def test_nosplit():
'It test that we can set some input files to be not split'
bin = create_test_binary()
#with infile
in_file = NamedTemporaryFile()
content = 'hola1\nhola2\n'
in_file.write(content)
in_file.flush()
out_file = NamedTemporaryFile()
cmd = [bin]
cmd.extend(['-i', in_file.name, '-t', out_file.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in',
'special':['no_split']},
{'options': ('-t', '--output'), 'io': 'out'}]
splits = 4
popen = Popen(cmd, stdout=stdout, stderr=stderr, cmd_def=cmd_def,
splits=splits)
assert popen.wait() == 0 #waits till finishes and looks to the retcod
assert not open(stdout.name).read()
assert not open(stderr.name).read()
assert open(out_file.name).read() == content * splits
in_file.close()
os.remove(bin)
def test_lots_splits_outfile():
'It tests that we can set 2 input files and an output file'
bin = create_test_binary()
splits = 200
content = ['hola%d\n' % split for split in range(splits)]
content = ''.join(content)
in_file1 = NamedTemporaryFile()
in_file1.write(content)
in_file1.flush()
in_file2 = NamedTemporaryFile()
in_file2.write(content)
in_file2.flush()
out_file1 = NamedTemporaryFile()
out_file2 = NamedTemporaryFile()
cmd = [bin]
cmd.extend(['-i', in_file1.name, '-t', out_file1.name])
cmd.extend(['-x', in_file2.name, '-z', out_file2.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in', 'splitter':''},
{'options': ('-x', '--input'), 'io': 'in', 'splitter':''},
{'options': ('-t', '--output'), 'io': 'out'},
{'options': ('-z', '--output'), 'io': 'out'}]
popen = Popen(cmd, stdout=stdout, stderr=stderr, cmd_def=cmd_def,
splits=splits)
assert popen.wait() == 0 #waits till finishes and looks to the retcod
assert not open(stdout.name).read()
assert not open(stderr.name).read()
assert open(out_file1.name).read() == content
assert open(out_file2.name).read() == content
in_file1.close()
in_file2.close()
os.remove(bin)
def test_2_infile_outfile():
'It tests that we can set 2 input files and an output file'
bin = create_test_binary()
#with infile
content = 'hola1\nhola2\nhola3\nhola4\nhola5\nhola6\nhola7\nhola8\n'
content += 'hola9\nhola10|n'
in_file1 = NamedTemporaryFile()
in_file1.write(content)
in_file1.flush()
in_file2 = NamedTemporaryFile()
in_file2.write(content)
in_file2.flush()
out_file1 = NamedTemporaryFile()
out_file2 = NamedTemporaryFile()
cmd = [bin]
cmd.extend(['-i', in_file1.name, '-t', out_file1.name])
cmd.extend(['-x', in_file2.name, '-z', out_file2.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in', 'splitter':''},
{'options': ('-x', '--input'), 'io': 'in', 'splitter':''},
{'options': ('-t', '--output'), 'io': 'out'},
{'options': ('-z', '--output'), 'io': 'out'}]
popen = Popen(cmd, stdout=stdout, stderr=stderr, cmd_def=cmd_def)
assert popen.wait() == 0 #waits till finishes and looks to the retcod
assert not open(stdout.name).read()
assert not open(stderr.name).read()
assert open(out_file1.name).read() == content
assert open(out_file2.name).read() == content
in_file1.close()
in_file2.close()
os.remove(bin)
def xtest_infile_outfile_condor():
'It tests that we can set an input file and an output file'
bin = create_test_binary()
#with infile
in_file = NamedTemporaryFile()
content = 'hola1\nhola2\nhola3\nhola4\nhola5\nhola6\nhola7\nhola8\n'
content += 'hola9\nhola10|n'
in_file.write(content)
in_file.flush()
out_file = NamedTemporaryFile()
cmd = [bin]
cmd.extend(['-i', in_file.name, '-t', out_file.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in', 'splitter':''},
{'options': ('-t', '--output'), 'io': 'out'}]
from psubprocess import CondorPopen
popen = Popen(cmd, stdout=stdout, stderr=stderr, cmd_def=cmd_def,
runner=CondorPopen,
runner_conf={'transfer_executable':True})
assert popen.wait() == 0 #waits till finishes and looks to the retcode
assert not open(stdout.name).read()
assert not open(stderr.name).read()
assert open(out_file.name).read() == content
in_file.close()
os.remove(bin)
def test_run_condor_retcode():
'It test that we can run condor job and get the retcode'
bin = create_test_binary()
#a simple job
cmd = [bin]
cmd.extend(['-r', '10'])
popen = Popen(cmd, runner_conf={'transfer_executable':True})
assert popen.wait() == 10 #waits till finishes and looks to the retcode
os.remove(bin)
def test_retcode():
'It tests that we get the correct returncode'
bin = create_test_binary()
cmd = [bin]
cmd.extend(['-r', '20'])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
popen = Popen(cmd, stdout=stdout, stderr=stderr, cmd_def=[])
assert popen.wait() == 20 #waits till finishes and looks to the retcod
assert not open(stdout.name).read()
assert not open(stderr.name).read()
os.remove(bin)
def test_run_condor_kill():
'It test that we can kill a condor job'
bin = create_test_binary()
#a simple job
cmd = [bin]
cmd.extend(['-w'])
popen = Popen(cmd, runner_conf={'transfer_executable':True})
pid = str(popen.pid)
popen.kill()
stdout = call(['condor_q', pid])[0]
assert pid not in stdout
os.remove(bin)
def test_kill_subjobs():
'It tests that we can kill the subjobs'
bin = create_test_binary()
cmd = [bin]
cmd.extend(['-w'])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
popen = Popen(cmd, stdout=stdout, stderr=stderr, cmd_def=[])
assert popen.returncode is None
popen.kill()
assert not open(stdout.name).read()
assert not open(stderr.name).read()
os.remove(bin)
def test_run_condor_stdout():
'It test that we can run condor job and retrieve stdout and stderr'
bin = create_test_binary()
#a simple job
cmd = [bin]
cmd.extend(['-o', 'hola', '-e', 'caracola'])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
popen = Popen(cmd, runner_conf={'transfer_executable':True},
stdout=stdout, stderr=stderr)
assert popen.wait() == 0 #waits till finishes and looks to the retcode
assert open(stdout.name).read() == 'hola'
assert open(stderr.name).read() == 'caracola'
os.remove(bin)
def test_run_condor_stdin():
'It test that we can run condor job with stdin'
bin = create_test_binary()
#a simple job
cmd = [bin]
cmd.extend(['-s'])
stdin = NamedTemporaryFile()
stdout = NamedTemporaryFile()
stdin.write('hola')
stdin.flush()
popen = Popen(cmd, runner_conf={'transfer_executable':True},
stdout=stdout, stdin=stdin)
assert popen.wait() == 0 #waits till finishes and looks to the retcode
assert open(stdout.name).read() == 'hola'
os.remove(bin)
def test_job_no_in_stream():
'It test that a job with no in stream is run splits times'
bin = create_test_binary()
cmd = [bin]
cmd.extend(['-o', 'hola', '-e', 'caracola'])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in', 'splitter':''}]
splits = 4
popen = Popen(cmd, stdout=stdout, stderr=stderr, cmd_def=cmd_def,
splits=splits)
assert popen.wait() == 0 #waits till finishes and looks to the retcod
assert open(stdout.name).read() == 'hola' * splits
assert open(stderr.name).read() == 'caracola' * splits
os.remove(bin)
def test_file_in():
'It tests the most basic behaviour'
bin = create_test_binary()
#with infile
in_file = NamedTemporaryFile()
in_file.write('hola')
in_file.flush()
cmd = [bin]
cmd.extend(['-i', in_file.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in', 'splitter':''}]
popen = Popen(cmd, stdout=stdout, stderr=stderr, cmd_def=cmd_def)
assert popen.wait() == 0 #waits till finishes and looks to the retcode
assert open(stdout.name).read() == 'hola'
in_file.close()
os.remove(bin)
def test_run_condor_in_file():
'It test that we can run condor job with an input file'
bin = create_test_binary()
in_file = NamedTemporaryFile()
in_file.write('hola')
in_file.flush()
cmd = [bin]
cmd.extend(['-i', in_file.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in'}]
popen = Popen(cmd, runner_conf={'transfer_executable':True},
stdout=stdout, stderr=stderr, cmd_def=cmd_def)
assert popen.wait() == 0 #waits till finishes and looks to the retcod
assert open(stdout.name).read() == 'hola'
os.remove(bin)
def test_run_condor_in_out_file(self):
'It test that we can run condor job with an output file'
bin = create_test_binary()
in_file = NamedTemporaryFile()
in_file.write('hola')
in_file.flush()
out_file = open('output.txt', 'w')
cmd = [bin]
cmd.extend(['-i', in_file.name, '-t', out_file.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in'},
{'options': ('-t', '--output'), 'io': 'out'}]
popen = Popen(cmd, runner_conf={'transfer_executable':True},
stdout=stdout, stderr=stderr, cmd_def=cmd_def)
popen.wait()
assert popen.wait() == 0 #waits till finishes and looks to the retcod
assert open(out_file.name).read() == 'hola'
os.remove(out_file.name)
#and output file with path won't be allowed unless the transfer file
#mechanism is not used
out_file = NamedTemporaryFile()
cmd = [bin]
cmd.extend(['-i', in_file.name, '-t', out_file.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in'},
{'options': ('-t', '--output'), 'io': 'out'}]
try:
popen = Popen(cmd, runner_conf={'transfer_executable':True},
stdout=stdout, stderr=stderr, cmd_def=cmd_def)
self.fail('ValueError expected')
#pylint: disable-msg=W0704
except ValueError:
pass
os.remove(bin)
def test_stdin():
'It test that stdin works as input'
bin = create_test_binary()
#with stdin
content = 'hola1\nhola2\nhola3\nhola4\nhola5\nhola6\nhola7\nhola8\n'
content += 'hola9\nhola10|n'
stdin = NamedTemporaryFile()
stdin.write(content)
stdin.flush()
cmd = [bin]
cmd.extend(['-s'])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options':STDIN, 'io': 'in', 'splitter':''}]
popen = Popen(cmd, stdout=stdout, stderr=stderr, stdin=stdin,
cmd_def=cmd_def)
assert popen.wait() == 0 #waits till finishes and looks to the retcod
assert open(stdout.name).read() == content
assert open(stderr.name).read() == ''
os.remove(bin)
def test_prunner_with_cmddef():
'It tests that we can run the prunner setting the cmd_def in the cmd'
bin = create_test_binary()
#with infile
in_file = NamedTemporaryFile()
content = 'hola1\nhola2\nhola3\nhola4\nhola5\nhola6\nhola7\nhola8\n'
content += 'hola9\nhola10|n'
in_file.write(content)
in_file.flush()
out_file = NamedTemporaryFile()
cmd = [bin]
cmd.extend(['>splitter=#-i#', in_file.name,
'<#-t#', out_file.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
popen = Popen(cmd, stdout=stdout, stderr=stderr)
assert popen.wait() == 0 #waits till finishes and looks to the retcod
assert not open(stdout.name).read()
assert not open(stderr.name).read()
assert open(out_file.name).read() == content
in_file.close()
os.remove(bin)
def test_bam_infile_outfile():
'It tests that we can set an bam input and output file'
bin = create_test_binary()
#with infile
in_file = open(os.path.join(DATA_DIR, 'seq.bam'))
out_file = NamedTemporaryFile()
cmd = [bin]
cmd.extend(['-i', in_file.name, '-t', out_file.name])
stdout = NamedTemporaryFile()
stderr = NamedTemporaryFile()
cmd_def = [{'options': ('-i', '--input'), 'io': 'in', 'splitter':'bam'},
{'options': ('-t', '--output'), 'io': 'out', 'joiner':'bam'}]
popen = Popen(cmd, stdout=stdout, stderr=stderr, cmd_def=cmd_def)
assert popen.wait() == 0 #waits till finishes and looks to the retcod
# print open(out_file.name).read()
# print out_file.name
in_file.close()
os.remove(bin)
