search

ome / docker-example-omero

OMERO Docker compose example
BSD 2-Clause "Simplified" License
24 stars 27 forks source link

omero server is failing? #1

Closed cudmore closed 5 years ago

cudmore commented 5 years ago

Omero server is failing? I did a git clone and then from the docker-example-omero directory ran

docker-compose up -d

docker ps -a

CONTAINER ID        IMAGE                                     COMMAND                  CREATED             STATUS                      PORTS                    NAMES
5194f138bba9        openmicroscopy/omero-web-standalone:5.5   "/usr/local/bin/entr…"   20 seconds ago      Up 18 seconds               0.0.0.0:4080->4080/tcp   docker-example-omero_omeroweb_1
c67df2fb8c9b        postgres:10                               "docker-entrypoint.s…"   20 seconds ago      Up 18 seconds               5432/tcp                 docker-example-omero_database_1
baeb73e1a25f        openmicroscopy/omero-server:5.5           "/usr/local/bin/entr…"   20 seconds ago      Exited (1) 12 seconds ago                            docker-example-omero_omeroserver_1

docker logs -t docker-example-omero_omeroserver_1

2019-06-25T23:58:27.882034265Z CREATE FUNCTION
2019-06-25T23:58:27.882036244Z CREATE TRIGGER
2019-06-25T23:58:27.882038199Z ALTER TABLE
2019-06-25T23:58:27.882040138Z ALTER TABLE
2019-06-25T23:58:27.882042092Z 
2019-06-25T23:58:27.882044581Z stderr: psql:omero-20190625-235824-637626.sql:2842: NOTICE:  identifier "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapco"
2019-06-25T23:58:27.882048220Z psql:omero-20190625-235824-637626.sql:4712: NOTICE:  identifier "fklogicalchannel_photometricinterpretation_photometricinterpretation" will be truncated to "fklogicalchannel_photometricinterpretation_photometricinterpret"
2019-06-25T23:58:27.882050571Z psql:omero-20190625-235824-637626.sql:5697: NOTICE:  identifier "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcont"
2019-06-25T23:58:27.882052861Z psql:omero-20190625-235824-637626.sql:9478: ERROR:  relation "i_logicalchannel_emissionwave" already exists
2019-06-25T23:58:27.882054960Z

I am on macOS Mojave, Docker Desktop Community 2..0.0.3 (31259)

jburel commented 5 years ago

This is due to a problem with PostgreSQL. Hopefully a new version of PostgreSQL will be released soon See https://forum.image.sc/t/fyi-not-possible-to-create-new-omero-instance-with-latest-postgresql-versions/26929

You will need to pin your Postgres docker to 9.6.13 for now

joshmoore commented 5 years ago

@cudmore : see also: https://github.com/ome/docker-example-omero/pull/2

joshmoore commented 5 years ago

This has now been corrected upstream. See https://github.com/ome/omero-install/issues/212 for more information.