[ome-users] OMERO username and password

Tue Feb 28 15:46:45 GMT 2017

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:\
> 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>
> 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/
>> demo-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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/429efcd1/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: javapath.PNG
Type: image/png
Size: 43596 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/429efcd1/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: jdk18.PNG
Type: image/png
Size: 69265 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/429efcd1/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pythonpath.PNG
Type: image/png
Size: 19551 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/429efcd1/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: configSet.PNG
Type: image/png
Size: 36146 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/429efcd1/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pgAdmin4Setting.PNG
Type: image/png
Size: 102133 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/429efcd1/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: databaseSetting.PNG
Type: image/png
Size: 108269 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170228/429efcd1/attachment-0005.png>