[ome-users] Omero 4.4.9 to 5.0.0 RC1 upgrade - Error connecting to database table dbpatch

[Aleksandra Tarkowska]

I am gad is working.


Kind regards
Ola

> On 9 Jan 2014, at 18:26, "Paulo Almeida" <palmeida at igc.gulbenkian.pt> wrote:
>
> Hello,
>
> I finally figured it out... The variable name is omero.db.pass and in
> 5.0.0 I wrote omero.db.password. I corrected it and the server started.
>
> Sorry for the waste of time, and thanks for pointing me in the right
> direction.
>
> Cheers,
> Paulo
>
>> On Thu, 2014-01-09 at 17:14 +0000, Paulo Almeida wrote:
>> Hi Ola,
>>
>> Apparently you're right, because now I also saw lines like this in the
>> log:
>>
>> Caused by: org.postgresql.util.PSQLException: FATAL: password
>> authentication failed for user "omero"
>>
>> I'm a bit puzzled by that, because it was working before the upgrade.
>> Initially I had thought it might be something with the settings, because
>> when I first ran omero, after the upgrade, it complained about a missing
>> "/OMERO" folder. But I set that up, along with DB name, user and
>> password, so the output of "omero config get" is this:
>>
>> omero.data.dir=/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/OMERO/binary-repository
>> omero.db.name=omero
>> omero.db.password=secret
>> omero.db.user=omero
>>
>> "secret" is the password that I successfully use to check the database
>> using:
>>
>> psql -h localhost -U omero
>>
>> And this is the beginning of \l inside psql:
>>
>>   Name    |  Owner   | Encoding |   Collate   |    Ctype    |   Access
>> privileges
>> -----------+----------+----------+-------------+-------------+-----------------------
>> omero     | omero    | UTF8     | en_US.UTF-8 | en_US.UTF-8 |
>>
>>
>> Is there anything else I can do to check what credentials omero is
>> using, if not those in etc/grid/config.xml? I even tried setting the
>> password in etc/omero.properties, with no success (I guess I'm not
>> supposed to do that anyway).
>>
>> Thanks,
>> Paulo
>>
>>
>>> On Thu, 2014-01-09 at 16:04 +0000, Aleksandra Tarkowska wrote:
>>> Dear Paulo
>>>
>>> 2014-01-09 13:55:05,796 ERROR [ome.services.db.SelfCorrectingDataSource] (
>>>     main) Failed to acquire connection after retries=3
>>> java.sql.SQLException: unable to get a connection from pool of a
>>> PoolingDataSource containing an XAPool of resource
>>> 99566f22-65bf-46b2-803e-835dad8ad75f with 0 connection(s) (0 still
>>> available)
>>>
>>> Sounds like wrong db username and/or password.
>>>
>>>
>>> Could you check your omero properties?
>>> Is your sql server running?
>>>
>>>
>>> Kind regards
>>> Ola
>>>
>>>
>>>
>>>
>>>
>>>> On 09/01/2014 15:58, "Paulo Almeida" <palmeida at igc.gulbenkian.pt> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I just upgraded to Omero 5.0.0 and apparently it went well, but the
>>>> server failed to restart, with exceptions in Blitz-0.log and the
>>>> following message:
>>>>
>>>> Error connecting to database table dbpatch. You may need to bootstrap.
>>>>
>>>> I did run the database script and the dbpatch table exists, with this as
>>>> the second and last entry (result of "SELECT * from db_patch"):
>>>>
>>>> 2 |            0 | OMERO5.0       |         -52 | 2014-01-09
>>>> 13:51:28.813421 | Database updated. |             0 | OMERO4.4        |
>>>>
>>>> I was using Java 6, but I saw an old Omero bug report mentioning a
>>>> similar message with this version of Java, so I tried upgrading to 7.
>>>> Nothing changed though. This is the bug report:
>>>>
>>>> http://trac.openmicroscopy.org.uk/ome/ticket/1269
>>>>
>>>> It's very old and the only thing in common is the message about not
>>>> being able to connect to dbpatch, so I don't know if it's relevant.
>>>>
>>>> I'm attaching the output of bin/omero admin diagnostics, as well as
>>>> Blitz-0.log and master.err , in case it helps diagnosing.
>>>>
>>>> Thanks,
>>>> Paulo Almeida
>>>> Instituto Gulbenkian de Ciência
>>>> _______________________________________________
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>>>> ome-users at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>>
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