def test_pbmerge_indexing(self):
log.debug("Test through API")
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(aln.toExternalFiles()), 2)
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'merged.bam')
log.info(outfn)
consolidateXml(aln, outfn, cleanup=False)
self.assertTrue(os.path.exists(outfn))
self.assertTrue(os.path.exists(outfn + '.pbi'))
cons = AlignmentSet(outfn)
self.assertEqual(len(aln), len(cons))
orig_stats = os.stat(outfn + '.pbi')
cons.externalResources[0].pbi = None
self.assertEqual(None, cons.externalResources[0].pbi)
# test is too quick, stat times might be within the same second
time.sleep(1)
cons.induceIndices()
self.assertEqual(outfn + '.pbi', cons.externalResources[0].pbi)
self.assertEqual(orig_stats, os.stat(cons.externalResources[0].pbi))
cons.externalResources[0].pbi = None
self.assertEqual(None, cons.externalResources[0].pbi)
# test is too quick, stat times might be within the same second
time.sleep(1)
cons.induceIndices(force=True)
self.assertNotEqual(orig_stats, os.stat(cons.externalResources[0].pbi))
def test_pbmerge_indexing(self):
log.debug("Test through API")
aln = AlignmentSet(data.getXml(11))
assert len(aln.toExternalFiles()) == 2
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'merged.bam')
log.info(outfn)
consolidateXml(aln, outfn, cleanup=False)
assert os.path.exists(outfn)
assert os.path.exists(outfn + '.pbi')
cons = AlignmentSet(outfn)
assert len(aln) == len(cons)
orig_stats = os.stat(outfn + '.pbi')
cons.externalResources[0].pbi = None
assert cons.externalResources[0].pbi is None
# test is too quick, stat times might be within the same second
time.sleep(1)
cons.induceIndices()
assert outfn + '.pbi' == cons.externalResources[0].pbi
assert orig_stats == os.stat(cons.externalResources[0].pbi)
cons.externalResources[0].pbi = None
assert cons.externalResources[0].pbi is None
# test is too quick, stat times might be within the same second
time.sleep(1)
cons.induceIndices(force=True)
assert orig_stats != os.stat(cons.externalResources[0].pbi)
def test_pbmerge_indexing(self):
log.debug("Test through API")
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(aln.toExternalFiles()), 2)
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'merged.bam')
log.info(outfn)
consolidateXml(aln, outfn, cleanup=False)
self.assertTrue(os.path.exists(outfn))
self.assertTrue(os.path.exists(outfn + '.pbi'))
cons = AlignmentSet(outfn)
self.assertEqual(len(aln), len(cons))
orig_stats = os.stat(outfn + '.pbi')
cons.externalResources[0].pbi = None
self.assertEqual(None, cons.externalResources[0].pbi)
# test is too quick, stat times might be within the same second
time.sleep(1)
cons.induceIndices()
self.assertEqual(outfn + '.pbi', cons.externalResources[0].pbi)
self.assertEqual(orig_stats, os.stat(cons.externalResources[0].pbi))
cons.externalResources[0].pbi = None
self.assertEqual(None, cons.externalResources[0].pbi)
# test is too quick, stat times might be within the same second
time.sleep(1)
cons.induceIndices(force=True)
self.assertNotEqual(orig_stats, os.stat(cons.externalResources[0].pbi))