[ome-devel] Questions on OMERO.server (BETA) 4.0 RC1

[josh.moore at gmx.de]

Mario Valle writes:
 > Ciao Josh!

Ah, ciao Mario! I was waiting to hear from you. :)

 > The beta4-rc1 build went on without a single problem!

Great to hear.

 > Well, I cannot access webadmin, but read on.

K.

 > I have only a suggestion and a few questions.
 > I suggest to put in the instructions that the environment variable 

 > PYTHONPATH=/Users/mvalle/Ice-3.3.0/py/python:/omero-4.0-rc1/dist/lib/python
 > should be set before running bin/omero config

Definitely. However, dist/lib/python shouldn't be necesssary since
bin/omero will add itself. (Let me know if that doesn't work for
you). But very much, the Ice python directory does need to be added,
but that is specific to how and where you installed it. We'll do our
best to make that straight-forward for everyone.
 
 > Questions:
 > 1) Should the bin/omero admin start command be run under sudo? Seems do not make any 
 > difference

This is something you will need to decide. Once you run it under sudo,
you will need to ALWAYS run it under sudo because the directories
created will be owned by root. In general, we suggest *not* running as
root, since there is really no need to do so.

 > 2) Which are the db.user and db.name that you set to me/mydb?
 > Should they be omero/omero?

omero/omero are the defaults. They are respectively the name of the
postgres user and the name of the database which the server should
access. The actual values are completely up to you.

 > 3) Should the data.dir an empty directory and not the old Beta3.2 /OMERO directory?

There should be no problem using the previous /OMERO directory, but
you should only do so if you successfully applied the upgrade script
and are using the previous database. If you are using a fresh
database, also use a fresh data.dir, otherwise the pixel data will be
overwritten. (And as ALWAYS, please, please make backups when
upgrading and more so for release candidates)

 > 4) The new db is omero and no more omero3, correct?

That is your choice. If you'd like to use omero3, just be sure to set
omero.db.name to "omero3"

 > 5) I have opened the ports 1098, 4063, 4444, 3873, 8000. Is this
 > correct?

No. From this release on, only 4063 is needed, unless you configure
your server for using SSL in which case you only need 4064. However,
these are just the IANA assigned ports for the Glacier2 router. You
are welcome to use any port you'd like, as long as you change the
client-endpoints configuration in etc/grid/default.xml

 > 6) How can I build the standard clients?

The importer is built by default when building the server (via "ant"),
and you can package a zip with "ant release-zip". See target/*.zip

Building insight is as it always was, and the various test builds are
available for download from:

  http://hudson.openmicroscopy.org.uk/job/OMERO/
  http://hudson.openmicroscopy.org.uk/job/INSIGHT/

 > And now the scoop:
 > Seems the server doesn't start because I run on Mac PPC with OSX 10.4 . Instead the 
 > master.err (attached) show that 10.5 is required.

There are now *several* processes started when you run "bin/omero
admin start", so my assumption is that only DropBox did not run. I'll
comment below.
 
 > I hope this is only an oversight and not a hard
 > prerequisite. Otherwise I'm cut out again from the OME world...

No chance! :)

 > Let me know.
 > Ciao!
 > 	mario

~Josh.


-------------------------------------------------------------
Traceback (most recent call last):
  File "lib/python/runFSServer.py", line 12, in ?
    import FSServer
  File "/omero-4.0-rc1/dist/lib/python/FSServer.py", line 13, in ?
    import MonitorServer 
  File "/omero-4.0-rc1/dist/lib/python/MonitorServer.py", line 97, in ?
    raise Exception(errorString)
Exception: Mac Os 10.5 or above required. You have: 10.4.9
-------------------------------------------------------------

Right. This means that the OMERO.fs process didn't start properly. It
*is* 10.5 minimum. However, as with all the OMERO.grid processes, you
could start it individually on a separate server. Let me know if this
is of interest, and I'll outline how to do that.



-------------------------------------------------------------
Starting django... 
Traceback (most recent call last):
  File "manage.py", line 27, in ?
    import settings # Assumed to be in the same directory.
  File "/omero-4.0-rc1/dist/lib/omeroweb/settings.py", line 152, in ?
    filemode='w')
TypeError: basicConfig() takes no arguments (5 given)
-------------------------------------------------------------

This is an error from the webclient / webadmin. We assume it's due to your
python version being pre-10.4. Can you confirm this? If so, try
upgrading to 2.4+.



-------------------------------------------------------------
java.io.FileNotFoundException: var/log/Blitz-0.log (Permission denied)
	at java.io.FileOutputStream.openAppend(Native Method)	at java.io.FileOutputStream.openAppend(Native Method)
-------------------------------------------------------------

This comes from running as root, and probably *is* preventing your
server from starting. You may want to either create a new deployment
directory, or chown all the files.



-------------------------------------------------------------
03/10/09 10:37:33.557 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier at BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
03/10/09 10:37:33.561 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
-------------------------------------------------------------

These are truly just startup warnings. Once blitz comes up, the
Glacier2 router will connect to it.


 > josh.moore at gmx.de wrote:
 > > Hi everyone,
 > > 
 > > as promised, an update on the upcoming release. We've just tagged
 > > release candidate 1 for internal testing (url below). You are welcome
 > > to start examining the tag or downloading from Hudson, but obviously
 > > there is still work to do and changes to be made.
 > > 
 > > In order to use this pre-docs version, some explanation is necessary:
 > > 
 > >  * First, the database has "evolved" as opposed to clearly being
 > >    versioned during our development, so anyone who has tested the
 > >    waters will need to re-create their database.
 > > 
 > >  * Another important change is how the database gets created. To
 > >    simplify the distribution, ant has been removed, which means the
 > >    "ant setup-db" target is gone. For the moment, we are delegating
 > >    database creation to your tool of choice (probably psql). See below
 > >    on how to do this.
 > > 
 > >  * The logging location has changed. Deployment starts up at least two
 > >    server instances, one with a lower memory requirement, solely for
 > >    indexing your database. To prevent confusion from duplications,
 > >    there are now two files. See var/log/Blitz-0.log and
 > >    var/log/Indexer-0.log after starting your instance.
 > > 
 > >  * Finally, server configuration has changed. Rather than editing
 > >    local.properties and executing "ant update", Java's Preferences API
 > >    (e.g. ~/.java/userPrefs on Linux) is being used (see below). This
 > >    keeps the distribution directory (other than the logs) read-only so
 > >    it can be installed globally.
 > > 
 > > 
 > > The final workflow, which we will be writing up online for release,
 > > can be summarized like this: (note this assumes that Ice, Java,
 > > Python, and Postgres are already installed)
 > > 
 > > 
 > >     svn co \
 > >       http://svn.openmicroscopy.org.uk/svn/omero/tags/omero-4.0-rc1 \
 > >       omero-4.0-rc1
 > > 
 > >     cd omero-4.0-rc1
 > >      # Calls "java omero" to prevent memory issues on 64bit
 > >     ./build.py
 > >     cd dist
 > > 
 > >     #
 > >     # All default properties are shown in etc/omero.properties
 > >     # If you would like to change any property, use the
 > >     # "bin/omero config" command.
 > >     #
 > >     bin/omero config set omero.data.dir /opt/OMERO
 > >     bin/omero config set omero.db.user me
 > >     bin/omero config set omero.db.name mydb
 > > 
 > > 
 > >     #
 > >     # To create a password script which also contains your
 > >     # (OMERO) root user's password, use the "bin/omero db" command
 > >     #
 > >     bin/omero db script    # Asks for root pass and creates OMERO__4.sql
 > > 
 > > 
 > >     #
 > >     # Postgresql commands:
 > >     # ==========================
 > >     # These commands assume the default values as in etc/omero.properties
 > >     #
 > >     sudo -u postgres createdb -O omero omero
 > >     sudo -u postgres createlang plpgsql omero
 > >     psql -U omero omero < OMERO4__0.sql
 > > 
 > > 
 > >     # Starting your server
 > >     bin/omero admin start
 > >     # No deploy needed.
 > > 
 > > 
 > > Once "OMERO.blitz now accepting connections." appears in your
 > > var/log/Blitz-0.log, you can browse to:
 > > 
 > >   http://localhost:8000/webadmin
 > > 
 > > and begin adding new users.
 > > 
 > > 
 > > Known issues:
 > > =============
 > > 
 > >  * Server builds on Windows but will not deploy properly.
 > > 
 > >  * To get the Eclipse projects to compile, it is necessary to run
 > >    "ant test-compile".
 > > 
 > > 
 > > Thanks ever so much for your patience and and the upcoming
 > > feedback. And, as always, we'll keep you posted on the further release
 > > schedule.
 > > 
 > > 
 > > Best wishes,
 > > Josh