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

Tue Oct 7 13:26:06 BST 2014

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
>>>
>>>
>>>
>>
>>
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>
>
>

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