[ome-devel] questions about OMERO

[Curtis Rueden]

Hi,

With Chris's help, I was able to get OMERO working pretty well -- it
was largely an issue of documentation. To anyone else installing
OMERO, I suggest following the "manual install" instructions, and
ignoring the "quick install" option. As time allows, we plan to
investigate implementation of a "Download from OMERO" plugin for
ImageJ as part of our plugin suite.

I do have some questions about the system, though:

1) Can OMERO export original files with no programming (e.g., from
OMERO.insight)? If not, is this functionality planned? We would like
to start by using OMERO as a "smart file server," with the ability to
freely download original files from the database for use in external
applications.

2) Is there currently a way to view all associated metadata for an
Image -- such as a list of linked structures as in OME's web
interface, or perhaps an XML view? It would be useful to get a nice,
neat view of an Image's relevant metadata within OMERO.insight.

3) Is there a command-line or other automation-friendly importer for
OMERO? It would be helpful for some acquisition systems -- the
acquired data could be uploaded to a dedicated machine (probably the
OMERO server machine), which would perform an automated import.

4) Is there a timeline for OMERO being able to import OME-TIFF and
OME-XML, or some subset thereof? It seems like the ability to freely
handle OME-XML could be very useful for exchanging data between OME
and OMERO. I suppose there is a sticking point with custom
SemanticTypes, but I don't know enough about OMERO's architecture to
have a feel for how difficult a problem that poses.

Thanks,
Curtis

On 2/9/07, Chris Allan <callan at blackcat.ca> wrote:
>
> On 8 Feb 2007, at 17:11, Curtis Rueden wrote:
>
> > Hi,
>
> Hi Curtis.
>
> >
> > I installed OMERO today, but am having problems getting it to work.
> >
> > I am running Ubuntu 6.06 "Dapper" with PostgreSQL 8.0.7 and Java
> > 1.5.0_06.
> >
> > For the OMERO server, I followed the installation instructions on the
> > OmeroLinuxInstallHowto tiki page. A few notes:
> > * The -R and -S flags are not valid for createuser on my system, so I
> > left them off.
> > * I told createuser that the "omero" user should not have permission
> > to create additional users.
> > * I eventually figured out that you must update the
> > etc/local.properties file to reflect the chosen password for the
> > "omero" postgres user. The "Quick Install" instructions do not mention
> > it.
>
> http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?
> page=OmeroLinuxInstallHowto
>
> Just assuming you're using this documentation page. If you're not, is
> there somewhere else you retrieved the information from Curtis?
>
>
> The Quick Install assumes that you're going to use "omero"/"omero" as
> your database user and password, it states:
>
> * NOTE: For a Quick Install it is assumed that you will follow the
> examples laid out here with an password of omero for the omero
> database user.
>
>
> If you want to change these settings you must follow the "Manual
> Install" instructions, where it states:
>
> * Edit the etc/local.properties file in the OMERO distribution based
> upon your database user and password choices.
>
>
> Happy to modify the text and/or make it more explicit (Font size 32
> maybe? :)). Thoughts?
>
>
> So, have you followed the "Manual Install" instructions? As you've
> changed the local.properties file, you must:
>
> export JBOSS_HOME=~/Desktop/omero-3.0-Beta1/jboss-4.0.4.GA
> java omero update deploy
>
> (These instructions are in the "Reconfiguration" section of the
> Install document)
>
> You can confirm proper deployment by examining the $JBOSS_HOME/server/
> default/deploy directory.
>
> >
>
> ...snip...
>
> > 10:33:53,199 WARN  [SettingsFactory] Could not obtain connection
> > metadata
> > org.jboss.util.NestedSQLException: Could not create connection; -
> > nested throwable: (org.jboss.resource.JBossResourceException:
> > Apparently wrong driver class specified for URL: class:
> > org.postgresql.Driver, url: jdbc:postgresql://localhost/omero3); -
> > nested throwable: (org.jboss.resource.JBossResourceException: Could
> > not create connection; - nested throwable:
> > (org.jboss.resource.JBossResourceException: Apparently wrong driver
> > class specified for URL: class: org.postgresql.Driver, url:
> > jdbc:postgresql://localhost/omero3))
> >   at org.jboss.resource.adapter.jdbc.WrapperDataSource.getConnection
> > (WrapperDataSource.java:94)
> > ---
> >
> > Are these messages normal, or is something wrong with my
> > configuration?
>
> Yes, it's normal.
>
> ...snip...
>
> >
> > Any advice?
>
> See above.
>
> >
> > -Curtis
>
> Ciao.
>
> -Chris
>