def test_get_from_taxonomy_db(self):
"""EUtils access from taxonomy database should work"""
#note: this is more fragile than the nucleotide databases
g = EUtils(db='taxonomy', rettype='xml', retmode='xml')
ids = '9606[taxid] OR 28901[taxid]'
fh = StringIO()
fh.write(g[ids].read())
fh.seek(0)
data = parse_taxonomy_using_elementtree_xml_parse(fh)
result = sorted([item['ScientificName'] for item in data])
self.assertEqual(result, ['H**o sapiens', 'Salmonella enterica'])
def test_get_from_taxonomy_db(self):
"""EUtils access from taxonomy database should work"""
#note: this is more fragile than the nucleotide databases
g = EUtils(db='taxonomy', rettype='xml', retmode='xml')
ids = '9606[taxid] OR 28901[taxid]'
fh = StringIO()
fh.write(g[ids].read())
fh.seek(0)
data = parse_taxonomy_using_elementtree_xml_parse(fh)
result = sorted([item['ScientificName'] for item in data])
self.assertEqual(result, ['H**o sapiens', 'Salmonella enterica'])
def test_parse_taxonomy_using_elementtree_xml_parse(self):
"""parse_taxonomy_using_elementtree_xml_parse should return taxonomy associated information"""
g = EUtils(db='taxonomy', rettype='xml', retmode='xml')
ids = '28901[taxid]'
fh = StringIO()
fh.write(g[ids].read())
fh.seek(0)
data = parse_taxonomy_using_elementtree_xml_parse(fh)[0]
obs = (data['Lineage'],data['TaxId'],data['ScientificName'],\
data['Rank'])
exp = ('cellular organisms; Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella',\
'28901','Salmonella enterica','species')
self.assertEqual(obs,exp)
def test_parse_taxonomy_using_elementtree_xml_parse(self):
"""parse_taxonomy_using_elementtree_xml_parse should return taxonomy associated information"""
g = EUtils(db='taxonomy', rettype='xml', retmode='xml')
ids = '28901[taxid]'
fh = StringIO()
fh.write(g[ids].read())
fh.seek(0)
data = parse_taxonomy_using_elementtree_xml_parse(fh)[0]
obs = (data['Lineage'],data['TaxId'],data['ScientificName'],\
data['Rank'])
exp = ('cellular organisms; Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella',\
'28901','Salmonella enterica','species')
self.assertEqual(obs, exp)
