[ome-users] Initialize the OMERO database
josh.moore at gmx.de
josh.moore at gmx.de
Mon Apr 20 09:26:11 BST 2009
This is one of the major bugs in 4.0.0. "bin\omero config" was setting
the values for the current user in the registry, while the server
starts up as the local services user. This is also why "bin\omero
config" is not used under Windows in 4.0.1. If anyone is interested in
pursuing running the server as another user, please say so on the
list.
Cheers,
~Josh.
Smith, Stuart C writes:
> Hi Colin, no worries as if everything ran smoothly, we wouldn't learn
> anything :o)
>
> find the requested info...
>
> C:\omero-Beta4.0.0>bin\omero config get
> omero.data.dir='D:\\OMERO'
> omero.db.name=omero
> omero.db.pass=omero
> omero.db.user=omero
>
> C:\omero-Beta4.0.0>bin\omero config set omero.data.dir
> 'C:\OMERO'
>
> C:\omero-Beta4.0.0>bin\omero config get
> omero.data.dir='C:\OMERO'
> omero.db.name=omero
> omero.db.pass=omero
> omero.db.user=omero
>
> I noticed the data.dir was pointing to a non-existant D:\ Drive,
> although I'm sure I changed it (but can't have) and therefore configured
> to C:\
>
> I then stopped & restarted the server with "bin\omero admin start"
>
> C:\omero-Beta4.0.0>bin\omero admin stop
>
> SERVICE_NAME: OMERO.master
> TYPE : 10 WIN32_OWN_PROCESS
> STATE : 4 RUNNING
>
> (STOPPABLE,NOT_PAUSABLE,ACCEPTS_SHUTDOWN)
> WIN32_EXIT_CODE : 0 (0x0)
> SERVICE_EXIT_CODE : 0 (0x0)
> CHECKPOINT : 0x0
> WAIT_HINT : 0x0
>
> [SC] DeleteService SUCCESS
>
> Waiting on shutdown. Use CTRL-C to exit
> icegridadmin: could not contact the default locator:
> Network.cpp:1218: Ice::ConnectionRefusedException:
> connection refused: WSAECONNREFUSED
>
>
>
> C:\omero-Beta4.0.0>bin\omero admin start
> No descriptor given. Using etc/grid/default.xml
> [SC] CreateService SUCCESS
>
> SERVICE_NAME: OMERO.master
> TYPE : 10 WIN32_OWN_PROCESS
> STATE : 2 START_PENDING
>
> (NOT_STOPPABLE,NOT_PAUSABLE,IGNORES_SHUTDOWN)
> WIN32_EXIT_CODE : 0 (0x0)
> SERVICE_EXIT_CODE : 0 (0x0)
> CHECKPOINT : 0x0
> WAIT_HINT : 0x7d0
> PID : 1004
> FLAGS :
>
> Waiting on startup. Use CTRL-C to exit
> icegridadmin: could not contact the default locator:
> Network.cpp:1218: Ice::ConnectionRefusedException:
> connection refused: WSAECONNREFUSED
> .
> C:\omero-Beta4.0.0>
>
>
> Stuart
>
>
> -----Original Message-----
> From: Colin Blackburn [mailto:c.blackburn at dundee.ac.uk]
> Sent: 14 April 2009 14:15
> To: Smith, Stuart C
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Initialize the OMERO database
>
> Hi Stuart,
>
> sorry to hear you are having problems with Windows, it seems to throw up
>
> a few interesting issues on some machines and not on others.
>
> Can you let me know what the response is to:
>
> C:\omero-Beta4.0.0>bin\omero config get
>
> And, what your omero data directory actually is?
>
> Cheers,
>
> Colin
>
>
> Smith, Stuart C wrote:
> > Hi, for "stop" I get...
> >
> > C:\omero-Beta4.0.0>bin\omero admin stop
> >
> > SERVICE_NAME: OMERO.master
> > TYPE : 10 WIN32_OWN_PROCESS
> > STATE : 4 RUNNING
> > (STOPPABLE,NOT_PAUSABLE,ACCEPTS_SHUTDO
> > WIN32_EXIT_CODE : 0 (0x0)
> > SERVICE_EXIT_CODE : 0 (0x0)
> > CHECKPOINT : 0x0
> > WAIT_HINT : 0x0
> >
> > [SC] DeleteService SUCCESS
> >
> > Waiting on shutdown. Use CTRL-C to exit
> > icegridadmin: could not contact the default locator:
> > Network.cpp:1218: Ice::ConnectionRefusedException:
> > connection refused: WSAECONNREFUSED
> >
> > and when I restart, I get...
> >
> > C:\omero-Beta4.0.0>bin\omero admin start
> > No descriptor given. Using etc/grid/default.xml
> > [SC] CreateService SUCCESS
> >
> >
> > SERVICE_NAME: OMERO.master
> > TYPE : 10 WIN32_OWN_PROCESS
> > STATE : 2 START_PENDING
> >
> > (NOT_STOPPABLE,NOT_PAUSABLE,IGNORES_SHUTDOWN)
> > WIN32_EXIT_CODE : 0 (0x0)
> > SERVICE_EXIT_CODE : 0 (0x0)
> > CHECKPOINT : 0x0
> > WAIT_HINT : 0x7d0
> > PID : 3412
> > FLAGS :
> >
> > Waiting on startup. Use CTRL-C to exit
> > icegridadmin: could not contact the default locator:
> > Network.cpp:1218: Ice::ConnectionRefusedException:
> > connection refused: WSAECONNREFUSED
> > .
> > C:\omero-Beta4.0.0>
> >
> > Thanks in advance,
> >
> > Stu
> >
> >
> > -----Original Message-----
> > From: ome-users-bounces at lists.openmicroscopy.org.uk
> > [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of
> > Paulo Almeida
> > Sent: 14 April 2009 13:31
> > To: ome-users at lists.openmicroscopy.org.uk
> > Subject: Re: [ome-users] Initialize the OMERO database
> >
> > Hi Stuart,
> >
> > If you haven't done that yet, I would try:
> >
> > bin\omero admin stop
> >
> > and then:
> >
> > bin\omero admin start
> >
> > Good luck,
> > Paulo
> >
> > On Tuesday 14 April 2009 12:24:26 Smith, Stuart C wrote:
> >> Hi Josh, thanks for that. I have now downgraded to ICE 3.3.0 and
> upon
> >> running the "start sever" command I get...
> >>
> >> C:\omero-Beta4.0.0>bin\omero admin start
> >> No descriptor given. Using etc/grid/default.xml
> >> [SC] StartService FAILED 1056:
> >>
> >> An instance of the service is already running.
> >>
> >> Waiting on startup. Use CTRL-C to exit
> >>
> >> C:\omero-Beta4.0.0>
> >>
> >> I guess, trying not to state the obvious, that the required services
> > are
> >> already running. Of which, I have checked & the "postgreSQ" & "OMERO
> >> Master" services are both running.
> >>
> >> But when I try to view the webadmin page, it cannot be displayed.
> Any
> >> idea's?
> >>
> >> Stuart
> >>
> >>
> >> p.s. I will be installing 4.0.1 upon release, but by trying to get
> > 4.0.0
> >> working its helping me understand the app :o)
> >>
> >>
> >> -----Original Message-----
> >> From: josh.moore at gmx.de [mailto:josh.moore at gmx.de]
> >> Sent: 09 April 2009 15:23
> >> To: Smith, Stuart C; ome-users at lists.openmicroscopy.org.uk
> >> Subject: Re: [ome-users] Initialize the OMERO database
> >>
> >> Smith, Stuart C writes:
> >> > Hi Josh,
> >>
> >> Hi Stuart,
> >>
> >> > Anyway, with your help I sorted that that. I know you mentioned
> >>
> >> that
> >>
> >> > 4.0.1 will be released soon, but i decided to carry on with 4.0 as
> > a
> >> > test installation until 4.0.1 in available. Everything else went
> > ok,
> >> > until i tried to start the server and got the below error...
> >> >
> >> > ...
> >> > No descriptor given. Using etc/grid/default.xml
> >> > [SC] StartService FAILED 3:
> >> >
> >> > The system cannot find the path specified.
> >> >
> >> > Waiting on startup. Use CTRL-C to exit
> >> > icegridadmin: could not contact the default locator:
> >> > Network.cpp:1220: Ice::ConnectionRefusedException:
> >> > connection refused: WSAECONNREFUSED
> >> >
> >> > Any ideas?
> >>
> >> This is one of the errors fixed in 4.0.1. Though your best bet is to
> >> wait for the release, I can give you a quick tip and you can go from
> >> there: if you've installed Ice-3.3.1 which you probably have, move it
> >> to C:\Ice-3.3.0 since the path is hard-coded. In the upcoming
> release,
> >> it's not hard-coded, but after install it requires a reboot. Those
> are
> >> the types of trade-offs in this business. :)
> >>
> >> Best wishes,
> >> ~Josh.
> >>
> >> > Thanks,
> >> >
> >> > Stuart
> >> >
> >> >
> >> > -----Original Message-----
> >> > From: josh.moore at gmx.de [mailto:josh.moore at gmx.de]
> >> > Sent: 08 April 2009 19:09
> >> > To: Smith, Stuart C
> >> > Cc: ome-users at lists.openmicroscopy.org.uk
> >> > Subject: [ome-users] Initialize the OMERO database
> >> >
> >> >
> >> > Hi Stuart,
> >> >
> >> > before I begin a minor warning, we'll be releasing 4.0.1 in the
> > next
> >> > day or two with improved Windows support. So, though it doesn't
> >>
> >> change
> >>
> >> > any of the instructions for getting your database setup, it may
> > make
> >> > sense to wait for the final installation until then.
> >> >
> >> > But first, your db...
> >> >
> >> > Smith, Stuart C writes:
> >> > > Hi, I'm sure this will be a very basic question to most of you
> > but
> >> > > I have been asked to set up a PC running the OMERO server
> >> > > installation and have followed the Windows installation
> document
> >> > > upto the point where you are asked to "Initialize the OMERO
> >> > > database" with the script...
> >> > >
> >> > > $ cd C:\omero-Beta4.0.0\
> >> > > $ bin\omero db script
> >> > > Please enter omero.db.version [OMERO4]:
> >> > > Please enter omero.db.patch [0]:
> >> > > Please enter password for new OMERO root user:
> >> > > Please re-enter password for new OMERO root user:
> >> > > Saving to C:\omero-Beta4.0.0\OMERO4__0.sql
> >> > > $
> >> > >
> >> > > But have tried pasting into a cmd window, but it doesn't like
> > it.
> >> I
> >>
> >> > > therefore tried the first line & realised that it wasn't even
> >> >
> >> > changing
> >> >
> >> > > directories, therefore removed the 1st "$" char & that worked,
> > but
> >> >
> >> > then
> >> >
> >> > > got stuck on the 2nd line. Can someone please help me
> > initialize
> >> the
> >>
> >> > > DB.
> >> >
> >> > The dollar signs are a copy-n-paste issue from the non-Windows
> >> > instructions. Sorry about that. I've fixed them in the
> > documentation
> >> > for the coming release.
> >> >
> >> > > Also, as I was unsure if it had worked, although I wasn't
> > prompted
> >> >
> >> > for
> >> >
> >> > > the password as I added it to the script manually so I tried
> the
> >>
> >> next
> >>
> >> > > step of populating the database by copying the script in the
> >> > > installation document into "SQL Shell (psql)" and this errored,
> >>
> >> but
> >>
> >> > was
> >> >
> >> > > this because I hadn't initialized the db?
> >> > >
> >> > > Any help you guys can offer would be great as I have been asked
> > to
> >> >
> >> > set
> >> >
> >> > > this up to see if the software is useful to us.
> >> >
> >> > Alright. I'm a bit lost in what you tried, and what did and didn't
> >> > work. What you should use to create your database script is:
> >> >
> >> > cd C:\omero-Beta4.0.0\
> >> > bin\omero db script
> >> >
> >> > Then you should be asked the questions about version and
> >> > password. You said you weren't asked for a password. That seems
> >> > odd. How did you go about adding that manually?
> >> >
> >> > Once you've done that, then opening the SQL Shell as mentioned in
> > the
> >> > docs is certainly correct. The statement "\i ... OMERO4__0.sql" is
> >>
> >> the
> >>
> >> > process of initializing your db, so that can't be why it errored.
> > Can
> >> > you send us the error that it produced?
> >> >
> >> > > Thanks in advance,
> >> > > Stuart
> >> >
> >> > Hope that helps somewhat.
> >> > Best wishes,
> >> > ~Josh.
> >>
> >> _______________________________________________
> >> ome-users mailing list
> >> ome-users at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >
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>
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