cubes.piws.importer.processings.Processings

class cubes.piws.importer.processings.Processings(session, project_name, center_name, processings, processing_type, can_read=True, can_update=False, data_filepath=None, use_store=True, piws_security_model=True, check_assessment_with_rql=False)

This class enables us to load the processing data to CW.

__init__(session, project_name, center_name, processings, processing_type, can_read=True, can_update=False, data_filepath=None, use_store=True, piws_security_model=True, check_assessment_with_rql=False)

Initialize the Processings class.

Parameters:

session: Session (mandatory) :

a cubicweb session.

project_name: str (mandatory) :

the name of the project.

center_name: str (mandatory) :

the center name.

processings: dict of list of dict (mandatory) :

the processing description: the first dictionary contains the subject name as keys and then a list of dictionaries with two keys ( Assessment - Processings) that contains the entities parameter decriptions.

processing_type: str (mandatory) :

a processing type used to gather together similar processings.

can_read: bool (optional, default True) :

set the read permission to the imported data.

can_update: bool (optional, default False) :

set the update permission to the imported data.

data_filepath: str (optional, default None) :

the path to folder containing the current study dataset.

use_store: bool (optional, default True) :

if True use an SQLGenObjectStore, otherwise the session.

piws_security_model: bool (optional, default True) :

if True apply the PIWS security model.

check_assessment_with_rql: bool (optional, default False) :

if True check if the Assessment entity already exists using an rql.

Notes

Here is an axemple of the definiton of the ‘processings’ parameter:

processings = {
    "subjects1": [ {
        "Assessment": {
            "identifier": u"toy_V1_subject1",
            "timepoint": u"V1"},
        "Processings": [ {
            "Inputs": ["Any X Where X is Scan"],
            "ExternalResources": [[{
                "absolute_path": True, "name": u"p1",
                "identifier": u"toy_V1_subject1_p1_1",
                "filepath": u"/tmp/demo/V1/subject1/images/t1/t1.nii.gz"}]],
            "FileSets": [{
                "identifier": u"toy_V1_subject1_p1", "name": u"p1"}],
            "ProcessingRun": {
                "identifier": u"toy_V1_subject1_p1",
                "name": u"p1", "label": u"segmentation",
                "tool": u"spm", "version": u"8.1",
                "parameters": u"{'a': 1, 'r': 'mypath'}"}
        } ]
    } ]
}

Depreciated example:

processings = {
    "subjects1": [ {
        "Assessment": {
            "identifier": u"toy_V1_subject1",
            "timepoint": u"V1"},
        "Processings": [ {
            "Inputs": ["Any X Where X is Scan"],
            "ExternalResources": [ {
                "absolute_path": True, "name": u"p1",
                "identifier": u"toy_V1_subject1_p1_1",
                "filepath": u"/tmp/demo/V1/subject1/images/t1/t1.nii.gz"}],
            "FileSet": {
                "identifier": u"toy_V1_subject1_p1", "name": u"p1"},
            "ProcessingRun": {
                "identifier": u"toy_V1_subject1_p1",
                "name": u"p1", "label": u"segmentation",
                "tool": u"spm", "version": u"8.1",
                "parameters": u"{'a': 1, 'r': 'mypath'}"}
        }]
    } ]
}

Methods

__init__(session, project_name, center_name, ...)	Initialize the Processings class.
cleanup()	Method to cleanup temporary items and to commit changes.
import_data()	Method that import the processing data in the db.
schema(outfname[, text_font, node_text_size])	Create a view of the schema described in a python structure.

Attributes

assessment_relations
device_relations
fileset_relations
relations

__module__ = 'cubes.piws.importer.processings'

_create_processing(processing_struct, fset_structs, extfiles_structs, scores, processing_inputs, subject_eid, study_eid, assessment_eid)

Create a processing and its associated relations.

import_data()

Method that import the processing data in the db.

Note

Below the schema used to insert the scans:

Warning

This method assumes that all the subjects and groups have already been inserted in the database.

relations = [['Scan', 'filesets', 'FileSet'], ('FileSet', 'in_assessment', 'Assessment'), ('FileSet', 'external_files', 'ExternalFile'), ('ExternalFile', 'fileset', 'FileSet'), ('ExternalFile', 'in_assessment', 'Assessment'), ('Assessment', 'study', 'Study'), ('Study', 'assessments', 'Assessment'), ('Subject', 'assessments', 'Assessment'), ('Assessment', 'subjects', 'Subject'), ('Center', 'assessments', 'Assessment'), ('Assessment', 'center', 'Center'), ('CWGroup', 'can_read', 'Assessment'), ('CWGroup', 'can_update', 'Assessment'), ('Assessment', 'device', 'Device'), ('Device', 'device_assessments', 'Assessment'), ('ProcessingRun', 'study', 'Study'), ('Study', 'study_processing_runs', 'ProcessingRun'), ('ProcessingRun', 'subjects', 'Subject'), ('Subject', 'subject_processing_runs', 'ProcessingRun'), ('Assessment', 'processing_runs', 'ProcessingRun'), ('Scan', 'processing_runs', 'ProcessingRun'), ('GenomicMeasure', 'processing_runs', 'ProcessingRun'), ('ProcessingRun', 'inputs', 'GenomicMeasure'), ('ProcessingRun', 'inputs', 'Scan'), ('ProcessingRun', 'in_assessment', 'Assessment'), ('ProcessingRun', 'score_values', 'ScoreValue'), ('ScoreValue', 'in_assessment', 'Assessment')]