[ome-users] Initialize the OMERO database
Smith, Stuart C
Stuart.C.Smith at pfizer.com
Tue Apr 14 14:33:37 BST 2009
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.
>>
>> _______________________________________________
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>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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