class PhenotypeResourceTestCase(AuthenticatedBaseTestCase):
def setUp(self):
# Create a new phenotype objects and store it
self.phenotype = Phenotype(term="Hyterazygoze")
self.phenotype.save()
super(PhenotypeResourceTestCase, self).setUp()
def test_get_empty(self):
response = self.client.get('/api/phenotypes/999/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.not_found)
def test_get(self):
response = self.client.get('/api/phenotypes/{0}/'.format(
self.phenotype.id),
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.ok)
self.assertTrue(response.content)
# Testing phenotype query
response = self.client.get('/api/phenotypes/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.ok)
response_obj = json.loads(response.content)
# Query should return 1 phenotype and code should be ok
self.assertEqual(response_obj['result_count'], 1)
def setUp(self):
# Creating objects needed for variant
self.pubmed = PubMed(pmid=1)
self.pubmed.save()
self.phenotype = Phenotype(term='Hymocompos',
hpo_id=1)
self.phenotype.save()
# Retrive a Chromosome and varianttype
self.chromo = Chromosome.objects.get(pk=1)
self.chromo.save()
self.varianttype = VariantType.objects.get(pk=1)
self.varianttype.save()
super(VariantsResourcesTestCase, self).setUp()
def load_hgmd_snp(self, cursor, using=None):
cursor.execute('''
select distinct
cl.acc_num as hgmd_id,
c.value as chr,
c.id as chr_id,
v.id as variant_id,
trim(both from cl.disease) as phenotype,
ph.id as phenotype_id,
cl.gene as gene,
g.id as gene_id,
cl.pmid as pubmed,
pm.pmid as pubmed_id
from (
select m.acc_num, m.disease, m.gene, m.pmid, c.chromosome, c."coordSTART" as pos
from raw.hgmd_mutation m inner join raw.hgmd_hg19_coords c on (m.acc_num = c.acc_num)
) cl
left outer join chromosome c on (cl.chromosome = c.value)
left outer join variant v on (c.id = v.chr_id and cl.pos = v.pos)
left outer join variant_type vt on (v.type_id = vt.id)
left outer join phenotype ph on (lower(trim(both from regexp_replace(cl.disease, '\s*\?$', ''))) = lower(ph.term))
left outer join pubmed pm on (cl.pmid::varchar = pm.pmid::varchar)
left outer join gene g on (cl.gene::text = g.symbol::text)
left outer join variant_phenotype vp on (vp.variant_id = v.id)
where vt.value = 'SNP'
and cl.disease not like '%%?'
and v.id is not null and g.id is not null
order by c.id
''')
keys = ['hgmd_id', 'chr', 'chr_id', 'variant_id',
'phenotype', 'phenotype_id', 'gene', 'gene_id',
'pubmed', 'pubmed_id']
count = 0
new_pubmed_map = {}
new_phenotype_map = {}
chrs = dict(Chromosome.objects.values_list('value', 'id'))
while True:
rows = cursor.fetchmany(100)
if not rows:
break
for row in rows:
record = dict(zip(keys, row))
# Get or create a pubmed record
if record['pubmed_id']:
pubmed = PubMed(pmid=record['pubmed_id'])
pubmed._state.db = using
# Some records have a bogus PMID. Only proces the valid ones.
elif type(record['pubmed']) is int or record['pubmed'].isdigit():
pmid = int(record['pubmed'])
if pmid in new_pubmed_map:
pubmed = new_pubmed_map[pmid]
else:
pubmed = PubMed(pmid=pmid)
pubmed.save()
new_pubmed_map[pmid] = pubmed
else:
pubmed = None
# Get or create a the phenotype, associate the HGMD id with
if record['phenotype_id']:
phenotype = Phenotype(pk=record['phenotype_id'])
phenotype._state.db = using
else:
term = record['phenotype']
# Check newly added objects
if term in new_phenotype_map:
phenotype = new_phenotype_map[term]
else:
phenotype = Phenotype(term=record['phenotype'])
phenotype.save()
new_phenotype_map[term] = phenotype
_chr = Chromosome(pk=chrs[record['chr']])
_chr._state.db = using
if record['gene_id']:
gene = Gene(pk=record['gene_id'])
gene._state.db = using
try:
gp = GenePhenotype.objects.get(gene=gene, phenotype=phenotype)
except GenePhenotype.DoesNotExist:
gp = GenePhenotype(gene=gene, phenotype=phenotype)
gp.hgmd_id = record['hgmd_id']
gp.save()
else:
gene = None
if record['variant_id']:
variant = Variant(pk=record['variant_id'])
variant._state.db = using
try:
vp = VariantPhenotype.objects.get(variant=variant, phenotype=phenotype)
except VariantPhenotype.DoesNotExist:
vp = VariantPhenotype(variant=variant, phenotype=phenotype)
vp.hgmd_id = record['hgmd_id']
vp.save()
else:
variant = None
if pubmed:
phenotype.articles.add(pubmed)
if variant:
variant.articles.add(pubmed)
if gene:
gene.articles.add(pubmed)
count += 1
sys.stdout.write('{0}\r'.format(count))
sys.stdout.flush()
return count
def load_hgmd_phenotypes(label, keys, cursor, using):
count = 0
total = 0
# Local storage for new instances
pmids = {}
phenotypes = {}
while True:
rows = cursor.fetchmany(100)
if not rows:
break
for row in rows:
record = dict(zip(keys, row))
pubmed = gene = variant = None
new_phenotype = saved = False
# PubMed IDs
if record["pubmed_id"]:
pubmed = PubMed(pk=record["pubmed_id"])
pubmed._state.db = using
# Some records have a bogus PMID. Only proces the valid ones.
elif type(record["pubmed"]) is int or record["pubmed"].isdigit():
pmid = int(record["pubmed"])
if pmid in pmids:
pubmed = PubMed(pk=pmids[pmid])
pubmed._state.db = using
else:
pubmed = PubMed(pmid=pmid)
pubmed.save()
pmids[pmid] = pubmed.pk
# Phenotypes
if record["phenotype_id"]:
phenotype = Phenotype(pk=record["phenotype_id"])
phenotype._state.db = using
else:
new_phenotype = True
term = record["phenotype"]
if term in phenotypes:
phenotype = Phenotype(pk=phenotypes[term])
phenotype._state.db = using
else:
phenotype = Phenotype(term=term)
phenotype.save()
phenotypes[term] = phenotype.pk
# Variants
variant = Variant(pk=record["variant_id"])
variant._state.db = using
if (
new_phenotype
or not VariantPhenotype.objects.filter(
variant=variant, phenotype=phenotype, hgmd_id=record["hgmd_id"]
).exists()
):
vp = VariantPhenotype(variant=variant, phenotype=phenotype, hgmd_id=record["hgmd_id"])
vp.save()
saved = True
# Genes
if record["gene_id"]:
gene = Gene(pk=record["gene_id"])
gene._state.db = using
if (
new_phenotype
or not GenePhenotype.objects.filter(
gene=gene, phenotype=phenotype, hgmd_id=record["hgmd_id"]
).exists()
):
gp = GenePhenotype(gene=gene, phenotype=phenotype, hgmd_id=record["hgmd_id"])
gp.save()
saved = True
# Associate articles with other objects
if pubmed:
phenotype.articles.add(pubmed)
if variant:
variant.articles.add(pubmed)
if gene:
gene.articles.add(pubmed)
total += 1
if saved:
count += 1
if count % BATCH_SIZE == 0:
transaction.commit()
log.debug("Loading {0}...{1}/{2}".format(label, count, total))
# Print a newline for the terminal prompt
print
def setUp(self):
# Create a new phenotype objects and store it
self.phenotype = Phenotype(term="Hyterazygoze")
self.phenotype.save()
super(PhenotypeResourceTestCase, self).setUp()
class VariantsResourcesTestCase(AuthenticatedBaseTestCase):
fixtures = ['initial_data.json']
def setUp(self):
# Creating objects needed for variant
self.pubmed = PubMed(pmid=1)
self.pubmed.save()
self.phenotype = Phenotype(term='Hymocompos',
hpo_id=1)
self.phenotype.save()
# Retrive a Chromosome and varianttype
self.chromo = Chromosome.objects.get(pk=1)
self.chromo.save()
self.varianttype = VariantType.objects.get(pk=1)
self.varianttype.save()
super(VariantsResourcesTestCase, self).setUp()
def test_get_empty(self):
response = self.client.get('/api/variants/999/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.not_found)
def test_get_all(self):
count_before = Variant.objects.count()
new_variant = Variant(chr=self.chromo,
pos=1,
ref="jon",
alt="ba",
md5="kid",
type=self.varianttype,)
new_variant.save()
count_after = Variant.objects.count()
# Now try making a get request with the objects id
response = self.client.get('/api/variants/{0}/'.format(new_variant.id),
HTTP_ACCEPT='application/json')
# Request should be good and the count should have changed
self.assertEqual(response.status_code, codes.ok)
self.assertEqual(count_after, count_before+1)
def test_get_empty_metrics(self):
Variant.objects.all().delete()
# Bad request, should return 404
response = self.client.get('/api/variants/1/assessment-metrics/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.not_found)
def test_get_metrics(self):
# Create a variant object
new_variant = Variant(chr=self.chromo,
pos=1,
ref="jon",
alt="ba",
md5="kid",
type=self.varianttype,)
new_variant.save()
response = self.client.get('/api/variants/{0}/assessment-metrics/'.
format(new_variant.id),
HTTP_ACCEPT='application/json')
# Should be ok
self.assertEqual(response.status_code, codes.ok)
