def __init__(self, config):
super(PadeRunner, self).__init__()
self.secret_key = ""
self.register_blueprint(pade.http.jobdetails.bp)
self.register_blueprint(pade.http.newjob.bp, url_prefix="/new_job")
self.register_blueprint(pade.http.inputfile.bp,
url_prefix="/input_files")
self.register_blueprint(pade.http.jobbrowser.runner)
session_db = Redis(host=config.session_host,
port=config.session_port,
db=config.session_db)
metadb_db = Redis(host=config.metadb_host,
port=config.metadb_port,
db=config.metadb_db)
self.session_interface = pade.redis_session.RedisSessionInterface(
session_db)
mdb = MetaDB(config.metadb_dir, metadb_db)
modules = [
pade.http.jobdetails, pade.http.newjob, pade.http.inputfile,
pade.http.jobbrowser
]
for m in modules:
m.mdb = mdb
self.add_url_rule('/', 'index', pade.http.jobbrowser.index)
def setUp(self):
(this_dir, this_file) = os.path.split(__file__)
config = pade.config.test
try:
redis_db = Redis(host=config.metadb_host,
port=config.metadb_port,
db=config.metadb_db)
redis_db.flushdb()
except redis.exceptions.ConnectionError as e:
self.skipTest("No redis")
return
self.mdb = MetaDB(config.metadb_dir, redis_db)
self.mdb.redis.flushdb()
self.app = PadeRunner(config).test_client()
def setUp(self):
(this_dir, this_file) = os.path.split(__file__)
config = pade.config.test
try:
redis_db = Redis(host=config.metadb_host,
port=config.metadb_port,
db=config.metadb_db)
redis_db.flushdb()
except redis.exceptions.ConnectionError as e:
self.skipTest("No redis")
return
self.mdb = MetaDB(config.metadb_dir, redis_db)
self.mdb.redis.flushdb()
self.app = PadeRunner(config).test_client()
class PadeRunnerTestCase(unittest.TestCase):
def setUp(self):
(this_dir, this_file) = os.path.split(__file__)
config = pade.config.test
try:
redis_db = Redis(host=config.metadb_host,
port=config.metadb_port,
db=config.metadb_db)
redis_db.flushdb()
except redis.exceptions.ConnectionError as e:
self.skipTest("No redis")
return
self.mdb = MetaDB(config.metadb_dir, redis_db)
self.mdb.redis.flushdb()
self.app = PadeRunner(config).test_client()
def test_setup_job(self):
self.assertOk("/")
def assertOk(self, route):
self.assertStatus(route, 200)
def assertStatus(self, route, status):
rv = self.app.get(route)
self.assertEquals(rv.status_code, status)
def test_new_job_workflow(self):
r = self.app.get("/new_job/clear_workflow")
self.assertEquals(r.status_code, 302)
r = self.app.get("/input_files/")
self.assertEquals(r.status_code, 200)
r = self.app.get("/input_files/upload_raw_file")
self.assertEquals(r.status_code, 200)
with open(
'sample_jobs/two_cond_nuisance/sample_data_2_cond_nuisance.txt'
) as f:
infile = self.mdb.add_input_file(name="test.txt",
description="Some comments",
stream=f)
r = self.app.get("/input_files/" + str(infile.obj_id))
self.assertEquals(r.status_code, 200)
self.assertTrue('c1r1' in r.data)
with open(infile.path) as f:
self.assertTrue('c1r2' in f.next())
r = self.app.get("/new_job/select_input_file?input_file_id=" +
str(infile.obj_id),
follow_redirects=True)
self.assertTrue('Feature ID' in r.data)
self.assertTrue('Sample' in r.data)
r = self.app.post("/new_job/column_roles",
data={
'roles-0': 'feature_id',
'roles-1': 'sample',
'roles-2': 'sample',
'roles-3': 'sample',
'roles-4': 'sample',
'roles-5': 'sample',
'roles-6': 'sample',
'roles-7': 'sample',
'roles-8': 'sample',
'roles-9': 'sample',
'roles-10': 'sample',
'roles-11': 'sample',
'roles-12': 'sample',
'roles-12': 'sample',
'roles-13': 'sample',
'roles-14': 'sample',
'roles-15': 'sample',
'roles-16': 'sample',
},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('Factor name' in r.data)
self.assertTrue('Possible values' in r.data)
r = self.app.post("/new_job/add_factor",
data={
'factor_name': 'treated',
'possible_values-0': 'no',
'possible_values-1': 'yes',
'possible_values-2': '',
'possible_values-3': '',
},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('treated' in r.data)
self.assertTrue('no' in r.data)
self.assertTrue('yes' in r.data)
r = self.app.post("/new_job/add_factor",
data={
'factor_name': 'gender',
'possible_values-0': 'male',
'possible_values-1': 'female',
'possible_values-2': '',
'possible_values-3': '',
},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('treated' in r.data)
self.assertTrue('no' in r.data)
self.assertTrue('yes' in r.data)
self.assertTrue('male' in r.data)
self.assertTrue('female' in r.data)
r = self.app.post("/new_job/column_labels",
data={
'assignments-0': 'no',
'assignments-1': 'male',
'assignments-2': 'no',
'assignments-3': 'male',
'assignments-4': 'no',
'assignments-5': 'male',
'assignments-6': 'no',
'assignments-7': 'male',
'assignments-8': 'no',
'assignments-9': 'female',
'assignments-10': 'no',
'assignments-11': 'female',
'assignments-12': 'no',
'assignments-13': 'female',
'assignments-14': 'no',
'assignments-15': 'female',
'assignments-16': 'yes',
'assignments-17': 'male',
'assignments-18': 'yes',
'assignments-19': 'male',
'assignments-20': 'yes',
'assignments-21': 'male',
'assignments-22': 'yes',
'assignments-23': 'male',
'assignments-24': 'yes',
'assignments-25': 'female',
'assignments-26': 'yes',
'assignments-27': 'female',
'assignments-28': 'yes',
'assignments-29': 'female',
'assignments-30': 'yes',
'assignments-31': 'female'
},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('block and condition factors' in r.data)
r = self.app.post("/new_job/setup_job_factors",
data={
'factor_roles-0': 'condition',
'factor_roles-1': 'block'
},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('Other settings' in r.data)
r = self.app.post("/new_job/other_settings",
data={
'statistic': 'f',
'tuning_params':
"0.001 0.01 0.1 1 3 10 30 100 300 1000 3000",
'bins': '1000',
'permutations': '1000',
'summary_min_conf_level': '0.1',
'summary_step_size': '0.05'
},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('confirm' in r.data)
class PadeRunnerTestCase(unittest.TestCase):
def setUp(self):
(this_dir, this_file) = os.path.split(__file__)
config = pade.config.test
try:
redis_db = Redis(host=config.metadb_host,
port=config.metadb_port,
db=config.metadb_db)
redis_db.flushdb()
except redis.exceptions.ConnectionError as e:
self.skipTest("No redis")
return
self.mdb = MetaDB(config.metadb_dir, redis_db)
self.mdb.redis.flushdb()
self.app = PadeRunner(config).test_client()
def test_setup_job(self):
self.assertOk("/")
def assertOk(self, route):
self.assertStatus(route, 200)
def assertStatus(self, route, status):
rv = self.app.get(route)
self.assertEquals(rv.status_code, status)
def test_new_job_workflow(self):
r = self.app.get("/new_job/clear_workflow")
self.assertEquals(r.status_code, 302)
r = self.app.get("/input_files/")
self.assertEquals(r.status_code, 200)
r = self.app.get("/input_files/upload_raw_file")
self.assertEquals(r.status_code, 200)
with open('sample_jobs/two_cond_nuisance/sample_data_2_cond_nuisance.txt') as f:
infile = self.mdb.add_input_file(name="test.txt", description="Some comments", stream=f)
r = self.app.get("/input_files/" + str(infile.obj_id))
self.assertEquals(r.status_code, 200)
self.assertTrue('c1r1' in r.data)
with open(infile.path) as f:
self.assertTrue('c1r2' in f.next())
r = self.app.get("/new_job/select_input_file?input_file_id=" + str(infile.obj_id),
follow_redirects=True)
self.assertTrue('Feature ID' in r.data)
self.assertTrue('Sample' in r.data)
r = self.app.post("/new_job/column_roles",
data={
'roles-0': 'feature_id',
'roles-1': 'sample',
'roles-2': 'sample',
'roles-3': 'sample',
'roles-4': 'sample',
'roles-5': 'sample',
'roles-6': 'sample',
'roles-7': 'sample',
'roles-8': 'sample',
'roles-9': 'sample',
'roles-10': 'sample',
'roles-11': 'sample',
'roles-12': 'sample',
'roles-12': 'sample',
'roles-13': 'sample',
'roles-14': 'sample',
'roles-15': 'sample',
'roles-16': 'sample',
},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('Factor name' in r.data)
self.assertTrue('Possible values' in r.data)
r = self.app.post("/new_job/add_factor",
data={
'factor_name': 'treated',
'possible_values-0': 'no',
'possible_values-1': 'yes',
'possible_values-2': '',
'possible_values-3': '',},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('treated' in r.data)
self.assertTrue('no' in r.data)
self.assertTrue('yes' in r.data)
r = self.app.post("/new_job/add_factor",
data={
'factor_name': 'gender',
'possible_values-0': 'male',
'possible_values-1': 'female',
'possible_values-2': '',
'possible_values-3': '',},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('treated' in r.data)
self.assertTrue('no' in r.data)
self.assertTrue('yes' in r.data)
self.assertTrue('male' in r.data)
self.assertTrue('female' in r.data)
r = self.app.post("/new_job/column_labels",
data={
'assignments-0' : 'no',
'assignments-1' : 'male',
'assignments-2' : 'no',
'assignments-3' : 'male',
'assignments-4' : 'no',
'assignments-5' : 'male',
'assignments-6' : 'no',
'assignments-7' : 'male',
'assignments-8' : 'no',
'assignments-9' : 'female',
'assignments-10' : 'no',
'assignments-11' : 'female',
'assignments-12' : 'no',
'assignments-13' : 'female',
'assignments-14' : 'no',
'assignments-15' : 'female',
'assignments-16' : 'yes',
'assignments-17' : 'male',
'assignments-18' : 'yes',
'assignments-19' : 'male',
'assignments-20' : 'yes',
'assignments-21' : 'male',
'assignments-22' : 'yes',
'assignments-23' : 'male',
'assignments-24' : 'yes',
'assignments-25' : 'female',
'assignments-26' : 'yes',
'assignments-27' : 'female',
'assignments-28' : 'yes',
'assignments-29' : 'female',
'assignments-30' : 'yes',
'assignments-31' : 'female'},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('block and condition factors' in r.data)
r = self.app.post("/new_job/setup_job_factors",
data={
'factor_roles-0' : 'condition',
'factor_roles-1' : 'block'},
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('Other settings' in r.data)
r = self.app.post("/new_job/other_settings",
data={
'statistic' : 'f',
'tuning_params': "0.001 0.01 0.1 1 3 10 30 100 300 1000 3000",
'bins' : '1000',
'permutations' : '1000',
'summary_min_conf_level' : '0.1',
'summary_step_size' : '0.05' },
follow_redirects=True)
self.assertEquals(r.status_code, 200)
self.assertTrue('confirm' in r.data)