Python set_individual_phenotypes_from_dict Examples

Example #1

File: project_views.py Project: obonyojimmy/seqr

def save_individual_from_json_dict(project, indiv_dict):
    individual = Individual.objects.get_or_create(
        indiv_id=indiv_dict['indiv_id'], project=project)[0]
    individual.gender = indiv_dict.get('gender')
    individual.affected = indiv_dict.get('affected')
    individual.nickname = indiv_dict.get('nickname', '')
    individual.paternal_id = indiv_dict.get('paternal_id', '')
    individual.maternal_id = indiv_dict.get('maternal_id', '')
    individual.save()

    try:
        seqr_individual = get_seqr_individual_from_base_individual(individual)
        seqr_individual.sex = individual.gender
        seqr_individual.affected = individual.affected
        seqr_individual.display_name = individual.nickname
        seqr_individual.paternal_id = individual.paternal_id
        seqr_individual.maternal_id = individual.maternal_id
        seqr_individual.save()
    except Exception as e:
        print("Exception when updating SeqrIndividual: " + str(e))

    sample_management.set_family_id_for_individual(
        individual, indiv_dict.get('family_id', ''))
    sample_management.set_individual_phenotypes_from_dict(
        individual, indiv_dict.get('phenotypes', {}))

Example #2

File: project_views.py Project: burkesquires/xbrowse

def save_individual_from_json_dict(project, indiv_dict):
    individual = Individual.objects.get_or_create(indiv_id=indiv_dict['indiv_id'], project=project)[0]
    individual.gender = indiv_dict.get('gender')
    individual.affected = indiv_dict.get('affected')
    individual.nickname = indiv_dict.get('nickname', '')
    individual.paternal_id = indiv_dict.get('paternal_id', '')
    individual.maternal_id = indiv_dict.get('maternal_id', '')
    individual.save()
    sample_management.set_family_id_for_individual(individual, indiv_dict.get('family_id', ''))
    sample_management.set_individual_phenotypes_from_dict(individual, indiv_dict.get('phenotypes', {}))

Example #3

def save_individual_from_json_dict(project, indiv_dict):
    individual = Individual.objects.get_or_create(indiv_id=indiv_dict['indiv_id'], project=project)[0]
    individual.gender = indiv_dict.get('gender')
    individual.affected = indiv_dict.get('affected')
    individual.nickname = indiv_dict.get('nickname', '')
    individual.paternal_id = indiv_dict.get('paternal_id', '')
    individual.maternal_id = indiv_dict.get('maternal_id', '')
    individual.save()
    sample_management.set_family_id_for_individual(individual, indiv_dict.get('family_id', ''))
    sample_management.set_individual_phenotypes_from_dict(individual, indiv_dict.get('phenotypes', {}))

Example #4

File: project_views.py Project: batsal/xbrowse

def save_individual_from_json_dict(project, indiv_dict):
    individual = Individual.objects.get_or_create(indiv_id=indiv_dict["indiv_id"], project=project)[0]
    individual.gender = indiv_dict.get("gender")
    individual.affected = indiv_dict.get("affected")
    individual.nickname = indiv_dict.get("nickname", "")
    individual.paternal_id = indiv_dict.get("paternal_id", "")
    individual.maternal_id = indiv_dict.get("maternal_id", "")
    individual.save()
    sample_management.set_family_id_for_individual(individual, indiv_dict.get("family_id", ""))
    sample_management.set_individual_phenotypes_from_dict(individual, indiv_dict.get("phenotypes", {}))

Example #5

File: project_views.py Project: macarthur-lab/seqr

def save_individual_from_json_dict(project, indiv_dict):
    individual = get_or_create_xbrowse_model(Individual, indiv_id=indiv_dict['indiv_id'], project=project)[0]
    update_xbrowse_model(
        individual,
        gender = indiv_dict.get('gender'),
        affected = indiv_dict.get('affected'),
        nickname = indiv_dict.get('nickname', ''),
        paternal_id = indiv_dict.get('paternal_id', ''),
        maternal_id = indiv_dict.get('maternal_id', ''))

    sample_management.set_family_id_for_individual(individual, indiv_dict.get('family_id', ''))
    sample_management.set_individual_phenotypes_from_dict(individual, indiv_dict.get('phenotypes', {}))

Example #6

File: project_views.py Project: evrimulgen/seqr

def save_individual_from_json_dict(project, indiv_dict):
    individual = get_or_create_xbrowse_model(Individual, indiv_id=indiv_dict['indiv_id'], project=project)[0]
    update_xbrowse_model(
        individual,
        gender = indiv_dict.get('gender'),
        affected = indiv_dict.get('affected'),
        nickname = indiv_dict.get('nickname', ''),
        paternal_id = indiv_dict.get('paternal_id', ''),
        maternal_id = indiv_dict.get('maternal_id', ''))

    sample_management.set_family_id_for_individual(individual, indiv_dict.get('family_id', ''))
    sample_management.set_individual_phenotypes_from_dict(individual, indiv_dict.get('phenotypes', {}))