[ome-users] OMERO.web installation under Ubuntu 14

Tue Oct 7 14:38:19 BST 2014

Hi Simon

I haven't set any enviroment variable.

I login as the omero user using:
$sudo -s -u omero

Regards,
Unai

Simon Li <s.p.li at dundee.ac.uk> escribió:

> Hi Unai
>
> It looks like OMERO is trying to write to a non-standard temporary
> directory. Have you set any environment variables? Try running
>
> $ set | grep -E 'TEMP|TMP'
>
> How did you logon as the omero user- with sudo, su, or directly?
>
> Simon
>
> P.S. When you reply could you ensure you use reply-all so that
> ome-users at lists.openmicroscopy.org.uk gets copied in.
>
> On 07/10/2014 11:40, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es> wrote:
>
>> Hi Simon,
>>
>> Thanks for the tip yo gave me yesterday! I set the correct path and I
>> could finally download and unzip OMERO.web.
>>
>> Unluckily, I get more permission errors while I'm setting OMERO.server
>> as the omero system user. At some point, the script is trying to acces
>> the administrator account:
>>
>> omero at imServer:/home/omero$ OMERO.server/bin/omero config set
>> omero.db.name "$OMERO_DB_NAME"
>> + OMERO.server/bin/omero config set omero.db.name omeroubf
>> WARNING:omero.util.TempFileManager:Invalid tmp dir: /home/jribecarios
>> Traceback (most recent call last):
>>   File
>> "/home/omero/OMERO.server/lib/python/omero/util/temp_files.py", line
>> 166, in tmpdir
>>     name = self.mkstemp(prefix=".lock_test", suffix=".tmp", dir=target)
>>   File
>> "/home/omero/OMERO.server/lib/python/omero/util/temp_files.py", line
>> 246, in mkstemp
>>     fd, name = tempfile.mkstemp(prefix = prefix, suffix = suffix, dir
>> = dir, text = text)
>>   File "/usr/lib/python2.7/tempfile.py", line 308, in mkstemp
>>     return _mkstemp_inner(dir, prefix, suffix, flags)
>>   File "/usr/lib/python2.7/tempfile.py", line 239, in _mkstemp_inner
>>     fd = _os.open(file, flags, 0600)
>> OSError: [Errno 13] Permission denied:
>> '/home/jribecarios/.lock_testrsfzij.tmp'
>>
>> I don't really understand why, because apparently the omero user
>> account has been set as the owner of the /OMERO folder, inside the
>> administrator account.
>> Does it mean that the OMERO repository should be also set inside the
>> omero user account?
>>
>> Cheers,
>> Unai
>>
>>
>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>
>>> Hi Unai
>>>
>>> Which directory were you in (run `pwd` if you’re not sure) when you ran
>>> wget?
>>>
>>> Simon
>>>
>>> On 06/10/2014 15:19, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es> wrote:
>>>
>>>>
>>>> Dear Simon,
>>>>
>>>> Since I had so much problems trying to install OMERO I decided to
>>>> reset the computer, rei-nstall Ubuntu 14.04, and try to install OMERO
>>>> once again from the beginning, following these instructions:
>>>>
>>>>
>>>> http://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-
>>>> li
>>>> nux-walkthrough.html
>>>>
>>>> According to them, I created an omero system user:
>>>> useradd -m omero
>>>> chmod a+X ~omero
>>>>
>>>> Then I got "permission denied" errors when I tried to download and
>>>> unzip OMERO.server as the omero system user with the following code:
>>>>
>>>>
>>>> SERVER=http://downloads.openmicroscopy.org/omero/5.0.5/artifacts/OMERO.s
>>>> er
>>>> ver-5.0.5-ice35-b47.zip
>>>> wget $SERVER
>>>> unzip -q `basename $SERVER`
>>>>
>>>> If I use "sudo" with both commands, the terminal needs the password of
>>>> the omero account to execute them, and it hasn't been set (for safety
>>>> reason, I guess...).
>>>>
>>>> Should I create the omero system user with more permissions? Do you
>>>> think is a good idea to create an omero system user with a password
>>>> and sudo wget and unzip?
>>>>
>>>>
>>>> Thanks,
>>>> Unai
>>>>
>>>>
>>>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>>>
>>>>> On 02/10/2014 12:36, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>> Dear Simon,
>>>>>>
>>>>>> I symlinked the 'nginx.conf.template' file to the
>>>>>> '/etc/nginx/sites-enabled' folder, restarted nginx, and I couldn't
>>>>>> success once again.
>>>>>
>>>>> Did you check both port 80 and 8080? You might need to disable
>>>>> sites-available/default.
>>>>>
>>>>>>
>>>>>> Appart from that I've also tried to login from OMERO.insight, and I
>>>>>> couldn't run the 'OMEROinsight_unix.sh' file from the terminal due to
>>>>>> an abnormal termination:
>>>>>>
>>>>>> Abnormal termination due to an uncaught exception.
>>>>>> java.awt.HeadlessException
>>>>>
>>>>> This is a separate issue. It could be because the server walkthrough
>>>>> assumes you¹ll be running Insight from a different computer, so the
>>>>> headless version of Java is specified (openjdk-7-jre-headless) to
>>>>> reduce
>>>>> the number of dependencies that are instacommandlled.
>>>>>
>>>>> You could try installing the full JRE instead:
>>>>> apt-get install openjdk-7-jre
>>>>>
>>>>>
>>>>> Simon
>>>>> command
>>>>>> at
>>>>>>
>>>>>>
>>>>>> java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:20
>>>>>> 7)
>>>>>> at java.awt.Window.<init>(Window.java:535)
>>>>>> at java.awt.Frame.<init>(Frame.java:420)
>>>>>> at javax.swing.JFrame.<init>(JFrame.java:218)
>>>>>> at
>>>>>>
>>>>>>
>>>>>> org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(ScreenLogin
>>>>>> .j
>>>>>> av
>>>>>> a:1033)
>>>>>> at
>>>>>>
>>>>>>
>>>>>> org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView(S
>>>>>> pl
>>>>>> as
>>>>>> hScreenManager.java:176)
>>>>>> at
>>>>>>
>>>>>>
>>>>>> org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(SplashScre
>>>>>> en
>>>>>> Ma
>>>>>> nager.java:241)
>>>>>> at
>>>>>>
>>>>>>
>>>>>> org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashScreen
>>>>>> Pr
>>>>>> ox
>>>>>> y.java:123)
>>>>>> at
>>>>>>
>>>>>>
>>>>>> org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFactory.
>>>>>> ja
>>>>>> va
>>>>>> :59)
>>>>>> at
>>>>>>
>>>>>>
>>>>>> org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(SplashScre
>>>>>> en
>>>>>> In
>>>>>> it.java:99)
>>>>>> at
>>>>>>
>>>>>>
>>>>>> org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java
>>>>>> :2
>>>>>> 76
>>>>>> )
>>>>>> at
>>>>>>
>>>>>>
>>>>>> org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.
>>>>>> ja
>>>>>> va
>>>>>> :128)
>>>>>> at
>>>>>> org.openmicroscopy.shoola.env.Container.access$000(Container.java:78)
>>>>>> at org.openmicroscopy.shoola.env.Container$1.run(Container.java:174)
>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>> Exception in thread "Initializer"
>>>>>>
>>>>>> Exception: java.awt.HeadlessException thrown from the
>>>>>> UncaughtExceptionHandler in thread "Initializer"
>>>>>>
>>>>>>
>>>>>> Maybe this error is related to the connection problems, or maybe this
>>>>>> is an extra problem...
>>>>>>
>>>>>> Thanks,
>>>>>> Unai
>>>>>> command
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> The University of Dundee is a registered Scottish Charity, No:
>>>>> SC015096
>>>>
>>>>
>>>>
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>
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>>
>>
>>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> Esta cabecera ha sido añadida automáticamente por la Vicegerencia de las TIC:
> --------------------------------------------------------------------------------
> ATENCION!! Este correo contiene la palabra "contraseña" y puede  
> tratarse de un fraude.
> No proporcione nunca sus credenciales por correo electrónico.
> Si tiene alguna duda consulte con el CAU (154400).
> UPV/EHU, Vicegerencia de las TIC
>
> ERNE!! Mezu honek "contraseña" hitza dauka eta iruzurrezko mezua  
> izan daiteke.
> Ez eman inoiz zure pasahitza posta elektronikoaren bidez.
> Zalantzarik izanez gero deitu BAZren telefonora (154400)
> UPV/EHU, IKT Gerenteordetza
> --------------------------------------------------------------------------------
> ·