def test_load_csv_loader(self):
with self.assertRaises(Exception):
data = util.load_csv(self.path_csv, csv.reader)
data = util.load_csv(self.path_csv, csv.reader, non_unicode="replace")
self.assertEqual(data, self.data_exp_mask)
data = util.load_csv(self.path_csv, csv.reader, non_unicode="strip")
self.assertEqual(data, self.data_exp_strip)
with self.assertRaises(Exception):
data = util.load_csv(self.path_csv, csv.reader, non_unicode=None)
def run(self):
dest = self.task_dir_parent(self.name) / "Metadata"
dest.mkdir(parents=True, exist_ok=True)
paths = []
paths.append(self.proj.alignment.paths["sample_sheet"]) # Sample Sheet
paths.append(self.proj.path) # Project metadata YAML file (as it currently stands)
for path in paths:
shutil.copy(path, dest)
# metadata is special: need to filter out other projects
path_md_out = dest / self.proj.exp_path.name
# Read in all the rows in the original metadata spreadsheet. We'll
# ignore anything non-unicode here since it should have already been
# complained about when first parsed. (There's also the already-parsed
# data structure within self.proj but the original line-by-line CSV is
# already gone at that point.) Ideally the non_unicode behavior would
# be defined in one place instead of both here and in ProjectData.
data = load_csv(self.proj.exp_path, csv.DictReader, non_unicode="strip")
with open(path_md_out, "w") as f_out:
# Write out the experiment spreadsheet but only include our rows
writer = csv.DictWriter(f_out, fieldnames=data[0].keys())
writer.writeheader()
for row in data:
if row["Project"] == self.proj.name:
writer.writerow(row)
def test_load_csv_dict_loader(self):
"""Test that a csv.DictReader works too."""
data = util.load_csv(self.path / "test.csv", csv.DictReader)
self.assertEqual(data, self.dict_exp)
def test_load_csv_loader(self):
"""Test that a specific reader object can be supplied."""
data = util.load_csv(self.path / "test.csv", csv.reader)
self.assertEqual(data, self.data_exp)
def test_load_csv(self):
"""Test that a list of lists is created."""
data = util.load_csv(self.path / "test.csv")
self.assertEqual(data, self.data_exp)
def test_load_csv_dict_loader(self):
"""Test that a csv.DictReader works too."""
with self.assertRaises(FileNotFoundError):
util.load_csv(self.path / "test.csv", csv.DictReader)
def test_load_csv_loader(self):
"""Test that a specific reader object can be supplied."""
with self.assertRaises(FileNotFoundError):
util.load_csv(self.path / "test.csv", csv.reader)
def test_load_csv(self):
"""Test that a list of lists is created."""
with self.assertRaises(FileNotFoundError):
util.load_csv(self.path / "test.csv")