def test_migrate_one_variant(mongo_adapter):
##GIVEN a adapter to an empty old database
adapter = mongo_adapter
assert adapter.get_variants().count() == 0
##WHEN inserting a old style variant and updating the database
chrom = '1'
pos = 880086
ref = 'T'
alt = 'C'
hom = hem = 0
obs = 3
families = ['recessive_trio', '1', '2']
variant = {
'_id': '_'.join([chrom, str(pos), ref, alt]),
'homozygote': hom,
'hemizygote': hem,
'observations': obs,
'families': families,
}
adapter.db.variant.insert_one(variant)
##THEN assert that the variant was updated correct
nr_updated = migrate_database(adapter)
assert nr_updated == 1
migrated_variant = adapter.db.variant.find_one()
assert migrated_variant['chrom'] == chrom
assert migrated_variant['start'] == pos
assert migrated_variant['end'] == pos
assert migrated_variant['homozygote'] == hom
assert migrated_variant['hemizygote'] == hem
assert migrated_variant['observations'] == obs
assert migrated_variant['families'] == families
def test_migrate_one_variant(mongo_adapter):
##GIVEN a adapter to an empty old database
adapter = mongo_adapter
assert sum(1 for i in adapter.get_variants()) == 0
##WHEN inserting a old style variant and updating the database
chrom = "1"
pos = 880086
ref = "T"
alt = "C"
hom = hem = 0
obs = 3
families = ["recessive_trio", "1", "2"]
variant = {
"_id": "_".join([chrom, str(pos), ref, alt]),
"homozygote": hom,
"hemizygote": hem,
"observations": obs,
"families": families,
}
adapter.db.variant.insert_one(variant)
##THEN assert that the variant was updated correct
nr_updated = migrate_database(adapter)
assert nr_updated == 1
migrated_variant = adapter.db.variant.find_one()
assert migrated_variant["chrom"] == chrom
assert migrated_variant["start"] == pos
assert migrated_variant["end"] == pos
assert migrated_variant["homozygote"] == hom
assert migrated_variant["hemizygote"] == hem
assert migrated_variant["observations"] == obs
assert migrated_variant["families"] == families
def migrate(ctx, ):
"""Migrate an old loqusdb instance to 1.0"""
adapter = ctx.obj["adapter"]
start_time = datetime.now()
nr_updated = migrate_database(adapter)
LOG.info("All variants updated, time to complete migration: {}".format(
datetime.now() - start_time))
LOG.info("Nr variants that where updated: %s", nr_updated)