Project Class¶

Documentation of the Project class.

class qmenta.client.Project(account, project_id, max_upload_retries=5)¶

This class is used to work with QMENTA projects. The class is instantiated passing as argument a Connection object and the id

Parameters

account (qmenta.client.Account) – A QMENTA Account instance
project_id (Int or string) – The ID (or name) of the project you want to work with

add_metadata_parameter(title, param_id=None, param_type='string', visible=False)¶

Add a metadata parameer to the project.

Parameters

title (str) – Identificator of this new parameter
param_id (str) – Title of this new parameter
param_type (str) – Type of the parameter. One of: “integer”, “date”, “string”, “list”, “decimal”
visible (bool) – whether the parameter will be visible in the table of patients

Returns

True if parameter was correctly added, False otherwise.

Return type

bool

add_subject(subject)¶

Add a subject to the project.

Parameters: subject (Subject) – Instance of Subject representing the subject to add.
Returns: True if correctly added, False otherwise
Return type: bool

change_file_metadata(container_id, filename, modality, tags)¶

Change modality and tags of filename in container_id

Parameters

container_id (int) – Container identifier.
filename (str) – Name of the file to be edited.
modality (str or None) – Modality identifier, or None if the file shouldn’t have any modality
tags (list[str] or None) – List of tags, or None if the filename shouldn’t have any tags

check_subject_name(subject_name)¶

Check if a given subject name exists in the selected project.

Parameters: subject_name (str) – name of the subject to check
Returns: True if subject name exists in project, False otherwise
Return type: bool

copy_container_to_project(container_id, project_id)¶

Copy a container to another project.

Parameters

container_id (int) – ID of the container to copy.
project_id (int or str) – ID of the project to retireve, either the numeric ID or the name

Returns

True on success, False on fail

Return type

bool

delete_analysis(analysis_id)¶

Delete an analysis

Parameters: analysis_id (Int) – id of the analysis to be deleted

delete_session(subject_name, session_id, cache=False)¶

Delete a session from a subject within a project.

Parameters

subject_name (str) – Name of the subject
session_id (int) – The SSID of the session that will be deleted
cache (bool) – Whether to use the cached metadata or not

Returns

True if correctly deleted, False otherwise.

Return type

bool

delete_subject(subject_name)¶

Delete a subject from the project.

Parameters: name (str) – Name of the subject to be deleted.
Returns: True if correctly deleted, False otherwise.
Return type: bool

download_file(container_id, file_name, local_filename=False, overwrite=False)¶

Download a single file from a specific container.

Parameters

container_id (int) – ID of the container inside which the file is.
file_name (str) – Name of the file in the container.
local_filename (str) – Name of the file to be created. By default, the same as file_name.
overwrite (bool) – Whether or not to overwrite the file if existing.

download_files(container_id, filenames, zip_name='files.zip', overwrite=False)¶

Download a set of files from a given container.

Parameters

container_id (int) – ID of the container inside which the file is.
filenames (list[str]) – List of files to download.
overwrite (bool) – Whether or not to overwrite the file if existing.
zip_name (str) – Name of the zip where the downloaded files are stored.

get_analysis(analysis_name_or_id)¶

get_container(subject_name)¶

get_file_metadata(container_id, filename)¶

Retrieve the metadata from a particular file in a particular container.

Parameters

container_id (str) – Container identifier.
filename (str) – Name of the file.

Returns

Dictionary with the metadata.

Return type

dict

get_subject(subject_name, cache=True)¶

Return a subject object, representing a subject from the project.

Parameters: subject_name (str) – Name of the subject.
Returns: A Subject instance representing the desired subject, or False if the subject was not found.
Return type: Subject or bool

get_subject_id(subject_name, cache=False)¶

Given a subject name, return its ID in the project.

Parameters

subject_name (str) – Name of the subject in the project.
cache (bool) – Whether to use the cached metadata or not

Returns

The ID of the subject in the project, or False if the subject is not found.

Return type

int or bool

get_subjects_metadata(cache=True)¶

List all subject data from the selected project.

Returns: A list of dictionary of {“metadata_name”: “metadata_value”}
Return type: dict

list_analysis(limit=10000000)¶

List the analysis available to the user.

Parameters: limit (int) – Max number of results
Returns: List of analysis, each a dictionary
Return type: dict

list_container_files(container_id)¶

List the name of the files available inside a given container.

Parameters: container_id (str) – Container identifier.
Returns: List of file names (strings)
Return type: list[str]

list_container_files_metadata(container_id)¶

List all the metadata of the files available inside a given container.

Parameters: container_id (str) – Container identifier.
Returns: Dictionary of {“metadata_name”: “metadata_value”}
Return type: dict

list_input_containers(search_condition=None, limit=1000)¶

List the containers available to the user.

Parameters

search_condition (dict) – d_n: container_name s_n: subject_id from_d: from date to_d: to date sets: data sets (modalities)
limit (int) – Max number of results

Returns

List of containers, each a dictionary {“name”: “container-name”, “id”: “container_id”}

Return type

dict

list_result_containers(limit=1000)¶

List the result containers available to the user.

Parameters: limit (int) – Max number of results
Returns: List of containers, each a dictionary {“name”: “container-name”, “id”: “container_id”}
Return type: dict

property metadata_parameters¶

List all the parameters in the subject metadata.

Each project has a set of parameters that define the subjects metadata. This function returns all this parameters and its properties.

Returns

dictionary {“param_name”:: { “order”: Int, “tags”: [tag1, tag2, …, ], “title: “Title”, “type”: “integer|string|date|list|decimal”, “visible”: 0|1 }}

Return type

dict[str] -> dict[str] -> x

set_qc_status(analysis_id, status=QCStatus.PASS, comments='')¶

Changes the analysis QC status.

Parameters

analysis_id (int) – Analysis ID number
status (QCStatus) – QCStatus.PASS or QCStatus.FAIL
comments (str, optional) – Additional comments explaining why the QC status has been set to pass or fail.

start_analysis(script_name, version, in_container_id=None, analysis_name=None, analysis_description=None, ignore_warnings=False, settings=None, tags=None, preferred_destination=None)¶

Starts an analysis on a subject.

Parameters

script_name (str) – Name of the script to be run. One of: “volumetry”, “diffusion_connectome”, “morphology”
in_container_id (int or dict) – The ID of the container to get the data from, or a dictionary with one or more container names as keys, and IDs as values. Input container names are generally prefixed with “input_”. If not, the prefix will be automatically added.
analysis_name (str) – Name of the analysis (optional)
analysis_description (str) – Description of the analysis (optional)
ignore_warnings (bool) – If False, warnings by server cause failure.
settings (dict) – The input settings used to run the analysis. Use either settings or in_container_id. Input specification in the settings dict can be done by using the key “input”.
tags (list[str]) – The tags of the analysis.
destination (preferred) – The machine on which to run the analysis

Returns

The analysis ID if correctly started, None otherwise.

Return type

int

property subjects¶

Return the list of subject names from the selected projet.

Returns: a list of subject names
Return type: List(Strings)

property subjects_metadata¶

List all subject data from the selected project.

Returns: A list of dictionary of {“metadata_name”: “metadata_value”}
Return type: dict

upload_file(file_path, subject_name, ssid='', date_of_scan='', description='', result=False, name='', input_data_type='qmenta_mri_brain_data:1.0', add_to_container_id=0, chunk_size=512, split_data=False)¶

Upload a file to the platform, associated with the current user.

Parameters

file_path (str) – Path to the file to upload.
subject_name (str) – Subject to which this file will belong
ssid (str) – The ID of the timepoint
data_of_scan (str) – Date of scan/creation of the file
description (str) – Description of the file
result (bool) – If result=True then the upload will be taken as an offline analysis
name (str) – Name of the file in the platform
input_data_type (str) – mri_brain_data:1.0 or gametection:1.0
add_to_container_id (int) – ID of the container to which this file should be added (if id > 0)
chunk_size (int) – Size in kB of each chunk. Should be expressed as a power of 2: 2**x. Default value of x is 9 (chunk_size = 512 kB)
split_data (bool) – If True, the platform will try to split the uploaded file into different sessions. It will be ignored when the ssid is given.

Returns

True if correctly uploaded, False otherwise.

Return type

bool

upload_gametection(file_path, subject_name)¶

Upload new Gametection data to the subject.

Parameters: file_path (str) – Path to the file to upload
Returns: True if upload was correctly done, False otherwise.
Return type: bool

upload_mri(file_path, subject_name)¶

Upload new MRI data to the subject.

Parameters: file_path (str) – Path to the file to upload
Returns: True if upload was correctly done, False otherwise.
Return type: bool

upload_result(file_path, subject_name)¶

Upload new result data to the subject.

Parameters: file_path (str) – Path to the file to upload
Returns: True if upload was correctly done, False otherwise.
Return type: bool