Open Microscopy Environment

Hi all,

I have a quick quesiton for OMERO 4.3 (NEW RELEASED VERSION) upgrade.
My current version of OMERO server is 4.2.2 , and I tried to upgrade it into 4.3 version.

So, I tried to follow instructions based on official omero site.

And, I tried to execute follows commands.

Code: Select all


cd /omero_dist

bin/omero admin stop

cd ..

mv omero_dist omero_dist_old

tar jxvf omero-Beta4.3.0.tar.bz2

cp omero_dist_old/etc/grid/config.xml omero_dist/etc/grid


Update database
psql -h localhost -U omero omero < sql/psql/OMERO4.3__0/OMERO4.2__0.sql


Fixing metadata
psql -h localhost -U omero omero < sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql


cd /omero-dist/
bin omero admin start


Once I executed the command for updating database,
it generated several error message like as follows.

Code: Select all

[omerouser@europa omero_dist]$ psql -h localhost -U omero omero < sql/psql/OMERO4.3__0/OMERO4.2__0.sql
BEGIN
Timing is on.
CREATE FUNCTION
Time: 2.423 ms
ERROR:  too many parameters specified for RAISE
CONTEXT:  PL/pgSQL function "omero_43_check_pg_advisory_lock" line 15 at raise
ERROR:  current transaction is aborted, commands ignored until end of transaction block

ERROR:  current transaction is aborted, commands ignored until end of transaction block
..........................................................................................................................
ERROR:  current transaction is aborted, commands ignored until end of transaction block
ERROR:  syntax error at or near "EXISTS" at character 17
LINE 1: DROP TRIGGER IF EXISTS annotation_trigger ON annotation;
                        ^
ERROR:  current transaction is aborted, commands ignored until end of transaction block
ERROR:  current transaction is aborted, commands ignored until end of transaction block
ERROR:  syntax error at or near "EXISTS" at character 17
LINE 1: DROP TRIGGER IF EXISTS dataset_annotation_link_event_trigger...
                        ^
................................................................................................................
                        ^
ERROR:  current transaction is aborted, commands ignored until end of transaction block
ERROR:  syntax error at or near "EXISTS" at character 17
LINE 1: DROP TRIGGER IF EXISTS experimenter_annotation_link_event_tr...
                        ^
ERROR:  current transaction is aborted, commands ignored until end of transaction block
ERROR:  current transaction is aborted, commands ignored until end of transaction block
ERROR:  current transaction is aborted, commands ignored until end of transaction block
ROLLBACK


So, I executed as follows.

Code: Select all

[omerouser@europa omero_dist]$ psql -h localhost -U omero omero < sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
BEGIN
UPDATE 0
UPDATE 0
UPDATE 0
COMMIT


But, it seems that it generated same error message even though I executed above command.
Can I keep going on next step like "executing cd /omero-dist/
bin omero admin start" ?

Or is there anyway I need to fix these errors ?

It would be great help to give me any advices.

Thanks,
Steve

by the way, my current os is cent os 5.6 !!

Hi Steve,

what version of postgresql do you have installed? (psql --version or similar). The database upgrade is not running to completion because your version of postgresql does not support the syntax "DROP TRIGGER IF EXISTS..."). You won't be able to continue the upgrade until that is sorted. Since that syntax is available in 8.2, it probably means you are using 8.1 which is no longer supported in OMERO, and which will need to be upgraded before you can proceed.

~Josh.

Thanks for your quick response.

Yes, you are right. the current version of psql is 8.1.23 version.

But, I don't know how I can update psql from 8.1 to 8.2 version without any problems.

Could you let me know where i can find those information ?

Thanks in advance,
Steve

I found a good resource for updating of postgreSQL from 8.1 to 8.2 below site.
http://www.westnet.com/~gsmith/content/ ... /pgrpm.htm

Thanks,
Steve Oh

Hi,

I tried to upgrade postgresql 8.1 to 8.4 on cent os by following below site instructions.

http://blog.lystor.org.ua/2010/05/upgra ... 6642672999

In summary, I executed below commands step by step.

mkdir /pgbak
chown postgres:postgres /pgbak
su - postgres
pg_dumpall > /pgbak/backup.sql
exit
service postgresql stop
cp /var/lib/pgsql/data/pg_hba.conf /pgbak
mv /var/lib/pgsql/data /pgbak
yum remove postgresql*
yum install postgresql84-server
/etc/init.d/postgresql initdb
cp /pgbak/pg_hba.conf /var/lib/pgsql/data/pg_hba.conf
chkconfig --level 35 postgresql on
service postgresql start
su - postgres
psql -f /pgbak/backup.sql postgres
vacuumdb -a -z
exit

I have trouble "service postgresql start" command.
It said that 'starting postgresql service is failed'

How I can fix this error ?
It would be great help if you give me any advice.

Thanks,
Steve Oh

Hi Steve,

are there any log files under /var/lib/pgsql/data/ or /var/log which may be of relevance (and which you could send us)? Is there any more console output from the failed command? If not, you may want to try

Code: Select all

su - postgres
pg_ctl -D /var/lib/pgsql/data start


and send us what you see.

Cheers,
~Josh.

Hi Josh,

Thanks for your suggestions.

I am not sure whether this file is right log file for psql.

but, I found the file, 'postgresql-Thu.log' , which seems log file under "/var/lib/pgsql/data/pg_log/"

Code: Select all

LOG:  authentication option not in name=value format: sameuser

CONTEXT:  line 67 of configuration file "/var/lib/pgsql/data/pg_hba.conf"
LOG:  authentication option not in name=value format: sameuser

CONTEXT:  line 73 of configuration file "/var/lib/pgsql/data/pg_hba.conf"
FATAL:  could not load pg_hba.conf
LOG:  authentication option not in name=value format: sameuser

CONTEXT:  line 67 of configuration file "/var/lib/pgsql/data/pg_hba.conf"
LOG:  authentication option not in name=value format: sameuser

CONTEXT:  line 73 of configuration file "/var/lib/pgsql/data/pg_hba.conf"
FATAL:  could not load pg_hba.conf
LOG:  authentication option not in name=value format: sameuser

CONTEXT:  line 67 of configuration file "/var/lib/pgsql/data/pg_hba.conf"
LOG:  authentication option not in name=value format: sameuser

CONTEXT:  line 73 of configuration file "/var/lib/pgsql/data/pg_hba.conf"
FATAL:  could not load pg_hba.conf


Also, below file is pg_hba.conf file under "/var/lib/pgsql/data"

Code: Select all

# TYPE  DATABASE    USER        CIDR-ADDRESS          METHOD

# "local" is for Unix domain socket connections only
local   all         all                               ident sameuser
# IPv4 local connections:
#host    all         all         127.0.0.1/32          ident sameuser
host    all         all         127.0.0.1/32          trust

# IPv6 local connections:
host    all         all         ::1/128               ident sameuser



Under '/var/log/', I can only find 'yum.log file' that seems correct to me.

I attached at the end of yum log file as a reference.

Code: Select all

Jun 13 14:38:45 Updated: 4:perl-5.8.8-32.el5_6.3.i386
Jun 16 13:37:12 Erased: mod_ssl
Jun 16 13:37:13 Erased: subversion
Jun 16 13:37:15 Erased: webalizer
Jun 16 13:37:15 Erased: gnome-user-share
Jun 16 13:37:16 Erased: system-config-httpd
Jun 16 13:37:18 Erased: mod_perl
Jun 16 13:37:20 Erased: dovecot
Jun 16 13:37:22 Erased: postgresql-server
Jun 16 13:37:24 Erased: httpd
Jun 16 13:37:26 Erased: subversion-perl
Jun 16 13:37:27 Erased: mod_python
Jun 16 13:37:28 Erased: httpd-manual
Jun 16 13:37:31 Erased: git-svn
Jun 16 13:37:31 Erased: postgresql-libs
Jun 16 13:37:32 Erased: git-all
Jun 16 13:37:32 Erased: apr-util
Jun 16 13:37:33 Erased: postgresql
Jun 16 13:37:36 Erased: php
Jun 16 13:38:33 Installed: postgresql84-libs-8.4.7-1.el5_6.1.x86_64
Jun 16 13:38:36 Installed: postgresql84-8.4.7-1.el5_6.1.x86_64
Jun 16 13:38:40 Installed: postgresql84-server-8.4.7-1.el5_6.1.x86_64


I can't see any more console output except 'failed' message.

It seems that server starts now... could you explain what was my problem ?

Code: Select all

[root@europa log]# su - postgres
-bash-3.2$ pg_ctl -D /var/lib/pgsql/data start
server starting


Thanks for your help !!!

Steve

Is it fine to continue on executing below commands from now ?
Or do I need to do something for next step ?

Code: Select all

su - postgres
psql -f /pgbak/backup.sql postgres
vacuumdb -a -z
exit


Thanks in advance, Josh !!
Steve

It seems not working..

I got below error messages..

psql: could not connect to server: No such file or directory
Is the server running locally and accepting
connections on Unix domain socket "/tmp/.s.PGSQL.5432"?

Could you help me out how I can fix this problem ?

Thanks,

Steve