[ome-users] OMERO username and password

Tue Feb 28 18:36:11 GMT 2017

Hello Dominik,

I edit the path. Now, omero can find java but it still has problem as
attachment. I think the problem might come from "bin\omero db script
--password testOmero". Do I correct use database user password at here? The
error comes from python lib. I think I installed the correct python
extension for windows. Thank you

Regards,
Qi

On Tue, Feb 28, 2017 at 11:58 AM, Dominik Lindner (Staff) <
d.lindner at dundee.ac.uk> wrote:

> Hi,
>
> that sounds right, just make sure to use the password of the omero
> database user (the login role you set up before) when setting the
> 'omero.db.pass' parameter.
>
> And yes, I'd remove the "C:\Program Files\Java\jdk1.8.0_65\bin" entry from
> PATH. Just maybe check afterwards in the command line with "java -version"
> that the java executable can still be found on the system.
>
> I'm just thinking if there could be something else you missed... Did you
> install the "Python extensions for Windows", respectively the right
> version, matching your architecture and python version (which should be
> amd64 and  py2.7)? https://sourceforge.net/projects/pywin32/files/
> pywin32/Build%20220/
>
> Regards,
> Dominik
>
>
> On 28 Feb 2017, at 15:46, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>
> Hello Dominik,
>
> Thank you for your reply.
>
> 1. As attachment, in attachment "javapath", "jdk18", the
> "C:\ProgramData\Oracle\Java\javapath" folder has the three files, but
> they are only short cut. And the "C:\Program Files\Java\jdk1.8.0_65\bin"
> folder has all the files. Do I still need remove "C:\Program
> Files\Java\jdk1.8.0_65\bin" from path?
>
> 2. I created a new system variable "PYTHONPATH"
>
> 3. I use 2 passwords in pgAdmin4 "gq900107". One is when I log in the
> software. The other is when I set the testOmero longin/Group Roles
> "testOmero" (same as user name). I am not sure whether the Roles and the
> database settings in attachments are correct.
>
> Regards,
> Qi
>
> On Tue, Feb 28, 2017 at 8:36 AM, Dominik Lindner (Staff) <
> d.lindner at dundee.ac.uk> wrote:
>
>> Sorry, I missed the Ice entry in your PATH. That looks correct. But could
>> you please check the other points I mentioned, thanks.
>>
>> Regards,
>> Dominik
>>
>>
>> On 28 Feb 2017, at 13:33, Dominik Lindner (Staff) <d.lindner at dundee.ac.uk>
>> wrote:
>>
>> Hi Qi,
>>
>> just to make sure that we're not missing something in the documenation I
>> just installed 5.2.7 on a Windows 2012 server VM, which was working fine.
>>
>> Could you check the following things:
>> - There are two Java entries in your PATH variable. Could you go to the
>> location "C:\ProgramData\Oracle\Java\javapath" (ProgramData is hidden,
>> so just copy/paste the path into the navigation bar in the windows
>> explorer) and make sure it exists (there should be three files in the
>> directory, java, javaw and javaws).
>> If the directory exists, remove the entry "C:\Program
>> Files\Java\jdk1.8.0_65\bin;" from your PATH variable.
>> - You don't have the ICE directory in your PATH. Did you download and
>> extract ICE? If not, do so. And add "C:\Ice-3.5.1\bin;" (in case you
>> extracted it to C:\Ice-3.5.1) to your PATH.
>> - Also make sure you add a system variable PYTHONPATH which points to
>> ICE's python directory (C:\Ice-3.5.1\python; ) in case you missed that.
>> - And just to get sure, check that you run the "omero config" commands
>> with the right usernames and passwords! According to your screenshots, your
>> omero user is testOmero and your database is also called testOmero , and
>> the password is whatever you set for the testOmero login role in the
>> "Database setup" step.
>>
>> Regards,
>> Dominik
>>
>>
>> On 27 Feb 2017, at 16:45, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>>
>> Hello Josh,
>>
>> 1. As attachment, I think the version is 5.2.7
>>
>> 2. I use the "-db" command it still has the same problem. I didn't
>> remember I set ICE_CONFIG. I only set config following instruction.
>> "C:\OMERO.server\> bin\omero config set omero.db.name omero_database
>>
>> C:\OMERO.server\> bin\omero config set omero.db.user db_user
>> C:\OMERO.server\> bin\omero config set omero.db.pass db_password"
>>
>> 3. This is the Path for System variable (not user variable)
>> C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Program Files (x86)\AMD
>> APP\bin\x86;*C:\Program
>> Files\Java\jdk1.8.0_65\bin;C:\ProgramData\Oracle\Java\javapath;*C:\Program
>> Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Wi
>> ndows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windo
>> ws\System32\WindowsPowerShell\v1.0\;C:\Program Files
>> (x86)\Aperio\Common;C:\Program Files (x86)\Point Grey Research\PGR
>> FlyCapture\bin64\;C:\Program Files\TortoiseSVN\bin;C:\Program Files
>> (x86)\MiKTeX 2.9\miktex\bin\;C:\Program Files\MATLAB\R2016a\runtime\win64;C:\Program
>> Files\MATLAB\R2016a\bin;C:\Program Files (x86)\MATLAB\R2013a\runtime\win32;C:\Program
>> Files (x86)\MATLAB\R2013a\bin;C:\Program Files\MATLAB\MATLAB Compiler
>> Runtime\v715\runtime\win64;C:\Program Files\TortoiseGit\bin;C:\Program
>> Files (x86)\Git\cmd;C:\Program Files (x86)\ATI
>> Technologies\ATI.ACE\Core-Static;C:\Program Files\Point Grey
>> Research\FlyCapture2\bin64;C:\Program Files\MATLAB\MATLAB
>> Runtime\v901\runtime\win64;C:\Ice-3.5.1-b4-win-x64-Release\b
>> in;C:\Python27
>>
>> Does this correct? Thank you.
>>
>> Regards,
>> Qi
>>
>> On Mon, Feb 27, 2017 at 11:18 AM, Josh Moore <josh at glencoesoftware.com>
>> wrote:
>>
>>> On Mon, Feb 27, 2017 at 4:54 PM, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>>> > Hello Josh,
>>>
>>> Hi Qi,
>>>
>>>
>>> > 1. At first I downloaded and installed the 5.3 version OMERO server, I
>>> found
>>> > the problem and reinstall 5.2.7 version. But in the cmd.png attachment
>>> blue
>>> > square, there are warning about 5.3 version, do you know how to check
>>> the
>>> > version?
>>>
>>> You can use:
>>>
>>>    bin\omero version
>>>
>>> to see which version you are using. We added the warning in the 5.2
>>> line to make sure that everyone was aware.
>>>
>>>
>>> >
>>> > 2. Follow the instruction, I create database in pgAdmin4. As
>>> pgAdmin4.png
>>> > attachment, I set database, login role and password to "testOmero". In
>>> the
>>> > cmd.png attachment blue square, what command should I use to initialize
>>> > database? "bin\omero db script --password testOmero" or  "bin\omero db
>>> > script --password root_password"?
>>>
>>> You want:
>>>
>>>   --password testOmero
>>>
>>> The documentation uses "root_password" as an example.
>>>
>>>
>>> > 3. In the same square(blue), I face AttributeError? Did you face
>>> similar
>>> > error before?
>>>
>>> This error is unexpected. Have you set ICE_CONFIG perhaps? If not,
>>> could you try running this command with -d1:
>>>
>>>   bin\omero -d1 db script --password testOmero
>>>
>>>
>>> > 4. In cmd.png attachment, the red square shows I have java installed.
>>> But in
>>> > the green square, It says Java could not be found.
>>>
>>> This looks like the environment setting is not propagating to
>>> subprocesses. Is the Java installation new or have you used it
>>> previously? In which %PATH% variable is it defined?
>>>
>>> Cheers,
>>> ~Josh.
>>>
>>>
>>> > Thank you very much for your time and help.
>>> >
>>> > Regards,
>>> > Qi
>>> >
>>> >
>>> > On Mon, Feb 27, 2017 at 6:26 AM, Josh Moore <josh at glencoesoftware.com>
>>> > wrote:
>>> >>
>>> >> Hi Qi,
>>> >>
>>> >>
>>> >> On Fri, Feb 24, 2017 at 8:31 PM, Qi Gong <qigong at gwmail.gwu.edu>
>>> wrote:
>>> >> > Hello William,
>>> >> >
>>> >> > I tried to install a OMERO server on my local computer follow:
>>> >> >
>>> >> > https://www.openmicroscopy.org/site/support/omero5.2/sysadmi
>>> ns/windows/server-installation.html
>>> >>
>>> >> Just in case you hadn't seen it, Windows support will be ending with
>>> >> the 5.2 version. OMERO 5.3 which is intended for release next month
>>> >> has _not_ been tested on Windows. See
>>> >>
>>> >> http://blog.openmicroscopy.org/tech-issues/future-plans/depl
>>> oyment/2016/03/22/windows-support/
>>> >> for more information.
>>> >>
>>> >> If you'd like to try using Docker or VirtualBox to run a Linux-image
>>> >> on Windows, please let us know.
>>> >>
>>> >>
>>> >> > But I am facing some problem and have some questions.
>>> >> > 1. May I skip this command? C:\OMERO.server> bin\omero db script
>>> >> > --password
>>> >> > root_password?
>>> >>
>>> >> No. This generates the PostgreSQL script which will initialize your
>>> >> database.
>>> >>
>>> >>
>>> >> > 2. I am sure we have Java installed, but when I enter command:
>>> >> > bin\omero
>>> >> > admin start, system says Java could not be found.
>>> >> >
>>> >> > I attach a screenshot of cmd window. Have you ever faced similar
>>> problem
>>> >> > before? Thank you.
>>> >>
>>> >> Is Java set on the system PATH like the variables for Ice & Python
>>> >> from
>>> >> https://www.openmicroscopy.org/site/support/omero5.2/sysadmi
>>> ns/windows/server-installation.html#environment-variables
>>> >> ?
>>> >>
>>> >> Cheers,
>>> >> ~Josh
>>> >>
>>> >>
>>> >> > Regards,
>>> >> > Qi
>>> >> >
>>> >> >
>>> >> > On Wed, Feb 1, 2017 at 6:07 AM, William Moore (Staff)
>>> >> > <W.Moore at dundee.ac.uk>
>>> >> > wrote:
>>> >> >>
>>> >> >> Hi Qi,
>>> >> >>
>>> >> >>  I’m afraid that you do need to install and run an OMERO server.
>>> >> >>
>>> >> >> You might want to sign up for an account on our “demo” server that
>>> will
>>> >> >> allow you
>>> >> >> to import some data and get started with OMERO.
>>> >> >> Although this should not be used as a repository for any important
>>> >> >> data.
>>> >> >>
>>> >> >>  See
>>> >> >>
>>> >> >> https://www.openmicroscopy.org/site/support/omero5.2/users/d
>>> emo-server.html
>>> >> >> for details.
>>> >> >>
>>> >> >> Regards,
>>> >> >>
>>> >> >>   Will.
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> On 31 Jan 2017, at 20:27, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>>> >> >>
>>> >> >> Hello Kenneth,
>>> >> >>
>>> >> >> We want to use OMERO to view WSI images on our computer. Do we
>>> need to
>>> >> >> install and run a server or is there a stand alone browser? Thank
>>> you.
>>> >> >>
>>> >> >> Regards,
>>> >> >> Qi
>>> >> >>
>>> >> >> On Thu, Jan 26, 2017 at 4:14 PM, Kenneth Gillen (Staff)
>>> >> >> <k.h.gillen at dundee.ac.uk> wrote:
>>> >> >>>
>>> >> >>> Hi Qi,
>>> >> >>>
>>> >> >>> Generally you’d be given these by someone at your institution or
>>> >> >>> organisation. Your local IT support may also be able to suggest
>>> >> >>> something.
>>> >> >>>
>>> >> >>> Perhaps the person who suggested you use OMERO in the first place
>>> will
>>> >> >>> be
>>> >> >>> able to point you in the right direction?
>>> >> >>>
>>> >> >>> All the best,
>>> >> >>>
>>> >> >>> Kenny
>>> >> _______________________________________________
>>> >> ome-users mailing list
>>> >> ome-users at lists.openmicroscopy.org.uk
>>> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > mobile phone: 2024060862
>>> >
>>> > _______________________________________________
>>> > ome-users mailing list
>>> > ome-users at lists.openmicroscopy.org.uk
>>> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>> >
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>
>>
>>
>> --
>> mobile phone: 2024060862 <(202)%20406-0862>
>> <cmd.PNG>_______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
>
> --
> mobile phone: 2024060862 <(202)%20406-0862>
> <javapath.PNG><jdk18.PNG><pythonpath.PNG><configSet.PNG>
> <pgAdmin4Setting.PNG><databaseSetting.PNG>__________
> _____________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>

-- 
mobile phone: 2024060862
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/350fb557/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: cmd.PNG
Type: image/png
Size: 56063 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/350fb557/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pythonWin.PNG
Type: image/png
Size: 23498 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/350fb557/attachment-0001.png>