def _create_save_to_db(self):
"""
Create and save phenotype
Requires creating a participant
Create a phenotype and add it to participant as kwarg
Save participant
"""
# Create study
study = Study(external_id='phs001')
# Create phenotype
kwargs = {
'external_id': 'test_phenotype_0',
'source_text_phenotype': 'Hand Tremor',
'hpo_id_phenotype': 'HP:0002378',
'snomed_id_phenotype': '38033009',
'observed': 'Positive',
'age_at_event_days': 365
}
ph = Phenotype(**kwargs)
# Create and save participant with phenotype
participant_id = 'Test subject 0'
p = Participant(external_id=participant_id,
phenotypes=[ph],
is_proband=True,
study=study)
db.session.add(p)
db.session.commit()
kwargs['participant_id'] = p.kf_id
kwargs['kf_id'] = ph.kf_id
return kwargs
def _create_phenotypes(self):
"""
Create phenotypes and required entities
"""
# Create Study
study = Study(external_id='phs001')
# Create two phenotypes
pheno = ['test phenotype 1', 'test phenotype 2']
ph1 = Phenotype(source_text_phenotype=pheno[0],
external_id='test_phenotype_0')
ph2 = Phenotype(source_text_phenotype=pheno[1],
external_id='test_phenotype_0')
p = Participant(external_id='p1', is_proband=True, study=study)
# Add to participant and save
p.phenotypes.extend([ph1, ph2])
db.session.add(p)
db.session.commit()
return [ph1, ph2], p, pheno
def test_foreign_key_constraint(self):
"""
Test that a phenotype cannot be created without an existing
reference Participant. This checks foreign key constraint
"""
# Create phenotype
data = {
'source_text_phenotype': 'phenotype_1',
'participant_id': '' # empty blank foreign key
}
d = Phenotype(**data)
# Add to db
self.assertRaises(IntegrityError, db.session.add(d))
def test_not_null_constraint(self):
"""
Test that a phenotype cannot be created without required
parameters such as participant_id
"""
# Create phenotype
data = {
'source_text_phenotype': 'phenotype_1',
# non-existent required param: participant_id
}
d = Phenotype(**data)
# Add to db
self.assertRaises(IntegrityError, db.session.add(d))
def _create_phenotypes(self, total):
"""
Create phenotypes
"""
phen_list = []
for i in range(total):
ph = random.choice(self.phenotype_chosen_list)
phen = {
'phenotype': ph[0],
'hpo_id': ph[1],
'observed': random.choice(self.observed_list),
'age_at_event_days': random.randint(0, 32872)
}
phen_list.append(Phenotype(**phen))
return phen_list
def test_create_and_find(self):
"""
Test create phenotype
"""
dt = datetime.now()
# Create Study
study = Study(external_id='phs001')
# Create and save participant
participant_id = 'Test subject 0'
p = Participant(external_id=participant_id,
is_proband=True,
study=study)
db.session.add(p)
db.session.commit()
kwarg_dict = {}
# Create phenotypes
for i in range(2):
data = {
'external_id': 'test_phenotype_{}'.format(i),
'source_text_phenotype': 'test phenotype_{}'.format(i),
'hpo_id_phenotype': 'HP:0000118',
'snomed_id_phenotype': '38033009',
'age_at_event_days': 120,
'participant_id': p.kf_id
}
ph = Phenotype(**data)
kwarg_dict[ph.external_id] = data
db.session.add(ph)
db.session.commit()
self.assertEqual(Phenotype.query.count(), 2)
for k, kwargs in kwarg_dict.items():
ph = Phenotype.query.filter_by(external_id=k).one()
for key, value in kwargs.items():
self.assertEqual(value, getattr(ph, key))
self.assertGreater(ph.created_at, dt)
self.assertGreater(ph.modified_at, dt)
self.assertIs(type(uuid.UUID(ph.uuid)), uuid.UUID)
def participants(client):
# Add a bunch of studies for pagination
for i in range(101):
s = Study(external_id='Study_{}'.format(i))
db.session.add(s)
for i in range(101):
ca = CavaticaApp(name='app', revision=0)
db.session.add(ca)
# Add a bunch of study files
s0 = Study.query.filter_by(external_id='Study_0').one()
s1 = Study.query.filter_by(external_id='Study_1').one()
for i in range(101):
sf = StudyFile(file_name='blah', study_id=s0.kf_id)
db.session.add(sf)
# Add a bunch of investigators
for _ in range(102):
inv = Investigator(name='test')
inv.studies.extend([s0, s1])
db.session.add(inv)
# Add a bunch of families
families = []
for i in range(101):
families.append(Family(external_id='Family_{}'.format(i)))
db.session.add_all(families)
db.session.flush()
participants = []
f0 = Family.query.filter_by(external_id='Family_0').one()
f1 = Family.query.filter_by(external_id='Family_1').one()
seq_cen = None
for i in range(102):
f = f0 if i < 50 else f1
s = s0 if i < 50 else s1
data = {
'external_id': "test",
'is_proband': True,
'race': 'Asian',
'ethnicity': 'Hispanic or Latino',
'diagnosis_category': 'Cancer',
'gender': 'Male'
}
p = Participant(**data, study_id=s.kf_id, family_id=f.kf_id)
diag = Diagnosis()
p.diagnoses = [diag]
outcome = Outcome()
p.outcomes = [outcome]
phen = Phenotype()
p.phenotypes = [phen]
participants.append(p)
db.session.add(p)
db.session.flush()
seq_data = {
'external_id': 'Seq_0',
'experiment_strategy': 'WXS',
'library_name': 'Test_library_name_1',
'library_strand': 'Unstranded',
'is_paired_end': False,
'platform': 'Test_platform_name_1'
}
gf_kwargs = {
'external_id': 'gf_0',
'file_name': 'hg38.fq',
'data_type': 'Aligned Reads',
'file_format': 'fastq',
'size': 1000,
'urls': ['s3://bucket/key'],
'hashes': {
'md5': str(uuid.uuid4())
},
'controlled_access': False
}
seq_cen = SequencingCenter.query.filter_by(name="Baylor")\
.one_or_none()
if seq_cen is None:
seq_cen = SequencingCenter(external_id='SC_0', name="Baylor")
db.session.add(seq_cen)
db.session.flush()
seq_exp = SequencingExperiment(**seq_data,
sequencing_center_id=seq_cen.kf_id)
db.session.add(seq_exp)
samp = Biospecimen(analyte_type='an analyte',
sequencing_center_id=seq_cen.kf_id,
participant=p)
db.session.add(samp)
p.biospecimens = [samp]
gf = GenomicFile(**gf_kwargs,
sequencing_experiment_id=seq_exp.kf_id)
db.session.add(gf)
samp.genomic_files.append(gf)
samp.diagnoses.append(diag)
db.session.flush()
rg = ReadGroup(lane_number=4, flow_cell='FL0123')
rg.genomic_files.append(gf)
ct = CavaticaTask(name='task_{}'.format(i))
ct.genomic_files.append(gf)
ca.cavatica_tasks.append(ct)
# Family relationships
for participant1, participant2 in iterate_pairwise(participants):
gender = participant1.gender
rel = 'mother'
if gender == 'male':
rel = 'father'
r = FamilyRelationship(participant1=participant1,
participant2=participant2,
participant1_to_participant2_relation=rel)
db.session.add(r)
db.session.commit()