def test_help():
returncode, stdout, stderr = exec_command(
['dcos-cassandra', 'cassandra', '--help'])
assert returncode == 0
assert stdout.startswith(b"Usage:")
assert stderr == b''
def test_help():
returncode, stdout, stderr = exec_command(
['dcos-kubectl', 'kubectl', '--help'])
assert returncode == 0
expected_first_line = b'kubectl controls the Kubernetes cluster manager'
assert stdout.startswith(expected_first_line)
assert stderr == b''
def _exec_shark(msg, cmdline):
logger.info('%s with command line: %s', msg,
subprocess.list2cmdline(cmdline))
out, err, code = common.exec_command(cmdline)
if code != 0:
logger.error(
'Error while executing %s (exit code %d):\n' +
'stdout:\n%s\nstderr:\n%s', cmdline[0], code, b2s(out), b2s(err))
raise RuntimeError('%s error' % cmdline[0])
def uploadBinary(logger):
cmd = "st-flash write {}/kernel.bin 0x8000000 2>&1 | tee -a {}/logs/buildLog"
output = common.exec_command(cmd.format(path, dname))
if "Flash written and verified! jolly good!" not in output:
msg = "ERROR: exec_command() - build all faild.\n\nOutput msg:\n{}"
msgf = msg.format(output)
logger.info(msgf)
raise AssertionError(msgf)
else:
logger.info("Binary successfully written to flash.\n")
def uploadBinary(logger):
cmd = "st-flash write {}/kernel.bin 0x8000000 2>&1 | tee -a {}/logs/buildLog"
output = common.exec_command(cmd.format(path, dname))
if "Flash written and verified! jolly good!" not in output:
msg = "ERROR: exec_command() - build all faild.\n\nOutput msg:\n{}"
msgf = msg.format(output)
logger.info(msgf)
raise AssertionError(msgf)
else:
logger.info("Binary successfully written to flash.\n")
def test_help():
returncode, stdout, stderr = exec_command(
['dcos-kubernetes', 'kubernetes', '--help'])
assert returncode == 0
assert stdout == b"""DCOS Kubernetes Subcommand
Usage:
dcos kubectl parameters...
"""
assert stderr == b''
def apply_topup(context, apply_topup_files, topup_out):
"""Applies a calculated topup correction to a list of files.
Args:
context (class: `flywheel.gear_context.GearContext`): flywheel gear context
apply_topup_files (list): A list of files to apply topup correction to
index_list (list): A list that corresponds 1:1 with apply_topup_files, this indicates which row to use from the
"acquisition_parameters" text file for the associated file. This essentially tells topup what PE direction each
image is.
topup_out (string): the base directory/filename for the topup analysis that was run previously.
Returns:
output_files (list): a list of topup corrected files
"""
# Get the acquisition parameter file for the "--datain" option of topup
acq_par = context.get_input_path('acquisition_parameters')
output_files = []
# For all the files we're applying topup to, loop through them with their associated row in the acquisition parameter file
for fl, ix in apply_topup_files:
# Generate an output name: "topup_corrected_" appended to the front of the original filename
base = os.path.split(fl)[-1]
output_file = os.path.join(context.output_dir, 'topup-corrected-{}'.format(base))
output_files.append(output_file)
# Generate the applytopup command
cmd = ['applytopup',
'--imain={}'.format(fl),
'--datain={}'.format(acq_par),
'--inindex={}'.format(ix),
'--topup={}'.format(topup_out),
'--method=jac',
'--interp=spline',
'--out={}'.format(output_file)]
# Execute the command
exec_command(cmd)
return (output_files)
def bakeSrcCode(logger):
path = getBaseDir()
path = path + "/build"
cmd = "make all 2>&1 | tee -a {}/logs/buildLog"
output = common.exec_command(cmd.format(path))
if "text data bss dec hex filename" not in output:
msg = "ERROR: exec_command() - build all faild.\n\nOutput msg:\n{}"
msgf = msg.format(output)
logger.info(msgf)
raise AssertionError(msgf)
else:
msg = "make all successful.\n"
logger.info(msg)
def bakeSrcCode(logger):
path = getBaseDir()
path = path + "/build"
cmd = "make all 2>&1 | tee -a {}/logs/buildLog"
output = common.exec_command(cmd.format(path))
if "text data bss dec hex filename" not in output:
msg = "ERROR: exec_command() - build all faild.\n\nOutput msg:\n{}"
msgf = msg.format(output)
logger.info(msgf)
raise AssertionError(msgf)
else:
msg = "make all successful.\n"
logger.info(msg)
def count_jobs(job_name):
"""Returns how many jobs with self.jobs_name are currently queued or running"""
try:
out, err, code = common.exec_command("squeue")
except OSError:
raise RuntimeError("Couldn't run squeue, is it installed?")
if code:
raise RuntimeError(
"squeue failed with code %d: stdout: %s, stderr: %s" %
(code, out, err))
lines_with_jobname = [l for l in out.splitlines() if job_name in l]
return len(lines_with_jobname)
def test_help():
returncode, stdout, stderr = exec_command(
['dcos-introspect', 'introspect', '--help'])
assert returncode == 0
assert stdout == b"""DCOS Introspect Example Subcommand
Usage:
dcos introspect --info
Options:
--help Show this screen
--version Show version
"""
assert stderr == b''
def test_help():
returncode, stdout, stderr = exec_command(
['dcos-helloworld', 'helloworld', '--help'])
assert returncode == 0
assert stdout == b"""DCOS HelloWorld Example Subcommand
Usage:
dcos helloworld --info
Options:
--help Show this screen
--version Show version
"""
assert stderr == b''
def test_help():
returncode, stdout, stderr = exec_command(
['dcos-quobyte', 'quobyte', '--help'])
assert returncode == 0
assert stdout == b"""DCOS Quobyte Example Subcommand
Usage:
dcos quobyte info
Options:
--help Show this screen
--version Show version
"""
assert stderr == b''
def test_help():
returncode, stdout, stderr = exec_command(["dcos-helloworld", "helloworld", "--help"])
assert returncode == 0
assert (
stdout
== b"""DCOS HelloWorld Example Subcommand
Usage:
dcos helloworld info
Options:
--help Show this screen
--version Show version
"""
)
assert stderr == b""
def generate_topup_input(context):
"""Takes gear input files and generates a merged input file for TOPUP.
Args:
context (class: `flywheel.gear_context.GearContext`): flywheel gear context
Returns:
merged (string): the path to the merged file for use in TOPUP
"""
# Capture the paths of the input files from the gear context
image1_path = context.get_input_path('image_1')
image2_path = context.get_input_path('image_2')
work_dir = context.work_dir
# Create a base directory in the context's working directory for image 1
base_out1 = os.path.join(work_dir, 'Image1')
# If image 1 is 4D, we will only use the first volume (Assuming that a 4D image is fMRI and we only need one volume)
# TODO: Allow the user to choose which volume to use for topup correction
if is4D(image1_path):
im_name = os.path.split(image1_path)[-1]
log.info('Using volume 1 in 4D image {}'.format(im_name))
# Generate a command to extract the first volume
cmd = ['fslroi', image1_path, base_out1, '0', '1']
else:
# If the image is 3D, simply copy the image to our working directory using fslmaths because it's extension agnostic
cmd = ['fslmaths', image1_path, base_out1]
# Execute the command, resulting in a single volume from image_1 in the working directory
exec_command(cmd)
# Repeat the same steps with image 2
base_out2 = os.path.join(work_dir, 'Image2')
if is4D(image2_path):
im_name = os.path.split(image2_path)[-1]
log.info('Using volume 1 in 4D image {}'.format(im_name))
cmd = ['fslroi', image2_path, base_out2, '0', '1']
else:
cmd = ['fslmaths', image2_path, base_out2]
exec_command(cmd)
# Merge the two volumes (image_1 then image_2)
merged = os.path.join(work_dir, 'topup_vols')
cmd = ['fslmerge', '-t', merged, base_out1, base_out2]
exec_command(cmd)
return (merged)
def test_help():
returncode, stdout, stderr = exec_command(
['dcos-spark', 'spark', '--help'])
assert returncode == 0
assert stderr == b''
#! /usr/bin/env python
import os
import subprocess
import common
import traceback
abspath = os.path.abspath(__file__)
dname = os.path.dirname(abspath)
os.chdir(dname)
path = common.exec_command("pwd")
path = path.strip("\n")
def getBaseDir():
out = os.listdir(".")
while "Makefile" not in out:
os.chdir("..")
out = os.listdir(".")
else:
basePath = os.getcwd()
return basePath
def bakeSrcCode(logger):
path = getBaseDir()
path = path + "/build"
cmd = "make all 2>&1 | tee -a {}/logs/buildLog"
output = common.exec_command(cmd.format(path))
if "text data bss dec hex filename" not in output:
msg = "ERROR: exec_command() - build all faild.\n\nOutput msg:\n{}"
msgf = msg.format(output)
def test_config_schema():
returncode, stdout, stderr = exec_command(
['dcos-spark', 'spark', '--config-schema'])
assert returncode == 0
assert stderr == b''
def test_help():
returncode, stdout, stderr = exec_command(["dcos-hdfs", "hdfs", "--help"])
assert returncode == 0
assert stderr == b""
#! /usr/bin/env python
import os
import subprocess
import common
import traceback
abspath = os.path.abspath(__file__)
dname = os.path.dirname(abspath)
os.chdir(dname)
path = common.exec_command("pwd")
path = path.strip("\n")
def getBaseDir():
out = os.listdir(".")
while "Makefile" not in out:
os.chdir("..")
out = os.listdir(".")
else:
basePath = os.getcwd()
return basePath
def bakeSrcCode(logger):
path = getBaseDir()
path = path + "/build"
cmd = "make all 2>&1 | tee -a {}/logs/buildLog"
output = common.exec_command(cmd.format(path))
if "text data bss dec hex filename" not in output:
def run_topup(context, input):
"""Runs topup on a given input image.
Requires acquisition parameters and input options from the gear context.
Args:
context (class: `flywheel.gear_context.GearContext`): flywheel gear context
input (string): the path to the input file for topup's 'imain' input option
Returns:
out (string): the topup root path
"""
# Get the output directory and config file from the gear context
output_dir = context.output_dir
config_path = context.get_input_path('config_file')
acq_par = context.get_input_path('acquisition_parameters')
# If the user didn't provide a config file, use the default
if not config_path:
config_path = DEFAULT_CONFIG
# Setup output directories
fout = os.path.join(output_dir, 'topup-fmap')
iout = os.path.join(output_dir, 'topup-input-corrected')
out = os.path.join(output_dir, 'topup')
logout = os.path.join(output_dir, 'topup-log.txt')
# Get output options from the gear context (which commands to include in the topup call)
dfout = context.config['displacement_field']
jacout = context.config['jacobian_determinants']
rbmout = context.config['rigid_body_matrix']
verbose = context.config['verbose']
debug = context.config['topup_debug_level']
# lout = context.config['mystery_output']
# Begin generating the command arguments with the default commands that are always present
argument_dict = {'imain': input, 'datain': acq_par, 'out': out, 'fout': fout,
'iout': iout, 'logout': logout, 'config': config_path}
# Add the optional commands defined by the user in the config settings
if dfout:
argument_dict['dfout'] = out + '-dfield'
if jacout:
argument_dict['jacout'] = out + '-jacdet'
if rbmout:
argument_dict['rbmout'] = out + '-rbmat'
if verbose:
argument_dict['verbose'] = True
if debug:
argument_dict['debug'] = debug
# Print the config file settings to the log
log.info('Using config settings:\n\n{}\n\n'.format(open(config_path, 'r').read()))
# Build the command and execute
command = build_command_list(['topup'], argument_dict)
exec_command(command)
return (out)
def test_help():
returncode, stdout, stderr = exec_command(
['dcos-arangodb3', 'arangodb3', '--help'])
assert returncode == 0
assert stderr == b''
def test_help():
returncode, stdout, stderr = exec_command(
['dcos-arangodb', 'arangodb', '--help'])
assert returncode == 0
assert stderr == b''
