OpenREM Release Notes version 0.5.1

Headline changes

  • Major database modification to remove table name length errors
  • Extended the field value lengths to better incorporate all possible values and decimal places
  • Improved import of grid and filter information from DX images
  • Improved DX summary and detail web pages
  • Any item in a row can now be clicked to move between the home and filtered pages

Upgrades: Convert to South

Always make sure you have converted your database to South before attempting an upgrade

Quick reminder of how, if you haven’t done it already

# Linux: Debian/Ubuntu and derivatives
python /usr/local/lib/python2.7/dist-packages/openrem/manage.py convert_to_south remapp
# Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
python /usr/local/lib/python2.7/site-packages/openrem/manage.py convert_to_south remapp

# Windows, assuming no virtualenv
python C:\Python27\Lib\site-packages\openrem\manage.py convert_to_south remapp

Upgrading from before 0.5.0

Upgrading from version 0.3.9 or earlier

  • Back up your database

  • pip install openrem==0.4.2

  • Migrate the schema

    # Linux: Debian/Ubuntu and derivatives
python /usr/local/lib/python2.7/dist-packages/openrem/manage.py schemamigration --auto remapp
# Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
python /usr/local/lib/python2.7/site-packages/openrem/manage.py schemamigration --auto remapp
# Windows:
python C:\Python27\Lib\site-packages\openrem\manage.py schemamigration --auto remapp

    When South has considered the changes to the schema, you will see the following message:

    ? The field 'Observer_context.device_observer_name' does not have a default specified, yet is NOT NULL.
? Since you are making this field nullable, you MUST specify a default
? value to use for existing rows. Would you like to:
?  1. Quit now.
?  2. Specify a one-off value to use for existing columns now
?  3. Disable the backwards migration by raising an exception; you can edit the migration to fix it later
? Please select a choice: 3
    • As per the final line above, please select option 3, and then execute the migration:
    # Linux: Debian/Ubuntu and derivatives
python /usr/local/lib/python2.7/dist-packages/openrem/manage.py migrate remapp
# Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
python /usr/local/lib/python2.7/site-packages/openrem/manage.py migrate remapp

# Windows, assuming no virtualenv
python C:\Python27\Lib\site-packages\openrem\manage.py migrate remapp

  • Create and populate the database settings in the new local_settings.py file

    The openrem/openrem folder can be found at:

    # Linux: Debian/Ubuntu and derivatives
/usr/lib/python2.7/dist-packages/openrem/openrem
# Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
/usr/lib/python2.7/site-packages/openrem/openrem
# Windows:
C:\Python27\Lib\site-packages\openrem\openrem

    In the openrem/openrem folder, create a new file called local_settings.py and copy the contents of this link into a the file and save it. Alternatively, rename local_settings.py.example to local_settings.py - this is an older version of the file.

    Copy the database details from settings.py into local_settings.py

  • Change the secret key - you can use http://www.miniwebtool.com/django-secret-key-generator/ to generate a new one

  • Move the existing settings.py out of the python directories (delete or move somewhere as a backup)

  • Rename the settings.py.new to settings.py

  • Restart your webserver to check everything looks ok

  • Add some users

    • Go to the admin interface (eg http://localhost:8000/admin) and log in with the user created when you originally created the database (the manage.py syncdb command - Do you want to create a superuser)

    • Create some users and add them to the appropriate groups (if there are no groups, go to the OpenREM homepage and they should be there when you go back to admin).

      • viewgroup can browse the data only
      • exportgroup can do as view group plus export data to a spreadsheet, and will be able to import height and weight data in due course (See Issue #21)
      • admingroup can delete studies in addition to anything the export group can do

Upgrading from versions 0.4.0 - 0.4.2

  • Back up your database

  • Install version 0.5.0

    • pip install openrem==0.5.0

  • Install RabbitMQ

  • Move local_settings.py details from openrem to openremproject

    The inner openrem Django project folder has now been renamed openremproject The customised local_settings.py file and the wsgi.py file have remain in the old openrem folder. The openrem/openrem folder can be found as detailed in the upgrade from ‘0.3.9 or earlier’ instructions above, and the new openrem/openremproject folder is in the same place.

    • Move local_settings.py to openremproject. If you have kept the older local_settings file, you may like to instead rename the local_settings.py.example file instead, then transfer the database settings and change the secret key.
    • Set the path for MEDIA_ROOT. The webserver needs to be able to write to this location - it is where OpenREM will store export files etc so that they can be downloaded. For suggestions, see the main _install instructions.
    • Set ALLOWED_HOSTS. For details see the Django docs A '*' allows any host - see the Django docs for the risk of this.

  • Move wsgi.py from openrem to openremproject or rename wsgi.py.example in openremproject

    If you haven’t edited it, simply rename the new version in openremproject. Otherwise, move the old version and edit the following line as follows:

    # Old:
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "openrem.settings")
# New:
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "openremproject.settings")

  • Tidying up - you should delete the old openrem folder - you might like to take a backup first!

  • Update web server configuration

    The configuration of the webserver will need to be updated to reflect the new location for the settings.py file and the wsgi.py file.

    If you are using the built-in test webserver, static files will no-longer be served unless you use the insecure option:

    python manage.py runserver x.x.x.x:8000 --insecure

  • Migrate the schema

    # Linux: Debian/Ubuntu and derivatives
python /usr/local/lib/python2.7/dist-packages/openrem/manage.py schemamigration --auto remapp
python /usr/local/lib/python2.7/dist-packages/openrem/manage.py migrate remapp
# Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
python /usr/local/lib/python2.7/site-packages/openrem/manage.py schemamigration --auto remapp
python /usr/local/lib/python2.7/site-packages/openrem/manage.py migrate remapp
# Windows:
python C:\Python27\Lib\site-packages\openrem\manage.py schemamigration --auto remapp
python C:\Python27\Lib\site-packages\openrem\manage.py migrate remapp

After restarting the webserver, you should now have OpenREM 0.5.0 up and running. If you wish to test export functionality at this stage, start the Celery task queue - instructions in the Installing OpenREM docs or at the end of this guide.

Now move to Upgrading from version 0.5.0.

Upgrading from version 0.4.3

  • Back up your database

  • The 0.5.1 upgrade must be made from a 0.5.0 database, so a schema migration is required:

    pip install openrem==0.5.0

    # Linux: Debian/Ubuntu and derivatives
    python /usr/local/lib/python2.7/dist-packages/openrem/manage.py schemamigration --auto remapp
    python /usr/local/lib/python2.7/dist-packages/openrem/manage.py migrate remapp
    # Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
    python /usr/local/lib/python2.7/site-packages/openrem/manage.py schemamigration --auto remapp
    python /usr/local/lib/python2.7/site-packages/openrem/manage.py migrate remapp
    # Windows:
    python C:\Python27\Lib\site-packages\openrem\manage.py schemamigration --auto remapp
    python C:\Python27\Lib\site-packages\openrem\manage.py migrate remapp

Upgrading from version 0.5.0

  • Back up your database

  • Install 0.5.1:

    pip install openrem==0.5.1

  • Find out how many migration files you have

    Method 1:

    Use a file browser or terminal to list the contents of the migrations folder, eg:

    # Linux: Debian/Ubuntu and derivatives
ls /usr/local/lib/python2.7/dist-packages/openrem/remapp/migrations/
# Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
ls /usr/local/lib/python2.7/site-packages/openrem/remapp/migrations/
# Windows (alternatively use the file browser):
dir C:\Python27\Lib\site-packages\openrem\remapp\migrations\

    Method 2:

    Use the Django manage.py program to list the existing migrations:

    # Linux: Debian/Ubuntu and derivatives
python /usr/local/lib/python2.7/dist-packages/openrem/manage.py migrate --list remapp
# Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
python /usr/local/lib/python2.7/site-packages/openrem/manage.py migrate --list remapp
# Windows
python C:\Python27\Lib\site-packages\openrem\manage.py migrate --list remapp

    The output should look something like this - there can be any number of existing migrations (though 0001_initial will always be present):

    remapp
(*) 0001_initial
(*) 0002_auto__chg_field_ct_accumulated_dose_data_ct_dose_length_product_total_
(*) 0003_auto__chg_field_general_equipment_module_attributes_station_name
(*) 0004_auto__chg_field_ct_radiation_dose_comment__chg_field_accumulated_proje
(*) 0005_auto__add_exports__add_size_upload
(*) 0006_auto__chg_field_exports_filename
(*) 0007_auto__add_field_irradiation_event_xray_detector_data_relative_xray_exp
( ) 000x_051datamigration
( ) 000x_051schemamigration

  • Rename the two 051 migration files to follow on from the existing migrations, for example 0008_051schemamigration.py and 0009_051datamigration.py for the existing migrations above, or 0002_051schemamigration.py and 0003_051datamigration.py if the only migration is the initial migration. The 051schemamigration must come before the 051datamigration.

    If you are using linux, you might like to do it like this (from within the openrem folder):

    mv remapp/migrations/000{x,8}_051schemamigration.py
mv remapp/migrations/000{x,9}_051datamigration.py

  • If you now re-run migrate --list remapp you should get a listing with the 051schemamigration and the 051datamigration listed at the end:

    remapp
 (*) 0001_initial
 (*) 0002_auto__chg_field_ct_accumulated_dose_data_ct_dose_length_product_total_
 (*) 0003_auto__chg_field_general_equipment_module_attributes_station_name
 (*) 0004_auto__chg_field_ct_radiation_dose_comment__chg_field_accumulated_proje
 (*) 0005_auto__add_exports__add_size_upload
 (*) 0006_auto__chg_field_exports_filename
 (*) 0007_auto__add_field_irradiation_event_xray_detector_data_relative_xray_exp
 ( ) 0008_051schemamigration
 ( ) 0009_051datamigration

    The star indicates that a migration has already been completed. If you have any that are not completed apart from the 051schemamigration and the 051datamigration then please resolve these first.

  • Now execute the migrations:

    # Linux: Debian/Ubuntu and derivatives
python /usr/local/lib/python2.7/dist-packages/openrem/manage.py migrate remapp
# Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
python /usr/local/lib/python2.7/site-packages/openrem/manage.py migrate remapp
# Windows
python C:\Python27\Lib\site-packages\openrem\manage.py migrate remapp

Restart the web server

If you are using the built-in test web server (not for production use):

python manage.py runserver x.x.x.x:8000 --insecure

Otherwise restart using the command for your web server

Restart the Celery task queue

For testing, in a new shell:

# Linux: Debian/Ubuntu and derivatives
cd /usr/local/lib/python2.7/dist-packages/openrem/
# Linux: other distros. In a virtualenv replace all up to lib/ as appropriate
cd /usr/local/lib/python2.7/site-packages/openrem/
# Windows
cd C:\Python27\Lib\site-packages\openrem\

# All
celery -A openremproject worker -l info

For production use, see http://celery.readthedocs.org/en/latest/tutorials/daemonizing.html