def data_upgrades():
"""
COPY read_group.genomic_file_id TO read_group_genomic_file.read_group_id
COPY read_group.kf_id TO read_group_genomic_file.read_group_id
"""
connection = op.get_bind()
read_group_genomic_file = sa.Table(
'read_group_genomic_file', sa.MetaData(),
sa.Column('kf_id', KfId(length=11), default=kf_id_generator('RF')),
sa.Column('genomic_file_id', KfId(length=11)),
sa.Column('read_group_id', KfId(length=11)),
sa.Column('created_at', sa.DateTime(), default=datetime.now),
sa.Column('modified_at', sa.DateTime(), default=datetime.now),
sa.Column('uuid',
postgresql.UUID(),
nullable=True,
default=uuid_generator))
read_group = sa.Table('read_group', sa.MetaData(),
sa.Column('kf_id', KfId(length=11)),
sa.Column('genomic_file_id', KfId(length=11)))
results = connection.execute(
sa.select([read_group.c.genomic_file_id,
read_group.c.kf_id])).fetchall()
for gf, rg in results:
if not gf or not rg:
continue
connection.execute(read_group_genomic_file.insert().values(
genomic_file_id=gf, read_group_id=rg))
def data_upgrades():
"""
COPY sequencing_experiment.genomic_file_id TO
sequencing_experiment_genomic_file.sequencing_experiment_id
COPY sequencing_experiment.kf_id TO
sequencing_experiment_genomic_file.sequencing_experiment_id
"""
connection = op.get_bind()
sequencing_experiment_genomic_file = sa.Table(
'sequencing_experiment_genomic_file', sa.MetaData(),
sa.Column('kf_id', KfId(length=11), default=kf_id_generator('RF')),
sa.Column('genomic_file_id', KfId(length=11)),
sa.Column('sequencing_experiment_id', KfId(length=11)),
sa.Column('created_at', sa.DateTime(), default=datetime.now),
sa.Column('modified_at', sa.DateTime(), default=datetime.now),
sa.Column('uuid',
postgresql.UUID(),
nullable=True,
default=uuid_generator))
genomic_file = sa.Table(
'genomic_file', sa.MetaData(), sa.Column('kf_id', KfId(length=11)),
sa.Column('sequencing_experiment_id', KfId(length=11)))
results = connection.execute(
sa.select(
[genomic_file.c.kf_id,
genomic_file.c.sequencing_experiment_id])).fetchall()
for gf, seq_exp in results:
if not gf or not seq_exp:
continue
connection.execute(sequencing_experiment_genomic_file.insert().values(
genomic_file_id=gf, sequencing_experiment_id=seq_exp))
def data_upgrades():
"""
COPY genomic_file.biospecimen_id TO biospecimen_genomic_file.biospecimen_id
COPY genomic_file.kf_id TO biospecimen_genomic_file.genomic_file_id
DROP genomic_file.biospecimen_id
"""
connection = op.get_bind()
biospecimen_genomic_file = sa.Table(
'biospecimen_genomic_file',
sa.MetaData(),
sa.Column('kf_id',
dataservice.api.common.model.KfId(length=11),
default=kf_id_generator('BG')),
sa.Column('genomic_file_id',
dataservice.api.common.model.KfId(length=11)),
sa.Column('biospecimen_id',
dataservice.api.common.model.KfId(length=11)),
sa.Column('created_at', sa.DateTime(), default=datetime.now),
sa.Column('modified_at', sa.DateTime(), default=datetime.now),
)
genomic_file = sa.Table(
'genomic_file',
sa.MetaData(),
sa.Column('kf_id', dataservice.api.common.model.KfId(length=11)),
sa.Column('biospecimen_id',
dataservice.api.common.model.KfId(length=11)),
)
results = connection.execute(
sa.select([
genomic_file.c.biospecimen_id,
genomic_file.c.kf_id,
])).fetchall()
for bs, gf in results:
if not bs or not gf:
continue
connection.execute(biospecimen_genomic_file.insert().values(
biospecimen_id=bs, genomic_file_id=gf))
def test_kf_id():
"""
Test that kf_ids are generated correctly
Generates 1000 ids and makes sure they are correct length and dont
contain any invalid characters
"""
for _ in range(1000):
prefix = ''.join(random.sample(string.ascii_uppercase, 2))
kf_id = kf_id_generator(prefix)()
assert kf_id[:2] == prefix
assert len(kf_id) == 11
assert kf_id[2] == '_'
assert 'I' not in kf_id[2:]
assert 'L' not in kf_id[2:]
assert 'O' not in kf_id[2:]
assert 'U' not in kf_id[2:]
assert re.search(r'^' + prefix + r'_[A-HJ-KM-NP-TV-Z0-9]{8}', kf_id)
def data_downgrades():
"""
COPY read_group_genomic_file.genomic_file_id TO read_group.genomic_file_id
# NB This will lose all information relating many files to one read_group
"""
connection = op.get_bind()
read_group_genomic_file = sa.Table(
'read_group_genomic_file', sa.MetaData(),
sa.Column('kf_id', KfId(length=11), default=kf_id_generator('RF')),
sa.Column('genomic_file_id', KfId(length=11)),
sa.Column('read_group_id', KfId(length=11)),
sa.Column('created_at', sa.DateTime(), default=datetime.now),
sa.Column('modified_at', sa.DateTime(), default=datetime.now),
sa.Column('uuid',
postgresql.UUID(),
nullable=True,
default=uuid_generator))
read_group = sa.Table(
'read_group',
sa.MetaData(),
sa.Column('kf_id', KfId(length=11)),
sa.Column('genomic_file_id', KfId(length=11)),
)
results = connection.execute(
sa.select([
read_group_genomic_file.c.genomic_file_id,
read_group_genomic_file.c.read_group_id,
])).fetchall()
for gf, rg in results:
if not gf or not rg:
continue
connection.execute(read_group.update().where(
read_group.c.kf_id == rg).values(genomic_file_id=gf))
def data_downgrades():
"""
COPY sequencing_experiment_genomic_file.genomic_file_id TO
sequencing_experiment.genomic_file_id
# NB This will lose all information relating many files to
one sequencing_experiment
"""
connection = op.get_bind()
sequencing_experiment_genomic_file = sa.Table(
'sequencing_experiment_genomic_file', sa.MetaData(),
sa.Column('kf_id', KfId(length=11), default=kf_id_generator('RF')),
sa.Column('genomic_file_id', KfId(length=11)),
sa.Column('sequencing_experiment_id', KfId(length=11)),
sa.Column('created_at', sa.DateTime(), default=datetime.now),
sa.Column('modified_at', sa.DateTime(), default=datetime.now),
sa.Column('uuid',
postgresql.UUID(),
nullable=True,
default=uuid_generator))
genomic_file = sa.Table(
'genomic_file', sa.MetaData(), sa.Column('kf_id', KfId(length=11)),
sa.Column('sequencing_experiment_id', KfId(length=11)))
results = connection.execute(
sa.select([
sequencing_experiment_genomic_file.c.genomic_file_id,
sequencing_experiment_genomic_file.c.sequencing_experiment_id,
])).fetchall()
for gf, seq_exp in results:
if not gf or not seq_exp:
continue
connection.execute(
genomic_file.update().where(genomic_file.c.kf_id == gf).values(
sequencing_experiment_id=seq_exp))
def test_bad_foreign_key(self, client, entities, endpoint, method, field):
"""
Test bad foreign key
Foregin key is a valid kf_id but refers an entity that doesn't exist
"""
# Setup inputs
inputs = ENTITY_PARAMS['fields'][endpoint].copy()
model_cls = ENDPOINT_ENTITY_MAP.get(endpoint)
entity = entities.get(model_cls)[0]
_add_foreign_keys(inputs, entity)
inputs.update({field: id_service.kf_id_generator('ZZ')()})
# Setup endpoint
url = endpoint
if method.lower() in {'put', 'patch'}:
url = '{}/{}'.format(endpoint, entity.kf_id)
call_func = getattr(client, method.lower())
resp = call_func(url,
data=json.dumps(inputs),
headers={'Content-Type': 'application/json'})
body = json.loads(resp.data.decode('utf-8'))
assert body['_status']['code'] == 400
assert 'does not exist' in body['_status']['message']
def kf_id(cls):
kf_id = db.Column(KfId(),
primary_key=True,
doc="ID assigned by Kids First",
default=kf_id_generator(cls.__prefix__))
return kf_id
