def registry_with_biosources_and_biomaterials() -> CentralSubjectRegistry:
individuals = [Individual(individual_id='P1', birth_date='1950-05-05')]
diagnoses = [
Diagnosis(diagnosis_id='D1',
individual_id='P1',
diagnosis_date='2010-03-31')
]
biosources = [
Biosource(biosource_id='PMCBS000AAA',
individual_id='P1',
diagnosis_id='D1'),
Biosource(biosource_id='PMCBS000AAB',
individual_id='P1',
diagnosis_id='D1')
]
biomaterials = [
Biomaterial(biomaterial_id='PMCBM000AAA',
src_biosource_id='PMCBS000AAA'),
Biomaterial(biomaterial_id='PMCBM000AAB',
src_biosource_id='PMCBS000AAB')
]
return CentralSubjectRegistry.create({
'Individual': individuals,
'Diagnosis': diagnoses,
'Biosource': biosources,
'Biomaterial': biomaterials
})
def registry_with_diagnoses() -> CentralSubjectRegistry:
individuals = [
Individual(individual_id='P1', birth_date='1950-05-05'),
Individual(individual_id='P2', birth_date='2001-01-01'),
Individual(individual_id='P3',
birth_date='2001-01-01',
age_first_diagnosis=5),
Individual(individual_id='P4',
birth_date='2001-01-01',
diagnosis_count=3),
]
diagnoses = [
Diagnosis(diagnosis_id='D1.1',
individual_id='P1',
diagnosis_date='2010-03-31'),
Diagnosis(diagnosis_id='D1.2',
individual_id='P1',
diagnosis_date='2012-05-05'),
Diagnosis(diagnosis_id='D2.1',
individual_id='P2',
diagnosis_date='2011-12-01'),
Diagnosis(diagnosis_id='D3.1',
individual_id='P3',
diagnosis_date='2011-12-01'),
Diagnosis(diagnosis_id='D4.1',
individual_id='P4',
diagnosis_date='2011-12-01'),
]
return CentralSubjectRegistry.create({
'Individual': individuals,
'Diagnosis': diagnoses
})
def read_subject_data(self) -> CentralSubjectRegistry:
logger.info('Reading subject registry data ...')
subject_registry_data: Dict[str, Sequence[SubjectEntity]] = {}
for entity_type in list(SubjectEntity.__args__):
subject_registry_data[entity_type.__name__] = self.read_entity_data(entity_type)
return CentralSubjectRegistry.create(subject_registry_data)
def read_subject_registry(self) -> CentralSubjectRegistry:
try:
entity_data = {
entity_type.schema()['title']: self.read_entities(
path.join(self.input_dir, entity_filename(entity_type)),
entity_type)
for entity_type in list(SubjectEntity.__args__)
}
return CentralSubjectRegistry(entity_data=entity_data)
except FileNotFoundError as fnfe:
raise FileNotFoundError('File not found. {}'.format(fnfe))
def registry_with_missing_diagnosis_data() -> CentralSubjectRegistry:
individuals = [
Individual(individual_id='P1', birth_date='1950-05-05'),
Individual(individual_id='P2', birth_date='2001-01-01'),
Individual(individual_id='P3', birth_date='2002-07-07'),
Individual(individual_id='P4')
]
diagnoses = [
Diagnosis(diagnosis_id='D1.1',
individual_id='P1',
diagnosis_date='2010-03-31'),
Diagnosis(diagnosis_id='D2.1', individual_id='P2'),
Diagnosis(diagnosis_id='D2.2', individual_id='P2'),
Diagnosis(diagnosis_id='D4.1',
individual_id='P4',
diagnosis_date='2012-02-15')
]
return CentralSubjectRegistry.create({
'Individual': individuals,
'Diagnosis': diagnoses
})
def csr_subject_registry(csr_individuals) -> CentralSubjectRegistry:
return CentralSubjectRegistry.create({'Individual': csr_individuals})