def test_pipeline(self):
expected_counts = {
'batches':
2,
'cohorts':
2,
'genes':
65,
'projects':
1,
'results_per_sample': [
{
'batch': 'batch1',
'sample': 'NA12891',
'count': 1963,
},
{
'batch': 'batch1',
'sample': 'NA12892',
'count': 1963,
},
{
'batch': 'batch1',
'sample': 'NA12878',
'count': 1963,
},
{
'batch': 'batch2',
'sample': 'NA12891',
'count': 2094,
},
{
'batch': 'batch2',
'sample': 'NA12892',
'count': 2094,
},
{
'batch': 'batch2',
'sample': 'NA12878',
'count': 2094,
},
],
'samples':
6,
'transcripts':
108,
'variant_effects':
8788,
'variants':
4057,
'samples_per_batch': [(1, 3), (2, 3)],
}
expected_counts['results'] = \
sum([x['count'] for x in expected_counts['results_per_sample']])
# Immediately validates and creates a sample
management.call_command('samples', 'queue')
# Synchronously work on queue
worker1 = get_worker('variants')
worker2 = get_worker('default')
# Ensure sample-related entries are created..
self.assertEqual(Project.objects.count(), expected_counts['projects'])
self.assertEqual(Batch.objects.count(), expected_counts['batches'])
self.assertEqual(Sample.objects.count(), expected_counts['samples'])
# World and project cohort..
self.assertEqual(Cohort.objects.count(), expected_counts['cohorts'])
# Nothing published yet..
self.assertEqual(
Sample.objects.filter(published=False).count(),
expected_counts['samples'])
self.assertEqual(
Cohort.objects.filter(count=0, published=False).count(),
expected_counts['cohorts'])
self.assertEqual(
Batch.objects.filter(count=0, published=False).count(),
expected_counts['batches'])
# Manifests are stored
self.assertEqual(SampleManifest.objects.count(),
expected_counts['samples'])
for manifest in SampleManifest.objects.all():
self.assertNotEqual(manifest.content, '')
self.assertFalse(manifest.content_has_changed())
# Work on variants...
worker1.work(burst=True)
self.assertEqual(Variant.objects.count(), expected_counts['variants'])
# Work on effects...
worker2.work(burst=True)
self.assertEqual(Gene.objects.count(), expected_counts['genes'])
self.assertEqual(Transcript.objects.count(),
expected_counts['transcripts'])
self.assertEqual(VariantEffect.objects.count(),
expected_counts['variant_effects'])
self.assertEqual(Sift.objects.count(), 0)
self.assertEqual(PolyPhen2.objects.count(), 0)
self.assertEqual(ThousandG.objects.count(), 0)
self.assertEqual(EVS.objects.count(), 0)
# Results loaded..
self.assertEqual(Result.objects.count(), expected_counts['results'])
# Batches are now published..
self.assertEqual(
Batch.objects.filter(published=True).count(),
expected_counts['batches'])
# Ensure the counts are accurate for each sample..
for ec in expected_counts['results_per_sample']:
sample = Sample.objects.get(name=ec['sample'],
batch__name=ec['batch'])
self.assertTrue(sample.published)
self.assertEqual(sample.count, ec['count'])
# Batches are created with the samples, but are unpublished
for pk, count in expected_counts['samples_per_batch']:
batch = Batch.objects.get(pk=pk)
self.assertTrue(batch.published)
self.assertEqual(batch.count, count)
# Ensure the state changes were logged..
system = System.get(Sample.objects.all()[0])
self.assertEqual(len(system), 3)
def setUp(self):
self.system = System()
self.system.save()
def test_pipeline(self):
# Immediately validates and creates a sample
management.call_command('samples', 'queue')
# Synchronously work on queue
worker1 = get_worker('variants')
worker2 = get_worker('default')
# Ensure sample-related entries are created..
self.assertEqual(Project.objects.count(), 1)
self.assertEqual(Batch.objects.count(), 4)
self.assertEqual(Sample.objects.count(), 15)
# World and project cohort..
self.assertEqual(Cohort.objects.count(), 2)
# Nothing published yet..
self.assertEqual(Sample.objects.filter(published=False).count(), 15)
self.assertEqual(
Cohort.objects.filter(count=0, published=False).count(), 2)
self.assertEqual(
Batch.objects.filter(count=0, published=False).count(), 4)
# Manifests are stored
self.assertEqual(SampleManifest.objects.count(), 15)
for manifest in SampleManifest.objects.all():
self.assertNotEqual(manifest.content, '')
self.assertFalse(manifest.content_has_changed())
# Work on variants...
worker1.work(burst=True)
self.assertEqual(Variant.objects.count(), 674)
# Work on effects...
worker2.work(burst=True)
self.assertEqual(Gene.objects.count(), 104)
self.assertEqual(Transcript.objects.count(), 255)
self.assertEqual(VariantEffect.objects.count(), 1418)
self.assertEqual(Sift.objects.count(), 0)
self.assertEqual(PolyPhen2.objects.count(), 0)
self.assertEqual(ThousandG.objects.count(), 0)
self.assertEqual(EVS.objects.count(), 0)
# Results loaded..
self.assertEqual(Result.objects.count(), 3436)
# Batches are now published..
self.assertEqual(Batch.objects.filter(published=True).count(), 3)
# Ensure the counts are accurate for each sample..
for pk, count in [(1, 289), (2, 281), (3, 268), (4, 295), (5, 296),
(6, 293), (7, 264), (8, 289), (9, 264), (10, 293),
(11, 289), (12, 315)]:
sample = Sample.objects.get(pk=pk)
self.assertTrue(sample.published)
self.assertEqual(sample.count, count)
# Batches are created with the samples, but are unpublished
for pk, count in [(1, 5), (2, 3), (3, 4)]:
batch = Batch.objects.get(pk=pk)
self.assertTrue(batch.published)
self.assertEqual(batch.count, count)
# Ensure the state changes were logged..
system = System.get(Sample.objects.all()[0])
self.assertEqual(len(system), 3)
class SystemTestCase(TestCase):
def setUp(self):
self.system = System()
self.system.save()
def test_simple(self):
system = self.system
system.transition('Initialize', 'Initialized')
self.assertEqual(len(system), 1)
def test_long(self):
system = self.system
# Specify the event..
system.start_transition('Initialize')
self.assertTrue(system.in_transition())
self.assertEqual(system.current_state(), State.TRANSITION)
self.assertEqual(len(system), 1)
self.assertRaises(STSError, system.start_transition, 'Initialize')
# Sleep for 2 seconds..
time.sleep(2)
# Specify the state..
trans = system.end_transition('Initialized')
self.assertTrue(trans.duration, 2)
self.assertFalse(system.in_transition())
self.assertEqual(system.current_state().name, 'Initialized')
self.assertEqual(len(system), 1)
self.assertRaises(STSError, system.end_transition, 'Initialized')
system.transition('Saved', event='Save by foobar')
system.transition('Saved', event='Save by admin')
self.assertEqual(len(system), 3)
self.assertEqual(State.objects.count(), 3)
self.assertEqual(Event.objects.count(), 3)
def test_iteration(self):
system = self.system
system.transition('Shoe Buckled', event='Buckle Shoe')
system.transition('Door Closed', event='Close Door')
# Test iteration
self.assertEqual([str(t.state) for t in system], [
'Shoe Buckled',
'Door Closed',
])
def test_getitem(self):
system = self.system
self.assertEqual(system[:3], [])
self.assertEqual(system[2:3], [])
self.assertRaises(IndexError, system.__getitem__, 5)
self.assertRaises(IndexError, system.__getitem__, slice(None, None, 2))
self.assertRaises(ValueError, system.__getitem__, slice(None, None))
for i in range(1, 6):
system.transition('Count {0}'.format(i), event='Incr 1')
# Don't be confused.. indexing is zero-based, while counting is 1-based
self.assertEqual([str(t.state) for t in system[:3]],
['Count 1', 'Count 2', 'Count 3'])
self.assertEqual([str(t.state) for t in system[-3:]],
['Count 3', 'Count 4', 'Count 5'])
self.assertEqual([str(t.state) for t in system[:-3]],
['Count 1', 'Count 2'])
self.assertEqual([str(t.state) for t in system[1:3]],
['Count 2', 'Count 3'])
self.assertEqual(str(system[3].state), 'Count 4')
self.assertEqual(str(system[-1].state), 'Count 5')
# Bad slices..
self.assertEqual(system[-1:-3], [])
self.assertEqual(system[-1:2], [])
self.assertEqual(system[1:1], [])
def test_shortcuts(self):
from django.contrib.auth.models import User
from sts.shortcuts import transition, start_transition, end_transition
user = User.objects.create_user(username='******', password='******',
email='*****@*****.**')
transition(user, 'Creating User', 'User Created')
start_transition(user, 'Creating User')
end_transition(user, 'User Created')
def test_context_manager(self):
from sts.contextmanagers import transition
with transition('Sleeper', 'Awake', event='Nap') as trans:
time.sleep(2)
trans.message = 'That was a short nap!'
system = System.objects.get(name='Sleeper')
self.assertEqual(system.current_state().name, 'Awake')
trans = system[0]
self.assertEqual(trans.message, 'That was a short nap!')
self.assertTrue(2000 < trans.duration < 3000)
try:
with transition('Sleeper', 'Awake', event='Nap', fail_state='Annoyed'):
raise Exception
except:
pass
self.assertEqual(system.current_state().name, 'Annoyed')
def test_pipeline(self):
expected_counts = {
'batches': 2,
'cohorts': 2,
'genes': 65,
'projects': 1,
'results_per_sample': [
{
'batch': 'batch1',
'sample': 'NA12891',
'count': 1963,
},
{
'batch': 'batch1',
'sample': 'NA12892',
'count': 1963,
},
{
'batch': 'batch1',
'sample': 'NA12878',
'count': 1963,
},
{
'batch': 'batch2',
'sample': 'NA12891',
'count': 2094,
},
{
'batch': 'batch2',
'sample': 'NA12892',
'count': 2094,
},
{
'batch': 'batch2',
'sample': 'NA12878',
'count': 2094,
},
],
'samples': 6,
'transcripts': 108,
'variant_effects': 8788,
'variants': 4057,
'samples_per_batch': [(1, 3), (2, 3)],
}
expected_counts['results'] = \
sum([x['count'] for x in expected_counts['results_per_sample']])
# Immediately validates and creates a sample
management.call_command('samples', 'queue')
# Synchronously work on queue
worker1 = get_worker('variants')
worker2 = get_worker('default')
# Ensure sample-related entries are created..
self.assertEqual(Project.objects.count(), expected_counts['projects'])
self.assertEqual(Batch.objects.count(), expected_counts['batches'])
self.assertEqual(Sample.objects.count(), expected_counts['samples'])
# World and project cohort..
self.assertEqual(Cohort.objects.count(), expected_counts['cohorts'])
# Nothing published yet..
self.assertEqual(Sample.objects.filter(published=False).count(),
expected_counts['samples'])
self.assertEqual(
Cohort.objects.filter(count=0, published=False).count(),
expected_counts['cohorts'])
self.assertEqual(
Batch.objects.filter(count=0, published=False).count(),
expected_counts['batches'])
# Manifests are stored
self.assertEqual(SampleManifest.objects.count(),
expected_counts['samples'])
for manifest in SampleManifest.objects.all():
self.assertNotEqual(manifest.content, '')
self.assertFalse(manifest.content_has_changed())
# Work on variants...
worker1.work(burst=True)
self.assertEqual(Variant.objects.count(), expected_counts['variants'])
# Work on effects...
worker2.work(burst=True)
self.assertEqual(Gene.objects.count(), expected_counts['genes'])
self.assertEqual(Transcript.objects.count(),
expected_counts['transcripts'])
self.assertEqual(VariantEffect.objects.count(),
expected_counts['variant_effects'])
self.assertEqual(Sift.objects.count(), 0)
self.assertEqual(PolyPhen2.objects.count(), 0)
self.assertEqual(ThousandG.objects.count(), 0)
self.assertEqual(EVS.objects.count(), 0)
# Results loaded..
self.assertEqual(Result.objects.count(), expected_counts['results'])
# Batches are now published..
self.assertEqual(Batch.objects.filter(published=True).count(),
expected_counts['batches'])
# Ensure the counts are accurate for each sample..
for ec in expected_counts['results_per_sample']:
sample = Sample.objects.get(name=ec['sample'],
batch__name=ec['batch'])
self.assertTrue(sample.published)
self.assertEqual(sample.count, ec['count'])
# Batches are created with the samples, but are unpublished
for pk, count in expected_counts['samples_per_batch']:
batch = Batch.objects.get(pk=pk)
self.assertTrue(batch.published)
self.assertEqual(batch.count, count)
# Ensure the state changes were logged..
system = System.get(Sample.objects.all()[0])
self.assertEqual(len(system), 3)
