Data Model¶

Hierarchy¶

Data in a Flywheel system is organized in a tree-like hierarchy, as indicated in the following diagram.

flywheel.models.user.User - An authorized entity, usually referenced by email address.
flywheel.models.group.Group - A grouping of users and projects.
flywheel.models.project.Project - A project represents a grouping of subjects and sessions, e.g. within a study.
flywheel.models.subject.Subject - An individual under study.
flywheel.models.session.Session - A grouping of acquired data, typically data acquired within a limited timeframe.
flywheel.models.acquisition.Acquisition - A set of one or more files, typically acquired as part of the same process, at the same time.
flywheel.models.analysis_output.AnalysisOutput - A set of one or more derivative files from analyzing files after they have been acquired.

Permissions¶

Permissions in Flywheel are managed at the Group and Project level. Users that belong to a Group or a Project have a Role, which by default is one of:

Admin (admin) - Administrators can perform administrative-level actions such as setting permissions or creating and deleting projects.
Read-Write (rw) - Users can read, create and delete data, but cannot assign permissions or delete entire projects.
Read-Only (ro) - Users can only read data

By default when a new Project is created belonging to a Group, permissions will be copied from the Group to the Project, keeping user roles intact. From that point on, permissions for that Project must be managed at that project, changes made to the Group will not propagate to the project.

from pprint import pprint

# See project permissions
project = fw.get(project_id)
pprint(project.permissions)

# Add permission to a project
project.add_permission(flywheel.Permission('justinehlert@flywheel.io', 'ro'))

# Remove permission from a project
project.delete_permission('justinehlert@flywheel.io')

Custom Roles [NEW]¶

Custom roles can also be defined for more refined control over project access. To define a role, a label and list of allowed actions (for a full list of actions, see Available Actions).

# Edit these values to match a real group id and a project label that belongs to that group
group_id = 'group_id'
project_label = 'project_label'

# These actions (read_only actions) are required for any new role definition
REQUIRED_ACTIONS = [
        'containers_view_metadata',
        'files_view_metadata',
        'tags_view',
        'notes_view',
        'project_permissions_view',
        'data_views_view',
        'session_templates_view',
        'gear_rules_view',
        'jobs_view'
]
# Add files_modify_metadata to list
action_list = REQUIRED_ACTIONS + ['files_modify_metadata']
# Create a dictionary defining label and actions
role_dict = {'label': 'role_a_d20', 'actions': action_list}

# Add the role to Flywheel
role_a_d20 = fw.add_role(role_dict)

# Add the role to a group
fw.add_role_to_group(group_id, {'_id': role_a_d20.id})

# Get a project
project = fw.lookup(f'{group_id}/{project_label}')

# Add role for a user not yet on the project (but has been added to the Flywheel instance)
# Replace new_user@example.com with an email address belonging to a real user
user_id = 'new_user@example.com'
project.add_permission({'_id': user_id, 'role_ids': [role_a_d20.id]})

# Add role for user with existing permissions on the project
# Add containers_modify_metadata to list
action_list = REQUIRED_ACTIONS + ['containers_modify_metadata']
# Create a dictionary defining label and actions
role_dict = {'label': 'barrel_role', 'actions': action_list}
# Add the role to flywheel
barrel_role = fw.add_role(role_dict)
# Add the role to a group
fw.add_role_to_group(group_id, barrel_role.id)
# Get the current permission dictionary for user
permission_dict = fw.get_project_user_permission(project.id, user_id)
# Add role id to the current list of role ids
permission_dict['role_ids'].append(barrel_role.id)
# Update the user's permissions with the modified permission_dict
project.update_permission(user_id, permission_dict)

# List all roles
fw.get_all_roles()

# List all group roles
fw.get_all_group_roles(group_id)

# We need to remove the permission that uses the role before removing the role from group
project.delete_permission(user_id)

# Delete the role from group
fw.remove_role_from_group(group_id, barrel_role.id)

# Delete the role
fw.delete_role(barrel_role.id)

Available Actions¶

Action	Description
containers_view_metadata	View Container Metadata
containers_create_hierarchy	Create Container Hierarchy
containers_modify_metadata	Modify Container Metadata
containers_delete_hierarchy	Delete Container Hierarchy
containers_delete_project	Delete Project (Project Permission)
analyses_view_metadata	View Analysis Metadata
analyses_create_sdk	Create Adhoc Analysis
analyses_create_job	Create Job-Based Analysis
analyses_modify_metadata	Modify Analysis Metadata
analyses_delete	Delete Analysis
files_view_metadata	View File Metadata
files_view_contents	View File Contents
files_download	Download File
files_create_upload	Create/Upload File
files_modify_metadata	Modify File Metadata
files_delete_non_device_data	Delete Non-Device File Data
files_delete_device_data	Delete Device File Data
tags_view	View Tags
tags_manage	Manage Tags
notes_view	View Notes
notes_manage	Manage Notes
project_permissions_view	View Project Permissions
project_permissions_manage	Manage Project Permissions
gear_rules_view	View Project Gear Rules
gear_rules_manage	Manage Project Gear Rules
data_views_view	View Data Views
data_views_manage	Manage Data Views
session_templates_view	View Session Templates
session_templates_manage	Manage Session Templates
jobs_view	View Jobs
jobs_run_cancel	Run and Cancel Jobs
jobs_cancel_any	Cancel Any Job

Containers¶

Projects, Subjects, Sessions, Acquisitions and Analyses are all different types of Containers. Containers in Flywheel all support the following features:

Tags¶

Tags are concise labels that provide descriptive metadata that can be searched on. Available tags are managed on the Group.

# See tags on a session
session = fw.get(session_id)
print(', '.join(session.tags))

# Add a tag to a session
session.add_tag('Control')

# Remove a tag from a session
session.delete_tag('Analysis Required')

Notes¶

Notes are user-entered, human readable metadata attached to a container. They are timestamped and attributed to the user that entered them.

from pprint import pprint

# See notes on a session
session = fw.get(session_id)
pprint(session.notes)

# Add a note to a session
session.add_note('This is a note')

# Delete a note from a session
session.delete_note(session.notes[0].id)

Info¶

Info is free-form JSON metadata associated with a container or file.

from pprint import pprint

# Print the info for an acquisition
acquisition = fw.get(acquisition_id)
pprint(acquisition.info)

# Replace the entire contents of acquisition info
acquisition.replace_info({ 'splines': 34 })

# Add additional fields to acquisition info
acquisition.update_info({ 'curve': 'bezier' })

# Delete fields from acquisition info
acquisition.delete_info('splines')

Files¶

Files are a set of file attachments associated with a container. See also Dealing with Files.

from pprint import pprint

# List files on an acquisition
acquisition = fw.get(acquisition_id)

for f in acquisition.files:
  print('Name: %s, type: %s' % (f.name, f.type))

# Upload a file to an acquisition
acquisition.upload_file('/path/to/file.txt')

# Download a file to disk
acquisition.download_file('file.txt', '/path/to/file.txt')

# Files can also have metadata
pprint(acquisition.files[0].info)

acquisition.replace_file_info('file.txt', {'wordCount': 327})

File Classification¶

Flywheel supports an extensible, multi-dimenstional classification scheme for files. Each dimension of classification is referred to as an aspect. The available aspects are determined by the file’s modality.

For example, the MR modality provides the Intent, Measurement and Features aspects. In addition, the Custom aspect is always available, regardless of modality.

from pprint import pprint

# Display the aspects defined in the MR modality
mr = fw.get_modality('MR')
pprint(mr)

# Replace a file's modality and classification
acquisition.replace_file_classification('file.txt', {
        'Intent': ['Structural'],
        'Measurement': ['T2']
}, modality='MR')

# Update a file's Custom classification, without changing
# existing values or modality
acquisition.update_file_classification('file.txt', {
        'Custom': ['value1', 'value2']
})

# Delete 'value1' from Custom classification
acquisition.delete_file_classification('file.txt', {
        'Custom': ['value1']
})

Timestamps [NEW]¶

Objects with timestamps and created/modified dates provide helper accessors to get those dates in the local (system) timezone, as well as the original timezone in the case of acquisition and session timestamps.

For example:

# Acquisition Timestamp (tz=UTC)
print(acquisition.timestamp.isoformat())

# Acquisition Timestamp (tz=Local Timezone)
print(acquisition.local_timestamp.isoformat())

# Acquisition Timestamp (tz=Original Timezone)
print(session.original_timestamp.isoformat())

Age at Time of Session [NEW]¶

Sessions have a field for subject age at the time of the session, in seconds. There are also helper accessors to get age in years, months, weeks and days.

For example:

# Subject age in seconds
print('Subject was {} seconds old', session.age)

# Subject age in years
print('Subject was {} years old', session.age_years)