Skip to content

Commit

Permalink
update tests with /api/dataset change
Browse files Browse the repository at this point in the history
  • Loading branch information
@talavis
talavis committed Mar 29, 2019
1 parent 667eb31 commit 378e4ce
Show file tree
Hide file tree
Showing 2 changed files with 88 additions and 88 deletions.
54 changes: 27 additions & 27 deletions backend/modules/browser/tests/test_browser_handlers.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ def test_get_autocomplete():
dataset = 'SweGen'

query = 'PA'
response = requests.get('{}/api/datasets/{}/browser/autocomplete/{}'.format(BASE_URL, dataset, query))
response = requests.get('{}/api/dataset/{}/browser/autocomplete/{}'.format(BASE_URL, dataset, query))
data = json.loads(response.text)
assert set(data["values"]) == set(["PABPC1P9", "PACSIN2", "PANX2", "PARP4P3",
"PARVB", "PARVG", "PATZ1", "PAXBP1", "PAXBP1-AS1"])
Expand All @@ -28,7 +28,7 @@ def test_download():

data_type = 'transcript'
data_item = 'ENST00000438441'
response = requests.get('{}/api/datasets/{}/browser/download/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
response = requests.get('{}/api/dataset/{}/browser/download/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
assert len(response.text.split('\n')) == 180


Expand All @@ -40,15 +40,15 @@ def test_get_coverage():

data_type = 'transcript'
data_item = 'ENST00000438441'
response = requests.get('{}/api/datasets/{}/browser/coverage/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
response = requests.get('{}/api/dataset/{}/browser/coverage/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
data = json.loads(response.text)
assert len(data['coverage']) == 144
data_type = 'region'
data_item = '1-1-1000000'
response = requests.get('{}/api/datasets/{}/browser/coverage/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
response = requests.get('{}/api/dataset/{}/browser/coverage/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
assert response.status_code == 400
data_item = '1-1-5'
response = requests.get('{}/api/datasets/{}/browser/coverage/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
response = requests.get('{}/api/dataset/{}/browser/coverage/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
assert response.status_code == 404


Expand All @@ -59,7 +59,7 @@ def test_get_coverage_pos():
dataset = 'SweGen'
data_type = 'region'
data_item = '22-100001-100101'
response = requests.get('{}/api/datasets/{}/browser/coverage_pos/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
response = requests.get('{}/api/dataset/{}/browser/coverage_pos/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
cov_pos = json.loads(response.text)
assert cov_pos['start'] == 100001
assert cov_pos['stop'] == 100101
Expand All @@ -72,7 +72,7 @@ def test_get_gene():
"""
dataset = 'SweGen'
gene_id = 'ENSG00000015475'
response = requests.get('{}/api/datasets/{}/browser/gene/{}'.format(BASE_URL, dataset, gene_id))
response = requests.get('{}/api/dataset/{}/browser/gene/{}'.format(BASE_URL, dataset, gene_id))
expected = {"name": "BID", "canonicalTranscript": "ENST00000317361", "chrom": "22", "strand": "-", "geneName": "BID"}
gene = json.loads(response.text)

Expand All @@ -83,13 +83,13 @@ def test_get_gene():

dataset = 'SweGen'
gene_id = 'ENSG00000015475'
response = requests.get('{}/api/datasets/{}/browser/gene/{}'.format(BASE_URL, dataset, gene_id))
response = requests.get('{}/api/dataset/{}/browser/gene/{}'.format(BASE_URL, dataset, gene_id))
expected = {"name": "BID", "canonicalTranscript": "ENST00000317361", "chrom": "22", "strand": "-", "geneName": "BID"}
gene = json.loads(response.text)

dataset = 'SweGen'
gene_id = 'BAD_GENE_ID'
response = requests.get('{}/api/datasets/{}/browser/gene/{}'.format(BASE_URL, dataset, gene_id))
response = requests.get('{}/api/dataset/{}/browser/gene/{}'.format(BASE_URL, dataset, gene_id))
assert response.status_code == 404


Expand All @@ -99,7 +99,7 @@ def test_get_region():
"""
dataset = 'SweGen'
region_def = '22-46615715-46615880'
response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
response = requests.get('{}/api/dataset/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
region = json.loads(response.text)
expected = {'region': {'chrom': '22',
'start': 46615715,
Expand All @@ -110,7 +110,7 @@ def test_get_region():
assert region == expected

region_def = '22-16364870-16366200'
response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
response = requests.get('{}/api/dataset/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
region = json.loads(response.text)
expected = {'region': {'chrom': '22',
'start': 16364870,
Expand All @@ -121,11 +121,11 @@ def test_get_region():
assert region == expected

region_def = '22-46A1615715-46615880'
response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
response = requests.get('{}/api/dataset/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
assert response.status_code == 400

region_def = '22-1-1000000'
response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
response = requests.get('{}/api/dataset/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
assert response.status_code == 400


Expand All @@ -135,14 +135,14 @@ def test_get_transcript():
"""
dataset = 'SweGen'
transcript_id = 'ENST00000317361'
response = requests.get('{}/api/datasets/{}/browser/transcript/{}'.format(BASE_URL, dataset, transcript_id))
response = requests.get('{}/api/dataset/{}/browser/transcript/{}'.format(BASE_URL, dataset, transcript_id))
transcript = json.loads(response.text)
assert transcript['gene']['id'] == 'ENSG00000015475'
assert len(transcript['exons']) == 14

dataset = 'SweGen'
transcript_id = 'BAD_TRANSCRIPT'
response = requests.get('{}/api/datasets/{}/browser/transcript/{}'.format(BASE_URL, dataset, transcript_id))
response = requests.get('{}/api/dataset/{}/browser/transcript/{}'.format(BASE_URL, dataset, transcript_id))
assert response.status_code == 404


Expand All @@ -152,7 +152,7 @@ def test_get_variant():
"""
dataset = 'SweGen'
variant_id = '22-16080482-CAT-C'
response = requests.get('{}/api/datasets/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id))
response = requests.get('{}/api/dataset/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id))
variant = json.loads(response.text)
assert variant['variant']['variantId'] == '22-16080482-CAT-C'
assert set(variant['variant']['genes']) == set(['ENSG00000229286', 'ENSG00000235265'])
Expand All @@ -161,7 +161,7 @@ def test_get_variant():
assert len(variant['variant']['transcripts']) == len(['ENST00000448070', 'ENST00000413156'])

variant_id = '22-16269941-G-C'
response = requests.get('{}/api/datasets/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id))
response = requests.get('{}/api/dataset/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id))
variant = json.loads(response.text)
assert variant['variant']['variantId'] == '22-16269941-G-C'
assert set(variant['variant']['genes']) == set(['ENSG00000198062', 'ENSG00000236666'])
Expand All @@ -171,14 +171,14 @@ def test_get_variant():

variant_id = '21-9411609-G-T'
version = '20161223'
response = requests.get('{}/api/datasets/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id))
response = requests.get('{}/api/dataset/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id))
assert response.status_code == 404
response = requests.get('{}/api/datasets/{}/version/{}/browser/variant/{}'.format(BASE_URL, dataset, version, variant_id))
response = requests.get('{}/api/dataset/{}/version/{}/browser/variant/{}'.format(BASE_URL, dataset, version, variant_id))
variant = json.loads(response.text)
assert variant['variant']['variantId'] == '21-9411609-G-T'

variant_id = '22-94358sfsdfsdf52-T-C'
response = requests.get('{}/api/datasets/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id))
response = requests.get('{}/api/dataset/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id))
assert response.status_code == 400


Expand All @@ -190,24 +190,24 @@ def test_get_variants():

data_type = 'gene'
data_item = 'ENSG00000231565'
response = requests.get('{}/api/datasets/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
response = requests.get('{}/api/dataset/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
data = json.loads(response.text)
assert len(data['variants']) == 178

data_type = 'region'
data_item = '22-16360000-16361200'
response = requests.get('{}/api/datasets/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
response = requests.get('{}/api/dataset/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
data = json.loads(response.text)
assert len(data['variants']) == 13

data_type = 'region'
data_item = '22-46615715-46715880'
response = requests.get('{}/api/datasets/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
response = requests.get('{}/api/dataset/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
assert response.status_code == 400

data_type = 'transcript'
data_item = 'ENST00000438441'
response = requests.get('{}/api/datasets/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
response = requests.get('{}/api/dataset/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
data = json.loads(response.text)
assert len(data['variants']) == 178

Expand All @@ -219,20 +219,20 @@ def test_search():
dataset = 'SweGen'

query = 'NF1P3'
response = requests.get('{}/api/datasets/{}/browser/search/{}'.format(BASE_URL, dataset, query))
response = requests.get('{}/api/dataset/{}/browser/search/{}'.format(BASE_URL, dataset, query))
data = json.loads(response.text)
assert data['type'] == 'gene'
assert data['value'] == 'ENSG00000183249'

query = 'rs142856307'
response = requests.get('{}/api/datasets/{}/browser/search/{}'.format(BASE_URL, dataset, query))
response = requests.get('{}/api/dataset/{}/browser/search/{}'.format(BASE_URL, dataset, query))
data = json.loads(response.text)
assert data['type'] == 'dbsnp'
assert data['value'] == 142856307

query = '21-9411281-T-C'
version = '20161223'
response = requests.get('{}/api/datasets/{}/version/{}/browser/search/{}'.format(BASE_URL, dataset, version, query))
response = requests.get('{}/api/dataset/{}/version/{}/browser/search/{}'.format(BASE_URL, dataset, version, query))
data = json.loads(response.text)
assert data['type'] == 'variant'
assert data['value'] == '21-9411281-T-C'
Loading

0 comments on commit 378e4ce

Please sign in to comment.