Installing OntoWiki on Ubuntu 14.04 (using Docker)

[Maxim Kolchin]

Hi everyone,

I'm trying to install OntoWiki on Ubuntu 14.04 using Docker, but without success, it fails with the following error:

Setting up ontowiki-virtuoso (0.9.11-2) ...
---- starting postinst configure
ln: failed to create symbolic link '/etc/apache2/conf.d/ontowiki': No such file or directory
dpkg: error processing ontowiki-virtuoso (--configure):
 subprocess installed post-installation script returned error exit status 1

My Dockerfile is:
FROM ubuntu

ENV http_proxy http://proxy.ifmo.ru:3128
ENV DEBIAN_FRONTEND noninteractive

RUN echo "#!/bin/sh\nexit 0" > /usr/sbin/policy-rc.d && chmod 777 /usr/sbin/policy-rc.d
RUN apt-get install -y wget
RUN wget http://stack.lod2.eu/lod2repository_current_all.deb
RUN dpkg --no-debsig -i lod2repository_current_all.deb
RUN apt-get update
RUN apt-get install -y --force-yes ontowiki-virtuoso virtuoso-vad-conductor

Is 14.04 supported? Which version of Ubuntu is recommended?

P.S. I've tried to install OntoWiki on all version (12.04, 12.10, 13.04, 13.10 and 14.04) but with any success :(

Thank you in advance!
Max

[Natanael Arndt]

Hello Maxim,
basically the ubuntu version should not matter for running OntoWiki. I think in your case the problem might, be that no apache is installed or it keeps its configuration in a different place.

I don't know anything about docker but the line

RUN apt-get install -y --force-yes ontowiki-virtuoso virtuoso-vad-conductor

basically seams to be an ordinary apt-get command. So I recommand to not use force, but rather allow it to pull all necessary dependencies.

Did you create this docker file or was it provided by somebody? I think if it is in a condition, where it works we could add it to the OntoWiki git repo [1] so it might help others as well, if this is ok for you.

[1] https://github.com/AKSW/OntoWiki

All the best
Natanael

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[Maxim Kolchin]

Hi Natanael,

The log says that apache is being installed and successfully restarted, so the problem is in incorrect configuration path:

ln: failed to create symbolic link '/etc/apache2/conf.d/ontowiki': No such file or directory

I can't interact with the console during installation, so I have to use -y and --force-yes. Without --force-yes I get:
After this operation, 187 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
  liberfurt-php libjs-rdfauthor ontowiki-common ontowiki-virtuoso
E: There are problems and -y was used without --force-yes
2014/04/28 15:52:13 The command [/bin/sh -c apt-get install -y ontowiki-virtuoso virtuoso-vad-conductor] returned a non-zero code: 100

Yes this is mine Dockerfile, feel free to publish it, but it doesn't work actually, therefore I need help :)

Thanks,
Max

[Maxim Kolchin]

Maybe this is the reason I have to use --force-yes flag:

W: GPG error: http://stack.lod2.eu lod2/ Release: The following signatures were invalid: BADSIG 500905B62DFE00E3 Sebastian Tramp <tramp at informatik.uni-leipzig.de>

Max

[Maxim Kolchin]

So looks like I can't install OntoWiki on my "real" Ubuntu 13.10 too, because of the same reason:

Setting up ontowiki-virtuoso (0.9.11-2) ...
---- starting postinst configure
ln: failed to create symbolic link ‘/etc/apache2/conf.d/ontowiki’: No such file or directory
dpkg: error processing ontowiki-virtuoso (--configure):
 subprocess installed post-installation script returned error exit status 1

And I think this is the answer: http://askubuntu.com/questions/362682/ubuntu-13-10-server-403-error-after-upgrading-to-apache2-4
There is no /etc/apache2/conf.d in Ubuntu 13 at all.

The list of packages that are installed:
Reading package lists... Done
Building dependency tree      
Reading state information... Done
The following extra packages will be installed:
  apache2 apache2-bin apache2-data fontconfig-config fonts-dejavu-core ghostscript gsfonts imagemagick-common libapache2-mod-php5 libapr1 libaprutil1
  libaprutil1-dbd-sqlite3 libaprutil1-ldap libavahi-client3 libavahi-common-data libavahi-common3 libcups2 libcupsfilters1 libcupsimage2 liberfurt-php
  libfftw3-double3 libfontconfig1 libgomp1 libgs9 libgs9-common libijs-0.35 libjasper1 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-rdfauthor
  liblcms2-2 liblqr-1-0 libmagickcore5 libmagickwand5 libmarkdown-php libpaper-utils libpaper1 libphp-pclzip libtiff5 libvirtodbc0
  libzend-framework-php odbcinst odbcinst1debian2 ontowiki-common php5 php5-cli php5-common php5-curl php5-odbc php5-readline poppler-data ssl-cert
  tinymce ttf-dejavu-core virtuoso-opensource virtuoso-opensource-6.1 virtuoso-opensource-6.1-bin virtuoso-opensource-6.1-common virtuoso-server
  virtuoso-vsp-startpage zend-framework zend-framework-bin
Suggested packages:
  apache2-doc apache2-suexec-pristine apache2-suexec-custom apache2-utils ghostscript-x hpijs php-pear cups-common libfftw3-bin libfftw3-dev
  fonts-droid libjasper-runtime liblcms2-utils libmagickcore5-extra libjs-dojo-core libjs-dojo-dijit libjs-dojo-dojox owcli php5-json php5-user-cache
  poppler-utils fonts-japanese-mincho fonts-ipafont-mincho fonts-japanese-gothic fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming
  fonts-unfonts-core openssl-blacklist virtuoso-vad-doc virtuoso-vad-demo virtuoso-vad-tutorial virtuoso-vad-rdfmappers virtuoso-vad-sparqldemo
  virtuoso-vad-syncml virtuoso-vad-bpel virtuoso-vad-isparql virtuoso-vad-ods virtuoso-vad-dbpedia virtuoso-vad-facetedbrowser
The following NEW packages will be installed:
  apache2 apache2-bin apache2-data fontconfig-config fonts-dejavu-core ghostscript gsfonts imagemagick-common libapache2-mod-php5 libapr1 libaprutil1
  libaprutil1-dbd-sqlite3 libaprutil1-ldap libavahi-client3 libavahi-common-data libavahi-common3 libcups2 libcupsfilters1 libcupsimage2 liberfurt-php
  libfftw3-double3 libfontconfig1 libgomp1 libgs9 libgs9-common libijs-0.35 libjasper1 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-rdfauthor
  liblcms2-2 liblqr-1-0 libmagickcore5 libmagickwand5 libmarkdown-php libpaper-utils libpaper1 libphp-pclzip libtiff5 libvirtodbc0
  libzend-framework-php odbcinst odbcinst1debian2 ontowiki-common ontowiki-virtuoso php5 php5-cli php5-common php5-curl php5-odbc php5-readline
  poppler-data ssl-cert tinymce ttf-dejavu-core virtuoso-opensource virtuoso-opensource-6.1 virtuoso-opensource-6.1-bin virtuoso-opensource-6.1-common
  virtuoso-server virtuoso-vad-conductor virtuoso-vsp-startpage zend-framework zend-framework-bin
0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded.
Need to get 35.3 MB/43.6 MB of archives.
After this operation, 158 MB of additional disk space will be used.
Do you want to continue [Y/n]? Y

WARNING: The following packages cannot be authenticated!
  liberfurt-php libjs-rdfauthor ontowiki-common ontowiki-virtuoso

Install these packages without verification [y/N]? y

Thanks in advance!
Max

[Sebastian Tramp]

On Mon, Apr 28, 2014 at 04:56:58AM -0700, Maxim Kolchin wrote:
> Hi Natanael,
>
> The log says that apache is being installed and successfully restarted, so
> the problem is in incorrect configuration path:
> ln: failed to create symbolic link '/etc/apache2/conf.d/ontowiki': No such
> file or directory

Maxim, this package issue is already fixed in the latest version.
This version is not in the stable lod2 stack but in the testing lod2 stack.

Please try

RUN wget http://stack.lod2.eu/lod2testing-repository.deb
instead of
RUN wget http://stack.lod2.eu/lod2repository_current_all.deb

I will try this tomorrow myself ...

Best regards

Sebastian Tramp

> > email to ontowiki-use...@googlegroups.com <javascript:>.

> > For more options, visit https://groups.google.com/d/optout.
> >
> >
> >
>

--
WebID: http://aksw.org/SebastianTramp

[Maxim Kolchin]

I just tried the testing repository, but now ontowiki-virtuoso package can not be found, on the real OS and on Docker.

Thanks,
Max

[Maxim Kolchin]

Sorry, it was my fault with missing ontowiki-virtuoso.

But, now I get a dependency problem:
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 ontowiki-virtuoso : Depends: lod2-virtuoso-opensource but it is not going to be installed or
                              virtuoso-opensource-6.1 (>= 6.1.4) but it is not going to be installed
 virtuoso-vad-conductor : Depends: virtuoso-opensource but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

Max

[Natanael Arndt]

virtuoso-opensource-6.1 should be included in the standard ubuntu repository. You might try to explicitly install it

RUN apt-get install -y --force-yes ontowiki-virtuoso virtuoso-vad-conductor virtuoso-opensource-6.1

But seebi did those dependencies, maybe he can tell more.

Natanael

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[Maxim Kolchin]

I tried this already with 6.1 and 7.0 and without success :( The error:

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:

 virtuoso-opensource-6.1 : Depends: libvirtodbc0 (= 6.1.6+dfsg1-0ubuntu1) but 7.0.1 is to be installed
                           Depends: libmagickwand4 (>= 8:6.6.9.7) but it is not installable

 virtuoso-vad-conductor : Depends: virtuoso-opensource but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

Probably, the .deb's dependencies need to be fixed.

Max

[Natanael Arndt]

Are you able to just install virtuoso-opensource-6.1 on a plain ubuntu system, without lod2 repo?

Maybe the virtuoso-packages in the lod2 repo interfere here.

Natanael

[Maxim Kolchin]

Yes, I am. But when I try to install virtuoso-opensource-6.1 before
installing lod2testing-repository.deb, the installation fails because
virtuoso-vad-conductor requires virtuoso-opensource (without -6.1).
Therefore I tried to repeat the steps, but with virtuoso-opensource
and again got the problem with the incorrect path:

Setting up ontowiki-virtuoso (0.9.11-2) ...
---- starting postinst configure
ln: failed to create symbolic link '/etc/apache2/conf.d/ontowiki': No
such file or directory

dpkg: error processing package ontowiki-virtuoso (--configure):

subprocess installed post-installation script returned error exit status 1

BTW Does anyone else face similar problems? Or most of the users
install OntoWiki from the repo?

Maxim

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[Natanael Arndt]

Ok, so if I get you right, it works to install virtuoso-opensource and
virtuoso-vad-conductor on a plain ubuntu without any complications.
Installing lod2testing-repository.deb works fine as well.
The complications start as soon, as you want to install
ontowiki-virtuoso (from the lod2testing repo).

Did you install apache or nginx before installing ontowiki-virtuoso?
Because as I see ontowiki-virtuoso doesn't depend on any webserver even
though it should:

Depends: ontowiki-common (>= 0.9.11), lod2-virtuoso-opensource |
virtuoso-opensource-6.1 (>= 6.1.4), php5-odbc

@seebi is this correct? Is there any reason for it?

Anyways I will try to reproduce those steps in a virtual machine with
trusty.

[Maxim Kolchin]

Natanael,

Right.

I install OntoWiki on a minimal Ubuntu 14.04 image, so there is no
Apache2 yet and I see that something requires apache2:

Step 8 : RUN apt-get install -y --force-yes ontowiki-virtuoso
virtuoso-vad-conductor
---> Running in 95b092dd4e05
Reading package lists...
Building dependency tree...
Reading state information...

The following extra packages will be installed:

apache2 apache2-bin apache2-data libapache2-mod-php5 libapr1 libaprutil1
libaprutil1-dbd-sqlite3 libaprutil1-ldap libcurl3 libedit2 liberfurt-php
libjs-jquery libjs-rdfauthor libmarkdown-php libodbc1 libphp-pclzip librtmp0
libzend-framework-php lsof ontowiki-common php5 php5-cli php5-common
php5-curl php5-json php5-odbc php5-readline psmisc ssl-cert tinymce
zend-framework zend-framework-bin

Thank you!
Maxim

[Natanael Arndt]

Ok, I see. The directory “/etc/apache2/conf.d/” (as it was in raring
[1]) has moved to “/etc/apache2/conf-available/” (saucy [2]).

Maybe @seebi can fix that in the package, that it detects, which is the
correct directory.

For now, you could try a quick fix, which you have to run before the
ontowiki installation:

1. mkdir /etc/apache2
2. cd /etc/apache2
3. ln -s conf-enabled conf.d

I think the virtuoso dependencies in lod2 repo have to be fixed as well.
So make sure to install things in the following order:

0. Quick fix
1. virtuoso-opensource
2. lod2testing-repository.deb
3. ontowiki-virtuoso

This procedure worked for me on a plain ubuntu trusty (14.04 LTS).

@seebi, who is responsible for the virtuoso packages?

[1] http://packages.ubuntu.com/raring/amd64/apache2.2-common/filelist
[2] http://packages.ubuntu.com/saucy/amd64/apache2/filelist

All the best
Natanael

[Natanael Arndt]

Make sure after the quick fix, that “ls -l” shows “conf.d ->
conf-enabled” (should be in red, if color is enabled)

Natanael

[Maxim Kolchin]

So I should install apache2 before the quick fix, because there is no
conf-enabled dir in advance, right?

Max

[Natanael Arndt]

I think you can install it before, but you don't have to. The link
should just show to nothing and will become valid as soon, as the apache
installation creates the directory “conf-enabled”.

Natanael

[Maxim Kolchin]

Okay, now it seems that everything is installed successfully and I
started apache2 manually. What should I start to see OntoWiki working
(right now I see only apache on /)?

The steps are:

RUN echo "#!/bin/sh\nexit 0" > /usr/sbin/policy-rc.d && chmod 777
/usr/sbin/policy-rc.d

RUN apt-get install -y apache2

RUN cd /etc/apache2 && ln -s conf-enabled conf.d
RUN ls -al /etc/apache2

RUN apt-get install -y --force-yes wget virtuoso-opensource

RUN wget http://stack.lod2.eu/lod2testing-repository.deb
RUN dpkg -i lod2testing-repository.deb

RUN apt-get update

RUN apt-get install -y --force-yes ontowiki-virtuoso virtuoso-vad-conductor

Thank you!
Maxim

[Natanael Arndt]

I think after the installation from the debian package ontowiki is
available at /ontowiki . But you can also take a look in
/etc/apache2/conf./ontowiki (resp. /etc/apache2/conf-enabled/ontowiki)

Natanael

[Maxim Kolchin]

Finally I am able to install everything successfully (there was a
problem with virtuoso-opensource, because of --force-yes flag used and
the password during installation weren't provided the daemon was
disabled). Now I can open the Virtuoso Conductor UI on :8890 port.

But I get "404 Not Found" on /ontowiki path (apache2 is running and
I'm able to open / path). Can it be related to the quick fix?

root@0aad63a115f6:/# ls -al /etc/apache2/
total 80
drwxr-xr-x 11 root root 4096 Apr 29 18:23 .
drwxr-xr-x 112 root root 4096 Apr 29 18:21 ..
-rw-r--r-- 1 root root 7115 Apr 29 18:22 apache2.conf
drwxr-xr-x 2 root root 4096 Apr 29 18:09 conf-available
drwxr-xr-x 2 root root 4096 Apr 29 18:10 conf-enabled
lrwxrwxrwx 1 root root 12 Apr 29 18:09 conf.d -> conf-enabled
-rw-r--r-- 1 root root 1782 Jan 3 14:48 envvars
-rw-r--r-- 1 root root 31063 Jan 3 14:48 magic
drwxr-xr-x 2 root root 4096 Apr 29 18:10 mods-available
drwxr-xr-x 2 root root 4096 Apr 29 18:10 mods-enabled
-rw-r--r-- 1 root root 320 Jan 7 13:23 ports.conf
drwxr-xr-x 2 root root 4096 Apr 29 18:09 sites-available
drwxr-xr-x 2 root root 4096 Apr 29 18:09 sites-enabled

root@0aad63a115f6:/# cat /etc/apache2/conf.d/ontowiki
# OntoWiki Apache Configuration
<Directory /usr/share/ontowiki>
# needed for following the config.ini
Options +FollowSymLinks

# Give all right the the htaccess
AllowOverride All
</Directory>

Alias /ontowiki /usr/share/ontowiki


Thank you!
Maxim

[Natanael Arndt]

Hello Maxim,
sorry for not getting back to you. Did you solve the problem in the
meantime? I think this could be something with mod_rewrite, did you
install it?

I'm also going to build a docker image for OntoWiki but I think I will
take the current git develop branch. So maybe this will help you.

Natanael

[Maxim Kolchin]

Hi Natanael,

No, I've not solved the problem, actually I didn't have time to work on this, sorry.

I checked whether mode_rewrite is installed, so yes, it's:
root@d75ef35fb859:/# a2enmod rewrite
Module rewrite already enabled

What about you? Have you had a chance to prepare a working Docker image or Dockerfile?

Thanks,
Max

[Natanael Arndt]

Hi Max,
yes we managed to get a working Dockerfile, but we use nginx instead of Apache.

You can find the docker image/file on the hub:
https://registry.hub.docker.com/u/aksw/ontowiki-ubuntu-nginx/

Pleas tell us, if it works for you as well.

I think it is not cool to have virtuoso, nginx and php with ontowiki in one image I think we have to separate this at one point. And backup is an open issue.

All the best
Natanael

[Maxim Kolchin]

Awesome! It works for me! :)

Thank you!
Max

...

[Lucas de Oliveira Teixeira]

Hi,

I'm trying to create a dockerfile to create a image of OntoWiki and CubeViz.

So far I've added the following line to the dockerfile above:

RUN git clone https://github.com/AKSW/cubeviz.ontowiki.git /var/www/extensions/cubeviz

RUN cd /var/www/extensions/cubeviz/ && git checkout master

RUN cd /var/www/extensions/cubeviz/ && make install

Everything install fine.

But in the execution I keep getting SPARQL errors, like: Undefined namespace prefix at 'qb'

Have i missed something?

Thanks in advance.

>>>>>&g

...