Open Microscopy Environment

Dear all,

I've updated with homebrew our omero server from 5.1.4 to 5.2.2 on a MacOS 10.10 system.

I wanted to upgrade the database but it failed.
The error message is:
ome-www:bin benjaminS$ psql -h localhost -U omeroDBuser omeroDB < sql/psql/OMERO5.2__1/OMERO5.1__0.sql
-bash: sql/psql/OMERO5.2__1/OMERO5.1__0.sql: No such file or directory

I've checked the files, they 're not missing.
the brew info gives me

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ome-www:omero benjaminS$ brew info omero
ome/alt/omero: stable 5.2.2
http://www.openmicroscopy.org/site/products/omero
/usr/local/Cellar/omero/omero_distold (6,655 files, 750.7M)
  Built from source
/usr/local/Cellar/omero/omero_old_5_1_4 (8,083 files, 862.2M)
  Built from source
/usr/local/Cellar/omero/omerodistold_5_0_0 (7,621 files, 2.4G)
  Built from source
/usr/local/Cellar/omero/omerodistold_5_0_1 (6,650 files, 1.7G)
  Built from source
/usr/local/Cellar/omero/omerodistold_5_0_2 (6,667 files, 5.4G)
  Built from source
/usr/local/Cellar/omero/5.2.2 (3,789 files, 225.3M) *
  Built from source
From: https://github.com/ome/homebrew-alt/blob/master/Formula/omero.rb
==> Dependencies
Build: pkg-config ✔
Required: hdf5 ✔, jpeg ✔, zeroc-ice35 ✔
Recommended: ccache ✔, mplayer ✔
Optional: nginx ✘
==> Options
--with-cpp
   Build OmeroCpp libraries.
--with-nginx
   Build with nginx support
--without-ccache
   Build without ccache support
--without-mplayer
   Build without mplayer support
==> Caveats

For non-homebrew Python, you need to set your PYTHONPATH:
export PYTHONPATH=/usr/local/Cellar/omero/5.2.2/lib/python:$PYTHONPATH

To finish the installation, execute omero_python_deps in your
shell:
  ./usr/local/Cellar/omero/5.2.2/bin/omero_python_deps


the Blitz-log gives me the message to upgrade my database

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Caused by: ome.conditions.InternalException:
***************************************************************************************
DB version (OMERO5.1__1) does not match omero.properties (OMERO5.2__0). Please apply a db upgrade.
See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade.html
***************************************************************************************

   at ome.services.util.DBPatchCheck.start(DBPatchCheck.java:71) ~[server.jar:na]
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_55]
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_55]
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_55]
   at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_55]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1527) ~[spring-beans.jar:3.0.1.RELEASE]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1468) ~[spring-beans.jar:3.0.1.RELEASE]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400) ~[spring-beans.jar:3.0.1.RELEASE]
   ... 67 common frames omitted
ome-www:log benjaminS$ psql -h localhost -U omeroDBuser omeroDB < sql/psql/OMERO5.2__0/OMERO5.1__1
-bash: sql/psql/OMERO5.2__0/OMERO5.1__1: No such file or directory
ome-www:log benjaminS$ psql -h localhost -U omeroDBuser omeroDB < sql/psql/OMERO5.2__0/OMERO5.1__1.sql
-bash: sql/psql/OMERO5.2__0/OMERO5.1__1.sql: No such file or directory
ome-www:log benjaminS$ psql -h localhost -U omeroDBuser omeroDB < sql/psql/OMERO5.1__1/OMERO5.0__0.sql


Could it be that there're some read/write problems?
I thought to find a solution without pg_restore

Thanks Julia

Hi Julia,

the database upgrade did not happen because you need to either run the psql command from the main server directory or pass the full path to the upgrade script e.g.:

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psql -h localhost -U omeroDBuser omeroDB < /usr/local/Cellar/omero/5.2.2/sql/psql/OMERO5.2__1/OMERO5.1__0.sql


Best,
Sebastien

Dear Sebastien,

Thanks a lot. The server is running on 5.2.2.
I'm sorry. Sometimes it is such a stupid thing.

Have a nice day

No worries,

glad to hear the upgrade went well and the server is now running.

Best,
Sebastien