def read_distribution(dbs, confs):
description = [('Replicate', 'string'),
('Lane', 'string'),
('Start', 'number'),
('Transcript Length', 'number'),
('Read Coverage', 'number'),
]
chart = {}
chart['table_description'] = description
stats = []
for conf in confs['configurations']:
data = run_method_using_mysqldb(_read_distribution, dbs, conf, http.not_found)
if data == http.not_found:
print "Can't collect because of missing data."
else:
lines = []
for line in data:
lines.append((conf['replicateid'], line[0], line[1], line[2], line[3]))
stats.extend(lines)
if stats:
chart['table_data'] = stats
else:
chart['table_data'] = [['', '', 0, 0, 0]]
return chart
def read_distribution(dbs, confs):
description = [
('Replicate', 'string'),
('Lane', 'string'),
('Start', 'number'),
('Transcript Length', 'number'),
('Read Coverage', 'number'),
]
chart = {}
chart['table_description'] = description
stats = []
for conf in confs['configurations']:
data = run_method_using_mysqldb(_read_distribution, dbs, conf,
http.not_found)
if data == http.not_found:
print "Can't collect because of missing data."
else:
lines = []
for line in data:
lines.append(
(conf['replicateid'], line[0], line[1], line[2], line[3]))
stats.extend(lines)
if stats:
chart['table_data'] = stats
else:
chart['table_data'] = [['', '', 0, 0, 0]]
return chart
def test_running_method_using_mysqldb_with_operationalerror(self):
def dummy_method(dbs, confs):
raise OperationalError
method = dummy_method
dbs = {}
confs = {}
marker = None
result = run_method_using_mysqldb(method, dbs, confs, marker)
self.failUnless(result == marker)
def test_running_method_using_mysqldb_with_programmingerror(self):
def dummy_method(dbs, confs):
raise ProgrammingError
method = dummy_method
dbs = {}
confs = {}
marker = None
result = run_method_using_mysqldb(method, dbs, confs, marker)
self.failUnless(result == marker)
def test_running_method_using_mysqldb(self):
def dummy_method(dbs, confs):
return "Some result data from the MySQL database"
method = dummy_method
dbs = {}
confs = {}
marker = None
result = run_method_using_mysqldb(method, dbs, confs, marker)
self.failUnless(result == "Some result data from the MySQL database")
def test_running_method_using_mysqldb_with_attributerror(self):
def dummy_method(dbs, confs):
raise AttributeError
method = dummy_method
dbs = {}
confs = {}
marker = None
cla, exc, trbk = None, None, None
result = run_method_using_mysqldb(method, dbs, confs, marker)
self.failUnless(result == marker)
def test_running_method_using_mysqldb_with_operationalerror(self):
def dummy_method(dbs, confs):
raise OperationalError
method = dummy_method
dbs = {}
confs = {}
marker = None
result = run_method_using_mysqldb(method, dbs, confs, marker)
self.failUnless(result == marker)
def test_running_method_using_mysqldb_with_programmingerror(self):
def dummy_method(dbs, confs):
raise ProgrammingError
method = dummy_method
dbs = {}
confs = {}
marker = None
result = run_method_using_mysqldb(method, dbs, confs, marker)
self.failUnless(result == marker)
def test_running_method_using_mysqldb(self):
def dummy_method(dbs, confs):
return "Some result data from the MySQL database"
method = dummy_method
dbs = {}
confs = {}
marker = None
result = run_method_using_mysqldb(method, dbs, confs, marker)
self.failUnless(result == "Some result data from the MySQL database")
def test_running_method_using_mysqldb_with_attributerror(self):
def dummy_method(dbs, confs):
raise AttributeError
method = dummy_method
dbs = {}
confs = {}
marker = None
cla, exc, trbk = None, None, None
result = run_method_using_mysqldb(method, dbs, confs, marker)
self.failUnless(result == marker)
def collect(dbs, confs, method, strategy, **kwargs):
"""Collect results from multiple queries to the database using
a strategy."""
results = []
for conf in confs:
conf.update(kwargs)
data = run_method_using_mysqldb(method, dbs, conf, http.not_found)
if data == http.not_found:
print "Can't collect because of missing data."
else:
for line in data:
results.append(strategy(conf, line))
return results
def run(dbs, method, conf):
"""Run a method running sql code.
Returns a tuple of (data, success).
If the success value is True, the method could not be run properly.
If the success value is False, the method has been executed correctly.
"""
success = True
data = run_method_using_mysqldb(method, dbs, conf, http.not_found)
if data == http.not_found:
print "Error running sql method."
success = False
return data, success
def aggregate(dbs, confs, method, strategy, **kwargs):
"""Aggregate results from multiple queries to the database using
a strategy."""
stats = None
failed = 0
for conf in confs:
conf.update(kwargs)
data = run_method_using_mysqldb(method, dbs, conf, http.not_found)
if data == http.not_found:
print "Can't aggregate because of missing data."
failed = failed + 1
else:
if stats is None:
stats = data
else:
stats = merge(stats, data, strategy=strategy)
return stats, failed
def show(self, request):
"""Return the resource representation in the requested content type"""
if not self.method:
# The method needs to be set at least
return http.not_found([('Content-type', 'text/javascript')], '')
# Inject the project specific project databases
self.dbs = request.environ['dbs']
# Get the configurations for the given level of detail
confs = get_configurations(request, self.level, self.resolution,
self.partition, self.dbs, **self.kwargs)
# Run the method containing the code to access the database
data = run_method_using_mysqldb(self.method, self.dbs, confs,
http.not_found)
if data == http.not_found:
# If the returned value is the marker http.not_found, we know
# that something related to MySQL went wrong when the method
# was called. The marker is used so that no internals of the
# MySQL adapter need to be considered here.
return http.not_found()
if data is None:
log.warning("Method appears to be unimplemented: %s" % self.method)
return http.not_found([('Content-type', 'text/javascript')], '')
accept_header = request.headers.get('Accept', 'text/javascript')
body = None
# Different results are returned depending on whether this is a table
if 'table_description' in data and 'table_data' in data:
#print "Extract table info and return info"
# This chart is using the google visualization library
table = gviz_api.DataTable(data['table_description'])
try:
table.AppendData(data['table_data'])
except DataTableException:
print self.method
raise
if accept_header == 'text/plain':
body = table.ToJSonResponse()
elif accept_header == 'text/html':
body = table.ToHtml()
elif accept_header == 'text/x-cfg':
body = to_cfg(data)
elif accept_header == 'text/csv':
body = table.ToCsv()
elif accept_header == 'text/tab-separated-values':
body = table.ToCsv(separator="\t")
elif accept_header == 'text/x-python-pickled-dict':
body = pickle.dumps(data)
else:
try:
body = table.ToJSon()
except DataTableException:
print self.method
print data['table_description']
print data['table_data']
raise
except:
raise
else:
accept_header = request.headers.get('Accept', None)
if accept_header == 'text/x-python-pickled-dict':
body = pickle.dumps(data)
else:
body = json.dumps(data)
headers = [('Content-type', accept_header),
('Content-Length', len(body))]
return http.ok(headers, body)