def test_post_ndex(self):
pdict = {}
pdict[nbgwas_rest.ALPHA_PARAM] = 0.5
pdict[nbgwas_rest.NDEX_PARAM] = 'someid'
pdict['protein_coding'] = 'hg19'
pdict[nbgwas_rest.SNP_LEVEL_SUMMARY_PARAM] = (io.BytesIO(b'hi there'),
'yo.txt')
pdict[nbgwas_rest.SNP_LEVEL_SUMMARY_COL_LABEL_PARAM] = 'hi,how,are'
rv = self._app.post(nbgwas_rest.SNP_ANALYZER_NS, data=pdict,
follow_redirects=True)
self.assertEqual(rv.status_code, 202)
res = rv.headers['Location']
self.assertTrue(res is not None)
self.assertTrue(nbgwas_rest.SNP_ANALYZER_NS in res)
uuidstr = re.sub('^.*/', '', res)
nbgwas_rest.app.config[nbgwas_rest.JOB_PATH_KEY] = self._temp_dir
tpath = nbgwas_rest.get_task(uuidstr,
basedir=nbgwas_rest.get_submit_dir())
self.assertTrue(os.path.isdir(tpath))
jsonfile = os.path.join(tpath, nbgwas_rest.TASK_JSON)
self.assertTrue(os.path.isfile(jsonfile))
with open(jsonfile, 'r') as f:
jdata = json.load(f)
self.assertEqual(jdata[nbgwas_rest.ALPHA_PARAM], 0.5)
self.assertEqual(jdata[nbgwas_rest.NDEX_PARAM], 'someid')
self.assertEqual(jdata[nbgwas_rest.SNP_LEVEL_SUMMARY_COL_LABEL_PARAM],
'hi,how,are')
def test_get_task_for_validuuid(self):
somefile = os.path.join(self._temp_dir, '1')
open(somefile, 'a').close()
theuuid_dir = os.path.join(self._temp_dir, '1.2.3.4', '1234')
os.makedirs(theuuid_dir, mode=0o755)
someipfile = os.path.join(self._temp_dir, '1.2.3.4', '1')
open(someipfile, 'a').close()
self.assertEqual(nbgwas_rest.get_task('1234',
basedir=self._temp_dir),
theuuid_dir)
def test_get_task_for_nonexistantuuid(self):
self.assertEqual(nbgwas_rest.get_task(str(uuid.uuid4()),
basedir=self._temp_dir), None)
def test_get_task_for_none_uuid(self):
self.assertEqual(nbgwas_rest.get_task(None,
basedir=self._temp_dir), None)
def test_get_task_basedir_not_a_directory(self):
somefile = os.path.join(self._temp_dir, 'hi')
open(somefile, 'a').close()
self.assertEqual(nbgwas_rest.get_task('foo', basedir=somefile), None)
def test_get_task_basedir_none(self):
self.assertEqual(nbgwas_rest.get_task('foo'), None)