def test_get_file_line_count(self):
temp_dir = tempfile.mkdtemp()
try:
try:
# Try with double None
util.get_file_line_count(None)
self.fail('Expected TypeError')
except TypeError:
pass
try:
# try on non existant file
util.get_file_line_count(os.path.join(temp_dir, 'non'))
except IOError:
pass
# try on empty file
open(os.path.join(temp_dir, 'empty'), 'a').close()
self.assertEqual(
util.get_file_line_count(os.path.join(temp_dir, 'empty')), 0)
# try on file with data
util.append_string_to_file(os.path.join(temp_dir, 'three'),
'h\no\nw\n')
self.assertEqual(
util.get_file_line_count(os.path.join(temp_dir, 'three')), 3)
finally:
shutil.rmtree(temp_dir)
def test_append_string_to_file(self):
temp_dir = tempfile.mkdtemp()
try:
try:
# Try with double None
util.append_string_to_file(None, None)
self.fail('Expected TypeError')
except TypeError:
pass
try:
# Try with value set to None
util.append_string_to_file(os.path.join(temp_dir, 'foo'),
None)
except TypeError:
pass
# try on non existant file
util.append_string_to_file(os.path.join(temp_dir, 'non'), 'hi')
f = open(os.path.join(temp_dir, 'non'))
self.assertEqual(f.readline(), 'hi')
f.close()
# try on empty file
open(os.path.join(temp_dir, 'empty'), 'a').close()
util.append_string_to_file(os.path.join(temp_dir, 'empty'), 'hi')
f = open(os.path.join(temp_dir, 'empty'))
self.assertEqual(f.readline(), 'hi')
f.close()
# try on file with data
util.append_string_to_file(os.path.join(temp_dir, 'empty'), 'how')
f = open(os.path.join(temp_dir, 'empty'))
self.assertEqual(f.readline(), 'hihow')
finally:
shutil.rmtree(temp_dir)
def append_standard_to_files(self):
"""Appends standard 1FCZ to tsv files as mapped below
NONPOLYMER_TSV_STANDARD is appended to `get_nonpolymer_tsv()`
CRYSTALPH_TSV_STANDARD is appended to `get_crystalph_tsv()`
SEQUENCE_TSV_STANDARD is appended to `get_sequence_tsv()`
SEQUENCE_TSV_STANDARD is appended to `get_oldsequence_tsv()`
"""
logger.debug('Appending 1FCZ standard to tsv files')
try:
util.append_string_to_file(self.get_nonpolymer_tsv(),
DataImportTask.NONPOLYMER_TSV_STANDARD)
util.append_string_to_file(self.get_sequence_tsv(),
DataImportTask.SEQUENCE_TSV_STANDARD)
util.append_string_to_file(self.get_oldsequence_tsv(),
DataImportTask.SEQUENCE_TSV_STANDARD)
util.append_string_to_file(self.get_crystalph_tsv(),
DataImportTask.CRYSTALPH_TSV_STANDARD)
self.append_to_email_log('\nAppending 1FCZ standard to tsv'
' files\n')
nonpoly_count = util.get_file_line_count(self.get_nonpolymer_tsv())
seq_count = util.get_file_line_count(self.get_sequence_tsv())
crystal_count = util.get_file_line_count(self.get_crystalph_tsv())
inchi_count = util.get_file_line_count(
self.get_components_inchi_file())
self.append_to_email_log('Line counts:\n')
self.append_to_email_log(
str(inchi_count) + ' ' + DataImportTask.COMPINCHI_ICH + '\n')
self.append_to_email_log(
str(nonpoly_count) + ' ' + DataImportTask.NONPOLYMER_TSV +
'\n')
self.append_to_email_log(
str(seq_count) + ' ' + DataImportTask.SEQUENCE_TSV + '\n')
self.append_to_email_log(
str(seq_count) + ' ' + DataImportTask.OLDSEQUENCE_TSV + '\n')
self.append_to_email_log(
str(crystal_count) + ' ' + DataImportTask.CRYSTALPH_TSV + '\n')
except IOError:
logger.exception('Error appending standard to file')