def test_get_set_of_pdbid_from_crystalph_tsv_invalid_entries(self):
"""Header missing and 4rfr has 3 columns
"""
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('4X09\t6.5\n')
f.write('4rfr 7.5 8\n')
f.write('4XET\t6.2\n')
f.write('4XF1\t6.2\n')
f.write('4XF3\t6.2\n')
f.flush()
f.close()
pdbid_set = task.get_set_of_pdbid_from_crystalph_tsv()
self.assertEqual(os.path.isfile(task.get_crystalph_tsv()), True)
self.assertEqual(len(pdbid_set), 3)
self.assertEqual('4RFR' in pdbid_set, False)
self.assertEqual('4X09' in pdbid_set, False)
self.assertEqual('4XET' in pdbid_set, True)
self.assertEqual('4XF1' in pdbid_set, True)
self.assertEqual('4XF3' in pdbid_set, True)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pdbid_from_crystalph_tsv_valid_entries(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('PDB_ID _exptl_crystal_grow.pH\n')
f.write('4rfr 7.5\n')
f.write('4X09\t6.5\n')
f.write('4XET\t6.2\n')
f.write('4XF1\t6.2\n')
f.write('4XF3\t6.2\n')
f.flush()
f.close()
pdbid_set = task.get_set_of_pdbid_from_crystalph_tsv()
self.assertEqual(os.path.isfile(task.get_crystalph_tsv()), True)
self.assertEqual(len(pdbid_set), 5)
self.assertEqual('4RFR' in pdbid_set, True)
self.assertEqual('4X09' in pdbid_set, True)
self.assertEqual('4XET' in pdbid_set, True)
self.assertEqual('4XF1' in pdbid_set, True)
self.assertEqual('4XF3' in pdbid_set, True)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pdbid_from_crystalph_tsv_internal_exception(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
open(task.get_crystalph_tsv(), 'a').close()
os.chmod(task.get_crystalph_tsv(), 0o000)
pdbid_set = task.get_set_of_pdbid_from_crystalph_tsv()
self.assertEqual(len(pdbid_set), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pdbid_from_crystalph_tsv_no_header_invalid_lines(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('hello\nx\n')
f.flush()
f.close()
pdbid_set = task.get_set_of_pdbid_from_crystalph_tsv()
self.assertEqual(os.path.isfile(task.get_crystalph_tsv()), True)
self.assertEqual(len(pdbid_set), 0)
finally:
shutil.rmtree(temp_dir)
