def test_clean_alignments_cleans_only_old_alignemnts_sequences(self):
"""
Tests that only alignments older than 7 days are removed from the database when clean_alignments is run
"""
seq_ids_old = []
for i in range(2):
alignment_old = Alignment.objects.create_alignment(self.name, self.data)
alignment_old.created = datetime.now(timezone.utc) - timedelta(days=7)
alignment_old.save()
modified_old = Alignment.objects.get(pk=alignment_old.pk)
seq_ids_old.extend([m.pk for m in modified_old.seqs.all()])
alignment_new = Alignment.objects.create_alignment(self.name, self.data)
seq_ids_new = [a.pk for a in alignment_new.seqs.all()]
clean_alignments()
for s in seq_ids_new:
try:
new_seq = Seqrecord.objects.get(pk=s)
self.assertTrue(new_seq.pk in seq_ids_new, 'sequence %s was removed' % new_seq.pk)
except Seqrecord.DoesNotExist as error:
self.assertFalse(str(error) == 'Seqrecord matching query does not exist.', error)
for s in seq_ids_old:
try:
old_seq = Seqrecord.objects.get(pk=s)
self.assertFalse(old_seq.pk in seq_ids_old, 'sequence %s was not removed' % old_seq.pk)
except Seqrecord.DoesNotExist as error:
self.assertEqual(str(error), 'Seqrecord matching query does not exist.', error)
def test_clean_alignments_leaves_recent_alignments_untouched(self):
"""
Tests that an alignment not older than 7 days is not removed from the database when clean_alignments is run
"""
alignment = Alignment.objects.create_alignment(self.name, self.data)
alignment.created = datetime.now(timezone.utc) - timedelta(days=6)
alignment.save()
modified = Alignment.objects.get(pk=alignment.pk)
self.assertTrue(datetime.now(timezone.utc) - modified.created < timedelta(days=7), modified.created)
clean_alignments()
try:
new = Alignment.objects.get(name=self.name)
self.assertTrue(new.name == self.name, '%s was removed' % new.name)
except Alignment.DoesNotExist as error:
self.assertFalse(str(error) == 'Alignment matching query does not exist.', error)
def test_clean_alignments_removes_sequences_associated_to_old_alignments(self):
"""
Tests that all sequences associated to an alignment older than 7 days are removed from the database when
clean_alignments is run
"""
alignment = Alignment.objects.create_alignment(self.name, self.data)
alignment.created = datetime.now(timezone.utc) - timedelta(days=7)
alignment.save()
modified = Alignment.objects.get(pk=alignment.pk)
self.assertTrue(datetime.now(timezone.utc) - modified.created > timedelta(days=7), modified.created)
seq_ids = [m.pk for m in modified.seqs.all()]
clean_alignments()
for s in seq_ids:
try:
old_seq = Seqrecord.objects.get(pk=s)
self.assertFalse(old_seq.pk in seq_ids, 'sequence %s was not removed' % old_seq.pk)
except Seqrecord.DoesNotExist as error:
self.assertEqual(str(error), 'Seqrecord matching query does not exist.', error)
def test_clean_alignments_cleans_only_old_alignemnts(self):
"""
Tests that only alignments older than 7 days are removed from the database when clean_alignments is run
"""
alignment_old = Alignment.objects.create_alignment(self.name, self.data)
alignment_new = Alignment.objects.create_alignment(self.name, self.data)
alignment_old.created = datetime.now(timezone.utc) - timedelta(days=7)
alignment_old.save()
modified_old = Alignment.objects.get(pk=alignment_old.pk)
self.assertTrue(datetime.now(timezone.utc) - modified_old.created > timedelta(days=7), modified_old.created)
clean_alignments()
try:
new = Alignment.objects.get(pk=alignment_new.pk)
self.assertTrue(new.name == self.name, '%s was not removed' % new.name)
except Alignment.DoesNotExist as error:
self.assertFalse(str(error) == 'Alignment matching query does not exist.', error)
try:
old = Alignment.objects.get(pk=alignment_old.pk)
self.assertFalse(old.name == self.name, '%s was removed' % old.name)
except Alignment.DoesNotExist as error:
self.assertEqual(str(error), 'Alignment matching query does not exist.', error)
