def process(paths2process, db, wait=WAIT_TIME, logdir='log'):
cmd = 'ls -l {0}'
# if paths2process and
# time.time() - os.path.getmtime(paths2process[0]) > WAIT_TIME:
processed = []
for path, mod_time in paths2process.items():
if time.time() - mod_time > wait:
#process_me = paths2process.popleft().decode('utf-8')
process_me = path
cmd_ = cmd.format(process_me)
process_dict = {'input_path': process_me,
'accession_number': op.basename(process_me)}
print("Time to process {0}".format(process_me))
stdout, run_dict = run_heudiconv(cmd_)
process_dict.update(run_dict)
db.insert(process_dict)
# save log
logdir = localpath(logdir)
log = logdir.join(process_dict['accession_number'] + '.log')
log.write(stdout)
# if we processed it, or it failed,
# we need to remove it to avoid running it again
processed.append(path)
for processed_path in processed:
del paths2process[processed_path]
def process(paths2process, db, wait=WAIT_TIME, logdir='log'):
cmd = 'ls -l {0}'
# if paths2process and
# time.time() - os.path.getmtime(paths2process[0]) > WAIT_TIME:
processed = []
for path, mod_time in paths2process.items():
if time.time() - mod_time > wait:
#process_me = paths2process.popleft().decode('utf-8')
process_me = path
cmd_ = cmd.format(process_me)
process_dict = {
'input_path': process_me,
'accession_number': op.basename(process_me)
}
print("Time to process {0}".format(process_me))
stdout, run_dict = run_heudiconv(cmd_)
process_dict.update(run_dict)
db.insert(process_dict)
# save log
logdir = localpath(logdir)
log = logdir.join(process_dict['accession_number'] + '.log')
log.write(stdout)
# if we processed it, or it failed,
# we need to remove it to avoid running it again
processed.append(path)
for processed_path in processed:
del paths2process[processed_path]
import fabric.state
from fabric.decorators import task
from fabric.contrib.files import upload_template
from fabric.context_managers import settings, hide
from fabric.api import sudo, run, env, execute, put, reboot
from . import help # noqa
from .utils import tobool
fabric.state.output["running"] = False
env.output_prefix = False
TEMPLATES = localpath(__file__).new(basename="templates")
def check_docker(*args, **kwargs):
with settings(warn_only=True), hide("stdout", "running", "warnings"):
out = run("which docker")
if out == "":
install_docker()
def check_valid_os(*args, **kwargs):
with settings(warn_only=True), hide("stdout", "running", "warnings"):
out = run("which apt-get")
if out == "":
raise StandardError("Only Debian/Ubuntu are currently supported. Sorry.")
from py.path import local as localpath
import fabric.state
from fabric.decorators import task
from fabric.contrib.files import upload_template
from fabric.context_managers import settings, hide
from fabric.api import sudo, run, env, execute, put, reboot
from . import help # noqa
from .utils import tobool
fabric.state.output['running'] = False
env.output_prefix = False
TEMPLATES = localpath(__file__).new(basename="templates")
def check_docker(*args, **kwargs):
with settings(warn_only=True), hide('stdout', 'running', 'warnings'):
out = run('which docker')
if out == '':
install_docker()
def check_valid_os(*args, **kwargs):
with settings(warn_only=True), hide('stdout', 'running', 'warnings'):
out = run('which apt-get')
if out == '':
raise StandardError(
'Only Debian/Ubuntu are currently supported. Sorry.')
class Compile(Task):
name = "test"
def __init__(self, *args, **kwargs):
super(Compile, self).__init__(*args, **kwargs)
self.options = kwargs.get("options", {})
def run(self):
return execute(compile, **self.options)
p = localpath()
for target in p.join("targets").listdir("*.py"):
name = target.purebasename
name = name.split("_", 1)[1]
options = {
"tests": "no",
"target": str(target),
"output": str(p.join("build", name))
}
task = Compile(name=name, options=options)
setattr(task, "__doc__", "Compile {0:s} target".format(name))
globals()[name] = task
