OpenREM Release Notes version 0.8.1¶
Documentation: improved docs and added one-page complete install on Ubuntu instructions
Install: temporary fix for dependency error
Interface: added feature to allow users to change their own password
Charts: fixed problem where a blank category name may not be displayed correctly
Imports: reduced list of scanners that work with the legacy Toshiba CT extractor
Imports: improved handling of non-conformant DX images with text in filter thickness fields
Query-Retrieve: added non-standard option to work-around bug in Impax C-FIND SCP
Exports: fixed bug in mammography NHSBSP exports that incorrectly reported the filter material in some circumstances
Exports: fixed bug where sorting by AGD would cause duplicate entries for bilateral studies
Exports: fixed another non-ASCII bug
If upgrading from 0.7.4, see also OpenREM Release Notes version 0.8.0
Upgrading an OpenREM server with no internet access¶
Follow the instructions found at Upgrade an offline OpenREM installation, before returning here to update the database and configuration.
Upgrading from version 0.7.4 or 0.8.0¶
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 the new version of OpenREM:
pip install openrem==0.8.1
Update the configuration¶
no changes should be required if upgrading from 0.8.0
Locate and edit your local_settings file
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
# 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¶
Consider setting the timezone and language in
Add additional log file configuration¶
If the configuration is not added for the new
openrem_extractor.log you will find it being created whereever
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
local_settings_logfile settings in the install instructions.
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
INFO for whichever level of logging is desired.
Adding legacy Toshiba CT functionality¶
No change required if upgrading from 0.8.0
If you need to import data from older Toshiba CT scanners into OpenREM then the following tools need to be available on the same server as OpenREM:
The paths to these must be set in
local_settings.py for your system:
# Locations of various tools for DICOM RDSR creation from CT images DCMTK_PATH = 'C:/Apps/dcmtk-3.6.0-win32-i386/bin' DCMCONV = os.path.join(DCMTK_PATH, 'dcmconv.exe') DCMMKDIR = os.path.join(DCMTK_PATH, 'dcmmkdir.exe') JAVA_EXE = 'C:/Apps/doseUtility/windows/jre/bin/java.exe' JAVA_OPTIONS = '-Xms256m -Xmx512m -Xss1m -cp' PIXELMED_JAR = 'C:/Apps/doseUtility/pixelmed.jar' PIXELMED_JAR_OPTIONS = '-Djava.awt.headless=true com.pixelmed.doseocr.OCR -'
The example above is for Windows. On linux,
if you have installed the Offis DICOM toolkit with
sudo apt install dcmtk or similar, you can find the path for the
configuration above using the command
which dcmconv. This will be something like
/usr/bin/dcmconv, so the
DCMTK_PATH would be
'/usr/bin and the
DCMCONV would be
os.path.join(DCMTK_PATH, 'dcmconv'). Similarly
JAVA_EXE, which might be
/usr/bin/java. The pixelmed.jar file should be downloaded from
the link above, and you will need to provide the path to where you have saved it.
The list of CT scanners that the extractor works with has been reduced. You can add to this list, but you will need to verify that any systems you configure to use this extractor produce data in OpenREM that you expect.
Migrate the database¶
In a shell/command window, move into the
python manage.py makemigrations remapp # if changes are detected (not expected between most beta versions) 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
Restart all the services¶
Follow the guide at Start all the services.