Population of database fails

[Aking]

Hi
I'm getting a whole load of errors like one below when I'm up to the "Execute run the following to populate your database" stage of instructions on http://www.openmicroscopy.org/site/supp ... l-windows/. On windows 7 Pro 64bit, OMERO.server-4.4.1-ice34-b3035.

.....
psql:C:/omero_dist/OMERO4.4__0.sql:7200: ERROR: current transaction is aborted,
commands ignored until end of transaction block
ROLLBACK

Hence when I go to the next stage everything else in the admin diag looks OK except psql version and I have nothing to connect too.
Do you have any suggestions?
Thanks
Andy


c:\Omero_dist>bin\omero admin diagnostics

================================================================================

OMERO Diagnostics 4.4.1-ice34-b3035
================================================================================


Commands: java -version 1.6.0 (C:\Program Files (x86)\Jav
a\jre6\bin\java.EXE -- 2 others)
Commands: python -V 2.6.6 (C:\Python26\python.EXE)
Commands: icegridnode --version 3.4.2 (C:\Ice3.4.2\bin\icegridnod
e.EXE)
Commands: icegridadmin --version 3.4.2 (C:\Ice3.4.2\bin\icegridadm
in.EXE)
Commands: psql --version not found

Server: icegridnode running
Server: Blitz-0 active (pid = 6988, enabled)
Server: DropBox active (pid = 5764, enabled)
Server: FileServer active (pid = 6936, enabled)
Server: Indexer-0 active (pid = 4456, enabled)
Server: MonitorServer active (pid = 6048, enabled)
Server: OMERO.Glacier2 active (pid = 5852, enabled)
Server: OMERO.IceStorm active (pid = 6920, enabled)
Server: PixelData-0 active (pid = 7112, enabled)
Server: Processor-0 active (pid = 3696, enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)

Log dir: c:\Omero_dist\var\log exists

Log files: Blitz-0.log 246.0 KB errors=6 warnings=17

Log files: DropBox.log 8.0 KB errors=6 warnings=4

Log files: FileServer.log 1.0 KB
Log files: Indexer-0.log 205.0 KB errors=6 warnings=9

Log files: MonitorServer.log 2.0 KB
Log files: OMEROweb.log 29.0 KB errors=5 warnings=12
6
Log files: OMEROweb_request.log 19.0 KB errors=0 warnings=12
6
Log files: PixelData-0.log 146.0 KB errors=6 warnings=9

Log files: Processor-0.log 112.0 KB errors=32 warnings=65

Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 0.77 MB

Parsing Blitz-0.log:[line:802] => Server restarted <=
Parsing Blitz-0.log:[line:1208] => Server restarted <=

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=C:\Python26;C:\Program Files (x86)\Java\jre6\bin;C:\Program Fil
es (x86)\QuickTime\QTSystem\;C:\Ice3.4.2\bin;;C:\Windows\system32;C:\Windows;C:\
Windows\System32\Wbem;
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO.web status... DEVELOPMENT: You will have to check status by hand!

[bpindelski]

Hello Andy,

The error code that PostgreSQL is returning indicates that you already have an OMERO DB schema present and PostgreSQL is denying execution of any SQL DDL operations (as expected, due to the presence of the "BEGIN;" statement starting a new transaction).

You should be able to run the OMERO server and clients just fine, but if you want to make sure that you have a clean schema, I'd suggest dropping the current OMERO DB using the PostgreSQL CLI tool or PgAdmin III. Then you can again import the schema without any errors. Be aware that you will lose all your data (users, images etc.).

The fact that psql command is reported as missing from bin/omero admin diagnostics is a known issue on Windows, but it shouldn't stop you from using the clients. The PostgreSQL installer doesn't modify the PATH, hence the psql executable can't be located by the system. It can be rectified by manually adding "<PostgreSQL_install_dir>\bin" to the system PATH variable.

As a final note - I see you are running OMERO.web in development mode. I'd strongly suggest to look at https://www.openmicroscopy.org/site/support/omero4/server/install_web#section-6 and check if your settings are OK, before running bin/omero web start.

I hope that helps,

Regards,
Blazej

[Aking]

Thanks that resolved the errors.
Can I ask what the correct setting is for:
omero.web.application_server
if I'm running on IIS?
I'd changed the setting to development to try out the built in version but if I change to either of the fastcgi values it gives a warning not to use with Windows.
Thanks
Andy

[Aking]

Ignore that last but I see that its
web iis
to start and it just needs something acceptable in the field even if its not actually going to use it e.g. development in this case

[bpindelski]

Hi Andy,

You are right, Windows doesn't use bin/omero web start. I spent too much time in the *nix world and automatically added that to my previous reply.

Kind regards,
Blazej