[indivohealth] Indivo installation guides

[Maria Evangelia Chatzimina]

Hello,

I have created two installation guides for Indivo Health System, one for Ubuntu 11.10 and one for Ubuntu 14.04. I have tested them multiple times but if there is any problem maybe I can help.

Best regards,

Maria

--

Computational Medicine Laboratory (CML)
Institute of Computer Science (ICS) 
Foundation for Research and Technology - Hellas (FORTH)
N. Plastira 100 Vassilika Vouton, GR-700 13 Heraklion, Crete, Greece

Email: hatz...@ics.forth.gr

[Монгол Вьетнам]

Hello, thank you for your installation guide. But i have a problem when authenticate to Postgesql. It's installed correctly then i can.t find the line local all all ident in  /etc/postgresql/8.4/main/pg_hba.conf, mine is like local all all peer. is it OK? and also have problem when installing MySQL. after i change default storage to INNODB mysql can.t be restarted. BTW i couldn.t find [mysqld] from /etc/mysql/my.cnf, i found it from /etc/mysql/mysqld.../mysqld.cnf and replace that code in docs. (i.m working with ubuntu 15.04) Maybe i replaced the code in wrong place. Can you help me pls thank you in advance

[Maria Evangelia Chatzimina]

Hello,

Ok so for " i can.t find the line local all all ident in  /etc/postgresql/8.4/main/pg_hba.conf, mine is like local all all peer "  

Just change this line to all all md5. Your file should be like this: 

# Database administrative login by Unix domain socket

local   all             postgres                                peer

# TYPE  DATABASE        USER            ADDRESS                 METHOD

# "local" is for Unix domain socket connections only

local   all             all                                     md5

# IPv4 local connections:

host    all             all             0.0.0.0/0            md5

#host    all             all             127.0.0.1/32            md5

# IPv6 local connections:

host    all             all             ::1/128                 md5

0.0.0.0/0  is for every IP to access your postgresql database outside of the server. You can change it to something else if you want. There is another example in comments above as you can see that is about accessing postgreSQL only from localhost (127.0.0.1).

About MySQL I don't use it but I will try to help you.

Look for my.cnf in these paths: 

• /etc/my.cnf
• /etc/mysql/my.cnf
• $MYSQL_HOME/my.cnf
• [datadir]/my.cnf
• ~/.my.cnf

You can use this command in MySQL to see in which paths MySQL searches for the file 

$ mysqld --help --verbose

I don't know if mysqld.cnf is the same, so maybe this is why you can't restart mysql. [mysqld] is around line 31 in ubuntu 14.04 I don't think it will be different in ubuntu 15.04.  If it is not there maybe you can add it and test if MySQL restarts 

So write in the file 

[mysqld]

default-storage-engine = innodb

default-character-set = utf8

and restart the server

If you still have problem send me responses of the system or errors from log files and maybe I can help you. Also If you install postgreSQL you don't need also mysql for Indivo. 

Best regards,

Maria

[Монгол Вьетнам]

Really thank you for your great advice. So you mean not need mysql right? (of course, i already install postgres).  Then should i need oracle? 

Thank you very much

[Монгол Вьетнам]

And one more question. After configure setup in Indivo server succesfully, i can.t reset my database. when i run command "python utils/reset.py" it failed and display no module named codingsystems.data. Do you know about it? 

Thank you

Best regards

[Sudhakaran Packianathan]

Kindly copy these packages to the codingsystems folder https://github.com/chb/indivo_codingsystems

Regards,

Sudhakaran

[Монгол Вьетнам]

Great appreciation for your advice

Regards 

Nomin

[Sudhakaran Packianathan]

Welcome Nomin. Let me know of you face any more issues in set up and I would be glad to help.

Sudhakaran

[Maria Evangelia Chatzimina]

No you don't need oracle! They are three different databases for us to choose. If you still have issues with coding systems maybe I can help you.

Best regards,

Maria

[Монгол Вьетнам]

Thank you, Now i got basic ideas about indivo database. And i faced one more problem. When i test indivo it displays the error like below:

nomin@nomin-VirtualBox:~/Downloads/indivo_server$ sudo python manage.py test indivo
Creating test database for alias 'default'...
..............................................................................................................
==========================
RUNNING INTEGRATION TESTS:
==========================

=============================================================================
Report:
.......... pass : Document Handling Test
.......... pass : Sharing
.......... pass : PHA Document Handling
.......... pass : PHAing record_app delete
.......... pass : PHAing app delete
.......... pass : AppSpecific
.......... pass : Document Metadata Test
.......... pass : OAuthing
.......... pass : Binary Document Test
.......... pass : Accounting
.......... pass : Record Shares
.......... pass : Messaging
.......... pass : Special Document Handling
.......... pass : Auditing
.......... pass : Document Processing Test
.......... pass : Security
=============================================================================
......................................................................................................................E.........................................
======================================================================
ERROR: test_get_smart_ontology (indivo.tests.api.smart_tests.SMARTInternalTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/nomin/Downloads/indivo_server/indivo/tests/api/smart_tests.py", line 11, in test_get_smart_ontology
    response = self.client.get('/ontology')
  File "/usr/local/lib/python2.7/dist-packages/django/test/client.py", line 439, in get
    response = super(Client, self).get(path, data=data, **extra)
  File "/usr/local/lib/python2.7/dist-packages/django/test/client.py", line 241, in get
    return self.request(**r)
  File "/usr/local/lib/python2.7/dist-packages/django/core/handlers/base.py", line 111, in get_response
    response = callback(request, *callback_args, **callback_kwargs)
  File "/home/nomin/Downloads/indivo_server/indivo/lib/utils.py", line 38, in __call__
    return view_func(request, *args, **kwargs)
  File "/home/nomin/Downloads/indivo_server/indivo/views/smart_container.py", line 19, in smart_ontology
    ontology = urllib2.urlopen(url).read()
  File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/lib/python2.7/urllib2.py", line 431, in open
    response = self._open(req, data)
  File "/usr/lib/python2.7/urllib2.py", line 449, in _open
    '_open', req)
  File "/usr/lib/python2.7/urllib2.py", line 409, in _call_chain
    result = func(*args)
  File "/usr/lib/python2.7/urllib2.py", line 1227, in http_open
    return self.do_open(httplib.HTTPConnection, req)
  File "/usr/lib/python2.7/urllib2.py", line 1197, in do_open
    raise URLError(err)
URLError: <urlopen error [Errno -2] Name or service not known>

----------------------------------------------------------------------
Ran 270 tests in 306.346s

FAILED (errors=1)
Destroying test database for alias 'default'...

How to solve this error?

Thank you
Best regards
Nomin

[Монгол Вьетнам]

And i.m really new in indivo, apache, postgresql. Have one more question is where i test the user jsmith. I try to localhost but it displays Forbidden 403, You don.t have any permission to access. What is the cause of this error. Is it because of Apache or Indivo?

Thanks again

Best Regards 

Nomin

[Sudhakaran Packianathan]

Did you try with the correct password. This is an authenticaion issue. you should use password.example as the password for jsmith

[Sudhakaran Packianathan]

The test related to smart as failing as the smart server url which is reference in the sample apps is down. Smart apps now use a newer architecture.

You can ignore this test failure. You can run indivo without this test passing

[Монгол Вьетнам]

Hello Sudhakaran Packianathan

Actually i just type localhost from firefox, it doesn,t require me neither any password nor any username. Truth is i still don't know where i type those jsimth username and it's password. i mean don't know how to run indivo

Thanks

Best Regards

Nomin

[Maria Evangelia Chatzimina]

Hello! 

Ok I don't know the solution of the problem but check some things first:

go to your web folder and check your permissions or write

chown -R www-data:www-data web/

Also have you checked if your apache is working? if it is not working try to start indivo by running in two different terminals. Or stop apache and run it based on below  commands to see if everything is working fine and then you set up Apache.

/etc/init.d/apache2 stop

cd /web/indivo_server/

python manage.py runserver 8000

and 

cd /web/indivo_ui_server

python manage.py runserver 127.0.0.1:80

Also check this files to see if you have localhost or 127.0.0.1 for IP

web/indivo_server/settings.py

web/indivo_ui_server/settings.py

Try again localhost from browser. You should see a login form where you put your credentials of john smith. 

[Danielle Emmons]

I would like to be taken off this mailing list please

[Монгол Вьетнам]

Hello, is it still working if i installed apache2.4.10. Cuz in the instructor it is apache2.2

Thank you

Best Regards 

Nomin

[Maria Evangelia Chatzimina]

I tried to make it work with apache 2.4.10 but it is not working. So I have instructions for apache 2.2 . Maybe you can try in 2.4.10 but I don't know if it will work

Maria

[Монгол Вьетнам]

OMG guys i did it.i installed it. Thank you for your great advices. How happy i am :))))). BTW my problem with install is django old version. i upgraded it from 1.3.1 to 1.4.5 and problem solved. 

Huge thanks for you guys

Best Regards

Happy Nomin

[Maria Evangelia Chatzimina]

Well done! :)

[Matthias Rother]

hi Maria,

i followed your guide but my installation doesn't complete at all with ubuntu 14.04.5 Server Edtion (i tryed third times).

When i start the server the webserver says:

fapra@fapraVM:/web/indivo_server$ sudo python manage.py runserver indivo.fapra.edu:8000

Validating models...

0 errors found

Django version 1.3.1, using settings 'indivo_server.settings'

Development server is running at http://indivo.fapra.edu:8000/

Quit the server with CONTROL-C.

[14/May/2017 09:27:20] "GET / HTTP/1.1" 404 205

When i start the server ui another problem occours:

fapra@fapraVM:/web/indivo_ui_server$ sudo python manage.py runserver indivo.fapra.edu:80

Validating models...

0 errors found

Django version 1.3.1, using settings 'ui.settings'

Development server is running at http://indivo.fapra.edu:80/

Quit the server with CONTROL-C.

Traceback (most recent call last):

  File "/usr/local/lib/python2.7/dist-packages/django/core/servers/basehttp.py", line 283, in run

    self.result = application(self.environ, self.start_response)

  File "/usr/local/lib/python2.7/dist-packages/django/contrib/staticfiles/handlers.py", line 68, in __call__

    return self.application(environ, start_response)

  File "/usr/local/lib/python2.7/dist-packages/django/core/handlers/wsgi.py", line 250, in __call__

    self.load_middleware()

  File "/usr/local/lib/python2.7/dist-packages/django/core/handlers/base.py", line 47, in load_middleware

    raise exceptions.ImproperlyConfigured('Error importing middleware %s: "%s"' % (mw_module, e))

ImproperlyConfigured: Error importing middleware django.middleware.clickjacking: "No module named clickjacking"

[14/May/2017 09:33:50] "GET / HTTP/1.1" 500 808

Traceback (most recent call last):

  File "/usr/local/lib/python2.7/dist-packages/django/core/servers/basehttp.py", line 283, in run

    self.result = application(self.environ, self.start_response)

  File "/usr/local/lib/python2.7/dist-packages/django/contrib/staticfiles/handlers.py", line 68, in __call__

    return self.application(environ, start_response)

  File "/usr/local/lib/python2.7/dist-packages/django/core/handlers/wsgi.py", line 250, in __call__

    self.load_middleware()

  File "/usr/local/lib/python2.7/dist-packages/django/core/handlers/base.py", line 47, in load_middleware

    raise exceptions.ImproperlyConfigured('Error importing middleware %s: "%s"' % (mw_module, e))

ImproperlyConfigured: Error importing middleware django.middleware.clickjacking: "No module named clickjacking"

Traceback (most recent call last):

  File "/usr/local/lib/python2.7/dist-packages/django/core/servers/basehttp.py", line 283, in run

    self.result = application(self.environ, self.start_response)

  File "/usr/local/lib/python2.7/dist-packages/django/contrib/staticfiles/handlers.py", line 68, in __call__

    return self.application(environ, start_response)

  File "/usr/local/lib/python2.7/dist-packages/django/core/handlers/wsgi.py", line 250, in __call__

    self.load_middleware()

  File "/usr/local/lib/python2.7/dist-packages/django/core/handlers/base.py", line 47, in load_middleware

    raise exceptions.ImproperlyConfigured('Error importing middleware %s: "%s"' % (mw_module, e))

ImproperlyConfigured: Error importing middleware django.middleware.clickjacking: "No module named clickjacking"

My Settings are the following:

Hosts:

# The following lines are desirable for IPv6 capable hosts

::1     localhost ip6-localhost ip6-loopback

ff02::1 ip6-allnodes

ff02::2 ip6-allrouters

127.0.0.1 localhost

192.168.114.10 indivo.fapra.edu fapravm

Apache Cfg:

<VirtualHost *:8000>

        ServerAdmin admin@localhost

                ServerName indivo.fapra.edu

        ErrorLog ${APACHE_LOG_DIR}/error-8000.log

        CustomLog ${APACHE_LOG_DIR}/access-8000.log combined

        DocumentRoot /web/indivo_server

        Alias /static/ /web/indivo_server/static/

        EnableMMAP On

        EnableSendfile On

        LogLevel warn

        <Directory /web/indivo_server>

                Order deny,allow

                Allow from all

        </Directory>

        WSGIApplicationGroup %{GLOBAL}

        WSGIScriptAlias / /web/indivo_server/django.wsgi

        WSGIPassAuthorization On

</VirtualHost>

<VirtualHost *:80>

        ServerAdmin admin@localhost

                ServerName indivo.fapra.edu

                ErrorLog ${APACHE_LOG_DIR}/error-80.log

        CustomLog ${APACHE_LOG_DIR}/access-80.log combined

        DocumentRoot /web/indivo_ui_server

        Alias /static/ /web/indivo_ui_server/ui/static/

        EnableMMAP On

        EnableSendfile On

        LogLevel warn

        <Directory /web/indivo_ui_server>

         Order deny,allow

         Allow from all

        </Directory>

        WSGIDaemonProcess indivo_ui user=www-data group=www-data processes=1 maximum-requests=500 threads=10

        WSGIScriptAlias / /web/indivo_ui_server/django.wsgi

        WSGIPassAuthorization On

</VirtualHost>

Thats my little installtion Guide :)

<VirtualHost *:80>

        ServerAdmin ad...@indivo.fapra.edu

                ServerName indivo.fapra.edu

                ErrorLog ${APACHE_LOG_DIR}/error-80.log

        CustomLog ${APACHE_LOG_DIR}/access-80.log combined

        DocumentRoot /web/indivo_ui_server

        Alias /static/ /web/indivo_ui_server/ui/static/

        EnableMMAP On

        EnableSendfile On

        LogLevel warn

        <Directory /web/indivo_ui_server>

         Order deny,allow

         Allow from all

        </Directory>

        WSGIDaemonProcess indivo_ui user=www-data group=www-data processes=1 maximum-requests=500 threads=10

        WSGIScriptAlias / /web/indivo_ui_server/django.wsgi

        WSGIPassAuthorization On

</VirtualHost>

Could You please help my. I Stuck here 

greetings

[Maria Evangelia Chatzimina]

Hello Matthias,

I haven't seen "No module name clickjacking" error again. Can you check again you files web/indivo_server/settings.py  and web/indivo_ui_server/settings.py. I think there is something wrong with the middleware you are importing. For example in web/indivo_ui_server/my settings.py I don't have clickjacking. I have this:

MIDDLEWARE_CLASSES = (

    'django.middleware.common.CommonMiddleware',

    'django.contrib.sessions.middleware.SessionMiddleware',

    'django.contrib.auth.middleware.AuthenticationMiddleware',

     'django.middleware.locale.LocaleMiddleware', 

)

Check also if you have forgotter any "," in your middleware.

Also about the path you have added in your apache. You have added /web/indivo_server/...  is this the correct path? You have to add the complete path. For example for me is /home/maria/web/indivo_server 

Best regards, 

Maria

--

Computational BioMedicine Laboratory (CBML)

Institute of Computer Science (ICS) 
Foundation for Research and Technology - Hellas (FORTH)
N. Plastira 100 Vassilika Vouton, GR-700 13 Heraklion, Crete, Greece

Email: hatz...@ics.forth.gr

[Matthias Rother]

Thank you...this change gererate other problems  :)

is it possible that your share a pre configured vm ?

Am Dienstag, 4. August 2015 16:01:00 UTC+2 schrieb Maria Evangelia Chatzimina: