cubes.piws.importer.genetics.Genetics

class cubes.piws.importer.genetics.Genetics(session, project_name, center_name, genetics, can_read=True, can_update=True, data_filepath=None, use_store=True, piws_security_model=True)

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

__init__(session, project_name, center_name, genetics, can_read=True, can_update=True, data_filepath=None, use_store=True, piws_security_model=True)

Initialize the Genetics class.

Parameters:

session: Session (mandatory) :

a cubicweb session.

project_name: str (mandatory) :

the name of the project

center_name: str (mandatory) :

the center name

genetics: dict of list of dict (mandatory) :

the genetic measure description: the first dictionary contains the timepoint as keys and then a list of dictionaries with two keys (GenomicMeasures - Assessment) that contains the entities parameter descriptions.

can_read: bool (optional, default True) :

set the read permission to the imported data.

can_update: bool (optional, default True) :

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.

Notes

Here is an example of the definition of the ‘genetics’ parameter:

genetics = {
    "V1": [{
        "GenomicMeasures": [{
            "GenomicPlatform": {
                "related_snps": [
                    u"rs325623", u"rs272569", u"rs400",
                    u"rs1053026"
                ],
                "name": u"Illumina",
                "related_subjects": [
                    u"subject0", u"subject1", u"subject2",
                    u"subject3", u"subject4", u"subject5",
                    u"subject6", u"subject7", u"subject8",
                    u"subject9"
                ]
            },
            "GenomicMeasure": {
                "identifier": u"toy_V1_genetic_Illumina_raw_json",
                "label": u"toy_V1_genetic_Illumina_raw_json",
                "type": u"raw",
                "format": u"json"
            },
            "FileSet": {
                "identifier": u"toy_V1_genetic",
                "name": u"raw genetic measure"
            },
            "ExternalResources": [{
                "absolute_path": True,
                "identifier": u"toy_V1_genetic_1",
                "name": u"genetic",
                "filepath": u"/tmp/demo/V1/genetic/genetic.json"
            }]
        }],
        "Assessment": {
            "identifier": u"toy_V1_genetic",
            "timepoint": u"V1"}
    }]
}

Methods

__init__(session, project_name, center_name, ...)	Initialize the Genetics class.
cleanup()	Method to cleanup temporary items and to commit changes.
import_data()	Method that import some genetic 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.genetics'

_create_measure(measure_struct, fset_struct, extfiles, related_subjects, subjects_eid_map, study_eid, assessment_eid, platform_eid)

Create a genomic measure and its associated relations.

_create_platform(platform_struct, related_snps)

Create a genomic platform and its associated relations.

import_data()

Method that import some genetic data in the db.

Note

Below the schema used to insert the genetic data:

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'), ('GenomicMeasure', 'study', 'Study'), ('Study', 'study_genomic_measures', 'GenomicMeasure'), ('GenomicMeasure', 'subjects', 'Subject'), ('Subject', 'subject_genomic_measures', 'GenomicMeasure'), ('Assessment', 'genomic_measures', 'GenomicMeasure'), ('GenomicMeasure', 'in_assessment', 'Assessment'), ('GenomicMeasure', 'genomic_platform', 'GenomicPlatform'), ('GenomicPlatform', 'genomic_platform_genomic_measures', 'GenomicMeasure'), ('GenomicPlatform', 'snps', 'Snp')]