def test_builder_pipeline():
"""Test the entire builder pipeline."""
chanjo_db = Store(':memory:')
chanjo_db.set_up()
# test with minimal BED "file"
bed_stream = io.open('tests/fixtures/CCDS.mini.bed', 'r', encoding='utf-8')
init_db(chanjo_db, bed_stream)
block = chanjo_db.get('block', 'CCDS2.2')
assert block.start == 12
assert block.end == 35
superblock = chanjo_db.get('superblock', 'RFPL2')
assert superblock.start == 32586759
assert superblock.end == 32589260
block_ids = [block_.id for block_ in superblock.blocks]
assert set(block_ids) == set(['CCDS46694.1', 'CCDS54521.1'])
assert len(chanjo_db.find('block')) == 5
assert len(chanjo_db.find('superblock')) == 4
class TestBuildElement(object):
def setup(self):
self.store = Store(':memory:')
self.store.set_up()
self.interval = BaseInterval('1',
10,
100,
name='int1',
block_ids=['block1', 'block2'],
superblock_ids=['sblock1', 'sblock1'])
self.db_interval = StoreInterval(interval_id=self.interval.name,
contig=self.interval.contig,
start=self.interval.start,
end=self.interval.end,
strand=self.interval.strand)
self.interval_group = [('block2', self.db_interval, 'sblock1')]
def test_build_interval(self):
intervals = list(build_interval(self.store, self.interval))
self.store.save()
new_interval = self.store.get('interval', self.interval.name)
assert new_interval.id == self.interval.name
assert new_interval.start == self.interval.start
assert len(intervals) == 2
def test_build_block(self):
superblock_id, new_block = build_block(self.store, self.interval_group)
self.store.save()
db_block = self.store.get('block', self.interval_group[0][0])
assert superblock_id == 'sblock1'
assert new_block.id == db_block.id == self.interval_group[0][0]
assert new_block.start == db_block.start == self.interval_group[0][
1].start
class TestBuildElement(object):
def setup(self):
self.store = Store(":memory:")
self.store.set_up()
self.interval = BaseInterval(
"1", 10, 100, name="int1", block_ids=["block1", "block2"], superblock_ids=["sblock1", "sblock1"]
)
self.db_interval = StoreInterval(
interval_id=self.interval.name,
contig=self.interval.contig,
start=self.interval.start,
end=self.interval.end,
strand=self.interval.strand,
)
self.interval_group = [("block2", self.db_interval, "sblock1")]
def test_build_interval(self):
intervals = list(build_interval(self.store, self.interval))
self.store.save()
new_interval = self.store.get("interval", self.interval.name)
assert new_interval.id == self.interval.name
assert new_interval.start == self.interval.start
assert len(intervals) == 2
def test_build_block(self):
superblock_id, new_block = build_block(self.store, self.interval_group)
self.store.save()
db_block = self.store.get("block", self.interval_group[0][0])
assert superblock_id == "sblock1"
assert new_block.id == db_block.id == self.interval_group[0][0]
assert new_block.start == db_block.start == self.interval_group[0][1].start
