def test_run_logcmd():
test_script = textwrap.dedent("""
#!/usr/bin/env bash
echo output $@
exit 0
""").strip()
expcmd = './script.sh 1 2 3\n'
expstdout = 'output 1 2 3\n'
with tempdir.tempdir():
mkexec('script.sh', test_script)
with open('my_stdout', 'wt') as stdoutf:
stdout = run.run('./script.sh 1 2 3', log={'cmd': stdoutf})
assert stdout == expstdout
assert open('my_stdout', 'rt').read() == expcmd
with open('my_stdout', 'wt') as stdoutf:
stdout = run.run('./script.sh 1 2 3',
log={
'cmd': stdoutf,
"stdout": stdoutf
})
assert stdout == expstdout
assert open('my_stdout', 'rt').read() == expcmd + expstdout
def test_run_tee():
test_script = textwrap.dedent("""
#!/bin/bash
echo "standard output - arguments: $@"
echo "standard error" >&2
exit 0
""").strip()
with tempdir.tempdir():
mkexec('script.sh', test_script)
expstdout = "standard output - arguments: 1 2 3\n"
expstderr = "standard error\n"
capture = CaptureStdout()
with capture:
stdout = run.run('./script.sh 1 2 3', log={'tee': True})
assert stdout == expstdout
assert capture.stdout == expstdout
with capture.reset():
stdout, stderr = run.run('./script.sh 1 2 3',
stderr=True,
log={'tee': True})
assert stdout == expstdout
assert stderr == expstderr
assert capture.stdout == expstdout
assert capture.stderr == expstderr
with capture.reset():
stdout, stderr, ret = run.run('./script.sh 1 2 3',
stderr=True,
exitcode=True,
log={'tee': True})
assert ret == 0
assert stdout == expstdout
assert stderr == expstderr
assert capture.stdout == expstdout
assert capture.stderr == expstderr
with capture.reset():
stdout, ret = run.run('./script.sh 1 2 3',
exitcode=True,
log={'tee': True})
assert ret == 0
assert stdout == expstdout
assert capture.stdout == expstdout
def test_run_streams():
"""
"""
test_script = textwrap.dedent("""
#!/usr/bin/env bash
echo standard output
echo standard error >&2
exit 0
""").strip()
expstdout = 'standard output\n'
expstderr = 'standard error\n'
with tempdir.tempdir():
mkexec('./script.sh', test_script)
with open('my_stdout', 'wt') as stdout, \
open('my_stderr', 'wt') as stderr:
stdout, stderr = run.run('./script.sh',
stderr=True,
log={
'stdout': stdout,
'stderr': stderr
})
assert stdout == expstdout
assert stderr == expstderr
assert open('my_stdout', 'rt').read() == expstdout
assert open('my_stderr', 'rt').read() == expstderr
capture = CaptureStdout()
with open('my_stdout', 'wt') as stdout, \
open('my_stderr', 'wt') as stderr, \
capture.reset():
stdout, stderr = run.run('./script.sh',
stderr=True,
log={
'tee': True,
'stdout': stdout,
'stderr': stderr
})
assert stdout == expstdout
assert stderr == expstderr
assert capture.stdout == expstdout
assert capture.stderr == expstderr
assert open('my_stdout', 'rt').read() == expstdout
assert open('my_stderr', 'rt').read() == expstderr
def test_func_to_cmd():
cwd = os.getcwd()
with tempdir():
for tmp_dir in (None, '.'):
for clean in ('never', 'on_success', 'always'):
for verbose in (False, True):
cmd = fslsub.func_to_cmd(_good_func,
clean=clean,
tmp_dir=tmp_dir,
verbose=verbose)
fn = cmd.split()[-1]
assert op.exists(fn)
stdout, stderr, exitcode = run.run(cmd,
exitcode=True,
stdout=True,
stderr=True,
env={"PYTHONPATH": cwd})
assert exitcode == 0
if clean == 'never':
assert op.exists(
fn
), "Successful job got removed, even though this was not requested"
else:
assert not op.exists(
fn
), f"Successful job did not get removed after run for clean = {clean}"
if verbose:
assert stdout.strip() == f'running {fn}\nhello'
else:
assert stdout.strip() == 'hello'
cmd = fslsub.func_to_cmd(_bad_func,
clean=clean,
tmp_dir=tmp_dir)
fn = cmd.split()[-1]
assert op.exists(fn)
stdout, stderr, exitcode = run.run(cmd,
exitcode=True,
stdout=True,
stderr=True,
env={'PYTHONPATH': cwd})
assert exitcode != 0
if clean == 'always':
assert not op.exists(
fn
), "Failing job should always be removed if requested"
else:
assert op.exists(
fn
), f"Failing job got removed even with clean = {clean}"
def info(job_ids) -> Dict[str, Optional[Dict[str, str]]]:
"""Gets information on a given job id
The ``info`` function is deprecated - you should use the
``fsl_sub.report`` function from the ``fsl_sub`` Python library, which
is available in FSL 6.0.5 and newer.
Uses `qstat -j <job_ids>`
:arg job_ids: string with job id or (nested) sequence with jobs
:return: dictionary of jobid -> another dictionary with job information
(or None if job does not exist)
"""
if not hasattr(info, '_ncall'):
info._ncall = 0
info._ncall += 1
if info._ncall == 3:
warnings.warn("Please do not call `fslsub.info` repeatably, because it slows down the cluster. You can avoid this message by simply passing all the job IDs you are interested in to a single `fslsub.info` call.")
from fsl.utils.run import run
job_ids_string = _flatten_job_ids(job_ids)
try:
result = run(['qstat', '-j', job_ids_string], exitcode=True)[0]
except FileNotFoundError:
log.debug("qstat not found; assuming not on cluster")
return {}
return _parse_qstat(job_ids_string, result)
def test_run_submit():
def mkexec(path, contents):
with open(path, 'wt') as f:
f.write(contents)
os.chmod(path, 0o755)
test_script = textwrap.dedent("""
#!/usr/bin/env bash
echo test_script running
exit 0
""").strip()
with tempdir.tempdir(), \
mockFSLDIR(), \
mock.patch('fsl.utils.fslsub.submit', mock_submit):
mkexec(op.expandvars('$FSLDIR/bin/fsltest'), test_script)
jid = run.run('fsltest', submit=True)
assert jid == '12345'
stdout, stderr = fslsub.output(jid)
assert stdout == 'test_script running\n'
assert stderr == ''
# or can pass submit opts as a dict
kwargs = {'name': 'abcde', 'ram': '4GB'}
jid = run.run('fsltest', submit=kwargs)
assert jid == '12345'
stdout, stderr = fslsub.output(jid)
experr = '\n'.join(
['{}: {}'.format(k, kwargs[k])
for k in sorted(kwargs.keys())]) + '\n'
assert stdout == 'test_script running\n'
assert stderr == experr
# or can pass submit opts as kwargs
kwargs = {'name': 'abcde', 'ram': '4GB'}
jid = run.run('fsltest', submit=True, **kwargs)
assert jid == '12345'
stdout, stderr = fslsub.output(jid)
experr = '\n'.join(
['{}: {}'.format(k, kwargs[k])
for k in sorted(kwargs.keys())]) + '\n'
assert stdout == 'test_script running\n'
assert stderr == experr
def test_dryrun():
test_script = textwrap.dedent("""
#!/bin/bash
touch foo
""").strip()
with tempdir.tempdir():
mkexec('./script.sh', test_script)
run.run('./script.sh')
assert op.exists('foo')
os.remove('foo')
with run.dryrun():
run.run('./script.sh')
assert not op.exists('foo')
def test_run_passthrough():
test_script = textwrap.dedent("""
#!/bin/bash
echo "env: $RUN_TEST_ENV_VAR"
""").strip()
with tempdir.tempdir():
# return code == 0
mkexec('script.sh', test_script.format(0))
env = {'RUN_TEST_ENV_VAR': 'howdy ho'}
expstdout = "env: howdy ho\n"
assert run.run('./script.sh', env=env) == expstdout
def mock_submit(cmd, **kwargs):
if isinstance(cmd, six.string_types):
name = cmd.split()[0]
else:
name = cmd[0]
name = op.basename(name)
jid = '12345'
output = run.run(cmd)
with open('{}.o{}'.format(name, jid), 'wt') as f:
f.write(output)
with open('{}.e{}'.format(name, jid), 'wt') as f:
for k in sorted(kwargs.keys()):
f.write('{}: {}\n'.format(k, kwargs[k]))
return jid
#!/usr/bin/env python
# Script to publish the documentation on jalapeno
from fsl.utils.run import run
import os.path as op
from sphinx.cmd.build import main
main(('doc', 'doc/html'))
target = op.expanduser("~/www/doc/mcot/core")
if op.isdir(target):
run(f"rsync -aP doc/html/ {target}/")
def test_run():
test_script = textwrap.dedent("""
#!/bin/bash
echo "standard output - arguments: $@"
echo "standard error" >&2
exit {}
""").strip()
with tempdir.tempdir():
# return code == 0
mkexec('script.sh', test_script.format(0))
expstdout = "standard output - arguments: 1 2 3\n"
expstderr = "standard error\n"
# test:
# - single string
# - packed sequence
# - unpacked sequence
assert run.run('./script.sh 1 2 3') == expstdout
assert run.run(('./script.sh', '1', '2', '3')) == expstdout
assert run.run(*('./script.sh', '1', '2', '3')) == expstdout
# test stdout/stderr
stdout, stderr = run.run('./script.sh 1 2 3', stderr=True)
assert stdout == expstdout
assert stderr == expstderr
# test return code
res = run.run('./script.sh 1 2 3', exitcode=True)
stdout, ret = res
assert stdout == expstdout
assert ret == 0
stdout, stderr, ret = run.run('./script.sh 1 2 3',
stderr=True,
exitcode=True)
assert stdout == expstdout
assert stderr == expstderr
assert ret == 0
# stdout=False
res = run.run('./script.sh 1 2 3', stdout=False)
assert res == ()
stderr = run.run('./script.sh 1 2 3', stdout=False, stderr=True)
assert stderr == expstderr
# return code != 0
mkexec('./script.sh', test_script.format(255))
with pytest.raises(RuntimeError):
run.run('./script.sh 1 2 3')
stdout, ret = run.run('./script.sh 1 2 3', exitcode=True)
assert stdout == expstdout
assert ret == 255
def test_cmdonly():
assert run.run('script.sh', cmdonly=True) == ['script.sh']
assert run.run('script.sh 1 2 3',
cmdonly=True) == ['script.sh', '1', '2', '3']
assert run.run(['script.sh'], cmdonly=True) == ['script.sh']
assert run.run(['script.sh', '1'], cmdonly=True) == ['script.sh', '1']
