def run(self, **kwargs):
result = {}
command = kwargs['command']
out_opt = kwargs['out_opt']
parameters = kwargs['parameters']
bench_files = kwargs['bench_files']
in_opts = kwargs['in_opts']
if parameters:
if bench_files:
raise CommandError("Parameters or bench_files should be "
"provided, but not both.")
bench_str = make_bench_suite_parameters(command, parameters,
out_opt)
elif bench_files:
if not all(len(x) == len(in_opts) for x in bench_files):
raise CommandError(
"The length of bench_files and in_opts must "
"be the same.")
bench_str = make_bench_suite_files(command, in_opts, bench_files,
out_opt)
else:
raise CommandError("Must specify parameters or bench_files.")
result['bench_suite'] = bench_str
return result
def test_make_bench_suite_files_single(self):
"""Correctly generates the benchmark suite for single input option"""
cmd = "pick_otus.py"
in_opts = ["-i"]
bench_files = [["1000000.fna"], ["2000000.fna"], ["3000000.fna"]]
out_opt = "-o"
obs = make_bench_suite_files(cmd, in_opts, bench_files, out_opt)
self.assertEqual(obs, exp_bench_suite_files_single)
def test_make_bench_suite_files_single(self):
"""Correctly generates the benchmark suite for single input option"""
cmd = "pick_otus.py"
in_opts = ["-i"]
bench_files = [["1000000.fna"], ["2000000.fna"], ["3000000.fna"]]
out_opt = "-o"
obs = make_bench_suite_files(cmd, in_opts, bench_files, out_opt)
self.assertEqual(obs, exp_bench_suite_files_single)
def test_make_bench_suite_files_multiple(self):
"""Correctly generates the bench suite for multiple input options"""
cmd = "split_libraries_fastq.py -m mapping.txt"
in_opts = ["-i", "-b"]
bench_files = [["reads/1000000.fna", "barcodes/1000000.fna"],
["reads/2000000.fna", "barcodes/2000000.fna"],
["reads/3000000.fna", "barcodes/3000000.fna"]]
out_opt = "-o"
obs = make_bench_suite_files(cmd, in_opts, bench_files, out_opt)
self.assertEqual(obs, exp_bench_suite_files_multiple)
def test_make_bench_suite_files_multiple(self):
"""Correctly generates the bench suite for multiple input options"""
cmd = "split_libraries_fastq.py -m mapping.txt"
in_opts = ["-i", "-b"]
bench_files = [["reads/1000000.fna", "barcodes/1000000.fna"],
["reads/2000000.fna", "barcodes/2000000.fna"],
["reads/3000000.fna", "barcodes/3000000.fna"]]
out_opt = "-o"
obs = make_bench_suite_files(cmd, in_opts, bench_files, out_opt)
self.assertEqual(obs, exp_bench_suite_files_multiple)
def test_make_bench_suite_files_pbs(self):
"""Correctly generates the bench suite for a pbs environment"""
cmd = "pick_otus.py"
in_opts = ["-i"]
bench_files = [["1000000.fna"], ["2000000.fna"], ["3000000.fna"]]
out_opt = "-o"
pbs = True
job_prefix = "test"
queue = "friendlyq"
pbs_extra_args = "-m abe"
obs = make_bench_suite_files(cmd, in_opts, bench_files, out_opt, pbs,
job_prefix, queue, pbs_extra_args)
self.assertEqual(obs, exp_bench_suite_files_pbs)
def test_make_bench_suite_files_pbs(self):
"""Correctly generates the bench suite for a pbs environment"""
cmd = "pick_otus.py"
in_opts = ["-i"]
bench_files = [["1000000.fna"], ["2000000.fna"], ["3000000.fna"]]
out_opt = "-o"
pbs = True
job_prefix = "test"
queue = "friendlyq"
pbs_extra_args = "-m abe"
obs = make_bench_suite_files(cmd, in_opts, bench_files, out_opt, pbs,
job_prefix, queue, pbs_extra_args)
self.assertEqual(obs, exp_bench_suite_files_pbs)
def run(self, **kwargs):
# Get command parameters
command = kwargs['command']
out_opt = kwargs['out_opt']
parameters = kwargs['parameters']
bench_files = kwargs['bench_files']
in_opts = kwargs['in_opts']
pbs = kwargs['pbs']
job_prefix = kwargs['job_prefix']
queue = kwargs['queue']
pbs_extra_args = kwargs['pbs_extra_args']
# Check which type of bench suite are we generating
if parameters:
# We are generating a benchmark suite based on different parameter
# values. In such case, the user should not provide any bench file
if bench_files:
raise CommandError("Parameters or bench_files should be "
"provided, but not both.")
bench_str = make_bench_suite_parameters(command, parameters,
out_opt, pbs, job_prefix,
queue, pbs_extra_args)
elif bench_files:
# We are generating a benchmark suite based on input files,
# Check that the number of benchmark files for test case match
# the number of options to provide the input files
if not all(len(x) == len(in_opts) for x in bench_files):
raise CommandError("The length of bench_files and in_opts "
"must be the same.")
bench_str = make_bench_suite_files(command, in_opts, bench_files,
out_opt, pbs, job_prefix, queue,
pbs_extra_args)
else:
# Not enough parameters!
raise CommandError("Must specify parameters or bench_files.")
return {'bench_suite': bench_str}
def run(self, **kwargs):
# Get command parameters
command = kwargs['command']
out_opt = kwargs['out_opt']
parameters = kwargs['parameters']
bench_files = kwargs['bench_files']
in_opts = kwargs['in_opts']
pbs = kwargs['pbs']
job_prefix = kwargs['job_prefix']
queue = kwargs['queue']
pbs_extra_args = kwargs['pbs_extra_args']
# Check which type of bench suite are we generating
if parameters:
# We are generating a benchmark suite based on different parameter
# values. In such case, the user should not provide any bench file
if bench_files:
raise CommandError("Parameters or bench_files should be "
"provided, but not both.")
bench_str = make_bench_suite_parameters(command, parameters,
out_opt, pbs, job_prefix,
queue, pbs_extra_args)
elif bench_files:
# We are generating a benchmark suite based on input files,
# Check that the number of benchmark files for test case match
# the number of options to provide the input files
if not all(len(x) == len(in_opts) for x in bench_files):
raise CommandError("The length of bench_files and in_opts "
"must be the same.")
bench_str = make_bench_suite_files(command, in_opts, bench_files,
out_opt, pbs, job_prefix, queue,
pbs_extra_args)
else:
# Not enough parameters!
raise CommandError("Must specify parameters or bench_files.")
return {'bench_suite': bench_str}