def test_run_where_everything_is_successful(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = gzip.open(fakegz, 'wb')
f.write('hello\n')
f.flush()
f.close()
params.pdbsequrl = 'file://' + fakegz
params.makeblastdb = 'echo'
task = MakeBlastDBTask(temp_dir, params)
task._retrysleep = 0
task._maxretries = 1
task.run()
self.assertEqual(task.get_error(), None)
# check echo.stdout file for valid arguments
f = open(os.path.join(task.get_dir(), 'echo.stdout'), 'r')
line = f.readline()
self.assertEqual(
line, '-in ' + task.get_pdb_seqres_txt() + ' -out ' +
os.path.join(task.get_dir(), 'pdb_db') + ' -dbtype prot\n')
f.close()
lines = task.get_email_log().split('\n')
self.assertEqual(lines[2], '# sequence(s): 0')
f.close()
finally:
shutil.rmtree(temp_dir)
def test_run_where_pdbsequrl_is_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.run()
self.assertEqual(
task.get_error(), 'cannot download files cause '
'pdbsequrl not set')
finally:
shutil.rmtree(temp_dir)
def test_run_where_makeblastdb_is_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.pdbsequrl = 'pdbsequrl'
task = MakeBlastDBTask(temp_dir, params)
task.run()
self.assertEqual(
task.get_error(), 'cannot make blast database '
'cause makeblastdb not set')
finally:
shutil.rmtree(temp_dir)
def test_run_where_can_run_is_false(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
open(os.path.join(task.get_dir(), 'error'), 'a').close()
task.run()
self.assertEqual(task._can_run, False)
finally:
shutil.rmtree(temp_dir)
def test_run_where_download_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.pdbsequrl = 'file://doesnotexist'
params.makeblastdb = 'makeblastdb'
task = MakeBlastDBTask(temp_dir, params)
task._retrysleep = 0
task._maxretries = 1
task.run()
self.assertEqual(
task.get_error(),
'Unable to download file: ' + 'file://doesnotexist')
finally:
shutil.rmtree(temp_dir)
def test_run_where_gunzip_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = open(fakegz, 'w')
f.write('hello\n')
f.flush()
f.close()
params.pdbsequrl = 'file://' + fakegz
params.makeblastdb = 'makeblastdb'
task = MakeBlastDBTask(temp_dir, params)
task._retrysleep = 0
task._maxretries = 1
task.run()
self.assertEqual(
task.get_error(),
'Unable to uncompress file: ' + task.get_pdb_seqres_txt())
finally:
shutil.rmtree(temp_dir)
def test_run_where_makeblastdb_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = gzip.open(fakegz, 'wb')
f.write('hello\n')
f.flush()
f.close()
params.pdbsequrl = 'file://' + fakegz
params.makeblastdb = 'false'
task = MakeBlastDBTask(temp_dir, params)
task._retrysleep = 0
task._maxretries = 1
task.run()
self.assertEqual(
task.get_error(), 'Non zero exit code: 1 '
'received. Standard out:'
' Standard error: ')
finally:
shutil.rmtree(temp_dir)