Complete list of environment variables

This section explains how to set up the environment variables for SmartScope

General

  • ALLOWED_HOSTS Default: localhost

    Comma separated list domains that are allowed to be used to connect to the server. Usually, it is the IP an/or hostname of the computer where SmartScope is installed. If you have a domain name. e.g. locahost,myhostname,mydomain.com

  • DJANGO_SETTINGS_MODULE Default: Smartscope.settings.server_docker

    Useful to change if an instance will only be used as a worker. More details coming soon.

  • USE_STORAGE Default: True

    options: True|False If the instance should look in the main storage area for files. This option is required if the instance is connected to the microscope. Can be turned off if setting up an instance that can only view the results from other sources like a server that would only load files from AWS or long-term storage areas. This sotrage location is prioritized to load the files from as it should be the fastest accessible drive.

  • USE_LONGTERMSTORAGE Default: False

    options: True|False If you plan on backing up the storage drive to another area with more storage space, the server can look for files in that area for displaying on the website. This storage area has second priority to load the files from if the data isn’t present in the main storage any longer.

  • USE_AWS Default: False

    options: True|False If true, the AWS section of the file will need to be filled up. SmartScope will automatically back up the data for each specimen once they’re completed. The data can be loaded from AWS to display on the webpage after it’s been removed from the main storage. This area has third priority to load the files from.

  • USE_MICROSCOPE Default: True

    options: True|False If the instance of Smartscope being deployed is only going to serve as a viewing server that doesn’t connect to the microscope, set to False. It will disable the links to setup and run sessions.

  • WORKER_HOSTNAME Default: localhost

    If the webserver and worker (instance connected to the microscope) are not installed in the same computer. More details coming soon.

  • DEFAULT_UMASK Default: 003

    Set the way the permissions will be set on the files created by smartscope. With umask 003, the files will inherit a 774 (rwxrwxr–) permission set allowing group write.

  • LOGLEVEL Default=INFO

    options: INFO|DEBUG Set the sensitivity of logging. The default is INFO will print the most informative status updates while debug allows for more in-depth information.

  • DEBUG Default=True

    Sets the server in debug mode to return traceback of the error on webpage loading instead of the regular return code.

Fake-scope mode

  • TEST_FILES Default:/mnt/data/tmp/smartscope_testfiles/

    The location of the dummy files to run in “fake scope” mode.

Database

  • MYSQL_HOST Default:localhost

    IP address or hostname of the database server.

  • MYSQL_PORT Default:3306

    Port for the mysql server. 3306 is the default if the default port for mariabDB.

  • MYSQL_USERNAME Default:root

    Username for the mariaDB connection

  • MYSQL_ROOT_PASSWORD Default:

    Password for the user for mariaDB connection

  • DB_NAME Default:smartscope

    Name of the database in the mariaDB server

  • DB_PATH Default:/mnt/mariadb

    Path of the database. Only useful if MYSQL_HOST=localhost

AWS connection information

This section is required if the USE_AWS=True and if the information is not stored in ~/.aws Please view AWS S3 information on these variables