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upgraded pytests to cover more species specifically sanity checks for…
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… entrezgene
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@jal347
jal347 committed Oct 12, 2023
1 parent daf44b1 commit b4bfadf
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Showing 5 changed files with 454 additions and 293 deletions.
239 changes: 177 additions & 62 deletions src/tests/data_tests/test_1_annotation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,59 +2,143 @@


class TestAnnotationGET(BiothingsDataTest):
host = 'mygene.info'
prefix = 'v3'
host = "mygene.info"
prefix = "v3"

def test_101(self):

res = self.request('gene/1017').json()
res = self.request("gene/1017").json()

attr_li = [
'HGNC', 'MIM', '_id', 'accession', 'alias',
'ec', 'ensembl', 'entrezgene', 'genomic_pos',
'go', 'homologene', 'interpro', 'ipi', 'map_location',
'name', 'pir', 'pdb', 'pharmgkb', 'prosite', 'reagent',
'refseq', 'reporter', 'summary', 'symbol', 'taxid',
'type_of_gene', 'unigene', 'uniprot', 'exons', 'generif'
"HGNC",
"MIM",
"_id",
"accession",
"alias",
"ec",
"ensembl",
"entrezgene",
"genomic_pos",
"go",
"homologene",
"interpro",
"ipi",
"map_location",
"name",
"pir",
"pdb",
"pharmgkb",
"prosite",
"reagent",
"refseq",
"reporter",
"summary",
"symbol",
"taxid",
"type_of_gene",
"unigene",
"uniprot",
"exons",
"generif",
]
# Removed 'Vega' as an attribute in tests 2019/3

for attr in attr_li:
assert attr in res

def test_102(self):
res = self.request("gene/12566").json()
attr_li = [
"MGI",
"_id",
"accession",
"alias",
"ec",
"ensembl",
"entrezgene",
"genomic_pos",
"go",
"homologene",
"interpro",
"ipi",
"map_location",
"name",
"prosite",
"reagent",
"refseq",
"reporter",
"symbol",
"taxid",
"type_of_gene",
"unigene",
"uniprot",
"exons",
"generif",
]

for attr in attr_li:
assert attr in res

res = self.request("gene/245962").json()
attr_li = [
"RGD",
"_id",
"accession",
"alias",
"ensembl",
"entrezgene",
"genomic_pos",
"go",
"homologene",
"interpro",
"ipi",
"map_location",
"name",
"prosite",
"refseq",
"reporter",
"symbol",
"taxid",
"type_of_gene",
"unigene",
"uniprot",
"exons",
"generif",
]

for attr in attr_li:
assert attr in res

def test_102(self):
pairs = [
(12566, 'MGI'),
(245962, 'RGD'),
(493498, 'Xenbase'),
(406715, 'ZFIN'),
(824036, 'TAIR'),
(42453, 'FLYBASE')
(12566, "MGI"),
(245962, "RGD"),
(493498, "Xenbase"),
(406715, "ZFIN"),
(824036, "TAIR"),
(42453, "FLYBASE"),
]

for _id, attr in pairs:
res = self.request('gene/' + str(_id)).json()
res = self.request("gene/" + str(_id)).json()
assert attr in res

def test_103(self):
# pig
res = self.request('gene/397593').json()
assert 'reporter' in res
assert 'snowball' in res['reporter']
res = self.request("gene/397593").json()
assert "reporter" in res
assert "snowball" in res["reporter"]

def test_104(self):
# nematode
self.request('gene/172677').json()
self.request("gene/172677").json()

def test_105(self):
# this is not nematode, "taxid": 31234
res = self.request('gene/171911').json()
assert 'WormBase' in res
res = self.request("gene/171911").json()
assert "WormBase" in res

def test_106(self):
# fission yeast
self.request('gene/2539869').json()
self.request("gene/2539869").json()

def test_107(self):
# e coli.
Expand All @@ -63,89 +147,120 @@ def test_107(self):

def test_108(self):
# mirna
res = self.request('gene/406881').json()
assert 'miRBase' in res
res = self.request("gene/406881").json()
assert "miRBase" in res

def test_109(self):

res = self.request('gene/1017').json()
assert res['entrezgene'] == "1017"
res = self.request("gene/1017").json()
assert res["entrezgene"] == "1017"

def test_110(self):
# testing non-ascii character
self.request('gene/54097\xef\xbf\xbd\xef\xbf\xbdmouse', expect=404)
self.request("gene/54097\xef\xbf\xbd\xef\xbf\xbdmouse", expect=404)

def test_111(self):
# one test to /gene/Y105C5B.255 has been removed
# since dots in geneids are no longer supported
pass

def test_112(self):
""" GET /v3/gene/
"""GET /v3/gene/
{
"code": 400,
"success": false,
"error": "Bad Request",
"missing": "id"
}
"""
self.request('gene', expect=400)
self.request("gene", expect=400)

def test_113(self):

self.request('gene/', expect=400)
self.request("gene/", expect=400)


class TestAnnotationPOST(BiothingsDataTest):
host = 'mygene.info'
prefix = 'v3'
host = "mygene.info"
prefix = "v3"

def test_151(self):

res = self.request('gene', method='POST', data={'ids': '1017'}).json()
res = self.request("gene", method="POST", data={"ids": "1017"}).json()
assert len(res) == 1
assert res[0]['entrezgene'] == "1017"
assert res[0]["entrezgene"] == "1017"

# check default fields returned
default_fields = [
'symbol', 'reporter', 'refseq', 'pdb', 'interpro', 'entrezgene', 'summary',
'genomic_pos_hg19', 'unigene', 'ipi', 'taxid', 'pfam', 'homologene', 'ensembl', 'ec',
'type_of_gene', 'pathway', 'exons_hg19', 'MIM', 'generif', 'HGNC', 'name', 'reagent',
'uniprot', 'pharmgkb', 'alias', 'genomic_pos', 'accession', '_id', 'pir', 'prosite',
'wikipedia', 'go', 'query', 'map_location', 'exons', 'exac', 'other_names', 'umls',
'pantherdb', 'pharos', '_version']
"symbol",
"reporter",
"refseq",
"pdb",
"interpro",
"entrezgene",
"summary",
"genomic_pos_hg19",
"unigene",
"ipi",
"taxid",
"pfam",
"homologene",
"ensembl",
"ec",
"type_of_gene",
"pathway",
"exons_hg19",
"MIM",
"generif",
"HGNC",
"name",
"reagent",
"uniprot",
"pharmgkb",
"alias",
"genomic_pos",
"accession",
"_id",
"pir",
"prosite",
"wikipedia",
"go",
"query",
"map_location",
"exons",
"exac",
"other_names",
"umls",
"pantherdb",
"pharos",
"_version",
]

for field in default_fields:
assert field in res[0]
assert len(default_fields) <= len(res[0])

def test_152(self):

res = self.request('gene', method='POST', data={'ids': '1017, 1018'}).json()
res = self.request("gene", method="POST", data={"ids": "1017, 1018"}).json()
assert len(res) == 2
assert res[0]['_id'] == '1017'
assert res[1]['_id'] == '1018'
assert res[0]["_id"] == "1017"
assert res[1]["_id"] == "1018"

def test_153(self):

data = {'ids': '1017,1018',
'fields': 'symbol,name,entrezgene'}
res = self.request('gene', method='POST', data=data).json()
data = {"ids": "1017,1018", "fields": "symbol,name,entrezgene"}
res = self.request("gene", method="POST", data=data).json()
assert len(res) == 2
for _g in res:
assert set(_g) == set(['_id', '_version', 'query', 'symbol', 'name', 'entrezgene'])
assert set(_g) == set(
["_id", "_version", "query", "symbol", "name", "entrezgene"]
)

def test_154(self):

data = {'ids': '1017,1018',
'filter': 'symbol,go.MF'}
res = self.request('gene', method='POST', data=data).json()
data = {"ids": "1017,1018", "filter": "symbol,go.MF"}
res = self.request("gene", method="POST", data=data).json()
assert len(res) == 2
for _g in res:
assert set(_g) == set(['_id', '_version', 'query', 'symbol', 'go'])
assert set(_g) == set(["_id", "_version", "query", "symbol", "go"])
assert "MF" in _g["go"]

def test_155(self):
# get retired gene
res = self.request('gene', method='POST', data={'ids': '791256'}).json()
assert res[0]['_id'] == '50846' # this is the corresponding _id field
res = self.request("gene", method="POST", data={"ids": "791256"}).json()
assert res[0]["_id"] == "50846" # this is the corresponding _id field
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