[ome-devel] [ome-users] OME and OMERO: Release of OMERO3.0-Beta1
Curtis Rueden
ctrueden at wisc.edu
Thu Feb 8 17:11:57 GMT 2007
Hi,
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.
After launching the OMERO server, my JBoss environment looks good:
=========================================================================
JBoss Bootstrap Environment
JBOSS_HOME: /home/curtis/apps/omero-3.0-Beta1/jboss-4.0.4.GA
JAVA: /usr/lib/j2sdk1.5-sun/bin/java
JAVA_OPTS: -server -Xms128m -Xmx512m
-Dsun.rmi.dgc.client.gcInterval=3600000
-Dsun.rmi.dgc.server.gcInterval=3600000 -Dprogram.name=run.sh
CLASSPATH: /home/curtis/apps/omero-3.0-Beta1/jboss-4.0.4.GA/bin/run.jar:/usr/lib/j2sdk1.5-sun/lib/tools.jar
=========================================================================
After a whole lotta JBoss output, including some notes that omero.ear
was successfully deployed, I eventually see the following exception:
---
10:33:53,134 INFO [ConnectionProviderFactory] Initializing connection
provider: org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider
10:33:53,176 WARN [JBossManagedConnectionPool] Throwable while
attempting to get a new connection: null
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.local.LocalManagedConnectionFactory.createManagedConnection(LocalManagedConnectionFactory.java:177)
...
Caused by: 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.local.LocalManagedConnectionFactory.getDriver(LocalManagedConnectionFactory.java:274)
at org.jboss.resource.adapter.jdbc.local.LocalManagedConnectionFactory.createManagedConnection(LocalManagedConnectionFactory.java:168)
... 217 more
10:33:53,198 WARN [JDBCExceptionReporter] SQL Error: 0, SQLState: null
10:33:53,199 ERROR [JDBCExceptionReporter] 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))
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?
I then tried setting up users according to the instructions on the
Omero Getting Started tiki page:
---
curtis at skyking:~/apps/omero-3.0-Beta1/omero$ java -cp . omero addgroup
Buildfile: build.xml
addgroup:
+===========================================================================================+
|
| client
|
+===========================================================================================+
addgroup:
Please enter group name:
user
Please enter group description: (optional)
Please enter name of the group owner: (optional)
Feb 8, 2007 11:06:39 AM java.util.prefs.FileSystemPreferences$3 run
WARNING: Could not create system preferences directory. System
preferences are unusable.
Feb 8, 2007 11:06:39 AM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background
/home/curtis/.java/.userPrefs/prefs.xml
Feb 8, 2007 11:06:39 AM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background
/usr/lib/j2sdk1.5-sun/jre/.systemPrefs/prefs.xml
Exception in thread "main" javax.ejb.EJBAccessException: Authentication failure
at org.jboss.ejb3.security.Ejb3AuthenticationInterceptor.handleGeneralSecurityException(Ejb3AuthenticationInterceptor.java:68)
at org.jboss.aspects.security.AuthenticationInterceptor.invoke(AuthenticationInterceptor.java:71)
...
---
I am assuming this exception means that the group creation did not work?
I also tried creating a user, then logging in to the server with
OMERO.admin from a client, but needless to say that didn't work
either.
Any advice?
-Curtis
On 2/2/07, Jason Swedlow <jason at lifesci.dundee.ac.uk> wrote:
> Hi-
>
> The OME project is pleased to announce the release of OMERO3.0-
> Beta1. OMERO is a Java Enterprise port of the data management and
> visualization functions of the perl-based OME Server. The OMERO
> Server ships with a JBOSS Application Server, PostgreSQL RDMS, and
> uses three client applications: OMERO.insight, OMERO.importer, and
> OMERO.admin.
>
> All OMERO resources are available at our newly designed software
> download page:
>
> http://openmicroscopy.org/software/
>
> For new initiates, User Guides for OMERO client applications are
> available at our MilestoneDownloads page:
>
> http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
>
> OMERO installation on OS X is all by Mac packages and should be
> automatic. There are manual install instructions for Linux and OS X
> geeks.
>
> Please let us know any problems, wishes etc.
>
> **************
>
> Some background and resources:
>
> OMERO3 is a Java EE (formerly J2EE) application designed for the
> JBoss application server. OMERO3 runs under Linux and OS X and uses
> Hibernate for mapping to a PostgreSQL database (support for MySQL and
> Oracle are in progress, but have been demonstrated; contact us if
> interested). OMERO3 requires Java1.5. Our testing has all occurred
> on Pentium IV or AMD 250-series systems, with 1-2 GB RAM and a Gbit
> network connection. The OMERO3 docs page is at:
>
> http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=Omero
>
> Note that this is really for developers.
>
> OMERO.insight is our cross-platform Java client that uses an OMERO3
> server. OMERO.insight is our first client; OMERO3 is designed to
> support a number of different clients and client platforms (we are
> considering our long-term strategies for client environments).
> OMERO.insight seems to run well under Linux (so far, tested on RHE3),
> Windows XP-SP2, and OS X; the package requires Java1.5. We have
> used OMERO.insight on laptops with G4, Intel for Mac, and Intel P4
> processors, usually with 0.5 - 1 GB RAM and 100Mbit or Gbit NICs.
>
> OMERO.importer is our data importer. This is a Java client (requires
> Java1.5), that currently imports data from a client filesystem into
> an OMERO3 server. For import of external file formats, the OMERO
> project is using BioFormats- see http://loci.wisc.edu/ome/
> formats.html. Currently, OMEROImport supports two file formats--
> APLLC DV and MetaMorph's STK. We are of course working to include
> OMERO.importer as a component of OMERO.insight, as well as supporting
> server-side import. A major goal is the extension of proprietary
> file format support in OMERO.importer to include all files supported
> in Bio-Formats. We, along with our colleagues at LOCI, are working
> hard to expand the range of proprietary file formats supported in
> BioFormats. Stay tuned!
>
> What does OMERO do? Mostly, image visualization and image data
> management. There is not yet support for any management of image
> analysis results and data-- this continues to be one of the hallmarks
> of the released OME 2.x server (OME2.6.0 is now available at http://
> cvs.openmicroscopy.org.uk; we use this system in the lab for large-
> scale image analysis). The OMERO3-Beta1 package provides the ability
> to organize image data into Projects and Datasets and also user-
> defined CategoryGroups and Categories (see http://openmicroscopy.org/
> getting-started/manual_classification.html). In addition, our
> server-based Rendering Engine provides image visualization functions
> in a remote client environment. Our testing suggests that this that
> is a very useful tool for visualising image data in a client-server
> environment.
>
> Note that the OME and OMERO Servers are parallel, complementary
> projects. They are currently focussing on different function sets--
> see http://www.openmicroscopy.org/software/why2servers.html for more
> info.
>
> We have recognized the importance of getting feedback on the design,
> development, and documentation of OMERO and its clients. OMERO
> clients include an automatic bug logging system-- using this helps us
> to help you. As the above web pages suggest, we target our work
> around a series of milestones, and try to produce packages for
> testing these milestones. These should not be seen as finished,
> released software, but they are tested and (largely) work as
> promised. They are beta and should demonstrate what OMERO can achieve.
>
> Thanks again for your interest and support.
>
> Cheers,
>
> Jason
>
>
> **************************
> MSI/WTB Complex
> The University of Dundee
> Dow Street
> Dundee DD1 5EH
> United Kingdom
>
> phone (01382) 385819
> Intl phone: 44 1382 385819
> FAX (01382) 388072
> email: jason at lifesci.dundee.ac.uk
>
> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
> Open Microscopy Environment: http://openmicroscopy.org
> **************************
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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>
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