def test_run_with_error(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.blastnfilter = 'false'
params.postanalysis = 'true'
params.pdbdb = '/pdbdb'
blasttask = BlastNFilterTask(temp_dir, params)
blasttask._can_run = True
blasttask.run()
self.assertEqual(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
self.assertEqual(blasttask.get_error(), None)
complete_file = os.path.join(blasttask.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(complete_file), True)
error_file = os.path.join(blasttask.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(error_file), False)
std_err_file = os.path.join(blasttask.get_dir(), 'false.stderr')
self.assertEqual(os.path.isfile(std_err_file), True)
std_out_file = os.path.join(blasttask.get_dir(), 'false.stdout')
self.assertEqual(os.path.isfile(std_out_file), True)
finally:
shutil.rmtree(temp_dir)
def test_run_with_can_run_already_set_false(self):
params = D3RParameters()
params.blastnfilter = 'false'
params.postanalysis = 'false'
params.pdbdb = '/pdbdb'
blasttask = BlastNFilterTask(None, params)
blasttask._can_run = False
blasttask.run()
def test_run_fail_due_to_time_but_with_txt_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
foo_script = os.path.join(temp_dir, 'foo.py')
params.blastnfilter = foo_script
params.postanalysis = '/bin/echo'
params.pdbdb = '/pdbdb'
params.blastnfiltertimeout = 1
blasttask = BlastNFilterTask(temp_dir, params)
blasttask._can_run = True
txt_file = os.path.join(blasttask.get_dir(), '4za4.txt')
txt_contents = (
'query, 4za4\\n' + 'ph, 7.4\\n' + 'ligand, 4LU\\n\\n' +
'inchi, InChI=1S/C22H29N4O9P/c1-10-7-12-16-' +
'15(11(10)2)22(3,4)5-6-25(16)17-19(23-21(31)' +
'24-20(17)30)26(12)8-13(27)18(29)14(28)9-35-' +
'36(32,33)34/h6-7,13-14,18,27-29H,5,8-9H2,1-' +
'4H3,(H3-,23,24,30,31,32,33,34)/p+1/t13-,14+' + ',18-/m0/s1\\n'
'largest, 4zz3, 4PP\\n' + 'smallest, 3ax3, 4LP\\n' +
'holo, 2ax1, XDN\\n' + 'apo, 2ll3, GSS\\n')
# create fake blastnfilter script that makes csv files
f = open(foo_script, 'w')
f.write('#! /usr/bin/env python\n\n')
f.write('import time\n')
f.write('f = open(\'' + txt_file + '\', \'w\')\n')
f.write('f.write(\'' + txt_contents + '\\n\')\n')
f.write('f.flush()\nf.close()\n')
f.write('time.sleep(360)\n')
f.flush()
f.close()
os.chmod(foo_script, stat.S_IRWXU)
blasttask.run()
self.assertEqual(blasttask.get_error(), None)
self.assertEqual(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
complete_file = os.path.join(blasttask.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(complete_file), True)
std_err_file = os.path.join(blasttask.get_dir(), 'foo.py.stderr')
self.assertEqual(os.path.isfile(std_err_file), True)
std_out_file = os.path.join(blasttask.get_dir(), 'foo.py.stdout')
self.assertEqual(os.path.isfile(std_out_file), True)
res = blasttask.get_email_log().rstrip('\n')
res.index('/foo.py')
res.index('# txt files found: 1')
res.index('Output from summary.txt')
finally:
shutil.rmtree(temp_dir)
def test_run_with_blast_success_postanalysis_success_no_summary_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.blastnfilter = 'true'
params.postanalysis = '/bin/echo'
params.pdbdb = '/pdbdb'
blasttask = BlastNFilterTask(temp_dir, params)
blasttask._can_run = True
blasttask.run()
self.assertEqual(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
self.assertEqual(blasttask.get_error(), None)
complete_file = os.path.join(blasttask.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(complete_file), True)
std_err_file = os.path.join(blasttask.get_dir(), 'echo.stderr')
self.assertEqual(os.path.isfile(std_err_file), True)
std_out_file = os.path.join(blasttask.get_dir(), 'echo.stdout')
dataimport = DataImportTask(temp_dir, params)
f = open(std_out_file, 'r')
echo_out = f.read().replace('\n', '')
echo_out.index('--compinchi ' +
os.path.join(temp_dir, dataimport.get_dir_name(),
DataImportTask.COMPINCHI_ICH))
echo_out.index(' ' +
os.path.join(temp_dir, blasttask.get_dir_name()))
f.close()
self.assertEqual(os.path.isfile(std_out_file), True)
self.assertEquals(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
self.assertEquals(
os.path.exists(os.path.join(blasttask.get_dir(),
'true.stderr')), True)
self.assertEquals(
os.path.exists(os.path.join(blasttask.get_dir(),
'true.stdout')), True)
res = blasttask.get_email_log().rstrip('\n')
res.index('/bin/echo')
res.index('# txt files found: 0')
res.index('Output from summary.txt')
finally:
shutil.rmtree(temp_dir)
def test_run_with_exception(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.blastnfilter = 'falseasdfasdf'
params.postanalysis = 'true'
params.pdbdb = '/pdbdb'
blasttask = BlastNFilterTask(temp_dir, params)
blasttask._can_run = True
blasttask.run()
self.assertEqual(blasttask.get_status(), D3RTask.ERROR_STATUS)
self.assertEqual(blasttask.get_error().startswith('Caught'), True)
self.assertNotEqual(blasttask.get_error(), None)
finally:
shutil.rmtree(temp_dir)
def test_run_with_blast_success_useoldseq_and_postanalysis_fail(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.blastnfilter = '/bin/echo'
params.postanalysis = os.path.join(temp_dir, 'foo.py')
params.pdbdb = '/pdbdb'
blasttask = BlastNFilterTask(temp_dir, params)
blasttask._can_run = True
txt_file = os.path.join(blasttask.get_dir(), 'summary.txt')
txt_contents = ('INPUT SUMMARY\\n' + ' sequences: 177\\n' +
' complexes: 149\\n')
# create fake blastnfilter script that makes csv files
f = open(params.postanalysis, 'w')
f.write('#! /usr/bin/env python\n\n')
f.write('f = open(\'' + txt_file + '\', \'w\')\n')
f.write('f.write(\'' + txt_contents + '\\n\')\n')
f.write('f.flush()\nf.close()\n')
f.flush()
f.close()
os.chmod(params.postanalysis, stat.S_IRWXU)
blasttask.run()
self.assertEqual(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
self.assertEqual(blasttask.get_error(), None)
complete_file = os.path.join(blasttask.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(complete_file), True)
std_err_file = os.path.join(blasttask.get_dir(), 'echo.stderr')
self.assertEqual(os.path.isfile(std_err_file), True)
std_out_file = os.path.join(blasttask.get_dir(), 'echo.stdout')
dataimport = DataImportTask(temp_dir, params)
makeblast = MakeBlastDBTask(temp_dir, params)
f = open(std_out_file, 'r')
echo_out = f.read().replace('\n', '')
echo_out.index('--nonpolymertsv ' +
os.path.join(temp_dir, dataimport.get_dir_name(),
DataImportTask.NONPOLYMER_TSV))
echo_out.index(' --sequencetsv ' +
os.path.join(temp_dir, dataimport.get_dir_name(),
DataImportTask.OLDSEQUENCE_TSV))
echo_out.index(' --pdbblastdb ' +
os.path.join(temp_dir, makeblast.get_dir_name()))
echo_out.index(' --compinchi ' +
os.path.join(temp_dir, dataimport.get_dir_name(),
DataImportTask.COMPINCHI_ICH))
echo_out.index(' --outdir ' +
os.path.join(temp_dir, blasttask.get_dir_name()))
echo_out.index(' --crystalpH ' +
os.path.join(temp_dir, dataimport.get_dir_name(),
DataImportTask.CRYSTALPH_TSV))
echo_out.index(' --pdbdb /pdbdb ')
f.close()
self.assertEqual(os.path.isfile(std_out_file), True)
self.assertEquals(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
self.assertEquals(
os.path.exists(
os.path.join(blasttask.get_dir(), 'foo.py.stderr')), True)
self.assertEquals(
os.path.exists(
os.path.join(blasttask.get_dir(), 'foo.py.stdout')), True)
res = blasttask.get_email_log().rstrip('\n')
res.index('/bin/echo')
res.index('# txt files found: 0')
res.index('Output from summary.txt')
res.index(' sequences: 177')
res.index(' complexes: 149')
res.index(dataimport.get_sequence_tsv() +
' file not found falling back to ' +
dataimport.get_oldsequence_tsv())
finally:
shutil.rmtree(temp_dir)