Manual

TaskManager commands from the command line

Another way to interact with the TaskManager is via a set of scripts/executables available in the TaskManager environment (folders) after installing on a Windows or Linux server. These executables are especially useful if you want to upload or change a large number of tasks and/or templates. In that case, the REST API is not very convenient since actions/commands are given one by one.

Available and useful commands that can be used from the Windows or Linux command line box are shown below. Note that arguments between square brackets are optional.

taskmanager-add-task

Usage:

taskmanager-add-task [-h] [-db] -p PROJECT [-u USERS [USERS ...]]
    [-g GROUPS [GROUPS ...]] [-t TAGS [TAGS ...]] [-d DISTRIBUTE_GROUP]
    [-gen GENERATOR_URL] [-an APPLICATION_NAME] [-av APPLICATION_VERSION]
    [-cu CALLBACK_URL] [-cc CALLBACK_CONTENT] [--url URL] [--old] task

Example:

taskmanager-add-task -p glandula -u johndoe -t pinealis --url 10.20.30.40 --old task.json

By executing the example command above, a new task (JSON file task.json) is uploaded to the TaskManager running on URL 10.20.30.40. HOSTNAME can be a IP address or a server name known in the domain. The project related task is “glandula” and the specific user the task is assigned to is “johndoe”. The -t option is important here, since it means that this task, when carried out on the ViewR will use template ‘pinealis’. So when uploading the task to the TaskManager it is immediately linked to the task_template (ViewR template) that has to be used whule running the task. The –old option here is used because of a software version issue.

If the task would need to be assigned to a group of users (say with the name phds), so anyone of them can pick the task up to carry out, you should give the following:

taskmanager-add-task -g phds -u johndoe -t pinealis --url 10.20.30.40 --old task.json

taskmanager-add-user

Usage:

taskmanager-add-user [-h] -u USERNAME -p PASSWORD -n FULL_NAME -e EMAIL
    [-w ASSIGNMENT_WEIGHT] [-i] [-f]

This command adds a new user to the Task Manager. Most arguments will be trivial/clear. The argument -h or --help will show the help message and exit. The (optional) argument -I means that the new user should be ‘inactive’. The (optional) argument -f means that execution is forced without asking questions.

taskmanager-add-template

Usage:

taskmanager-add-template [-h] [--old] HOSTNAME template

Example:

taskmanager-add -add --old http://10.20.30.40:5000 template.json

By executing the example command above, a new template (JSON file template.json) will be uploaded to the Task Manager running on URL http://10.20.30.40 on port 5000.

Taskmanager-update-template

Usage:

taskmanager-update-template [-h] [--name NAME] [--user USER] [--old]
    HOSTNAME TEMPLATE.JSON

For example:

taskmanager-update-add --old http://10.20.30.40:5000 template.json

This command will update an existing template (known to and stored on the Task Manager).

Configuration

Most of the configuration of the app uses environment variables. The TaskManager uses the following configuration variables:

Environment variable	Description
TASKMANAGER_PORT	Port on which the TaskManager will isten
TASKMAN_INSTANCE_NAME	Instance name of the service, default Task Manager
TASKMAN_PROJECT_NAME	Project anme for the task manager, default DefaultProject
DB_SCHEMA	Database schema to use, see SQLAlchemy Engine Configuration
DB_NAME	Name of the database to use
DB_USER	User to use to connect to the database
DB_PASS	Password to connect to the database
DB_HOST	Hostname of the database server
DB_PORT	Port of the databse server
SECURITY_REGISTERABLE	Flag indicating if users are allowed to register themselves
SECURITY_CHANGEABLE	Flag indicating if users are allowed to change their passwords
SECURITY_RECOVERABLE	Flag indicating if users are allowed to recover their passwords
SECURITY_CONFIRMABLE	Flag indicating if users need to confirm their email before registration is complete
SECURITY_PASSWORD_SALT	Salt to use for the password hashing
SECRET_KEY	The Flask secret key

If use the TaskManager via docker-compose or kubernetes, you can automatically have it pull project data from a GIT repository. For that set the following environment variables:

Environment variable	Description
PROJECT_REPO	The GIT repository from where to get the project resources
PROJECT_BRANCH	The GIT branch from which to get the project resources
PROJECT_RELATIVE_PATH	The relative path inside the container in which to put the project resources

The following Gunicorn environment variables might be of interest:

Environment variable	Description
GUNICORN_WORKER_CLASS	Gunicorn work class
GUNICORN_WORKER_CONNECTIONS	Gunicorn work connection
GUNICORN_TIMEOUT	Gunicorn timeout

For the full Gunicorn settings see https://docs.gunicorn.org/en/stable/settings.html

Permissions and Roles

Roles

For the TaskManager the roles can be configured, but by default the following roles are defined:

Name	Permissions
admin	task_read_all, task_update_all, task_add, task_delete, template_add, template_update, template_delete, tag_add, tag_update, tag_delete, user_read_all, user_update_all, user_add, user_delete, group_read_all, group_add, group_update, group_delete, meta_read_all, meta_update, meta_add, meta_delete, roles_manage
superuser	task_read_all, task_update_status_all, task_update_user, task_update_lock_all, tag_add, tag_update, user_read_all, user_update_assignment_weight, group_read_all, group_update
user	task_read, task_update_status, user_read, group_read

Permissions

The permissions are defined as follows:

Permission	Description
task_read	Allows reading tasks assigned to itself. Please note: acquiring and releasing the lock field is part of this permission.
task_read_all	Allows reading all tasks.
task_update_status	Allows updating the status of tasks assigned to itself.
task_update_status_all	Allows updating the status of all tasks.
task_update_user	Allows updating the assigned users and/or groups of tasks.
task_update_lock_all	Allows updating or clear the lock of all tasks.
task_update_all	Allows updating all fields of all tasks.
task_add	Allows adding a task.
task_delete	Allows deleting a task.
template_add	Allows adding a template.
template_update	Allows updating templates.
template_delete	Allows deleting a template.
tag_add	Allows adding a tag.
tag_update	Allows updating a tag.
tag_delete	Allows deleting a tag.
user_read	Allows seeing your user information.
user_read_all	Allows seeing all users.
user_add	Allows adding users.
user_update_all	Allows updating all users.
user_update_assignment_weight	Allows changing the assignment weight of users.
user_delete	Allows deleting users.
group_read	Allows seeing the groups you are assigned to.
group_read_all	Allows seeing all groups.
group_add	Allows adding groups.
group_update	Allows updating groups. Please note: this is how user membership of a group can be managed.
group_delete	Allows deleting groups.
roles_manage	Allows adding and removing roles from users

Database Models

Database model of the TaskManager tables.