def test_species(self):
res, con = self.h.request(self.api + "/species/9606")
eq_(res.status, 200)
d = _d(con.decode('utf-8'))
eq_(set(d.keys()), set(['taxid', 'authority', 'lineage', '_id',
'common_name', 'genbank_common_name',
'_version', 'parent_taxid', 'scientific_name',
'has_gene', 'children', 'rank',
'uniprot_name']))
python类eq_()的实例源码
def test_query_dotstar_reporter(self):
human = self.json_ok(self.get_ok(self.api +
"/query?q=reporter:2842429&fields=reporter"),
filter=True)
mouse = self.json_ok(self.get_ok(self.api +
"/query?q=reporter:1452128_a_at&fields=reporter"),
filter=True)
rat = self.json_ok(self.get_ok(self.api +
"/query?q=reporter:1387540_at&fields=reporter"),
filter=True)
# human
eq_(human["total"], 3)
eq_(human["hits"][0]["reporter"]["HuGene-1_1"], "8110147")
assert "2889211" in human["hits"][0]["reporter"]["HuEx-1_0"]
assert "TC05002114.hg.1" in human["hits"][0]["reporter"]["HTA-2_0"]
eq_(human["hits"][0]["reporter"]["HG-U133_Plus_2"], "228805_at")
assert "gnf1h08801_at" in human["hits"][0]["reporter"]["GNF1H"]
eq_(human["hits"][0]["reporter"]["HuGene-1_1"], "8110147")
eq_(human["hits"][0]["reporter"]["HuGene-2_1"], "16992761")
# rat
eq_(rat["total"], 1)
eq_(rat["hits"][0]["reporter"]["RaEx-1_0"], "7082865")
eq_(rat["hits"][0]["reporter"]["Rat230_2"], "1387540_at")
eq_(rat["hits"][0]["reporter"]["RaGene-2_1"], "17661681")
eq_(rat["hits"][0]["reporter"]["RaGene-1_1"], "10747640")
assert "AF036760_at" in rat["hits"][0]["reporter"]["RG-U34A"]
# rat
eq_(mouse["total"], 1)
assert "1456141_x_at" in mouse["hits"][0]["reporter"]["Mouse430_2"]
eq_(mouse["hits"][0]["reporter"]["MTA-1_0"], "TC0X00000742.mm.1")
assert "165150_i_at" in mouse["hits"][0]["reporter"]["MG-U74Bv2"]
eq_(mouse["hits"][0]["reporter"]["MoEx-1_0"], "7012082")
eq_(mouse["hits"][0]["reporter"]["GNF1M"], "gnf1m11626_at")
eq_(mouse["hits"][0]["reporter"]["MoGene-2_1"], "17535957")
eq_(mouse["hits"][0]["reporter"]["MoGene-1_1"], "10600512")
def test_query_dotstar_interpro(self):
res = self.json_ok(self.get_ok(self.api +
"/query?q=interpro:IPR008389&fields=interpro&species=human,mouse,rat"))
eq_(res["total"], 6)
assert set([pro["id"] for hit in res["hits"]
for pro in hit["interpro"]]) == set(['IPR008389',
'IPR017385'])
def test_query_dotstar_reagent(self):
res = self.json_ok(self.get_ok(self.api +
"/query?q=reagent:GNF190467&fields=reagent"))
eq_(res["total"], 1)
hit = res["hits"][0]
assert {"relationship": "is", "id": "GNF168655"} in \
hit["reagent"]["GNF_Qia_hs-genome_v1_siRNA"]
assert {"relationship": "is", "id": "GNF277345"} in \
hit["reagent"]["GNF_mm+hs-MGC"]
assert {"relationship": "is", "id": "GNF110093"} in \
hit["reagent"]["NOVART_hs-genome_siRNA"]
def test_query_dotstar_uniprot(self):
swissid = self.json_ok(self.get_ok(self.api +
"/query?q=uniprot:Q8NEB7&fields=uniprot"),
filter=True)
trembid = self.json_ok(self.get_ok(self.api +
"/query?q=uniprot:F5H2C2&fields=uniprot"),
filter=True)
eq_(swissid["hits"], trembid["hits"])
eq_(trembid["total"], 1)
eq_(trembid["hits"][0]["uniprot"]["Swiss-Prot"], "Q8NEB7")
assert set(trembid["hits"][0]["uniprot"]["TrEMBL"]), \
set(["E7EP66", "F5H2C2", "F5H3P4", "F5H5S8"])
def test_sort_by_fields(self):
res = self.json_ok(self.get_ok(self.api + "/query?q=MTFMT&sort=entrezgene&species=human,mouse,rat"))
hits = res["hits"]
assert len(hits) == 3
eq_(hits[0]["entrezgene"],69606)
eq_(hits[1]["entrezgene"],123263)
eq_(hits[2]["entrezgene"],315763)
def test_caseinsensitive(self):
lower = self.json_ok(self.get_ok(self.api + "/query?q=cdk2"),filter=True)
upper = self.json_ok(self.get_ok(self.api + "/query?q=CDK2"),filter=True)
# old test...needs revisiting, sometimes the orders of results are *slightly* different for cdk2 and CDK2
#eq_(lower["hits"],upper["hits"])
eq_(sorted(lower["hits"],key=lambda e: e["entrezgene"]),sorted(upper["hits"],key=lambda e: e["entrezgene"]))
def test_symbolnamespecies_order(self):
res = self.json_ok(self.get_ok(self.api + "/query?q=cdk2&species=human,mouse,rat"))
hits = res["hits"]
# first is 1017, it's human and cdk2 is a symbol
eq_(hits[0]["_id"],"1017")
# second is 12566, mouse
eq_(hits[1]["_id"],"12566")
# third is 362817, rat
eq_(hits[2]["_id"],"362817")
def test_gene_other_names(self):
# this one has some
res = self.json_ok(self.get_ok(self.api + "/gene/107924918"))
assert "other_names" in res, "No other_names found in %s" % res
eq_(res["other_names"],['aquaporin NIP1-2-like', 'aquaporin NIP1;2', 'aquaporin NIP1;3'])
# that one not
res = self.json_ok(self.get_ok(self.api + "/gene/1246509"))
assert not "other_names" in res
# query by other_names:
res = self.json_ok(self.get_ok(self.api + "/query?q=other_names:p33&size=50"))
assert res["total"] > 30 # currently 35...
#eq_(len(res["hits"]),10)
ids = [h["_id"] for h in res["hits"]]
assert "1017" in ids, "Should have 1017 in results"
def test_pvs_effective_permittivity_real():
testpack = setup_func_pc(0.3e-3)
em = setup_func_mm(testpack)
# Allow 5% error
ok_(abs(em._effective_permittivity.real - 1.52441173e+00) < tolerance_pc * em._effective_permittivity.real)
# eq_(em._effective_permittivity.real, 1.52441173e+00)
def test_ks_pc_is_0p3_mm():
testpack = setup_func_pc(0.3e-3)
em = setup_func_em(testpack)
# Allow 5% error
memls_ks = 4.13718676e+00
# eq_(em.ks, memls_ks)
ok_(abs(em.ks - memls_ks) < tolerance_pc * em.ks)
def test_ks_pc_is_0p25_mm():
testpack = setup_func_pc(0.25e-3)
em = setup_func_em(testpack)
# Allow 5% error
memls_ks = 2.58158887e+00
# eq_(em.ks, memls_ks)
ok_(abs(em.ks - memls_ks) < tolerance_pc * em.ks)
def test_ks_pc_is_0p2_mm():
testpack = setup_func_pc(0.2e-3)
em = setup_func_em(testpack)
# Allow 5% error
memls_ks = 1.41304849e+00
# eq_(em.ks, memls_ks)
ok_(abs(em.ks - memls_ks) < tolerance_pc * em.ks)
def test_ks_pc_is_0p15_mm():
testpack = setup_func_pc(0.15e-3)
em = setup_func_em(testpack)
# Allow 5% error
memls_ks = 6.30218291e-01
# eq_(em.ks, memls_ks)
ok_(abs(em.ks - memls_ks) < tolerance_pc * em.ks)
def test_ks_pc_is_0p2_mm():
testpack = setup_func_pc(0.05e-3)
em = setup_func_em(testpack)
# Allow 5% error
memls_ks = 2.49851702e-02
# eq_(em.ks, memls_ks)
ok_(abs(em.ks - memls_ks) < tolerance_pc * em.ks)
def test_ks_pc_is_0p1_mm():
testpack = setup_func_pc(0.1e-3)
em = setup_func_mm(testpack)
# Allow 5% error
memls_ks = 1.94727497e-01
# eq_(em.ks, memls_ks)
ok_(abs(em.ks - memls_ks) < tolerance_pc * em.ks)
def test_memlsks_pc_is_0p05_mm():
testpack = setup_func_pc(0.05e-3)
em = setup_func_mm(testpack)
# Allow 5% error
memls_ks = 2.49851702e-02
# eq_(em.ks, memls_ks)
ok_(abs(em.ks - memls_ks) / em.ks < tolerance_pc)
def test_memls_ka():
testpack = setup_func_pc(0.05e-3) # Corr fn is irrelevant
em = setup_func_mm(testpack)
# Allow 5% error
memls_ka = 3.00937657e-01
# eq_(em.ka, memls_ka)
ok_(abs(em.ka - memls_ka) / em.ka < tolerance_pc)
def test_npol_passive_is_2():
em = setup_func_em()
eq_(em.npol, 2)
def test_query_with_several_rows(self):
conn, tracer = self._get_conn_tracer()
writer = tracer.writer
cursor = conn.cursor()
query = "SELECT n FROM (SELECT 42 n UNION SELECT 421 UNION SELECT 4210) m"
cursor.execute(query)
rows = cursor.fetchall()
eq_(len(rows), 3)
spans = writer.pop()
eq_(len(spans), 1)
span = spans[0]
eq_(span.get_tag('sql.query'), query)
# eq_(span.get_tag('sql.rows'), 3)
