[ome-users] OMERO username and password

Tue Feb 28 16:58:14 GMT 2017

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<mailto: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<mailto: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<mailto: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<mailto: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<http://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:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\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\bin;C:\Python27

Does this correct? Thank you.

Regards,
Qi

On Mon, Feb 27, 2017 at 11:18 AM, Josh Moore <josh at glencoesoftware.com<mailto:josh at glencoesoftware.com>> wrote:
On Mon, Feb 27, 2017 at 4:54 PM, Qi Gong <qigong at gwmail.gwu.edu<mailto: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<mailto:josh at glencoesoftware.com>>
> wrote:
>>
>> Hi Qi,
>>
>>
>> On Fri, Feb 24, 2017 at 8:31 PM, Qi Gong <qigong at gwmail.gwu.edu<mailto: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/sysadmins/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/deployment/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/sysadmins/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<mailto: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/demo-server.html
>> >> for details.
>> >>
>> >> Regards,
>> >>
>> >>   Will.
>> >>
>> >>
>> >>
>> >> On 31 Jan 2017, at 20:27, Qi Gong <qigong at gwmail.gwu.edu<mailto: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<mailto: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
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