Installing OpenREM¶
Install OpenREM 0.7.4¶
pip install openrem
Will need ``sudo`` or equivalent if installing on linux without using a virtualenv
Configuration¶
Locate install location¶
- Ubuntu linux:
/usr/local/lib/python2.7/dist-packages/openrem/
- Other linux:
/usr/lib/python2.7/site-packages/openrem/
- Linux virtualenv:
lib/python2.7/site-packages/openrem/
- Windows:
C:\Python27\Lib\site-packages\openrem\
- Windows virtualenv:
Lib\site-packages\openrem\
There are two files that need renaming:
openremproject/local_settings.py.example
toopenremproject/local_settings.py
openremproject/wsgi.py.example
toopenremproject/wsgi.py
Edit local_settings.py¶
Note
Windows notepad will not recognise the Unix style line endings. Please use an editor such as Notepad++ or Notepad2 if you can, else use WordPad – on the View tab you may wish to set the Word wrap to ‘No wrap’
Important
In local_settings.py, always use forward slashes and not backslashes, even for paths on Windows systems.
The directories in this local_settings.py file must already exist - OpenREM will not create them for you.
Database¶
Note
SQLite is great for getting things running quickly and testing if the setup works, but is not recommended for production use.
We recommend using PostgreSQL as it is the best supported database for Django, and the only one for which the median value will be calculated and displayed in OpenREM charts. Alternatively, other databases such as MySQL/MariaDB, Oracle, and some others with lower levels of support can be used.
There are some further guides to setting up PostgreSQL – see Databases
If you are using SQLite:
'ENGINE': 'django.db.backends.sqlite3',
'NAME': '/ENTER/PATH/WHERE/DB/FILE/CAN/GO',
- Linux example:
'NAME': '/home/user/openrem/openrem.db',
- Windows example:
'NAME': 'C:/Users/myusername/Documents/OpenREM/openrem.db',
If you are using PostgreSQL:
'ENGINE': 'django.db.backends.postgresql_psycopg2',
'NAME': 'openremdb',
'USER': 'openremuser',
'PASSWORD': 'openrem_pw',
Location for imports and exports¶
Csv and xlsx study information exports and patient size csv imports are
written to disk at a location defined by MEDIA_ROOT
.
The path set for MEDIA_ROOT
is up to you, but the user that runs the
webserver must have read/write access to the location specified because
it is the webserver than reads and writes the files. In a debian linux,
this is likely to be www-data for a production install. Remember to use
forward slashes for the config file, even for Windows.
Linux example:
MEDIA_ROOT = "/var/openrem/media/"
Windows example:
MEDIA_ROOT = "C:/Users/myusername/Documents/OpenREM/media/"
Secret key¶
Generate a new secret key and replace the one in the local_settings.py
file. You can use
http://www.miniwebtool.com/django-secret-key-generator/ for this.
Allowed hosts¶
The ALLOWED_HOSTS
needs to be defined, as the DEBUG
mode is now
set to False
. This needs to contain the server name or IP address that
will be used in the URL in the web browser. For example:
ALLOWED_HOSTS = [
'192.168.56.102',
'.doseserver.',
'localhost',
]
A dot before a hostname allows for subdomains (eg www.doseserver), a dot
after a hostname allows for FQDNs (eg doseserver.ad.trust.nhs.uk).
Alternatively, a single '*'
allows any host, but removes the security
the feature gives you.
Log file¶
There are two places logfiles need to be configured - here and when starting Celery. The logs defined here capture most of the information; the Celery logs just capture workers starting and tasks starting and finishing.
Configure the filename to determine where the logs are written. In linux, you might want to send them to a sub-folder of
/var/log/
. In this example, they are written to the MEDIA_ROOT
; change as appropriate:
import os
logfilename = os.path.join(MEDIA_ROOT, "openrem.log")
qrfilename = os.path.join(MEDIA_ROOT, "openrem_qr.log")
storefilename = os.path.join(MEDIA_ROOT, "openrem_store.log")
LOGGING['handlers']['file']['filename'] = logfilename # General logs
LOGGING['handlers']['qr_file']['filename'] = qrfilename # Query Retrieve SCU logs
LOGGING['handlers']['store_file']['filename'] = storefilename # Store SCP logs
If you want all the logs in one file, simply set them all to the same filename.
In the settings file, there are simple
and verbose
log message styles. We recommend you leave these as
verbose
:
LOGGING['handlers']['file']['formatter'] = 'verbose' # General logs
LOGGING['handlers']['qr_file']['formatter'] = 'verbose' # Query Retrieve SCU logs
LOGGING['handlers']['store_file']['formatter'] = 'verbose' # Store SCP logs
Finally you can set the logging level. Options are DEBUG
, INFO
, WARNING
, ERROR
, and CRITICAL
, with
progressively less logging.
LOGGING['loggers']['remapp']['level'] = 'INFO' # General logs
LOGGING['loggers']['remapp.netdicom.qrscu']['level'] = 'INFO' # Query Retrieve SCU logs
LOGGING['loggers']['remapp.netdicom.storescp']['level'] = 'INFO' # Store SCP logs
Create the database¶
In a shell/command window, move into the openrem folder:
- Ubuntu linux:
cd /usr/local/lib/python2.7/dist-packages/openrem/
- Other linux:
cd /usr/lib/python2.7/site-packages/openrem/
- Windows:
cd C:\Python27\Lib\site-packages\openrem\
- Virtualenv:
cd lib/python2.7/site-packages/openrem/
Create the database:
python manage.py makemigrations remapp
python manage.py migrate
python manage.py showmigrations
The last command will list each Django app migrations. Each should have a cross inside a pair of square brackets something like below:
admin
[X] 0001_initial
auth
[X] 0001_initial
[X] 0002_alter_permission_name_max_length
[X] 0003_alter_user_email_max_length
[X] 0004_alter_user_username_opts
[X] 0005_alter_user_last_login_null
[X] 0006_require_contenttypes_0002
contenttypes
[X] 0001_initial
[X] 0002_remove_content_type_name
remapp
[X] 0001_initial
sessions
[X] 0001_initial
sites
[X] 0001_initial
Finally, create a Django super user:
python manage.py createsuperuser
Answer each question as it is asked – this user is needed to set up the other users and the permissions.
Add the median database function: PostgreSQL databases only¶
Rename the file
remapp/migrations/0002_0_7_fresh_install_add_median.py.inactive
to
remapp/migrations/0002_0_7_fresh_install_add_median.py
and then run
python manage.py makemigrations --empty remapp
python manage.py migrate
The first command will create a skeleton 0001_initial.py
migration file. The
second command runs the migration files, and will display the text
Applying remapp.0002_0_7_fresh_install_add_median... OK
, indicating that the median function has been added.
Start all the services!¶
You are now ready to start the services to allow you to use OpenREM - go to Start all the services to see how!
Further instructions¶
Production webservers¶
Unlike the database, the production webserver can be left till later and can be changed again at any time.
For performance it is recommended that a production webserver is used instead of the inbuilt ‘runserver’. Popular choices would be either Apache or you can do as the cool kids do and use Gunicorn with nginx.
The django website has instructions and links to get you set up with Apache.
An advanced guide using Apache, including auto-restarting the server when the code changes, has been contributed here: Installing Apache on Windows Server 2012 with auto-restart
DICOM Store and query-retrieve¶
The best (and only practical way in a production environment) to get DICOM data into OpenREM is to have a DICOM store node (Store Service Class Provider/SCP) and possibly a query-retrieve service class user too.
To find out more about this, refer to the DICOM Store and QR docs.