Upgrade to OpenREM 0.9.1

Headline changes

  • Imports: fixed imports for GE surgical flat panel c-arm with irregular value types and value meanings
  • Interface: added feature to filter by specific number of exposure types – CT only
  • Query-retrieve: new option to get SR series when PACS returns empty series level response
  • Query-retrieve: handle illegal missing instance number in image level response
  • Query-retrieve: improved logging
  • Exports: added export to UK PHE 2019 CT survey format
  • General documentation and interface improvements, bug fixes, and changes to prepare for Python 3

Upgrade preparation

Version 0.9 of OpenREM has a minimum Python version of 2.7.9 (still needs to be 2.7 not 3) and a minimum version of setuptools. If your installation was originally for OpenREM 0.6 in 2014 or earlier, these may now be too old and need updating.

To check the Python version, activate the virtualenv if you are using one, then:

python -V

If the version is earlier than 2.7.9, then an upgrade is needed.

Ubuntu Linux

  • Check which version of Ubuntu is installed (lsb_release -a)
  • If it is 14.04 LTS (Trusty), then an operating system upgrade or migration to a new server is required. If migrating, ensure the version of OpenREM installed on the new server is the same as the one on the old server, then Restore the database following the instructions and when up and running again perform the upgrade on the new server
  • 16.04 LTS (Xenial) or later should have 2.7.11 or later available.
  • For other Linux distributions check in their archives for which versions are available.

Windows

  • A newer version of Python 2.7 can be downloaded from python.org and installed over the current version.

Linux and Windows

  • With a version of Python 2.7.9 or later, setuptools can be updated (activate virtualenv if using one):

    pip install setuptools -U

Upgrading an OpenREM server with no internet access

Follow the instructions found at Upgrade an offline OpenREM installation, before returning here to update the configuration, migrate the database and complete the upgrade.

Upgrading from version 0.7.1 or earlier

Follow the instructions to OpenREM Release Notes version 0.7.3 first, then return to these instructions to upgrade to 0.9.1.

Upgrading from version 0.7.3 or later

Upgrade

  • Back up your database

  • Stop any Celery workers

  • Consider temporarily disabling your DICOM Store SCP, or redirecting the data to be processed later

  • If you are using a virtualenv, activate it

  • Install specific version of Celery:

    Linux server:

    pip install celery==4.2.2

    Windows server:

    pip install celery==3.1.25

  • Install the new version of OpenREM:

    pip install openrem==0.9.1

Update the configuration

Locate and edit your local_settings file

  • Ubuntu linux: /usr/local/lib/python2.7/dist-packages/openrem/openremproject/local_settings.py
  • Other linux: /usr/lib/python2.7/site-packages/openrem/openremproject/local_settings.py
  • Linux virtualenv: vitualenvfolder/lib/python2.7/site-packages/openrem/openremproject/local_settings.py
  • Windows: C:\Python27\Lib\site-packages\openrem\openremproject\local_settings.py
  • Windows virtualenv: virtualenvfolder\Lib\site-packages\openrem\openremproject\local_settings.py

Date format - changed with 0.8

Set the date format for xlsx exports (need to check csv situation). Copy the following code into your local_settings.py file if you want to change it from dd/mm/yyy:

# Date format for exporting data to Excel xlsx files.
# Default in OpenREM is dd/mm/yyyy. Override it by uncommenting and customising below; a full list of codes is available
# at https://msdn.microsoft.com/en-us/library/ee634398.aspx.
# XLSX_DATE = 'mm/dd/yyyy'

Time zone and language - changed with 0.8

Consider setting the timezone and language in local_settings.py. See local_settings.py.example.

Add additional log file configuration - changed with 0.8

Warning

If the configuration is not added for the new openrem_extractor.log you will find it being created where ever you start the webserver from, and starting the webserver may fail.

Add the new extractor log file configuration to the local_settings.py - you can copy the ‘Logging configuration’ section from local_settings.py.example if you haven’t made many changes to this section. See the Log file settings in the install instructions.

Warning

If you are upgrading from an earlier beta with the Toshiba RDSR creation logs defined, this has changed names and must be modified in local_settings.py before the migration below. It should be changed to:

LOGGING['loggers']['remapp.extractors.ct_toshiba']['level'] = 'INFO'  # Toshiba RDSR creation extractor logs

substituting INFO for whichever level of logging is desired.

E-mail server settings - changed with 0.9.0

If you want selected OpenREM users to be automatically sent fluoroscopy high dose alerts then set the details of the e-mail server to be used in the E-mail server settings part of your local_settings.py file. Locate and edit your local_settings file

  • Ubuntu linux: /usr/local/lib/python2.7/dist-packages/openrem/openremproject/local_settings.py
  • Other linux: /usr/lib/python2.7/site-packages/openrem/openremproject/local_settings.py
  • Linux virtualenv: vitualenvfolder/lib/python2.7/site-packages/openrem/openremproject/local_settings.py
  • Windows: C:\Python27\Lib\site-packages\openrem\openremproject\local_settings.py
  • Windows virtualenv: virtualenvfolder\Lib\site-packages\openrem\openremproject\local_settings.py

Then change the e-mail section settings to reflect the e-mail server that is to be used:

EMAIL_HOST = 'localhost'
EMAIL_PORT = 25
EMAIL_HOST_USER = ''
EMAIL_HOST_PASSWORD = ''
EMAIL_USE_TLS = False
EMAIL_USE_SSL = False
EMAIL_DOSE_ALERT_SENDER = 'your.alert@email.address'
EMAIL_OPENREM_URL = 'http://your.openrem.server'

See the E-mail configuration documentation for full details.

Migrate the database

In a shell/command window, move into the openrem folder:

  • Ubuntu linux: /usr/local/lib/python2.7/dist-packages/openrem/
  • Other linux: /usr/lib/python2.7/site-packages/openrem/
  • Linux virtualenv: vitualenvfolder/lib/python2.7/site-packages/openrem/
  • Windows: C:\Python27\Lib\site-packages\openrem\
  • Windows virtualenv: virtualenvfolder\Lib\site-packages\openrem\
python manage.py makemigrations remapp
python manage.py migrate remapp

Update static files

In the same shell/command window as you used above run the following command to clear the static files belonging to your previous OpenREM version and replace them with those belonging to the version you have just installed (assuming you are using a production web server…):

python manage.py collectstatic --clear

Virtual directory users

If you are running your website in a virtual directory, you also have to update the reverse.js file. To get the file in the correct path, take care that you insert just after the declaration of STATIC_ROOT the following line in your local_settings.py:

JS_REVERSE_OUTPUT_PATH = os.path.join(STATIC_ROOT, 'js', 'django_reverse')

To update the reverse.js file execute the following command:

python manage.py collectstatic_js_reverse

See Running the OpenREM website in a virtual directory for more details.

Enable task management - changed in 0.9.0

RabbitMQ management interface

To make use of the RabbitMQ queue display and purge control, the management interface needs to be enabled. To do so, follow the instructions at Enable RabbitMQ queue management interface.

Celery management interface, Flower

To make use of the Celery task management, Flower needs to be running. To do so, follow the instructions in Celery task management: Flower. For ‘one-page Ubuntu’ installs, add the Flower related config and create, register and start the systemd service files as described in Celery and Flower. If you need to change the default Flower port of 5555 then make sure you do so in openremproject\local_settings.py to add/modify the line FLOWER_PORT = 5555 as well as when you start Flower.

Celery for Windows config - changed in 0.9.0

For best performance and reliability when using Celery on Windows, if your command for starting Celery specifies a pool option, for example -P solo, remove it so that Celery reverts to using the default prefork pool. This will enable multiple tasks to run concurrently and it will be possible to terminate tasks.

If you are a Windows user you may also wish to review Daemonising Celery and Flower on Windows as the example control batch files have been updated.

Ubuntu installs that followed One page complete Ubuntu install

Systemd service files have been renamed in these docs to use openrem-function rather than function-openrem. To update the service files accordingly, follow the following steps. This is optional, but will make finding them easier (e.g. sudo systemctl status openrem-[tab][tab] will list them!)

sudo systemctl stop gunicorn-openrem.service
sudo systemctl stop celery-openrem.service
sudo systemctl stop flower-openrem.service

sudo systemctl disable gunicorn-openrem.service
sudo systemctl disable celery-openrem.service
sudo systemctl disable flower-openrem.service

sudo mv /etc/systemd/system/{gunicorn-openrem,openrem-gunicorn}.service
sudo mv /etc/systemd/system/{celery-openrem,openrem-celery}.service
sudo mv /etc/systemd/system/{flower-openrem,openrem-flower}.service

sudo systemctl enable openrem-gunicorn.service
sudo systemctl enable openrem-celery.service
sudo systemctl enable openrem-flower.service

sudo systemctl start openrem-gunicorn.service
sudo systemctl start openrem-celery.service
sudo systemctl start openrem-flower.service

Restart all the services

Follow the guide at Start all the services.