OpIndividual

Bases: OpMessage

This class represents the individual or patient who is the subject of the phenopacket. It provides a DTO-like object to hold data that should be instantiated by factory methods corresponding to the data source. THe class can generate a GA4GH Phenopakcet Schema Individual message.

Note that we assume the species is always human, so taxonomy is always set to 9606 Homo sapiens

Parameters:

Name	Type	Description	Default
id	str	the individual identifier (application-specific)	required
alternate_ids	list	list of alternative identifiers, optional	[]
date_of_birth	timestamp, optional	date of birth of the individual (optional, should not be used without data privacy protection)	None
iso8601duration	str	age represented as an ISO 8601 Period, e.g., P42Y5M would be 42 years and 5 months	None
vital_status	PPkt.VitalStatus	An object representing the Vital status of the individual, optional	None
karyotypic_sex		the chromosomal sex (karyotypic sex), of the individual, e.g., XY or XX or XXY, optional	None
gender		the self-described gender of the individual, optional	None

Source code in src/oncoexporter/model/op_Individual.py

class OpIndividual(OpMessage):
    """
    This class represents the individual or patient who is the subject of the phenopacket.
    It provides a DTO-like object to hold data that should be instantiated by factory methods
    corresponding to the data source. THe class can generate a GA4GH Phenopakcet Schema Individual message.

    Note that we assume the species is always human, so taxonomy is always set to
    9606 Homo sapiens

    :param id: the individual identifier (application-specific)
    :type id: str
    :param alternate_ids: list of alternative identifiers, optional
    :type alternate_ids: list
    :param date_of_birth: date of birth of the individual (optional, should not be used without data privacy protection)
    :type date_of_birth: timestamp, optional
    :param iso8601duration: age represented as an ISO 8601 Period, e.g., P42Y5M would be 42 years and 5 months
    :type iso8601duration: str
    :param vital_status: An object representing the Vital status of the individual, optional
    :type vital_status: PPkt.VitalStatus
    :param karyotypic_sex: the chromosomal sex (karyotypic sex), of the individual, e.g., XY or XX or XXY, optional
    :param karyotypic_sex: str
    :param gender: the self-described gender of the individual, optional

    """
    def __init__(self, id,
                alternate_ids = [],
                date_of_birth=None,
                iso8601duration=None,
                vital_status=None,
                sex=None,
                karyotypic_sex=None,
                gender=None) -> None:
        """Constructor method
        """
        self._id = id
        # todo add check for date_of_birth, leaving out for now
        self._iso8601duration = iso8601duration
        male_sex = {"m", "male"}
        female_sex = {"f",  "female",}
        if sex.lower() in male_sex:
            self._sex = PPkt.MALE
        elif sex.lower() in female_sex:
            self._sex = PPkt.FEMALE
        else:
            self._sex = PPkt.UNKNOWN_SEX

        self._taxonomy = PPkt.OntologyClass()
        self._taxonomy.id = "NCBITaxon:9606"
        self._taxonomy.label = "Homo sapiens"

        self._vital_status = vital_status


    def to_ga4gh(self) -> PPkt.Individual:
        """Transform the data in the onject into a GA4GH Phenopacket Individual
        :return: An message corresponding to the GA4GH Phenopacket Individual
        :rtype: PPkt.Individual
        """
        individual =  PPkt.Individual()
        individual.id = self._id
        if self._iso8601duration is not None:
            individual.time_at_last_encounter.age.iso8601duration = self._iso8601duration
        individual.sex = self._sex
        if self._taxonomy is not None:
            individual.taxonomy.CopyFrom(self._taxonomy)
        if self._vital_status is not None:
            individual.vital_status.status = self._vital_status.status
        return individual

__init__(id, alternate_ids=[], date_of_birth=None, iso8601duration=None, vital_status=None, sex=None, karyotypic_sex=None, gender=None)

Constructor method

Source code in src/oncoexporter/model/op_Individual.py

def __init__(self, id,
            alternate_ids = [],
            date_of_birth=None,
            iso8601duration=None,
            vital_status=None,
            sex=None,
            karyotypic_sex=None,
            gender=None) -> None:
    """Constructor method
    """
    self._id = id
    # todo add check for date_of_birth, leaving out for now
    self._iso8601duration = iso8601duration
    male_sex = {"m", "male"}
    female_sex = {"f",  "female",}
    if sex.lower() in male_sex:
        self._sex = PPkt.MALE
    elif sex.lower() in female_sex:
        self._sex = PPkt.FEMALE
    else:
        self._sex = PPkt.UNKNOWN_SEX

    self._taxonomy = PPkt.OntologyClass()
    self._taxonomy.id = "NCBITaxon:9606"
    self._taxonomy.label = "Homo sapiens"

    self._vital_status = vital_status

to_ga4gh()

Transform the data in the onject into a GA4GH Phenopacket Individual

Returns:

Type	Description
PPkt.Individual	An message corresponding to the GA4GH Phenopacket Individual

Source code in src/oncoexporter/model/op_Individual.py

def to_ga4gh(self) -> PPkt.Individual:
    """Transform the data in the onject into a GA4GH Phenopacket Individual
    :return: An message corresponding to the GA4GH Phenopacket Individual
    :rtype: PPkt.Individual
    """
    individual =  PPkt.Individual()
    individual.id = self._id
    if self._iso8601duration is not None:
        individual.time_at_last_encounter.age.iso8601duration = self._iso8601duration
    individual.sex = self._sex
    if self._taxonomy is not None:
        individual.taxonomy.CopyFrom(self._taxonomy)
    if self._vital_status is not None:
        individual.vital_status.status = self._vital_status.status
    return individual