def main(filenames, input_format='json', outfile="~/out.txt"):
"""
Parse PCBA assay descriptions.
Parameters
----------
filenames : list
Filenames containing assay descriptions.
input_format : str, optional (default 'json')
Input file format.
"""
for filename in filenames:
if input_format == 'json':
handler = PcbaPandasHandler()
handler.add_dataset(filename)
else:
raise NotImplementedError(
'Unrecognized input format "{}"'.format(input_format))
handler.write(out_file)
class TestPcbaPandasHandler(unittest.TestCase):
"""
Tests for PcbaPandasHandler.
"""
def setUp(self):
self.handler = PcbaPandasHandler()
self.data_dir = os.path.split(os.path.realpath(__file__))[0]
self.parser = PcbaJsonParser(
os.path.join(self.data_dir, 'data/aid1.json'))
def test_add_dataset(self):
"""
Test for adding datasets.
"""
self.handler.add_dataset(
os.path.join(self.data_dir, "data/aid1.json"))
row = self.handler.get_dataset(0)
num_rows = len(self.handler.df)
assert num_rows == 1
assert row.get("comment") == self.parser.get_comment()
assert row.get("name") == self.parser.get_name()
assert row.get("aid") == self.parser.get_aid()
def test_to_csv(self):
"""
Test for witing to csv
"""
# Open and close a tempfile without deleting it. (On some systems
# cannot open tempfiles if they are already open, so need to close
# to use elsewhere in test)
f = tempfile.NamedTemporaryFile(delete=False)
f.close()
try:
self.handler.add_dataset(
os.path.join(self.data_dir, "data/aid1.json"))
self.handler.to_csv(f.name)
with open(f.name, "rb") as csvfile:
reader = csv.DictReader(csvfile)
#for row in reader:
row = reader.next()
assert row["comment"] == self.parser.get_comment()
assert row["name"] == self.parser.get_name()
assert int(row["aid"]) == self.parser.get_aid()
finally:
# Delete tempfile
os.remove(f.name)
class TestPcbaPandasHandler(unittest.TestCase):
"""
Tests for PcbaPandasHandler.
"""
def setUp(self):
self.handler = PcbaPandasHandler()
self.data_dir = os.path.split(os.path.realpath(__file__))[0]
self.parser = PcbaJsonParser(
os.path.join(self.data_dir, 'data/aid1.json'))
def test_add_dataset(self):
"""
Test for adding datasets.
"""
self.handler.add_dataset(os.path.join(self.data_dir, "data/aid1.json"))
row = self.handler.get_dataset(0)
num_rows = len(self.handler.df)
assert num_rows == 1
assert row.get("comment") == self.parser.get_comment()
assert row.get("name") == self.parser.get_name()
assert row.get("aid") == self.parser.get_aid()
def test_to_csv(self):
"""
Test for witing to csv
"""
# Open and close a tempfile without deleting it. (On some systems
# cannot open tempfiles if they are already open, so need to close
# to use elsewhere in test)
f = tempfile.NamedTemporaryFile(delete=False)
f.close()
try:
self.handler.add_dataset(
os.path.join(self.data_dir, "data/aid1.json"))
self.handler.to_csv(f.name)
with open(f.name, "rb") as csvfile:
reader = csv.DictReader(csvfile)
#for row in reader:
row = reader.next()
assert row["comment"] == self.parser.get_comment()
assert row["name"] == self.parser.get_name()
assert int(row["aid"]) == self.parser.get_aid()
finally:
# Delete tempfile
os.remove(f.name)
def main(filenames, input_format='json', outfile="~/out.txt"):
"""
Parse PCBA assay descriptions.
Parameters
----------
filenames : list
Filenames containing assay descriptions.
input_format : str, optional (default 'json')
Input file format.
"""
for filename in filenames:
if input_format == 'json':
handler = PcbaPandasHandler()
handler.add_dataset(filename)
else:
raise NotImplementedError(
'Unrecognized input format "{}"'.format(input_format))
handler.write(out_file)
def setUp(self):
self.handler = PcbaPandasHandler()
self.data_dir = os.path.split(os.path.realpath(__file__))[0]
self.parser = PcbaJsonParser(
os.path.join(self.data_dir, 'data/aid1.json'))
def setUp(self):
self.handler = PcbaPandasHandler()
self.data_dir = os.path.split(os.path.realpath(__file__))[0]
self.parser = PcbaJsonParser(
os.path.join(self.data_dir, 'data/aid1.json'))
