[ome-devel] Upgrading your OMERO4.1 database

[Josh Moore]

Alessandro Dellavedova writes:
 > Hi Josh,

Hi Alessandro,

 > thank you very much for your kind answer.

Gladly.

 > Together with the Imaging facility here at our Campus we decided to
 > adopt OMERO for centralized storage and management of the data
 > produced by:
 > 
 > - Timelapse microscopes;
 > - Spinning disks;
 > - Dual Photon microscope.
 > 
 > We tested version OMERO Beta-4.1.1-r5927-b91 and we spotted a
 > couple of bugs (one of those should be already fixed in LOCI):
 > 
 > https://trac.openmicroscopy.org.uk/omero/ticket/1979
 > https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=372
 > 
 > Basically I was trying to upgrade to the latest RC version in order to test the following things:

Understood. Though the database is going into RC, the code has not
yet. We need another couple of weeks before code freeze. But we'll
certainly contact the mailing lists to say when would be a good time
to test.

 > - LDAP authentication (here we have 600 users on an OpenLDAP
 >   directory based on RFC 2307 "Posix accounts");

 > - Group-based permissions (we do have a quite high number of small
 > teams, that are Posix groups, where scientists from different
 > scientific groups share some info in order to achieve their goals);

 > - Sharing of data via Web between groups;

These three items are all scheduled for the RC, and we'll be looking
very forward to your feedback.

 > - Stress testing.

 > For this project we bought a Sun X4540 fully loaded with 48x2TB
 > SATA II disks for a grand total of 96TB raw of disk space and we
 > will be using Solaris as Operating System, with ZFS filesystem.
 > 
 > If you do have some spare time I'd like to go indeep about the
 > choice we made about Solaris and ZFS, because the technical details
 > and the filesystem reliability are mandatory when dealing with
 > multi-terabyte storage pools, and ZFS features some very
 > interesting stuff (eg: block-level data deduplication directly
 > implemented in the filesystem, this can save a LOT of space).

I'll let others who have experience with ZFS speak up, but it will be
very exciting to hear how this works out for you.

 > As per your kind explainations I'll be waiting a little bit more
 > then I'll start over using OMERO4.2-RC__5 when available.
 
Sounds like a good plan.

 > Again, thank you very much for your time and for the efforts that
 > the OMERO team is putting into this great platform, you are really
 > changing the way we are doing microscopy and information management
 > here.

Very happy to hear it!

 > Best,
 > 
 > Alessandro

Cheers,
~Josh

 > On May 6, 2010, at 9:33 AM, Josh Moore wrote:
 > 
 > > 
 > > (forwarding to list from ticket:1434)
 > > 
 > > Hi Alessandro,
 > > 
 > >> While trying to upgrade the OMERO database from version 4.1 to
 > >> version 4.2 by using the script committed on:
 > >> http://trac.openmicroscopy.org.uk/omero/browser/trunk/sql/psql/OMERO4.2-DEV__0/OMERO4.1__0.sql?rev=6068
 > >> 
 > >> I get the following error:
 > > 
 > > Thanks for taking the time to let us know, but I can only say you
 > > almost certainly *don't* want to be doing this. We are currently
 > > on version OMERO4.2-RC__4, working towards a release within the
 > > next month. We don't provide upgrade scripts between the
 > > intermediate steps, so upgrading from OMERO4.1__0 to
 > > OMERO4.2-DEV__0 will get you into a dead-end.
 > > 
 > > If you would like to help us test 4.2, that'd be great, but you'll
 > > need to start from a fresh database and wait for things to calm down
 > > just a bit. (OMERO4.2-RC__5 should be coming out shortly).
 > > 
 > > If you were trying to do something else specifically, let us know and
 > > we'll see if we can't help you out.
 > > 
 > > Cheers,
 > > ~Josh.
 > > 
 > >> omero at omero:/opt/omero_dist/sql/psql/OMERO4.2-DEV__0$ psql -h localhost -U
 > >> omero < OMERO4.1__0.sql
 > >> Password for user omero:
 > >> BEGIN
 > >> CREATE FUNCTION
 > >> omero_assert_omero4_1_0
 > >> -------------------------
 > >> 
 > >> (1 row)
 > >> 
 > >> DROP FUNCTION
 > >> INSERT 0 1
 > >> ALTER TABLE
 > >> ERROR:  syntax error at or near "="
 > >> LINE 5:        AND experimenterid. = groupexperimentermap.child;
 > >>                                   ^
 > >> ERROR:  syntax error at or near "COLUMN"
 > >> LINE 1: ALTER TABLE groupexperimentermap SET COLUMN owner NOT NULL;
 > >>                                             ^
 > >> 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:  current transaction is aborted, commands ignored until end of
 > >> transaction block
 > >> ROLLBACK
 > >> 
 > >> And the upgrade of the database fails. I'm not sure if
 > >> commenting here is the best way to report this kind of problems,
 > >> just in case feel free to drop me a line at
 > >> alessandro.dellavedova<@>ifom-ieo-campus.it
 > >> 
 > >> Thank you for your continued efforts in developing OMERO !
 > >> 
 > >> Alessandro