def _create_entities(self):
# Create study
study = Study(external_id='phs001')
# Create participant
p = Participant(external_id='p1',
is_proband=True, study=study)
# Create sequencing_center
sc = SequencingCenter.query.filter_by(name="Baylor").one_or_none()
if sc is None:
sc = SequencingCenter(name="Baylor")
db.session.add(sc)
db.session.commit()
# Create sequencing experiments
se1 = SequencingExperiment(**self._make_seq_exp('se1'),
sequencing_center_id=sc.kf_id)
se2 = SequencingExperiment(**self._make_seq_exp('se2'),
sequencing_center_id=sc.kf_id)
# Create biospecimen
bs = Biospecimen(external_sample_id='bio1', analyte_type='dna',
participant_id=p.kf_id,
sequencing_center_id=sc.kf_id)
# Create genomic files
gfs = []
for i in range(4):
kwargs = {
'file_name': 'file_{}'.format(i),
'data_type': 'submitted aligned read',
'file_format': '.cram',
'urls': ['s3://file_{}'.format(i)],
'hashes': {'md5': str(uuid.uuid4())},
'controlled_access': True,
'is_harmonized': True,
'reference_genome': 'Test01'
}
gf = GenomicFile(**kwargs,
sequencing_experiment_id=se1.kf_id)
if i % 2:
se1.genomic_files.append(gf)
else:
se2.genomic_files.append(gf)
gfs.append(gf)
bs.genomic_files = gfs
p.biospecimens = [bs]
db.session.add(p)
db.session.commit()
def _create_participants_and_dependents(self):
"""
Create participant with required entities
"""
# Create study
study = Study(external_id='phs001')
names = ['Fred', 'Wilma', 'Pebbles', 'Dino']
proband = [True, False]
participants = []
for i, _name in enumerate(names):
# Participants
p = Participant(external_id=_name,
is_proband=random.choice(proband),
study=study)
db.session.add(p)
db.session.commit()
# Sequencing center
sc = SequencingCenter.query.filter_by(name="Baylor").one_or_none()
if sc is None:
sc = SequencingCenter(name="Baylor")
db.session.add(sc)
db.session.commit()
# SequencingExperiment
se = self._create_experiment('se_{}'.format(i),
sequencing_center_id=sc.kf_id)
# Biospecimen
s = self._create_biospecimen('s_{}'.format(i),
sequencing_center_id=sc.kf_id,
participant_id=p.kf_id)
# Input GF
gf_in = self._create_genomic_file(
'gf_{}_in'.format(i),
sequencing_experiment_id=se.kf_id)
# Output GF
gf_out = self._create_genomic_file(
'gf_{}_out'.format(i),
data_type='aligned read',
sequencing_experiment_id=se.kf_id)
s.genomic_files = [gf_in, gf_out]
p.biospecimens = [s]
participants.append(p)
return participants
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()