Users and user groups

NOTE

This documentation is a work in progress and is incomplete.

Please contact developers for more details.

• Users and passwords
• User configuration
  • Password requirements
  • User interface, workflow and ACMG
• User groups
  • User groups and gene panels

Users and passwords

ELLA users and associated data are defined in the file users.json.

To add new or update existing users, run the following command:

ella-cli users add_many <path to users.json>

This will print a one-time password to screen for each user that was added. This password is auto-expired and should be used by each user to set a new password upon first login.

NOTE

User configuration history is currently not tracked in the datamodel, so changes should be tracked externally.

User example:

[
    {
        "username": "testuser1",
        "first_name": "Henrik",
        "last_name": "Ibsen",
        "email": "testuser1@foo.bar",
        "group": "testgroup01"
    }
]

See also users.json (opens new window) and Reset user password.

NOTE

For simplicity, password and password_expiry are provided in the testdata version of users.json. However, this should not be done in production, as this may have undesired side effects. Instead, use the procedure above.

User configuration

Default settings for all users (shallow merged with usergroup's and user's config at runtime). See example_config.yml (opens new window) for examples.

• File: ella_config.yml (set by ELLA_CONFIG env variable)
• Key: user

Password requirements

Requirements for valid password.

• Key: user.auth

Subkey	Explanation	Values
password_expiry_days	Days before password has to be renewed.	[integer]
password_minimum_length	Minimum length of valid password.	[integer]
password_match_groups	Character types in valid password.	[regex]
password_match_groups_descr	Descriptions for character types.	[free text]
password_num_match_groups	Number of character types required for valid password.	[integer]

User interface, workflow and ACMG

Settings related to user interface, workflow and ACMG rules.

• Key: user.user_config

See:

• Overview (subkey: overview)
• Workflows (subkey: workflows)
• ACMG default values and thresholds (subkey: acmg)

User groups

A user group defines the configuration for different groups of users. This includes settings for:

• Gene panels
• Group settings for the ACMG rules engine
• Import and deposit
• User interface for groups

See usergroups.json (opens new window) for examples.

To update the user groups, run the following command:

ella-cli users add_groups <path to usergroups.json>

This will add new or update existing user groups with the new configurations options.

NOTE

User group configuration history is currently not tracked in the data model, so changes should be tracked externally.

User groups and gene panels

ELLA's current access model revolves around gene panels, which control which analyses and variants are available to a given user. It is therefore important to ensure that this is configured correctly, and if new gene panels (including updated versions) are added to the system, that the configuration is updated accordingly.

• File: usergroups.json
• Key: genepanels
• Value: [gene panel name], [version] (latter is optional)