEROPATH=/home/omero/OMERO.server
omeropyserver_1 | + '[' '' = true ']'
omeropyserver_1 | + /home/omero/OMERO.server/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeroserver_1 | ++ ls /tmp/OMERO.server-5.2.7-ice36-b40.zip
omeroserver_1 | + omegozip=/tmp/OMERO.server-5.2.7-ice36-b40.zip
omeroserver_1 | + omerodist=/tmp/OMERO.server-5.2.7-ice36-b40
omeroserver_1 | + rm -f /tmp/OMERO.server-5.2.7-ice36-b40.zip
omeroserver_1 | + mv /tmp/OMERO.server-5.2.7-ice36-b40 /home/omero/OMERO.server
omeroserver_1 | + /tmp/install/server.sh
omeroserver_1 | + COMPONENT=server
omeroserver_1 | + OMEROPATH=/home/omero/OMERO.server
omeroserver_1 | Waiting on Postgres...
omeroserver_1 | + echo 'Waiting on Postgres...'
omeroserver_1 | + psql -h postgres -p 5432 -U postgres -c '\l'
omeroserver_1 | List of databases
omeroserver_1 | Name | Owner | Encoding | Collate | Ctype | Access privileges
omeroserver_1 | -----------+----------+----------+------------+------------+-----------------------
omeroserver_1 | postgres | postgres | UTF8 | en_US.utf8 | en_US.utf8 |
omeroserver_1 | template0 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres +
omeroserver_1 | | | | | | postgres=CTc/postgres
omeroserver_1 | template1 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres +
omeroserver_1 | | | | | | postgres=CTc/postgres
omeroserver_1 | (3 rows)
omeroserver_1 |
omeroserver_1 | + echo 'postgres now accepts connections, creating database omero...'
omeroserver_1 | postgres now accepts connections, creating database omero...
omeroserver_1 | Loading config...
omeroserver_1 | + echo 'Loading config...'
omeroserver_1 | + /home/omero/OMERO.server/bin/omero config set omero.db.host postgres
omeropyserver_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropyserver_1 | !! 12/21/16 10:13:49.165 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropyserver_1 | OMERO.server is unavailable - sleeping
omeropyserver_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeroserver_1 | + /home/omero/OMERO.server/bin/omero config set omero.db.port 5432
omeropy_1 | !! 12/21/16 10:13:49.967 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeroserver_1 | + /home/omero/OMERO.server/bin/omero config set omero.db.user postgres
omeroserver_1 | + /home/omero/OMERO.server/bin/omero config set omero.db.name omero
omeroserver_1 | + '[' '' = true ']'
omeroserver_1 | + cut -d '|' -f 1
omeroserver_1 | + psql -h postgres -p 5432 -U postgres -lqt
omeroserver_1 | + grep -qw omero
omeroserver_1 | + createdb -h postgres -p 5432 -U postgres omero
omeroserver_1 | + echo 'INFO: omero was created.'
omeroserver_1 | + omego db upgrade --serverdir /home/omero/OMERO.server --dbname omero
omeroserver_1 | INFO: omero was created.
omeroserver_1 | 2016-12-21 10:13:52,727 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/OMERO.server ...
omeroserver_1 | 2016-12-21 10:13:52,728 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
omeroserver_1 | 2016-12-21 10:13:52,729 [omego.extern] INFO Executing [custom environment]: psql -d omero -h postgres -U postgres -w -A -t --version
omeroserver_1 | 2016-12-21 10:13:52,737 [omego.extern] INFO Completed [0.008 s]
omeroserver_1 | 2016-12-21 10:13:52,737 [ omego.db] INFO psql version: psql (PostgreSQL) 9.5.5
omeroserver_1 |
omeroserver_1 | 2016-12-21 10:13:52,738 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
omeroserver_1 | 2016-12-21 10:13:52,738 [omego.extern] INFO Executing [custom environment]: psql -d omero -h postgres -U postgres -w -A -t -c \conninfo
omeroserver_1 | 2016-12-21 10:13:52,754 [omego.extern] INFO Completed [0.015 s]
omeroserver_1 | 2016-12-21 10:13:52,754 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
omeroserver_1 | 2016-12-21 10:13:52,755 [omego.extern] INFO Executing [custom environment]: psql -d omero -h postgres -U postgres -w -A -t -c SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
postgres_1 | ERROR: relation "dbpatch" does not exist at character 42
postgres_1 | STATEMENT: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
omeroserver_1 | 2016-12-21 10:13:52,767 [omego.extern] ERROR Failed [0.012 s]
omeroserver_1 | Traceback (most recent call last):
omeroserver_1 | File "/usr/bin/omego", line 9, in <module>
omeroserver_1 | load_entry_point('omego==0.4.2', 'console_scripts', 'omego')()
omeroserver_1 | File "/usr/lib/python2.7/site-packages/omego/main.py", line 52, in entry_point
omeroserver_1 | (Version.NAME, Version)])
omeroserver_1 | File "/usr/lib/python2.7/site-packages/yaclifw/framework.py", line 197, in main
omeroserver_1 | ns.func(ns)
omeroserver_1 | File "/usr/lib/python2.7/site-packages/omego/db.py", line 309, in __call__
omeroserver_1 | DbAdmin(d, args.dbcommand, args, ext)
omeroserver_1 | File "/usr/lib/python2.7/site-packages/omego/db.py", line 78, in __init__
omeroserver_1 | getattr(self, command)()
omeroserver_1 | File "/usr/lib/python2.7/site-packages/omego/db.py", line 157, in upgrade
omeroserver_1 | currentsqlv = '%s__%s' % self.get_current_db_version()
omeroserver_1 | File "/usr/lib/python2.7/site-packages/omego/db.py", line 174, in get_current_db_version
omeroserver_1 | result = self.psql('-c', q)
omeroserver_1 | File "/usr/lib/python2.7/site-packages/omego/db.py", line 240, in psql
omeroserver_1 | stdout, stderr = External.run('psql', args, capturestd=True, env=env)
omeroserver_1 | File "/usr/lib/python2.7/site-packages/omego/external.py", line 223, in run
omeroserver_1 | "Non-zero return code", exe, args, r, stdout, stderr)
omeroserver_1 | omego.external.RunException: Non-zero return code
omeroserver_1 | command: psql -d omero -h postgres -U postgres -w -A -t -c SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
omeroserver_1 | return code: 1
omeroserver_1 | stdout:
omeroserver_1 | stderr: ERROR: relation "dbpatch" does not exist
omeroserver_1 | LINE 1: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id...
omeroserver_1 | ^
omeroserver_1 |
omeroserver_1 | + omego db init --serverdir /home/omero/OMERO.server --dbname omero
omeroserver_1 | 2016-12-21 10:13:53,353 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/OMERO.server ...
omeroserver_1 | 2016-12-21 10:13:53,355 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
omeroserver_1 | 2016-12-21 10:13:53,355 [omego.extern] INFO Executing [custom environment]: psql -d omero -h postgres -U postgres -w -A -t --version
omeroserver_1 | 2016-12-21 10:13:53,363 [omego.extern] INFO Completed [0.008 s]
omeroserver_1 | 2016-12-21 10:13:53,364 [ omego.db] INFO psql version: psql (PostgreSQL) 9.5.5
omeroserver_1 |
omeroserver_1 | 2016-12-21 10:13:53,365 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
omeroserver_1 | 2016-12-21 10:13:53,365 [omego.extern] INFO Executing [custom environment]: psql -d omero -h postgres -U postgres -w -A -t -c \conninfo
omeroserver_1 | 2016-12-21 10:13:53,377 [omego.extern] INFO Completed [0.012 s]
omeroserver_1 | 2016-12-21 10:13:53,377 [ omego.db] INFO Creating SQL: omero-20161221-101353-377721.sql
omeroserver_1 | 2016-12-21 10:13:53,377 [omego.extern] INFO Invoking CLI [current environment]: db script -f omero-20161221-101353-377721.sql omero
omeroserver_1 | WARNING: Positional arguments are deprecated
omeroserver_1 | Using OMERO5.2 for version
omeroserver_1 | Using 0 for patch
omeroserver_1 | Using password from commandline
omeroserver_1 | 2016-12-21 10:13:54,654 [ omego.db] INFO Creating database using omero-20161221-101353-377721.sql
omeroserver_1 | 2016-12-21 10:13:54,655 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
omeroserver_1 | 2016-12-21 10:13:54,655 [omego.extern] INFO Executing [custom environment]: psql -d omero -h postgres -U postgres -w -A -t -f omero-20161221-101353-377721.sql
omeropyserver_1 | + /home/omero/OMERO.server/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropyserver_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropyserver_1 | !! 12/21/16 10:13:59.755 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropyserver_1 | OMERO.server is unavailable - sleeping
omeropyserver_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:14:00.542 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropyserver_1 | + /home/omero/OMERO.server/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropyserver_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropyserver_1 | !! 12/21/16 10:14:10.360 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropyserver_1 | OMERO.server is unavailable - sleeping
omeropyserver_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:14:11.123 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropyserver_1 | + /home/omero/OMERO.server/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropyserver_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropyserver_1 | !! 12/21/16 10:14:20.935 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropyserver_1 | OMERO.server is unavailable - sleeping
omeropyserver_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:14:21.713 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeroserver_1 | 2016-12-21 10:14:22,054 [omego.extern] INFO Completed [27.398 s]
omeroserver_1 | 2016-12-21 10:14:22,054 [ omego.db] WARNI stderr: psql:omero-20161221-101353-377721.sql:2662: NOTICE: identifier "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapco"
omeroserver_1 | psql:omero-20161221-101353-377721.sql:4322: NOTICE: identifier "fklogicalchannel_photometricinterpretation_photometricinterpretation" will be truncated to "fklogicalchannel_photometricinterpretation_photometricinterpret"
omeroserver_1 | psql:omero-20161221-101353-377721.sql:5302: NOTICE: identifier "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcont"
omeroserver_1 |
omeroserver_1 | Creating data repo...
omeroserver_1 | + echo 'Creating data repo...'
omeroserver_1 | + mkdir -p /home/omero/data
omeroserver_1 | + /home/omero/OMERO.server/bin/omero config set omero.data.dir /home/omero/data
omeroserver_1 | Starting OMERO.server...
omeroserver_1 | + echo 'Starting OMERO.server...'
omeroserver_1 | + /home/omero/OMERO.server/bin/omero admin start --foreground
omeropyserver_1 | + /home/omero/OMERO.server/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropyserver_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropyserver_1 | !! 12/21/16 10:14:31.518 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropyserver_1 | OMERO.server is unavailable - sleeping
omeropyserver_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeroserver_1 | No descriptor given. Using etc/grid/default.xml
omeropy_1 | Ice.ConnectionRefusedException: omeroserver:4064 isn't running
omeropy_1 | !! 12/21/16 10:14:32.301 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropyserver_1 | + /home/omero/OMERO.server/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropy_1 | InternalException: Failed to connect: exception ::Glacier2::CannotCreateSessionException
omeropy_1 | {
omeropy_1 | reason = Server not fully initialized
omeropy_1 | }
omeropyserver_1 | InternalException: Failed to connect: exception ::Glacier2::CannotCreateSessionException
omeropyserver_1 | {
omeropyserver_1 | reason = Server not fully initialized
omeropyserver_1 | }
omeropy_1 | !! 12/21/16 10:14:44.969 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropy_1 | OMERO.server is unavailable - sleeping
omeropy_1 | + sleep 10
omeropyserver_1 | !! 12/21/16 10:14:44.978 error: communicator not destroyed during global destruction.+ echo 'OMERO.server is unavailable - sleeping'
omeropyserver_1 | OMERO.server is unavailable - sleeping
omeropyserver_1 | + sleep 10
omeropy_1 | + /home/omero/OMERO.py/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropyserver_1 | + /home/omero/OMERO.server/bin/omero login -s omeroserver -p 4064 -u root -w omero
omeropyserver_1 | Created session cdb07b76-9895-4164-a487-87145ad311be (root@omeroserver:4064). Idle timeout: 10 min. Current group: system
omeropy_1 | Created session 5efdb611-dde6-441e-99b6-3d90bb0d2090 (root@omeroserver:4064). Idle timeout: 10 min. Current group: system
omeropyserver_1 | + echo 'omeroserver:4064 now accepts connections'
omeropyserver_1 | omeroserver:4064 now accepts connections
omeropyserver_1 | + exec
omeropy_1 | + echo 'omeroserver:4064 now accepts connections'
omeropy_1 | omeroserver:4064 now accepts connections
omeropy_1 | + exec
test_omeropyserver_1 exited with code 0
Aborting on container exit...
Stopping test_omeroserver_1 ... done
Stopping test_postgres_1 ... done
++ docker inspect -f '{{.State.ExitCode}}' test_omeropy_1
+ exitcode=0
+ docker-compose -f test/docker-compose.yml rm -fv
WARNING: The SKIP_UPGRADE_CHECK variable is not set. Defaulting to a blank string.
WARNING: The OMEROBUILD variable is not set. Defaulting to a blank string.
Going to remove test_omeropy_1, test_omeropyserver_1, test_omeroserver_1, test_postgres_1
Removing test_omeropy_1 ... done
Removing test_omeropyserver_1 ... done
Removing test_omeroserver_1 ... done
Removing test_postgres_1 ... done
+ exit 0
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment